Load ncbi (6.1.20010709) into ncbi-tools6/branches/upstream/current.

16 files changed, 17331 insertions, 0 deletions

diff --git a/ddv/README b/ddv/README
new file mode 100644
index 00000000..8466e504
--- /dev/null
+++ b/ddv/README
@@ -0,0 +1,4 @@
+The code in this directory except ddvgraph is restricted checkin as it has
+been forked and placed in the C++ toolkit.  Please check in only bugfixes and
+make sure that these bugfixes are also checked into the C++ code.  New features 
+should only go into the C++ code.  For more info, contact lewisg.
diff --git a/ddv/ddv.dsp b/ddv/ddv.dsp
new file mode 100644
index 00000000..15eda6ca
--- /dev/null
+++ b/ddv/ddv.dsp
@@ -0,0 +1,121 @@
+# Microsoft Developer Studio Project File - Name="ddv" - Package Owner=<4>
+# Microsoft Developer Studio Generated Build File, Format Version 6.00
+# ** DO NOT EDIT **
+
+# TARGTYPE "Win32 (x86) Application" 0x0101
+
+CFG=ddv - Win32 Release
+!MESSAGE This is not a valid makefile. To build this project using NMAKE,
+!MESSAGE use the Export Makefile command and run
+!MESSAGE 
+!MESSAGE NMAKE /f "ddv.mak".
+!MESSAGE 
+!MESSAGE You can specify a configuration when running NMAKE
+!MESSAGE by defining the macro CFG on the command line. For example:
+!MESSAGE 
+!MESSAGE NMAKE /f "ddv.mak" CFG="ddv - Win32 Release"
+!MESSAGE 
+!MESSAGE Possible choices for configuration are:
+!MESSAGE 
+!MESSAGE "ddv - Win32 Debug" (based on "Win32 (x86) Application")
+!MESSAGE "ddv - Win32 Release" (based on "Win32 (x86) Application")
+!MESSAGE 
+
+# Begin Project
+# PROP AllowPerConfigDependencies 0
+# PROP Scc_ProjName ""
+# PROP Scc_LocalPath ""
+CPP=cl.exe
+MTL=midl.exe
+RSC=rc.exe
+
+!IF  "$(CFG)" == "ddv - Win32 Debug"
+
+# PROP BASE Use_MFC 0
+# PROP BASE Use_Debug_Libraries 1
+# PROP BASE Output_Dir "Debug"
+# PROP BASE Intermediate_Dir "Debug"
+# PROP BASE Target_Dir ""
+# PROP Use_MFC 0
+# PROP Use_Debug_Libraries 1
+# PROP Output_Dir "Debug"
+# PROP Intermediate_Dir "Debug"
+# PROP Ignore_Export_Lib 0
+# PROP Target_Dir ""
+# ADD BASE CPP /nologo /W3 /Gm /GX /ZI /Od /D "WIN32" /D "_DEBUG" /D "_WINDOWS" /D "_MBCS" /YX /FD /GZ /c
+# ADD CPP /nologo /W3 /Gm /GX /ZI /Od /I "..\biostruc\cdd" /I ".." /I "..\ddv" /I "..\cn3d" /I "..\access" /I "..\asnstat" /I "..\connect\lbapi" /I "..\connect" /I "..\asnlib" /I "..\vibrant" /I "..\biostruc" /I "..\object" /I "..\api" /I "..\cdromlib" /I "..\desktop" /I "..\tools" /I "..\corelib" /I "..\network\taxon1\common" /I "..\network\vibnet" /I "..\network\entrez\client" /I "..\network\nsclilib" /I "..\network\medarch\client" /I "..\network\id1arch" /I "..\network\taxon1\taxon2" /I "..\network\blast3\client" /D "WIN32" /D "_DEBUG" /D "_WINDOWS" /D "_MBCS" /YX /FD /GZ /c
+# SUBTRACT CPP /Fr
+# ADD BASE MTL /nologo /D "_DEBUG" /mktyplib203 /win32
+# ADD MTL /nologo /D "_DEBUG" /mktyplib203 /win32
+# ADD BASE RSC /l 0x409 /d "_DEBUG"
+# ADD RSC /l 0x409 /d "_DEBUG"
+BSC32=bscmake.exe
+# ADD BASE BSC32 /nologo
+# ADD BSC32 /nologo
+LINK32=link.exe
+# ADD BASE LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib /nologo /subsystem:windows /debug /machine:I386 /pdbtype:sept
+# ADD LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib opengl32.lib glu32.lib glaux.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib wsock32.lib ncbimmdb.lib ncbidesk.lib ncbitool.lib vibnet.lib ncbinacc.lib netcli.lib vibrant.lib ncbicdr.lib ncbiobj.lib ncbi.lib ddvlib.lib /nologo /subsystem:windows /debug /machine:I386 /pdbtype:sept /libpath:"..\cdromlib\debug" /libpath:"..\biostruc" /libpath:"..\cdromlib\ncbicdr___Win32_Debug" /libpath:"..\corelib\debug" /libpath:"..\vibrant\debug" /libpath:"..\object\debug" /libpath:"..\biostruc\debug" /libpath:"..\desktop\debug" /libpath:"..\tools\debug" /libpath:"..\network\entrez\client\debug" /libpath:"..\network\vibnet\debug" /libpath:"..\network\nsclilib\debug" /libpath:"..\network\taxon1\taxon2\debug" /libpath:"..\network\id1arch\debug" /libpath:"..\network\medarch\client\debug" /libpath:"..\network\blast3\client\debug" /libpath:"ddvlib___Win32_Debug"
+# SUBTRACT LINK32 /pdb:none
+
+!ELSEIF  "$(CFG)" == "ddv - Win32 Release"
+
+# PROP BASE Use_MFC 0
+# PROP BASE Use_Debug_Libraries 1
+# PROP BASE Output_Dir "ddv___Win32_Release"
+# PROP BASE Intermediate_Dir "ddv___Win32_Release"
+# PROP BASE Ignore_Export_Lib 0
+# PROP BASE Target_Dir ""
+# PROP Use_MFC 0
+# PROP Use_Debug_Libraries 1
+# PROP Output_Dir "ddv___Win32_Release"
+# PROP Intermediate_Dir "ddv___Win32_Release"
+# PROP Ignore_Export_Lib 0
+# PROP Target_Dir ""
+# ADD BASE CPP /nologo /W3 /Gm /GX /ZI /Od /I "..\biostruc\cdd" /I ".." /I "..\ddv" /I "..\cn3d" /I "..\access" /I "..\asnstat" /I "..\connect\lbapi" /I "..\connect" /I "..\asnlib" /I "..\vibrant" /I "..\biostruc" /I "..\object" /I "..\api" /I "..\cdromlib" /I "..\desktop" /I "..\tools" /I "..\corelib" /I "..\network\taxon1\common" /I "..\network\vibnet" /I "..\network\entrez\client" /I "..\network\nsclilib" /I "..\network\medarch\client" /I "..\network\id1arch" /I "..\network\taxon1\taxon2" /I "..\network\blast3\client" /D "WIN32" /D "_DEBUG" /D "_WINDOWS" /D "_MBCS" /YX /FD /GZ /c
+# SUBTRACT BASE CPP /Fr
+# ADD CPP /nologo /W3 /Gm /GX /Zi /I "..\biostruc\cdd" /I ".." /I "..\ddv" /I "..\cn3d" /I "..\access" /I "..\asnstat" /I "..\connect\lbapi" /I "..\connect" /I "..\asnlib" /I "..\vibrant" /I "..\biostruc" /I "..\object" /I "..\api" /I "..\cdromlib" /I "..\desktop" /I "..\tools" /I "..\corelib" /I "..\network\taxon1\common" /I "..\network\vibnet" /I "..\network\entrez\client" /I "..\network\nsclilib" /I "..\network\medarch\client" /I "..\network\id1arch" /I "..\network\taxon1\taxon2" /I "..\network\blast3\client" /D "_WINDOWS" /D "WIN32" /D "_MBCS" /YX /FD /c
+# ADD BASE MTL /nologo /D "_DEBUG" /mktyplib203 /win32
+# ADD MTL /nologo /mktyplib203 /win32
+# ADD BASE RSC /l 0x409 /d "_DEBUG"
+# ADD RSC /l 0x409
+BSC32=bscmake.exe
+# ADD BASE BSC32 /nologo
+# ADD BSC32 /nologo
+LINK32=link.exe
+# ADD BASE LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib opengl32.lib glu32.lib glaux.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib wsock32.lib ncbimmdb.lib ncbidesk.lib ncbitool.lib vibnet.lib ncbinacc.lib netcli.lib vibrant.lib ncbicdr.lib ncbiobj.lib ncbi.lib ddvlib.lib /nologo /subsystem:windows /debug /machine:I386 /pdbtype:sept /libpath:"..\cdromlib\debug" /libpath:"..\biostruc" /libpath:"..\cdromlib\ncbicdr___Win32_Debug" /libpath:"..\corelib\debug" /libpath:"..\vibrant\debug" /libpath:"..\object\debug" /libpath:"..\biostruc\debug" /libpath:"..\desktop\debug" /libpath:"..\tools\debug" /libpath:"..\network\entrez\client\debug" /libpath:"..\network\vibnet\debug" /libpath:"..\network\nsclilib\debug" /libpath:"..\network\taxon1\taxon2\debug" /libpath:"..\network\taxon1\common\debug" /libpath:"..\network\id1arch\debug" /libpath:"..\network\medarch\client\debug" /libpath:"..\network\blast3\client\debug" /libpath:"ddvlib___Win32_Debug"
+# SUBTRACT BASE LINK32 /pdb:none
+# ADD LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib opengl32.lib glu32.lib glaux.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib wsock32.lib ncbimmdb.lib ncbidesk.lib ncbitool.lib vibnet.lib ncbinacc.lib netcli.lib vibrant.lib ncbicdr.lib ncbiobj.lib ncbi.lib ddvlib.lib /nologo /subsystem:windows /debug /machine:I386 /pdbtype:sept /libpath:"..\cdromlib\ncbicdr___Win32_Release" /libpath:"..\cdromlib\ncbinacc___Win32_Release" /libpath:"..\corelib\ncbi___Win32_Release" /libpath:"..\vibrant\vibrant___Win32_Release" /libpath:"..\object\object___Win32_Release" /libpath:"..\biostruc\mmdb___Win32_Release" /libpath:"..\desktop\desktop___Win32_Release" /libpath:"..\tools\tools___Win32_Release" /libpath:"..\network\entrez\client\netentr___Win32_Release" /libpath:"..\network\vibnet\vibnet___Win32_Release" /libpath:"..\network\nsclilib\netcli___Win32_Release" /libpath:"..\network\taxon1\taxon2\ncbitxc2___Win32_Release" /libpath:"..\network\id1arch\ncbiid1___Win32_Release" /libpath:"..\network\medarch\client\medarch___Win32_Release" /libpath:"..\network\blast3\client\netblast___Win32_Release" /libpath:"..\cn3d\ncbicn3d___Win32_Release" /libpath:"..\ddv\ddvlib___Win32_Release"
+# SUBTRACT LINK32 /pdb:none
+
+!ENDIF 
+
+# Begin Target
+
+# Name "ddv - Win32 Debug"
+# Name "ddv - Win32 Release"
+# Begin Group "Source Files"
+
+# PROP Default_Filter "cpp;c;cxx;rc;def;r;odl;idl;hpj;bat"
+# Begin Source File
+
+SOURCE=..\link\mswin\ddv.rc
+# End Source File
+# Begin Source File
+
+SOURCE=..\ddv\ddvmain.c
+# End Source File
+# End Group
+# Begin Group "Header Files"
+
+# PROP Default_Filter "h;hpp;hxx;hm;inl"
+# Begin Source File
+
+SOURCE=..\ddv\ddvmain.h
+# End Source File
+# End Group
+# Begin Group "Resource Files"
+
+# PROP Default_Filter "ico;cur;bmp;dlg;rc2;rct;bin;rgs;gif;jpg;jpeg;jpe"
+# End Group
+# End Target
+# End Project
diff --git a/ddv/ddvclick.c b/ddv/ddvclick.c
new file mode 100644
index 00000000..ffeff805
--- /dev/null
+++ b/ddv/ddvclick.c
@@ -0,0 +1,2975 @@
+/*  $Id: ddvclick.c,v 1.65 2000/07/25 20:30:23 hurwitz Exp $
+* ===========================================================================
+*
+*                            PUBLIC DOMAIN NOTICE
+*            National Center for Biotechnology Information (NCBI)
+*
+*  This software/database is a "United States Government Work" under the
+*  terms of the United States Copyright Act.  It was written as part of
+*  the author's official duties as a United States Government employee and
+*  thus cannot be copyrighted.  This software/database is freely available
+*  to the public for use. The National Library of Medicine and the U.S.
+*  Government do not place any restriction on its use or reproduction.
+*  We would, however, appreciate having the NCBI and the author cited in
+*  any work or product based on this material
+*
+*  Although all reasonable efforts have been taken to ensure the accuracy
+*  and reliability of the software and data, the NLM and the U.S.
+*  Government do not and cannot warrant the performance or results that
+*  may be obtained by using this software or data. The NLM and the U.S.
+*  Government disclaim all warranties, express or implied, including
+*  warranties of performance, merchantability or fitness for any particular
+*  purpose.
+*
+* ===========================================================================
+*
+* File Name:  ddvclick.c
+*
+* Author:  Patrick Durand
+*
+* Version Creation Date:   09/20/99
+*
+* $Revision: 1.65 $
+*
+* File Description: mouse management code for DeuxD-Viewer (DDV)
+*
+* Modifications:
+* --------------------------------------------------------------------------
+* $Log: ddvclick.c,v $
+* Revision 1.65  2000/07/25 20:30:23  hurwitz
+* bug fixes: panel update when file is closed, double-click launches UDV from DDE, seqName agrees in status line and left col
+*
+* Revision 1.64  2000/07/24 22:00:08  hurwitz
+* fixed bug that 1/2 characters were displayed sometimes
+*
+* Revision 1.63  2000/07/20 22:25:57  hurwitz
+* bug fix.  mouse-mode query working again
+*
+* Revision 1.62  2000/07/14 22:24:55  lewisg
+* fix scroll, click, visual c++ build bugs.  add command line arg parse to ddv
+*
+* Revision 1.61  2000/07/12 22:22:41  hurwitz
+* added delete block to DDV
+*
+* Revision 1.60  2000/07/12 21:18:13  hurwitz
+* fixed display problems with select rectangle
+*
+* Revision 1.59  2000/07/12 15:38:08  hurwitz
+* made rectangle select much faster.  it's almost working.
+*
+* Revision 1.58  2000/07/05 19:23:13  lewisg
+* add two panes to ddv, update msvc project files
+*
+* Revision 1.57  2000/07/05 18:42:16  hurwitz
+* added split block function to DDV
+*
+* Revision 1.56  2000/06/30 22:31:51  hurwitz
+* added merge block function for DDV
+*
+* Revision 1.55  2000/06/28 19:41:31  hurwitz
+* auto vertical scroll working for rectangle selection
+*
+* Revision 1.54  2000/06/27 20:46:38  hurwitz
+* fixed bugs with select rectangle, added select row option
+*
+* Revision 1.53  2000/06/26 19:32:17  hurwitz
+* can select a rectangle instead of a single row, auto horizontal scroll works but not vertical scroll yet
+*
+* Revision 1.52  2000/06/22 20:56:52  hurwitz
+* assorted bug fixes
+*
+* Revision 1.51  2000/06/21 21:20:56  hurwitz
+* a couple bug fixes
+*
+* Revision 1.50  2000/06/20 19:35:11  hurwitz
+* use indexed seqAlign when necessary, make multiple when redrawing
+*
+* Revision 1.49  2000/06/16 18:40:02  lewisg
+* send mouseup message when drag ends off of sequence
+*
+* Revision 1.48  2000/06/15 20:26:05  hurwitz
+* added left/right/center justify for DDE
+*
+* Revision 1.47  2000/06/13 18:23:54  hurwitz
+* made ViewMgr_MakeMultiple routine, call this on each launch of DDE rather than launch of DDV
+*
+* Revision 1.46  2000/06/12 23:02:40  hurwitz
+* enable launch of DDE from Cn3D, swith from DDV_ComputeRuler to DDE_ReMakeRuler, get rid of styles option for DDE
+*
+* Revision 1.45  2000/06/06 20:09:22  lewisg
+* fix double redraw bug
+*
+* Revision 1.44  2000/05/31 23:07:26  hurwitz
+* made NoGaps a runtime parameter, fixed bug with vertical scroll of show/hide list, save edits query is not performed if nothing to save
+*
+* Revision 1.43  2000/05/25 21:40:42  hurwitz
+* rows hidden in DDV are hidden in DDE, can save edits when rows are hidden in DDE
+*
+* Revision 1.42  2000/05/24 21:42:59  hurwitz
+* getting hide/show rows to work with DDV and DDE together
+*
+* Revision 1.41  2000/05/19 13:48:31  hurwitz
+* made a version of DDE that doesn't allow aligned gaps, changed wording for adding new rows
+*
+* Revision 1.40  2000/05/16 19:43:01  hurwitz
+* grey out create block, delete block, undo, and redo as needed
+*
+* Revision 1.39  2000/05/08 22:48:33  hurwitz
+* on launch of DDE, merge nodes that are same MsaTxtDisp alignment and gap
+*
+* Revision 1.38  2000/05/05 20:24:13  hurwitz
+* some bug fixes, also redraw proper block in DDE after a save operation that causes a merge of 2 blocks
+*
+* Revision 1.37  2000/05/04 22:43:38  hurwitz
+* don't launch DDE on top of DDV, change some wording, redraw DDE after save to AlnMgr
+*
+* Revision 1.36  2000/05/02 19:50:38  hurwitz
+* fixed some bugs with launching DDE from DDV, added new alnMgr fn for positioning DDE on proper column
+*
+* Revision 1.35  2000/04/27 17:01:44  hurwitz
+* small fixes to shift row and shift boundary
+*
+* Revision 1.34  2000/04/26 21:54:27  hurwitz
+* added save function to tell AlnMgr about edits made in DDE
+*
+* Revision 1.33  2000/04/21 23:00:51  hurwitz
+* can launch DDE from DDV
+*
+* Revision 1.32  2000/04/13 18:57:03  hurwitz
+* for DDE: many bug fixes, also get rid of columns that are all unaligned gaps
+*
+* Revision 1.31  2000/04/10 20:58:42  hurwitz
+* added GUI controls for DeleteBlock in DDE
+*
+* Revision 1.30  2000/04/07 16:21:08  hurwitz
+* made delete block faster, added delete block to edit menu
+*
+* Revision 1.29  2000/04/05 20:52:35  hurwitz
+* added GUI control for shifting left and right alignment boundaries
+*
+* Revision 1.28  2000/04/04 22:18:43  lewisg
+* add defline to ddv, fix seq import bugs, set boundbox
+*
+* Revision 1.27  2000/04/03 22:26:31  hurwitz
+* can now shift a row with click and drag
+*
+* Revision 1.26  2000/03/30 23:35:22  hurwitz
+* fixed a bug involving scrolling while moving a row
+*
+* Revision 1.25  2000/03/29 20:02:48  hurwitz
+* keep track of master during move row operations
+*
+* Revision 1.24  2000/03/28 21:03:14  hurwitz
+* added gui control to re-order rows
+*
+* Revision 1.23  2000/03/27 18:07:48  hurwitz
+* page up and page down working, give panel focus on launch
+*
+* Revision 1.22  2000/03/25 00:22:09  hurwitz
+* put DDE_StackPtr in DDV_Main, add to stack inside DDE api's, added insert char, delete char, home and end keyboard control
+*
+* Revision 1.21  2000/03/01 22:49:41  lewisg
+* import bioseq, neatlyindex, get rid of dead code
+*
+* Revision 1.20  2000/03/01 20:23:39  durand
+* update select/deselect code to allow DDV sending correct message to Cn3D
+*
+* Revision 1.19  2000/02/15 22:40:57  lewisg
+* add ability to launch udv so that it colors by row, fixes to colormgr, track rows from viewmgr, fix visual c projects
+*
+* Revision 1.18  2000/02/07 18:57:58  durand
+*  fixed a selection problem
+*
+* Revision 1.17  2000/02/04 16:05:40  durand
+* add click action to select a row
+*
+* Revision 1.16  2000/02/02 14:44:29  durand
+* added function to create data structure for block editor, fixed some bugs
+*
+* Revision 1.15  2000/01/12 15:49:42  durand
+* add About dlg box and fix a bug in selection
+*
+* Revision 1.14  2000/01/10 15:09:45  durand
+* Use Entrez instead of ID1
+*
+* Revision 1.13  2000/01/05 21:11:13  durand
+* update mouse click actions and DrawSequence function for a better use from ddv and cn3d
+*
+* Revision 1.12  1999/12/07 21:40:13  durand
+* add mouse modes menu and caret facility for the editor
+*
+* Revision 1.11  1999/12/06 16:19:19  durand
+* add GoTo facility to DDV
+*
+* Revision 1.10  1999/12/03 23:17:22  lewisg
+* Patrick's new global update msg, argument passing when launching ddv, experimental editing
+*
+* Revision 1.9  1999/11/29 15:26:25  durand
+* designed a new GUI to fix problems under MacOS, Linux and SGI
+*
+* Revision 1.8  1999/11/18 00:21:42  lewisg
+* draw speedups and selection on mouseup
+*
+* Revision 1.7  1999/11/17 22:44:01  durand
+* speed up the selection manager for large SeqAlign
+*
+* Revision 1.6  1999/11/03 21:29:48  durand
+* add CTRL and SHFT keys for mouse selection. redesign the loader functions of DDV to properly register the message callbacks
+*
+* Revision 1.5  1999/10/29 14:15:39  durand
+* add simple mouse selection functions
+*
+* Revision 1.4  1999/10/22 14:19:05  durand
+* add new code for mouse selection
+*
+* Revision 1.3  1999/10/21 13:12:43  durand
+* update selection system
+*
+* Revision 1.2  1999/10/12 15:01:28  lewisg
+* resolve confict with internal/ddv
+*
+* Revision 1.1  1999/09/30 14:10:24  durand
+* add ddv to toolkit
+*
+* Revision 1.2  1999/09/22 20:41:17  durand
+* add mouse-click and drag functions
+*
+* Revision 1.1  1999/09/21 14:19:59  durand
+* add basic mouse management functions
+*
+*
+*
+* ==========================================================================
+*/
+
+#include <ncbi.h>
+#include <vibrant.h>
+
+#include <udviewer.h>
+#include <ddvpanel.h>
+#include <ddvclick.h>
+#include <ddvgraph.h>
+#include <alignmgr.h>
+#include <sqnutils.h>
+#include <seqmgr.h>
+#include <pgppop.h>
+#include <samutil.h>
+#include <tofasta.h>
+#include <viewmgr.h>
+
+/*static MonitorPtr  mon=NULL;*/
+static Boolean OnAlignmentBoundary(PoinT pt, PaneL p, DdvMainPtr dmp,
+                                   Int4* pBlockIndex, Boolean* pLeftBoundary,
+                                   Int4* pCol, Int4* pHPos);
+static Boolean GetBlockAndAlignment(PoinT pt, PaneL p, DdvMainPtr dmp,
+                                    Int4* pBlockIndex, Boolean* pIsUnAligned,
+                                    Int4* pCol, Int4* pOffset, Int4* pWidth, RecT* rcP);
+static Boolean GetBlockAndAlignmentForCol(DdvMainPtr dmp, Int4 Col, Int4* pBlockIndex,
+                                          Boolean* pIsUnAligned, Int4* pOffset, Int4* pWidth);
+static RecT DrawOutline(PaneL p, Int4 Line_num_start, Int4 Disp_coord_start,
+                        Int4 Line_num_stop, Int4 Disp_coord_stop, Boolean Draw);
+static RecT DrawOutlineGivenScroll(PaneL p, Int4 Line_num_start, Int4 Disp_coord_start,
+                                   Int4 Line_num_stop, Int4 Disp_coord_stop,
+                                   Int4 VScroll, Int4 HScroll, Boolean Draw);
+static void EraseOutline(PaneL p);
+static Boolean RectanglesAreSame(RecT rc1, RecT rc2);
+static void DDV_SelectRegion(DdvMainPtr dmp, PoinT pt, RecT rc,
+                             Int4 row_start, Int4 row_stop,
+                             Int4 col_start, Int4 col_stop);
+
+
+NLM_EXTERN Int4 DDV_GetHPixelPosGivenColNumberAndScroll(DdvMainPtr dmp, RecT rc,
+                                                        Int4 Col, Int4 ScrollPos) {
+/*****************************************************************************
+*  return number of pixels right to (0-based) Col.
+*****************************************************************************/
+  Int4  NumPixels;
+
+	InsetRect(&rc,4,4);
+	DDV_AdjustDrawingRect(&rc,&(dmp->GrData.udv_font),dmp);
+  NumPixels = (Col+1-ScrollPos) * dmp->GrData.udv_font.ColWidth;
+  NumPixels += dmp->GrData.udv_panel.cxName + dmp->GrData.udv_scale.cxLeftScale;
+  NumPixels += rc.left;
+  return(NumPixels);
+}
+
+
+NLM_EXTERN Int4 DDV_GetHPixelPosGivenColNumber(DdvMainPtr dmp, RecT rc, Int4 Col) {
+/*****************************************************************************
+*  return number of pixels right to (0-based) Col for current ScrollPos.
+*****************************************************************************/
+  return(DDV_GetHPixelPosGivenColNumberAndScroll(dmp, rc, Col, dmp->GrData.udv_hscrl.ScrollPos));
+}
+
+
+NLM_EXTERN Int4 DDV_GetVPixelPosGivenRowNumberAndScroll(DdvMainPtr dmp, RecT rc,
+                                                        Int4 Row, Int4 ScrollPos) {
+/*****************************************************************************
+*  return number of pixels down to (0-based) Row.
+*****************************************************************************/
+  Int4  NumPixels;
+
+	InsetRect(&rc,4,4);
+	DDV_AdjustDrawingRect(&rc,&(dmp->GrData.udv_font), dmp);
+  NumPixels = (Row+1-ScrollPos) * dmp->GrData.udv_font.LineHeight;
+  /* next line is copied from DDV_GetRowGivenMousePos */
+  NumPixels += 3*dmp->GrData.udv_panel.cyScale/2;
+  NumPixels += rc.top;
+  return(NumPixels);
+}
+
+
+NLM_EXTERN Int4 DDV_GetVPixelPosGivenRowNumber(DdvMainPtr dmp, RecT rc, Int4 Row) {
+/*****************************************************************************
+*  return number of pixels down to (0-based) Row for current scrollPos.
+*****************************************************************************/
+  return(DDV_GetVPixelPosGivenRowNumberAndScroll(dmp, rc, Row, dmp->GrData.udv_vscrl.ScrollPos));
+}
+
+
+NLM_EXTERN void DDV_GetVPixelPosOfEmptySpace(DdvMainPtr dmp, RecT rc, Int4* pTop, Int4* pBot) {
+/*****************************************************************************
+*  return Top:  number of pixels down to top of empty space.
+*  return Bot:  number of pixels down to bot of empty space.
+*****************************************************************************/
+	InsetRect(&rc,4,4);
+  *pTop = rc.top;
+  *pBot = rc.top + dmp->GrData.udv_panel.cyScale/2;
+  return;
+}
+
+
+NLM_EXTERN Int4 DDV_GetColNumberGivenMousePos(DdvMainPtr dmp, RecT rc, PoinT pt) {
+/*****************************************************************************
+*  return the display coordinate at this mouse position.
+*****************************************************************************/
+  Int4  mouse_col;
+
+	InsetRect(&rc,4,4);
+	DDV_AdjustDrawingRect(&rc,&(dmp->GrData.udv_font),dmp);
+	rc.left+=dmp->GrData.udv_panel.cxName + dmp->GrData.udv_scale.cxLeftScale;
+	mouse_col=(pt.x-rc.left)/dmp->GrData.udv_font.ColWidth+
+		dmp->GrData.udv_hscrl.ScrollPos;
+  return(mouse_col);
+}
+
+
+/*****************************************************************************
+
+Function: DDV_GetRowGivenMousePos()
+
+Purpose: given some graphical info, this function returns line_num, the row
+		number (absolute value) and the ParaGLine_Num (i.e. sequence/row
+
+		number; this value must be use to get data from TableHead).
+					
+Return value: line_num (-1 if not found ; otherwise a one-based value)
+
+*****************************************************************************/
+static Int4 DDV_GetRowGivenMousePos(DdvMainPtr dmp, RecT * rcP, PoinT * pt,
+
+			Int4Ptr ParaGLine_Num)
+{
+Int4 Line_num=(Int4)-1,mouse_row,i,n;
+ParaGPtr pgp;
+
+	/*size of the Panel; see also DDV_DrawPanelContent_H()*/
+	InsetRect(rcP,4,4);
+	DDV_AdjustDrawingRect(rcP,&(dmp->GrData.udv_font),dmp);
+	rcP->left+=dmp->GrData.udv_panel.cxName+dmp->GrData.udv_scale.cxLeftScale;
+	rcP->top+=3*dmp->GrData.udv_panel.cyScale/2;
+
+	/*mouse position*/
+	mouse_row=(pt->y-rcP->top)/dmp->GrData.udv_font.LineHeight+
+		dmp->GrData.udv_vscrl.ScrollPos;
+
+	/*use the first ParaG of each sequence and mouse_row to find 
+	row (==sequence) number*/
+	for(i=0;i<dmp->MSA_d.pgp_l.nBsp;i++){
+		pgp=(ParaGPtr)(dmp->MSA_d.pgp_l.TableHead[i]->data.ptrvalue);
+		if (pgp->ScaleStyle==SCALE_POS_NONE) n=0;
+		else n=1;
+		/*within each ParaG, the seq. in on line 0 or 1 (if ruler)*/
+		if (mouse_row>=pgp->StartLine && mouse_row<=(pgp->StartLine+n)){
+			Line_num=mouse_row+1;
+
+			*ParaGLine_Num=i+1;
+			break;
+		}
+	}
+
+	return(Line_num);
+}
+
+/*****************************************************************************
+
+Function: DDV_GetClosetSeqLocGivenBspPos()
+
+Purpose: given a position in the Bioseq, this function return the closest
+         selected region on that bioseq.
+		
+Parameters:	sip, eID, iID; bsioseq identifiers
+            bsp_pos; current position on that bioseq
+			old_pos; returns old_pos of a selection (used only if bModify is TRUE)
+			bModify; if TRUE, create a modified slp
+
+Note : sip can be null ONLY if bModify if FALSE.
+
+Return value: see Purpose.
+
+*****************************************************************************/
+static SeqLocPtr DDV_GetClosetSeqLocGivenBspPos(SeqIdPtr sip, Uint2 eID, 
+		Uint2 iID, Int4 bsp_pos, Int4Ptr old_pos, Boolean bModify)
+{
+SelStructPtr ssp;
+SeqLocPtr    slp=NULL;
+ValNodePtr   vnp_bsp,vnp;
+Int4         diff,old_diff,diff_l,diff_r,bsp_start,bsp_stop;
+Uint1        strand;
+
+	ssp=ObjMgrGetSelected();
+	if (ssp==NULL) return(NULL);
+	
+	vnp_bsp=DDV_GetSelectedRegions(ssp,eID,iID);
+	if (vnp_bsp==NULL) return(NULL);
+	vnp=vnp_bsp;
+	*old_pos=(Int4)-1;
+	old_diff=(Int4)INT4_MAX;
+
+	while(vnp){
+		bsp_start=SeqLocStart((SeqLocPtr)vnp->data.ptrvalue);
+		bsp_stop=SeqLocStop((SeqLocPtr)vnp->data.ptrvalue);
+		strand=SeqLocStrand((SeqLocPtr)vnp->data.ptrvalue);
+		if (bsp_pos<bsp_start){/*left of a selected region ?*/
+			diff=bsp_start-bsp_pos;
+			if (diff<old_diff){	
+				if (slp) slp=SeqLocFree(slp);
+				if (bModify){
+					slp = SeqLocIntNew (bsp_pos, bsp_stop, strand/*Seq_strand_minus*/, sip);
+					*old_pos=bsp_stop;
+				}
+				else{
+					slp = SeqLocIntNew (bsp_start, bsp_stop, strand, sip);
+					*old_pos=(Int4)-1;
+				}
+				old_diff=diff;
+			}
+		}
+		else if (bsp_pos>bsp_stop){/*right of a selected region ?*/
+			diff=bsp_pos-bsp_stop;
+			if (diff<old_diff){	
+				if (slp) slp=SeqLocFree(slp);
+				if (bModify){
+					slp = SeqLocIntNew (bsp_start, bsp_pos, strand/*Seq_strand_plus*/, sip);
+					*old_pos=bsp_start;
+				}
+				else{
+					slp = SeqLocIntNew (bsp_start, bsp_stop, strand, sip);
+					*old_pos=(Int4)-1;
+				}
+				old_diff=diff;
+			}
+		}
+		else{/*inside a selected region ?*/
+			if(bModify){
+				diff_l=bsp_pos-bsp_start;
+				diff_r=bsp_stop-bsp_pos;
+				if (diff_l<diff_r){
+					bsp_start=bsp_pos;
+					*old_pos=bsp_stop;
+					/*strand=Seq_strand_plus;*/
+				}
+				else{
+					bsp_stop=bsp_pos;
+					*old_pos=bsp_start;
+					/*strand=Seq_strand_minus;*/
+				}
+				slp = SeqLocIntNew (bsp_start, bsp_stop, strand, sip);
+				break;
+			}
+		}
+		vnp=vnp->next;
+	}
+	ValNodeFree(vnp_bsp);
+	return(slp);
+}
+
+/*****************************************************************************
+
+Function: DDV_IsFullBspAlreadySel()
+
+Purpose: check if a row is already selected.
+		
+Parameters:	bsp_eID,bsp_iID; bsp identifiers
+			bsp_start,bsp_stop; full sequence 
+			
+Return value: TRUE if the sequence is already fully selected
+
+*****************************************************************************/
+static Boolean DDV_IsFullBspAlreadySel(Uint2 bsp_eID,Uint2 bsp_iID,Int4 bsp_start,
+		Int4 bsp_stop)
+{
+SelStructPtr ssp;
+ValNodePtr   vnp_bsp,vnp;
+Int4         sel_bsp_start,sel_bsp_stop;
+
+	ssp=ObjMgrGetSelected();
+	if (ssp==NULL) return(FALSE);
+	
+	vnp_bsp=DDV_GetSelectedRegions(ssp,bsp_eID,bsp_iID);
+	if (vnp_bsp==NULL) return(FALSE);
+	vnp=vnp_bsp;
+
+	while(vnp){
+		sel_bsp_start=SeqLocStart((SeqLocPtr)vnp->data.ptrvalue);
+		sel_bsp_stop=SeqLocStop((SeqLocPtr)vnp->data.ptrvalue);
+		if (bsp_start==sel_bsp_start && bsp_stop==sel_bsp_stop)
+			return(TRUE);
+		vnp=vnp->next;
+	}
+	return(FALSE);
+}
+
+
+static Uint1 DDV_GetRegionInParaG(ParaGPtr pgp, Int4 Line_num) {
+/*****************************************************************************
+*  get region within ParaG
+*****************************************************************************/
+  Int4  mouse_row, diff;
+
+  mouse_row = Line_num-1;
+
+  if (pgp->ScaleStyle==SCALE_POS_NONE)
+    diff=0;
+  else
+    diff=1;
+
+  if (mouse_row==(pgp->StartLine+diff)){
+    return(PGP_REGION_SEQ);
+  }
+  else if (mouse_row >  (pgp->StartLine+ diff) && 
+           mouse_row <= (pgp->StartLine+ pgp->nLines-1)){
+    return(PGP_REGION_FEAT);
+  }
+  return(PGP_REGION_NOWHERE);
+}
+
+
+static void DDV_GetRowAndColGivenPtAndScroll(DdvMainPtr dmp, RecT rc, PoinT pt,
+                                             Int4 HScroll, Int4 VScroll,
+                                             Int4Ptr Disp_coord, Int4Ptr Line_num) {
+/*****************************************************************************
+*  get row and column where the mouse is clicked.  Provide scroll positions.
+*****************************************************************************/
+  Int4  mouse_row, mouse_col;
+
+  InsetRect(&rc,4,4);
+  DDV_AdjustDrawingRect(&rc, &(dmp->GrData.udv_font), dmp);
+  rc.left += dmp->GrData.udv_panel.cxName + dmp->GrData.udv_scale.cxLeftScale;
+  rc.top += 3*dmp->GrData.udv_panel.cyScale/2;
+
+  mouse_row = (pt.y - rc.top)/dmp->GrData.udv_font.LineHeight + VScroll;
+  mouse_col = (pt.x - rc.left)/dmp->GrData.udv_font.ColWidth + HScroll;
+
+  *Line_num=mouse_row+1;
+  *Disp_coord=mouse_col;
+}
+
+
+static void DDV_GetRowAndColGivenPt(DdvMainPtr dmp, RecT rc, PoinT pt,
+                                    Int4Ptr Disp_coord, Int4Ptr Line_num) {
+/***********************************************************************************
+*  get row and column where the mouse is clicked.  Assume current scroll positions.
+***********************************************************************************/
+  DDV_GetRowAndColGivenPtAndScroll(dmp, rc, pt,
+      dmp->GrData.udv_hscrl.ScrollPos, dmp->GrData.udv_vscrl.ScrollPos,
+      Disp_coord, Line_num);
+}
+
+
+static Int4 DDV_GetParaGLineNumGivenLineNum(DdvMainPtr dmp, Int4 Line_num) {
+/*****************************************************************************
+*  get the ParaGLine_Num for Line_num.
+*****************************************************************************/
+  Int4      i, row;
+  ParaGPtr  pgp;
+
+  row = Line_num-1;
+  for (i=0; i<dmp->MSA_d.pgp_l.nBsp; i++) {
+    pgp = (ParaGPtr)(dmp->MSA_d.pgp_l.TableHead[i]->data.ptrvalue);
+    if (row>=pgp->StartLine && row<=(pgp->StartLine + pgp->nLines-1)) {
+      return(i+1);
+    }
+  }
+  return(-1);
+}
+
+
+static Int4 DDV_GetSeqAlignCoordGivenCol(DdvMainPtr dmp, Int4 Disp_coord) {
+/*****************************************************************************
+*  get the SeqAlignCoord for Disp_coord.
+*****************************************************************************/
+  ValNodePtr        vnp;
+  DDVRulerDescrPtr  drdp;
+  Int4              diff;
+
+  vnp=dmp->MSA_d.pgp_l.RulerDescr;
+  while(vnp){
+    drdp=(DDVRulerDescrPtr)vnp->data.ptrvalue;
+    if (!drdp->bUnAligned){
+      diff = Disp_coord - drdp->disp_start;
+      if (Disp_coord>=drdp->disp_start && Disp_coord<=drdp->disp_stop){
+        return(drdp->align_start + diff);
+      }
+    }
+    vnp=vnp->next;
+  }
+  return(-1);
+}
+
+
+static ParaGPtr DDV_GetPGPGivenRowAndCol(DdvMainPtr dmp, Int4 Line_num, Int4 Disp_coord) {
+/*****************************************************************************
+*  get the ParaG ptr that contains (Line_num, Disp_coord)
+*****************************************************************************/
+  ParaGPtr    pgp=NULL;
+  ValNodePtr  vnp;
+
+  vnp=dmp->MSA_d.pgp_l.TableHead[Line_num-1];
+  while(vnp){
+    pgp=(ParaGPtr)vnp->data.ptrvalue;
+    if (Disp_coord>=pgp->StartLetter && Disp_coord<=pgp->StopLetter){
+      return(pgp);
+    }
+    vnp=vnp->next;
+  }
+  return(pgp);
+}
+
+
+static Boolean DDV_GetCoordsGivenAClickAndScrollPos(DdvMainPtr dmp, RecT * rcP, PoinT * pt,
+    Int4 HScroll, Int4 VScroll,
+		Int4Ptr bsp_coord, Int4Ptr SeqAlign_coord, Int4Ptr Disp_coord,
+		Int4Ptr Line_num, Int4Ptr ParaGLine_Num, Uint1Ptr uWhere, 
+		ParaGPtr PNTR cur_pgp)
+/*****************************************************************************
+*  variation on DDV_GetCoordsGivenAClick.
+*  pass: VScroll and HScroll -- the positions of the vertical and
+*        horizontal scroll bars.
+*****************************************************************************/
+{
+ValNodePtr     vnp;
+ParaGPtr       pgp,TheParaG;
+/*MsaTxtDispPtr  mtdp;*/
+DDVRulerDescrPtr drdp;
+Int4           mouse_row,mouse_col,i,diff;
+Boolean        bFound;
+
+  *ParaGLine_Num = -1;
+	/*size of the Panel; see also DDV_DrawPanelContent_H()*/
+	InsetRect(rcP,4,4);
+	DDV_AdjustDrawingRect(rcP,&(dmp->GrData.udv_font),dmp);
+	rcP->left+=dmp->GrData.udv_panel.cxName+dmp->GrData.udv_scale.cxLeftScale;
+	rcP->top+=3*dmp->GrData.udv_panel.cyScale/2;
+
+	/*mouse position*/
+	mouse_row=(pt->y-rcP->top)/dmp->GrData.udv_font.LineHeight+VScroll;
+	mouse_col=(pt->x-rcP->left)/dmp->GrData.udv_font.ColWidth+HScroll;
+
+	bFound=FALSE;
+
+	for(i=0;i<dmp->MSA_d.pgp_l.nBsp;i++){
+		/*use the first ParaG of each sequence and mouse_row to find 
+		row (==sequence) number; then go though the ParaG list of that
+		sequence to find The ParaG, using mouse_col*/
+		pgp=(ParaGPtr)(dmp->MSA_d.pgp_l.TableHead[i]->data.ptrvalue);
+		if (mouse_row>=pgp->StartLine && mouse_row<=(pgp->StartLine+pgp->nLines-1)){
+			vnp=dmp->MSA_d.pgp_l.TableHead[i];
+		    *ParaGLine_Num = i + 1;
+			while(vnp){
+				pgp=(ParaGPtr)vnp->data.ptrvalue;
+				if (mouse_col>=pgp->StartLetter && mouse_col<=pgp->StopLetter){
+					bFound=TRUE;
+					TheParaG=pgp;
+					break;
+				}
+				vnp=vnp->next;
+			}
+			if (bFound) break;
+		}
+	}
+	/*ok : the mouse is inside a ParaG*/
+	if (bFound){
+		*cur_pgp=TheParaG;
+		/*where is the mouse in the ParaG ?*/
+		*uWhere=PGP_REGION_NOWHERE;
+		if (TheParaG->ScaleStyle==SCALE_POS_NONE)
+			diff=0;
+		else
+			diff=1;
+		if (mouse_row==(TheParaG->StartLine+diff)){
+			*uWhere=PGP_REGION_SEQ;
+		}
+		else if (mouse_row>(TheParaG->StartLine+diff) && 
+				mouse_row<=(pgp->StartLine+pgp->nLines-1)){
+			*uWhere=PGP_REGION_FEAT;
+		}
+
+		/*a. get Disp Coord*/
+		*Line_num=mouse_row+1;/*base 1 value*/
+		*Disp_coord=mouse_col;
+
+		/*on the Sequence ? Then, get the coords. (BSP, DISP, SEQALIGN)*/
+		/*PGP_REGION_FEAT is not yet implemented...  ;-) */
+		if (*uWhere==PGP_REGION_SEQ){
+			/*b. get BSP coord*/
+			*bsp_coord=DDV_GetBspCoordGivenDispCoord(TheParaG,mouse_col);
+			
+			/*c. get SeqAlign Coord*/
+			vnp=dmp->MSA_d.pgp_l.RulerDescr;
+			while(vnp){
+				drdp=(DDVRulerDescrPtr)vnp->data.ptrvalue;
+				if (!drdp->bUnAligned){
+					diff=mouse_col-drdp->disp_start;
+					if (mouse_col>=drdp->disp_start && mouse_col<=drdp->disp_stop){
+						*SeqAlign_coord=drdp->align_start+diff;
+						break;
+					}
+				}
+				else{
+					*SeqAlign_coord=(Int4)-1;
+				}
+				vnp=vnp->next;
+			}
+		}
+	}
+
+	return(bFound);
+}
+
+
+/*****************************************************************************
+
+Function: DDV_GetCoordsGivenAClick()
+
+Purpose: given some graphical info, this function returns bsp_coord, SeqAlign_coord,
+         Disp_coord. Future implementation : will also return eID, iID, idx of
+		 a feature (if the nice user clicks on a feature).
+		
+Parameters:	dmp; panel main data block
+            rcP; panel size
+			pt; mouse position
+			bsp_coord, SeqAlign_coord, Disp_coord,Line_num; return values
+            uWhere; where the mouse is in a ParaG
+			
+Note : all but Line_num are zero-based values. Line_num is a one-based value.
+			
+Return value: TRUE if the user clicks within a ParaG (see also 
+		bsp_coord, SeqAlign_coord, Disp_coord, uWhere). NOTE : if the function 
+		returns FALSE then bsp_coord, SeqAlign_coord, Line_num, Disp_coord and 
+		uWhere are undefined !
+
+*****************************************************************************/
+static Boolean DDV_GetCoordsGivenAClick(DdvMainPtr dmp, RecT * rcP, PoinT * pt,
+		Int4Ptr bsp_coord, Int4Ptr SeqAlign_coord, Int4Ptr Disp_coord,
+		Int4Ptr Line_num, Int4Ptr ParaGLine_Num, Uint1Ptr uWhere, 
+		ParaGPtr PNTR cur_pgp)
+{
+  /* return coordinates for the current scroll position */
+  return(DDV_GetCoordsGivenAClickAndScrollPos(dmp, rcP, pt, 
+    dmp->GrData.udv_hscrl.ScrollPos, dmp->GrData.udv_vscrl.ScrollPos,
+    bsp_coord, SeqAlign_coord, Disp_coord, Line_num, ParaGLine_Num, uWhere, cur_pgp));
+}
+
+/*****************************************************************************
+
+Function: DDV_AutoHScroll()
+
+Purpose: used from drag/hold mouse to auto-scroll the panel horizontally when
+         the mouse reaches the left/right borders of the panel
+
+
+Return value: none
+
+*****************************************************************************/
+static void DDV_AutoHScroll(DdvMainPtr dmp,Int4 Disp_coord)
+{
+Int4 from_col,to_col,from_row,to_row,old_pos;
+BaR hsb;
+
+	DDV_GetCurrentDispRange(dmp->hWndDDV,&(dmp->GrData),dmp->MSA_d.pgp_l.LengthAli,
+			&from_col,&to_col,&from_row,&to_row);
+	
+	hsb = GetSlateHScrollBar ((SlatE) dmp->hWndDDV);
+	old_pos=GetBarValue(hsb);
+	if (Disp_coord>=to_col){/*scroll to the right*/
+		SetValue(hsb,old_pos+1);
+	}
+	else if (Disp_coord<=from_col){
+		SetValue(hsb,old_pos-1);
+	}
+
+}
+
+/*****************************************************************************
+
+Function: DDV_AutoVScroll()
+
+Purpose: used from drag/hold mouse to auto-scroll the panel vertically when
+         the mouse reaches the top/bottom borders of the panel
+
+
+Return value: none
+
+*****************************************************************************/
+static void DDV_AutoVScroll(DdvMainPtr dmp,Int4 Line_num)
+{
+Int4 from_col,to_col,from_row,to_row,old_pos;
+BaR vsb;
+
+	DDV_GetCurrentDispRange(dmp->hWndDDV,&(dmp->GrData),dmp->MSA_d.pgp_l.LengthAli,
+			&from_col,&to_col,&from_row,&to_row);
+	
+	vsb = GetSlateVScrollBar ((SlatE) dmp->hWndDDV);
+	old_pos=GetBarValue(vsb);
+	if (Line_num>=(to_row-1)){/*scroll down*/
+		SetValue(vsb,old_pos+1);
+	}
+	else if (Line_num<=(from_row+1)){/*scroll up*/
+		SetValue(vsb,old_pos-1);
+	}
+}
+
+
+/*****************************************************************************
+
+Function: DDV_DispSelRangeInStatus()
+
+Purpose: display position while selection is in progress. (mouse mode : selection)
+
+Return value: none
+
+*****************************************************************************/
+static void DDV_DispSelRangeInStatus(PrompT InfoPanel,Int4 bsp_start, Int4 bsp_stop,
+		Int4 line_num,CharPtr szSeqName)
+{
+Char szText[250];
+
+	sprintf(szText,"Selection : %s, [%i]:[%i..%i]",szSeqName,line_num,
+		bsp_start,bsp_stop);
+	SetTitle(InfoPanel,szText);
+}
+
+
+/*****************************************************************************
+
+Function: DDV_DispPositionInStatus()
+
+Purpose: display position (mouse mode : query).
+
+Return value: none
+
+*****************************************************************************/
+NLM_EXTERN void DDV_DispPositionInStatus(PrompT InfoPanel,Int4 bsp_pos,
+		Int4 line_num,CharPtr szSeqName)
+{
+Char szText[250];
+
+	sprintf(szText,"Position : %s, [%i]:[%i]",szSeqName,line_num,bsp_pos);
+	SetTitle(InfoPanel,szText);
+}
+
+
+static void DDV_DispStatus(DdvMainPtr dmp, Int4 Line_num_stop,
+                           Int4 Disp_coord_start, Int4 Disp_coord_stop) {
+/*****************************************************************************
+
+Function: DDV_DispStatus()
+
+Purpose: display position while selection is in progress. (mouse mode : selection)
+
+Return value: none
+
+*****************************************************************************/
+  DdvMainWinPtr  mWin_d;
+  Int4           ParaGLine_num, bsp_start, bsp_stop;
+  ParaGPtr       pgp;
+  char           szAccess[21];
+
+  mWin_d = (DdvMainWinPtr) GetObjectExtra(dmp->hParent);
+  if (mWin_d != NULL) {
+    ParaGLine_num = DDV_GetParaGLineNumGivenLineNum(dmp, Line_num_stop);
+    if (ParaGLine_num != -1) {
+      DDV_GetSeqNameGivenRow(dmp->MSA_d.pgp_l.TableHead, ParaGLine_num, szAccess);
+      pgp = DDV_GetPGPGivenRowAndCol(dmp, Line_num_stop, Disp_coord_stop);
+      bsp_stop = DDV_GetBspCoordGivenDispCoord(pgp, Disp_coord_stop);
+      if (dmp->MouseMode == DDV_MOUSEMODE_SELECT ||
+          dmp->MouseMode == DDV_MOUSEMODE_SELECT_ONE_ROW) {
+        pgp = DDV_GetPGPGivenRowAndCol(dmp, Line_num_stop, Disp_coord_start);
+        bsp_start = DDV_GetBspCoordGivenDispCoord(pgp, Disp_coord_start);
+        DDV_DispSelRangeInStatus(mWin_d->InfoPanel, bsp_start+1, bsp_stop+1,
+          ParaGLine_num, szAccess);
+      }
+      else {
+        DDV_DispPositionInStatus(mWin_d->InfoPanel, bsp_stop+1,
+          ParaGLine_num, szAccess);
+      }
+    }
+  }
+}
+
+
+/*****************************************************************************
+
+Function: DDV_GetSeqNameGivenRow()
+
+Purpose: get a sequence number, given a list of ParaG and a row number
+
+Note: row_num is a one-based value; this value must be in the range 0 to nBsp.
+
+(I don't check that here, so be carefull when calling this function)
+
+
+Return value: -
+
+*****************************************************************************/
+NLM_EXTERN void DDV_GetSeqNameGivenRow(ValNodePtr * ParaG_List, Int4 row_num,
+	CharPtr szSeqName)
+{
+  SeqIdPtr sip;
+  ParaGPtr pgp;
+  BioseqPtr bsp;
+  
+  pgp=(ParaGPtr)(ParaG_List[row_num-1]->data.ptrvalue);
+  
+  /*get a name*/	
+  bsp = BioseqLockById(pgp->sip);
+  if(bsp) {
+    /* get name but not gi */
+    sip = SeqIdFindBestAccession(bsp->id);
+    BioseqUnlock(bsp);
+  }
+  
+  if (!sip)
+    sip = SeqIdFindBest(pgp->sip, 0);
+  SeqIdWrite(sip, szSeqName,PRINTID_TEXTID_ACCESSION, 20);   
+}
+
+/*****************************************************************************
+
+Function: DDV_SendBSPSelectMsg_OLD()
+
+Purpose: send a message to select a range of letters on a bioseq.
+
+Return value: none
+
+*****************************************************************************/
+static void DDV_SendBSPSelectMsg_OLD(DdvMainPtr dmp,Int4 bsp_coord,Int4 SeqAlign_coord,
+		Int4 first_Disp_coord, Int4 Disp_coord,Int4 Line_num,Int4 ParaGLine_Num,
+    ParaGPtr cur_pgp,PoinT * pt, Boolean Display)
+{
+Int4        first_bsp_coord, bsp_pos;
+Uint1       direction;/*use to tell ObjMgr the direction of the mouse (left,right)*/
+SeqLocPtr   slp;/*to send an AlsoSelectMsg*/
+Uint2       bsp_eID,bsp_iID;
+Boolean     bDeselectAll=TRUE;
+DdvMainWinPtr dmwp;
+
+	/*analyse the bsp coords*/
+	if (bsp_coord==(Int4)-1){/*this is a gap*/
+		dmp->ms.oldPos=dmp->ms.newPos=*pt;
+		dmp->ms.old_row=Line_num;
+		dmp->ms.old_col=Disp_coord;
+		dmp->ms.old_pgp=cur_pgp;
+		return;
+	}
+
+	/*get the very first click (from DDV_ClickProc)*/
+	first_bsp_coord=
+		DDV_GetBspCoordGivenDispCoord(dmp->ms.first_pgps[Line_num-1],
+                                  dmp->ms.first_cols[Line_num-1]);
+	if (first_bsp_coord==(Int4)-1){/*the first time the user 
+		clicked, it was on a gap*/
+		/*if we are in this scope, that means we have a bsp coord*/
+		first_bsp_coord=bsp_coord;
+		dmp->ms.first_cols[Line_num-1]=Disp_coord;
+		dmp->ms.first_pgps[Line_num-1]=cur_pgp;
+	}
+
+	bsp_pos=bsp_coord;
+	
+	if (ctrlKey || shftKey)
+		bDeselectAll=FALSE;
+
+	/*the mouse is moving to the left or to the right ?*/
+	/*don't forget to check the strand...  ;-) */
+	if (AlnMgrGetNthStrand(dmp->MSA_d.pgp_l.sap, ParaGLine_Num)==Seq_strand_plus){
+		if (dmp->ms.oldPos.x<pt->x)
+			direction=Seq_strand_plus;
+		else
+			direction=Seq_strand_minus;
+	}
+	else{
+		if (dmp->ms.oldPos.x>pt->x)
+			direction=Seq_strand_minus;
+		else
+			direction=Seq_strand_plus;
+	}
+	/*'from' (first_bsp_coord) always less than 'to' (bsp_coord)*/
+	if (first_bsp_coord>bsp_coord)
+		swap(&first_bsp_coord,&bsp_coord);
+	/*save the new position*/
+	dmp->ms.oldPos=dmp->ms.newPos=*pt;
+	dmp->ms.old_row=Line_num;
+	dmp->ms.old_col=Disp_coord;
+	dmp->ms.old_pgp=cur_pgp;
+
+	/*now, we can send the Select message*/
+	/* first_pgp, old_pgp & cur_pgp have the same sip... 
+	they are on a same row; I can use one of them*/
+	slp = SeqLocIntNew (first_bsp_coord, bsp_coord, direction, cur_pgp->sip);
+	UDV_DecodeIdxFeat (dmp->MSA_d.pgp_l.entitiesTbl[ParaGLine_Num-1],&bsp_eID,&bsp_iID);
+  if (bsp_eID!=0 && bsp_iID!=0 && slp){
+    /*update InfoPanel*/
+    dmwp=(DdvMainWinPtr)GetObjectExtra(dmp->hParent);
+    if (dmwp){
+      Char szAccess[21];
+			
+      DDV_GetSeqNameGivenRow(dmp->MSA_d.pgp_l.TableHead, ParaGLine_Num, szAccess);
+	        
+      switch(dmp->MouseMode){
+        case DDV_MOUSEMODE_SELECT:
+        case DDV_MOUSEMODE_SELECT_ONE_ROW:
+          if (Display) {
+            DDV_DispSelRangeInStatus(dmwp->InfoPanel,first_bsp_coord+1,
+              bsp_coord+1,ParaGLine_Num,szAccess);/*+1 : switch to one-based value*/
+          }
+          break;
+        case DDV_MOUSEMODE_QUERY:
+        case DDV_MOUSEMODE_EDIT:
+          DDV_DispPositionInStatus(dmwp->InfoPanel, 
+            bsp_pos+1,ParaGLine_Num,szAccess);/*+1 : switch to one-based value*/
+          break;
+      }
+    }
+		/*send the message*/
+    if (dmp->MouseMode==DDV_MOUSEMODE_SELECT ||
+        dmp->MouseMode==DDV_MOUSEMODE_SELECT_ONE_ROW){
+      ObjMgrAlsoSelect (bsp_eID, bsp_iID, OBJ_BIOSEQ,OM_REGION_SEQLOC, slp);
+    }
+  }
+  else {
+    if (slp) 
+      SeqLocFree(slp);
+  }
+}
+
+
+/*****************************************************************************
+
+Function: DDV_SendBSPSelectMsg()
+
+Purpose: send a message to select a range of letters on a bioseq.
+         I've rewritten this.  Hope I did it right.  Dave H.
+
+Return value: none
+
+*****************************************************************************/
+static void DDV_SendBSPSelectMsg(DdvMainPtr dmp,
+		Int4 col_start, Int4 col_stop, Int4 row, Boolean Display)
+{
+  Int4           bsp_coord_start, bsp_coord_stop, ParaGLine_Num, col;
+  Uint1          direction;/*used to tell ObjMgr the direction of the mouse (left,right)*/
+  SeqLocPtr      slp;/*to send an AlsoSelectMsg*/
+  Uint2          bsp_eID, bsp_iID;
+  Boolean        bDeselectAll=TRUE;
+  ParaGPtr       pgp;
+  DdvMainWinPtr  dmwp;
+
+  if (col_start > col_stop) swap(&col_start, &col_stop);
+
+  /* calculate bsp_coord_start */
+  for (col=col_start; col<=col_stop; col++) {
+    pgp = DDV_GetPGPGivenRowAndCol(dmp, row, col);
+    bsp_coord_start = DDV_GetBspCoordGivenDispCoord(pgp, col);
+    if (bsp_coord_start != -1) break;
+  }
+
+  /* calculate bsp_coord_stop */
+  for (col=col_stop; col>=col_start; col--) {
+    pgp = DDV_GetPGPGivenRowAndCol(dmp, row, col);
+    bsp_coord_stop = DDV_GetBspCoordGivenDispCoord(pgp, col);
+    if (bsp_coord_stop != -1) break;
+  }
+
+  ParaGLine_Num = DDV_GetParaGLineNumGivenLineNum(dmp, row);
+
+	if (ctrlKey || shftKey)
+		bDeselectAll=FALSE;
+
+	/*the mouse is moving to the left or to the right ?*/
+	/*don't forget to check the strand...  ;-) */
+  if (AlnMgrGetNthStrand(dmp->MSA_d.pgp_l.sap, ParaGLine_Num)==Seq_strand_plus) {
+    direction=Seq_strand_plus;
+  }
+  else {
+    direction=Seq_strand_minus;
+  }
+
+  /*now, we can send the Select message*/
+  /* first_pgp, old_pgp & cur_pgp have the same sip... 
+  they are on a same row; I can use one of them*/
+  slp = SeqLocIntNew (bsp_coord_start, bsp_coord_stop, direction, pgp->sip);
+  UDV_DecodeIdxFeat (dmp->MSA_d.pgp_l.entitiesTbl[ParaGLine_Num-1],&bsp_eID,&bsp_iID);
+  if (bsp_eID!=0 && bsp_iID!=0 && slp){
+    /*update InfoPanel*/
+    dmwp=(DdvMainWinPtr)GetObjectExtra(dmp->hParent);
+    if (dmwp){
+      Char szAccess[21];
+			
+      DDV_GetSeqNameGivenRow(dmp->MSA_d.pgp_l.TableHead, ParaGLine_Num, szAccess);
+	        
+      switch(dmp->MouseMode){
+        case DDV_MOUSEMODE_SELECT:
+        case DDV_MOUSEMODE_SELECT_ONE_ROW:
+          if (Display) {
+            DDV_DispSelRangeInStatus(dmwp->InfoPanel, bsp_coord_start+1,
+              bsp_coord_stop+1, ParaGLine_Num, szAccess); /*+1 : switch to one-based value*/
+          }
+          break;
+        case DDV_MOUSEMODE_QUERY:
+        case DDV_MOUSEMODE_EDIT:
+          DDV_DispPositionInStatus(dmwp->InfoPanel, 
+            bsp_coord_stop+1, ParaGLine_Num, szAccess);/*+1 : switch to one-based value*/
+          break;
+      }
+    }
+		/*send the message*/
+    if (dmp->MouseMode==DDV_MOUSEMODE_SELECT ||
+        dmp->MouseMode==DDV_MOUSEMODE_SELECT_ONE_ROW){
+      ObjMgrAlsoSelect (bsp_eID, bsp_iID, OBJ_BIOSEQ, OM_REGION_SEQLOC, slp);
+    }
+  }
+  else {
+    if (slp) 
+      SeqLocFree(slp);
+  }
+}
+
+
+/*****************************************************************************
+
+Functions: DDV_ClickProcUpper() and DDV_ClickProcLower()
+
+Purpose: mouse click funcions attached to the upper
+            and lower panels in 2-panel mode.  They switch focus between the upper
+            and lower panels, then call the main DDV_ClickProc.
+		
+Parameters:	p; panel handle (currently unused)
+			pt; new mouse position
+
+Return value: none
+
+*****************************************************************************/
+
+NLM_EXTERN void DDV_ClickProcUpper(PaneL p, PoinT pt)
+{
+DdvMainWinPtr mWin_d;
+WindoW		  hWinMain;
+Boolean       tempClick;
+
+	hWinMain=(WindoW)ParentWindow(p);
+	if (hWinMain==NULL) return;
+	mWin_d = (DdvMainWinPtr) GetObjectExtra (hWinMain);
+	if (mWin_d==NULL) return;
+	mWin_d->hWndDDV = mWin_d->hUpperPanel;
+    DDV_SetMenuFocus(hWinMain);
+	mWin_d->InfoPanel = mWin_d->UpperInfoPanel;
+    tempClick = Nlm_dblClick;  /* keep vibrant from resetting double click */
+    SetTitle(mWin_d->InfoPanel,"Ready !");
+    SetTitle(mWin_d->LowerInfoPanel,"");
+    Nlm_dblClick = tempClick;
+
+    DDV_ClickProc(p, pt);
+}
+
+NLM_EXTERN void DDV_ClickProcLower(PaneL p, PoinT pt)
+{
+DdvMainWinPtr mWin_d;
+WindoW		  hWinMain;
+Boolean       tempClick;
+
+	hWinMain=(WindoW)ParentWindow(p);
+	if (hWinMain==NULL) return;
+	mWin_d = (DdvMainWinPtr) GetObjectExtra (hWinMain);
+	if (mWin_d==NULL) return;
+	mWin_d->hWndDDV = mWin_d->hLowerPanel;
+    DDV_SetMenuFocus(hWinMain);
+	mWin_d->InfoPanel = mWin_d->LowerInfoPanel;
+    tempClick = Nlm_dblClick;  /* keep vibrant from resetting double click */
+    SetTitle(mWin_d->InfoPanel,"Ready !");
+    SetTitle(mWin_d->UpperInfoPanel,"");
+    Nlm_dblClick = tempClick;
+
+    DDV_ClickProc(p, pt);
+}
+
+/*****************************************************************************
+
+Function: DDV_ClickProc()
+
+Purpose: manage Mouse-Click; this function is designed for the autonomous viewer
+		to manage the InfoPanel and the Features List Dialog Box
+		DON'T USE FOR EXTERNAL SOFTWARE...
+		
+Parameters:	p; panel handle (currently unused)
+			pt; new mouse position
+
+Return value: none
+
+*****************************************************************************/
+NLM_EXTERN void DDV_ClickProc(PaneL p, PoinT pt)
+{
+DdvMainPtr 	   dmp;
+DdvMainWinPtr  mWin_d;
+RecT           rcP, rcP2;
+Int4           bsp_coord, SeqAlign_coord, Disp_coord, Line_num,bsp_start,bsp_stop,
+               old_pos, ParaGLine_Num, VPos, HPos;
+Int4           from_row, to_row, from_col, to_col;
+Uint1          uWhere;
+ParaGPtr       cur_pgp=NULL;
+SeqLocPtr      slp;
+Uint2          bsp_eID,bsp_iID;
+Boolean        bDeselectAll=TRUE,bIsAlreadyFullSel;
+Int4           BlockIndex, Col, NumBlocks;
+Boolean        LeftBoundary, IsUnAligned;
+DdvMainWinPtr  dmwp;
+BioseqPtr      bsp;
+Char           buf[81], szAccess[21];
+ParaGPtr       pgp;
+Int4           i, NumRows, ColCnt, Offset, Width;
+
+MsaParaGPopListPtr  mpplp;
+SeqAlignPtr         sap;
+DDE_StackPtr        dsp;
+Boolean             IsEditable, *pNoGaps, NoGaps, FoundIt;
+
+	/*get the panel data*/
+	dmp = (DdvMainPtr) GetObjectExtra(p);
+	if (dmp==NULL) return;
+  mWin_d = (DdvMainWinPtr) GetObjectExtra(dmp->hParent);
+  if (mWin_d == NULL) return;
+	
+	ObjectRect(p,&rcP);
+
+	if (ctrlKey || shftKey)
+		bDeselectAll=FALSE;
+
+  /* handle the case when a block is being deleted in DDV */
+  if (dmp->MouseMode == DDV_MOUSEMODE_DELETEBLOCK) {
+    /* get block index, etc */
+    if (GetBlockAndAlignment(pt, p, dmp, &BlockIndex, &IsUnAligned, &Col, &Offset, &Width, &rcP)) {
+      /* if block is aligned */
+      if (!IsUnAligned) {
+        /* create display for single block */
+        sap = ViewMgr_GetBeginIndexed(dmp->MSA_d.pgp_l.sap);
+        dmp->MSA_d.pgp_l.viewed_sap = dmp->MSA_d.pgp_l.sap;
+        mpplp = DDE_CreateDisplay(sap, BlockIndex, IsUnAligned, &NumBlocks);
+        dsp = DDE_NewStack(mpplp);
+        /* record which block is being edited, etc */
+        dsp->LaunchBlock = BlockIndex;
+        dsp->NumBlocks =   NumBlocks;
+        dsp->IsUnAligned = IsUnAligned;
+        DDE_MergeNodesLists(dsp->pEdit);
+        /* delete block, tell AlnMgr to save edits, redraw DDV */
+        DDE_DeleteBlock(dsp, 0, FALSE);
+        dmp->dsp = dsp;
+        DDV_SaveEdits(dmp, TRUE);
+        /* free stack */
+        dsp = DDE_FreeStack(dsp);
+        dmp->dsp = dsp;
+      }
+    }
+    ArrowCursor();
+    dmp->MouseMode = dmp->SavedMouseMode;
+  }
+  
+  /* handle the click when splitting 2 blocks */
+  if (dmp->MouseMode == DDV_MOUSEMODE_SPLITBLOCK) {
+    FoundIt = FALSE;
+    /* adjust x position so vertical bar jumps when mouse is on center of char */
+    pt.x -= dmp->GrData.udv_font.ColWidth/2;
+    /* if user clicked on an aligned block */
+    if (GetBlockAndAlignment(pt, p, dmp, &BlockIndex, &IsUnAligned, &Col, &Offset, &Width, &rcP)) {
+      /* save col where vertical bar was last drawn */
+      dmp->SaveCol = Col;
+      /* draw vertical bar after this column */
+      HPos = DDV_GetHPixelPosGivenColNumber(dmp, rcP, Col);
+      UDV_draw_vertical_bar(rcP, HPos, FALSE);
+      dmp->ms.Action_type = MS_ACTION_SPLIT_BLOCK;
+      FoundIt = TRUE;
+    }
+    if (!FoundIt) {
+      ArrowCursor();
+    }
+    dmp->MouseMode = dmp->SavedMouseMode;
+  }
+  
+  /* handle the 1st click when merging 2 blocks */
+  /* for the 1st click just need to record the block */
+  else if (dmp->MouseMode == DDV_MOUSEMODE_MERGEBLOCKS1) {
+    FoundIt = FALSE;
+    /* if mouse is in a valid place, get BlockIndex and alignment status */
+    if (GetBlockAndAlignment(pt, p, dmp, &BlockIndex, &IsUnAligned, &Col, &Offset, &Width, &rcP)) {
+      if (!IsUnAligned) {
+        dmp->BlockIndex = BlockIndex;
+        dmp->MouseMode = DDV_MOUSEMODE_MERGEBLOCKS2;
+        FoundIt = TRUE;
+      }
+    }
+    if (!FoundIt) {
+      dmp->MouseMode = dmp->SavedMouseMode;
+      ArrowCursor();
+    }
+  }
+
+  /* handle the 2nd click when merging 2 blocks */
+  else if (dmp->MouseMode == DDV_MOUSEMODE_MERGEBLOCKS2) {
+    /* if mouse is in a valid place, get BlockIndex and alignment status */
+    if (GetBlockAndAlignment(pt, p, dmp, &BlockIndex, &IsUnAligned, &Col, &Offset, &Width, &rcP)) {
+      /* if 2 blocks are next to each other and both aligned */
+      if ((!IsUnAligned) && (ABS(BlockIndex - dmp->BlockIndex) == 1)) {
+        /* create a stack for the block on the right */
+        BlockIndex = MAX(BlockIndex, dmp->BlockIndex);
+        sap = ViewMgr_GetBeginIndexed(dmp->MSA_d.pgp_l.sap);
+        dmp->MSA_d.pgp_l.viewed_sap = dmp->MSA_d.pgp_l.sap;
+        mpplp = DDE_CreateDisplay(sap, BlockIndex, IsUnAligned, &NumBlocks);
+        dsp = DDE_NewStack(mpplp);
+        /* record which block is being edited, etc */
+        dsp->LaunchBlock = BlockIndex;
+        dsp->NumBlocks =   NumBlocks;
+        dsp->IsUnAligned = IsUnAligned;
+        DDE_MergeNodesLists(dsp->pEdit);
+        /* if block on right is flush left */
+        if (DDE_FirstColumnIsAligned(dsp->pEdit)) {
+          /* delete block on right.  count number of cols that were in block. */
+          ColCnt = DDE_DeleteBlock(dsp, 0, FALSE);
+          /* tell AlnMgr to save edits, don't redraw yet */
+          dmp->dsp = dsp;
+          DDV_SaveEdits(dmp, FALSE);
+          /* free stack for block on right.  create stack for block on left */
+          DDE_FreeStack(dsp);
+          sap = ViewMgr_GetBeginIndexed(dmp->MSA_d.pgp_l.sap);
+          dmp->MSA_d.pgp_l.viewed_sap = dmp->MSA_d.pgp_l.sap;
+          mpplp = DDE_CreateDisplay(sap, BlockIndex-1, IsUnAligned, &NumBlocks);
+          dsp = DDE_NewStack(mpplp);
+          /* record which block is being edited, etc */
+          dsp->LaunchBlock = BlockIndex-1;
+          dsp->NumBlocks =   NumBlocks;
+          dsp->IsUnAligned = IsUnAligned;
+          DDE_MergeNodesLists(dsp->pEdit);
+          DDE_Verify(dsp->pEdit);
+          /* shift right boundary of left block by number cols in right block */
+          DDE_ShiftRightBoundary(dsp, 0, ColCnt, FALSE);
+          /* tell AlnMgr to save edits, now redraw */
+          dmp->dsp = dsp;
+          DDV_SaveEdits(dmp, TRUE);
+        }
+        /* free remaining stack */
+        dsp = DDE_FreeStack(dsp);
+        dmp->dsp = dsp;
+      }
+    }
+    dmp->MouseMode = dmp->SavedMouseMode;
+    ArrowCursor();
+  }
+
+  
+  /* handle the case when we're launching the editor on a block */
+  else if (dmp->MouseMode == DDV_MOUSEMODE_LAUNCHEDITOR) {
+    /* if mouse is in a valid place, get BlockIndex and alignment status */
+    if (GetBlockAndAlignment(pt, p, dmp, &BlockIndex, &IsUnAligned, &Col, &Offset, &Width, &rcP)) {
+      /* don't allow editing when there are gaps and no gaps are allowed */
+      pNoGaps = (Boolean*) GetAppProperty("dde_nogaps");
+      if (pNoGaps == NULL) NoGaps = TRUE;
+      else NoGaps = *pNoGaps;
+      IsEditable = AlnMgrIsEditable(dmp->MSA_d.pgp_l.sap);
+      if (!(IsEditable == AM_EDITGAPS && NoGaps) && IsEditable) {
+        ViewMgr_MakeMultiple(dmp->MSA_d.pgp_l.sap);
+      }
+      else {
+        Message(MSG_OK, "%s", "Unable to convert this alignment\n into an editable form.");
+        dmp->MouseMode = dmp->SavedMouseMode;
+        ArrowCursor();
+        return;
+      }
+      /* get pointer to original seqAlign */
+      sap = ViewMgr_GetBeginIndexed(dmp->MSA_d.pgp_l.sap);
+      /* create display for editor */
+      mpplp = DDE_CreateDisplay(sap, BlockIndex, IsUnAligned, &NumBlocks);
+      mpplp->viewed_sap = dmp->MSA_d.pgp_l.sap;
+      /* create the stack used by editor */
+      dsp = DDE_NewStack(mpplp);
+      DDE_MergeNodesLists(dsp->pEdit);
+      /* record which block is being edited, etc */
+      dsp->LaunchBlock = BlockIndex;
+      dsp->NumBlocks =   NumBlocks;
+      dsp->IsUnAligned = IsUnAligned;
+      /* hide the rows in DDE that are hidden in DDV */
+      NumRows = dsp->pEdit->TotalNumRows;
+      for (i=0; i<NumRows; i++) {
+        if (ViewMgr_TRow2VRow(dmp->MSA_d.pgp_l.sap, i+1) == -1) {
+          DDE_HideRow(dsp, i, FALSE);
+        }
+      }
+      DDE_Add(dsp);
+      dsp->SomethingToSave = FALSE;
+      /* launch the editor as a slave */
+      SetAppProperty("ddeinterndata",(void*)dsp);
+      GatherProcLaunch(OMPROC_EDIT, FALSE, dmp->MSA_d.entityID, 
+					dmp->MSA_d.itemID, OBJ_SEQALIGN, 0, 0, OBJ_SEQALIGN, 0);
+      RemoveAppProperty("ddeinterndata");
+    }
+    dmp->MouseMode = dmp->SavedMouseMode;
+    ArrowCursor();
+  }
+  
+  /* handle the case when we're creating an aligned block */
+  else if (dmp->MouseMode == DDV_MOUSEMODE_CREATEBLOCK) {
+    ObjectRect(p, &rcP);
+    InsetRect(&rcP,4,4);
+    DDV_AdjustDrawingRect(&rcP,&(dmp->GrData.udv_font),dmp);
+    rcP.left += dmp->GrData.udv_panel.cxName + dmp->GrData.udv_scale.cxLeftScale;
+    /* if the point is in a valid spot */
+    if (PtInRect(pt, &rcP)) {
+      ObjectRect(p, &rcP);
+      Col = DDV_GetColNumberGivenMousePos(dmp, rcP, pt);
+      /* and the column's legal */
+      if ((Col >= 0) && (Col < dmp->MSA_d.pgp_l.LengthAli)) {
+        /* and there is no aligned block already */
+        if (DDE_GetNumBlocks(dmp->dsp->pEdit) == 0) {
+          /* save start col */
+          dmp->dsp->FromCol = Col;
+          /* save col where vertical bar was last drawn */
+          dmp->dsp->SaveCol = Col;
+          /* draw vertical bar before and after this column */
+          HPos = DDV_GetHPixelPosGivenColNumber(dmp, rcP, dmp->dsp->SaveCol);
+          UDV_draw_vertical_bar(rcP, HPos, TRUE);
+          HPos -= dmp->GrData.udv_font.ColWidth;
+          UDV_draw_vertical_bar(rcP, HPos, TRUE);
+          dmp->ms.Action_type = MS_ACTION_CREATE_BLOCK;
+        }
+        else {
+          dmp->MouseMode = dmp->SavedMouseMode;
+          ArrowCursor();
+        }
+      }
+      else {
+        dmp->MouseMode = dmp->SavedMouseMode;
+        ArrowCursor();
+      }
+    }
+    else {
+      dmp->MouseMode = dmp->SavedMouseMode;
+      ArrowCursor();
+    }
+  }
+
+  /*the mouse is located in a ParaG ?*/
+	/*if YES : the user is selecting either sequence letter(s) or a feature*/
+	else if ((pt.x>(rcP.left+dmp->GrData.udv_panel.cxName+
+       dmp->GrData.udv_scale.cxLeftScale)) &&
+		  (pt.y>(rcP.top+dmp->GrData.udv_panel.cyScale))) {
+			/*get the ParaG list and look for the ParaG where the mouse is located*/
+			/*note : only implemented for DDV_DISP_HORZ type of display...*/
+			if (dmp->MSA_d.pgp_l.DisplayType==DDV_DISP_HORZ){
+				if (DDV_GetCoordsGivenAClick(dmp,&rcP,&pt,
+					&bsp_coord,&SeqAlign_coord,&Disp_coord,&Line_num,
+					&ParaGLine_Num,&uWhere,&cur_pgp)){
+					if (uWhere==PGP_REGION_SEQ){
+						if (bDeselectAll && (dmp->MouseMode==DDV_MOUSEMODE_SELECT ||
+                                 dmp->MouseMode==DDV_MOUSEMODE_SELECT_ONE_ROW))
+							ObjMgrDeSelectAll ();
+						if (shftKey && bsp_coord!=(Int4)-1){
+							UDV_DecodeIdxFeat (dmp->MSA_d.pgp_l.entitiesTbl[ParaGLine_Num-1], 
+								&bsp_eID,&bsp_iID);
+							if (bsp_eID!=0 && bsp_iID!=0){
+								slp=DDV_GetClosetSeqLocGivenBspPos(cur_pgp->sip,bsp_eID, 
+									bsp_iID, bsp_coord, &old_pos, TRUE);
+								if (slp){
+									if (dmp->MouseMode==DDV_MOUSEMODE_SELECT ||
+                      dmp->MouseMode==DDV_MOUSEMODE_SELECT_ONE_ROW)
+										ObjMgrAlsoSelect (bsp_eID, bsp_iID, 
+											OBJ_BIOSEQ,OM_REGION_SEQLOC, slp);
+									if (old_pos!=(Int4)-1)
+										Disp_coord=old_pos;
+								}
+							}
+							dmp->ms.oldPos=pt;
+							dmp->ms.Action_type=MS_ACTION_SELECT_SEQ;
+							return;
+						}
+
+            /* display info about residues that's clicked */
+            if (ParaGLine_Num != -1) {
+              DDV_GetSeqNameGivenRow(dmp->MSA_d.pgp_l.TableHead, ParaGLine_Num, szAccess);
+              DDV_DispPositionInStatus(mWin_d->InfoPanel, bsp_coord+1, ParaGLine_Num, szAccess);
+            }
+
+						/*save the positions */
+						dmp->ms.oldPos=pt;
+						dmp->ms.newPos=pt;
+						dmp->ms.Action_type=MS_ACTION_SELECT_SEQ;
+						dmp->ms.old_row=Line_num;
+						dmp->ms.old_col=Disp_coord;
+						dmp->ms.old_pgp=cur_pgp;
+						dmp->ms.first_row=Line_num;
+            dmp->ms.first_col=Disp_coord;
+            dmp->ms.last_row=Line_num;
+            dmp->ms.last_col=Disp_coord;
+
+            /* show outline of highlighted area */
+            CopyMode();
+            DrawOutline(p, Line_num, Disp_coord, Line_num, Disp_coord, TRUE);
+
+            if (dmp->ms.first_cols == NULL) {
+              NumRows = dmp->MSA_d.pgp_l.nBsp;
+              dmp->ms.first_cols = MemNew(NumRows * sizeof(Int4));
+              dmp->ms.first_pgps = MemNew(NumRows * sizeof(ParaGPtr));
+            }
+						dmp->ms.first_cols[Line_num-1]=Disp_coord;
+						dmp->ms.first_pgps[Line_num-1]=cur_pgp;
+            dmp->ms.first_point=pt;
+            dmp->ms.first_HScroll=dmp->GrData.udv_hscrl.ScrollPos;
+            dmp->ms.first_VScroll=dmp->GrData.udv_vscrl.ScrollPos;
+            dmp->ms.old_HScroll = dmp->GrData.udv_hscrl.ScrollPos;
+            dmp->ms.old_VScroll = dmp->GrData.udv_vscrl.ScrollPos;
+						/*update caret pos, if needed only*/
+						if (dmp->MouseMode==DDV_MOUSEMODE_EDIT){
+							dmp->dci.old_row=dmp->dci.new_row;
+							dmp->dci.old_col=dmp->dci.new_col;
+						}
+            /* if we're in the editor and mousemode is query */
+            /* click and drag on sequence will cause the whole row to shift */
+            if (dmp->bEditor) {
+              if (dmp->MouseMode == DDV_MOUSEMODE_QUERY) {
+                /* make sure column is legit */
+                DDV_GetCurrentDispRange(dmp->hWndDDV,&(dmp->GrData),
+                  dmp->MSA_d.pgp_l.LengthAli,&from_col,&to_col,&from_row,&to_row);
+                /* Don't shift row if clicking on first or last column of */
+                /* display because then the screen scrolls */
+                if (((Disp_coord>from_col) && (Disp_coord<=to_col)) || (Disp_coord==0)) {
+                  /* draw a double rectangle around the selected char */
+                  /* to mark the from spot */
+                  ObjectRect(p, &rcP);
+                  VPos = DDV_GetVPixelPosGivenRowNumber(dmp, rcP, Line_num-1); /* 1-based */
+                  HPos = DDV_GetHPixelPosGivenColNumber(dmp, rcP, Disp_coord); /* 0-based */
+                  rcP2.left =    HPos - dmp->GrData.udv_font.ColWidth;
+                  rcP2.right =   HPos;
+                  rcP2.top =     VPos - dmp->GrData.udv_font.LineHeight;
+                  rcP2.bottom =  VPos;
+                  UDV_draw_rectangle(rcP2, FALSE);
+                  InsetRect(&rcP2, 1, 1);
+                  UDV_draw_rectangle(rcP2, FALSE);
+                  CrossCursor();
+                  dmp->dsp->FromCol = Disp_coord;
+                  dmp->dsp->FromRow = Line_num-1;
+                  dmp->dsp->SaveCol = Disp_coord;
+                  dmp->dsp->SaveRow = Line_num-1;
+                  dmp->ms.Action_type = MS_ACTION_SHIFT_ROW;
+                }
+              }
+            }
+						/*select a single letter*/
+            if (dmp->MouseMode == DDV_MOUSEMODE_SELECT ||
+                dmp->MouseMode == DDV_MOUSEMODE_SELECT_ONE_ROW) {
+/*
+              DDV_SendBSPSelectMsg(dmp, bsp_coord, SeqAlign_coord,
+                Disp_coord, Line_num, ParaGLine_Num, cur_pgp, &pt, TRUE);
+*/
+            }
+					}
+				}
+			}
+	}	
+	/*the mouse is located within the Name list region (left of ParaG) ?*/
+	else if (pt.x>=dmp->GrData.udv_panel.cxName-1 && 
+			pt.x<=dmp->GrData.udv_panel.cxName+3){
+				rcP.left=5*dmp->GrData.udv_font.cxChar; /*min value*/
+				rcP.right=2*PANEL_NAME_WIDTH*dmp->GrData.udv_font.cxChar;/*max val*/
+				pt.x=dmp->GrData.udv_panel.cxName;
+				dmp->ms.oldPos=pt;
+				dmp->ms.newPos=pt;
+				dmp->ms.rcClip=rcP;
+				dmp->ms.Action_type=MS_ACTION_RESIZE_WIN;
+				InvertMode();	
+				UDV_draw_double_cursor(dmp->ms.rcClip,
+					dmp->ms.oldPos);
+				CrossCursor();
+	}
+	/*the mouse is located on a sequence name ?*/
+	else if (pt.x<dmp->GrData.udv_panel.cxName &&
+			pt.y>(rcP.top+dmp->GrData.udv_panel.cyScale)){
+		Line_num=DDV_GetRowGivenMousePos(dmp, &rcP, &pt,&ParaGLine_Num);
+		if (Line_num!=(Int4)-1){
+		    UDV_DecodeIdxFeat (dmp->MSA_d.pgp_l.entitiesTbl[ParaGLine_Num-1], 
+				&bsp_eID,&bsp_iID);
+			if (dblClick /*&& !dmp->bEditor*/){/*load the sequence viewer on that sequence*/
+                {
+                    SAM_ViewGlobal vg;
+                    
+                    MemSet(&vg, 0, sizeof(SAM_ViewGlobal));
+                    vg.pCGlobal = dmp->Globals.colorp;
+                    vg.Row = Line_num;
+                    if(!dmp->bEditor) vg.MasterViewer = SAMVIEWDDV;
+                    else vg.MasterViewer = SAMVIEWDDE;
+                    SetAppProperty(SAM_ViewString, &vg);
+                    GatherSpecificProcLaunch(0, "OneD-Viewer", OMPROC_VIEW,
+                      FALSE, bsp_eID, bsp_iID, OBJ_BIOSEQ);
+                    RemoveAppProperty(SAM_ViewString);
+                }
+            }
+			else{
+				if (dmp->bEditor){
+					WindoW temport;
+					dmp->deri.curEditRow=ParaGLine_Num-1;
+					rcP.left=0;
+					rcP.right=rcP.left+dmp->GrData.udv_panel.cxName;
+					temport=SavePort(ParentWindow(p));
+					Select(p);
+					InvalRect(&rcP);
+					Update();
+					RestorePort(temport);
+          /* record the row that's moving */
+          dmp->dsp->FromRow = Line_num - 1;
+          /* keep track of where the underline is */
+          dmp->dsp->SaveRow = Line_num - 1;
+					dmp->ms.Action_type = MS_ACTION_MOVE_ROW;
+          /* make a rectangle of the sequence names region */
+          ObjectRect(p,&rcP);
+          rcP2.left =   rcP.left;
+          rcP2.right =  rcP.left + dmp->GrData.udv_panel.cxName - 10;
+          rcP2.top =    rcP.top;
+          rcP2.bottom = rcP.bottom;
+          /* draw the underline */
+          VPos = DDV_GetVPixelPosGivenRowNumber(dmp, rcP2, Line_num-1);
+          UDV_draw_horizontal_line(rcP2, VPos);
+          CrossCursor();
+				}
+        else  /* not editor */ {
+            dmwp=(DdvMainWinPtr)GetObjectExtra(dmp->hParent);
+            if(dmwp) {
+                pgp=(ParaGPtr)(dmp->MSA_d.pgp_l.TableHead[Line_num-1]->data.ptrvalue);
+		            bsp=BioseqLockById(pgp->sip);
+                CreateDefLine(NULL,bsp,buf,80,0,NULL,NULL);
+                BioseqUnlock(bsp);
+                SetTitle(dmwp->InfoPanel,buf);
+            }
+        }
+			}
+		}
+	}
+	/*the mouse is located  just on the left of a sequence ? 
+		If true, select the full sequence*/
+	else if ((pt.x>=dmp->GrData.udv_panel.cxName+3) /*after the name of the sequence ?*/
+			&&
+			(pt.x<=dmp->GrData.udv_panel.cxName+3+dmp->GrData.udv_scale.cxLeftScale+
+			dmp->GrData.udv_font.cxChar) /*before the sequence ?*/
+			&& 
+			(dmp->MouseMode==DDV_MOUSEMODE_SELECT ||
+       dmp->MouseMode==DDV_MOUSEMODE_SELECT_ONE_ROW)/*valid only if selection mode*/
+			){
+		if (pt.y>(rcP.top+dmp->GrData.udv_panel.cyScale)){
+			/*get the ParaG list and look for the ParaG where the mouse is located*/
+			/*note : only implemented for DDV_DISP_HORZ type of display...*/
+			if (dmp->MSA_d.pgp_l.DisplayType==DDV_DISP_HORZ){
+				Line_num=DDV_GetRowGivenMousePos(dmp, &rcP, &pt,&ParaGLine_Num);
+				if (Line_num!=(Int4)-1){
+					/*get min,max coord. of BSP*/
+					UDV_GetBspRangeinPGPList(dmp->MSA_d.pgp_l.TableHead[ParaGLine_Num-1],
+						&bsp_start,&bsp_stop);
+					if (bsp_start!=INT4_MAX && bsp_stop!=INT4_MIN){
+						/*now, we can send the Select message*/
+						/* first_pgp, old_pgp & cur_pgp have the same sip... 
+						they are on a same row; I can use one of them*/
+						cur_pgp=(ParaGPtr)(dmp->MSA_d.pgp_l.TableHead[ParaGLine_Num-1]->data.ptrvalue);
+						slp = SeqLocIntNew (bsp_start, bsp_stop, Seq_strand_plus, cur_pgp->sip);
+						UDV_DecodeIdxFeat (dmp->MSA_d.pgp_l.entitiesTbl[ParaGLine_Num-1], 
+							&bsp_eID,&bsp_iID);
+						if (bsp_eID!=0 && bsp_iID!=0 && slp){
+							bIsAlreadyFullSel=DDV_IsFullBspAlreadySel(bsp_eID,bsp_iID,
+								bsp_start,bsp_stop);
+							if (!bIsAlreadyFullSel){
+								if (!bDeselectAll){
+									ObjMgrAlsoSelect (bsp_eID, bsp_iID, 
+										OBJ_BIOSEQ,OM_REGION_SEQLOC, slp);
+								}
+								else{
+									ObjMgrDeSelectAll ();
+									ObjMgrSelect (bsp_eID, bsp_iID, 
+										OBJ_BIOSEQ,OM_REGION_SEQLOC, slp);
+								}
+							}
+							else{
+								if (bDeselectAll)
+									ObjMgrDeSelectAll ();
+								ObjMgrDeSelect (bsp_eID, bsp_iID, 
+									OBJ_BIOSEQ,OM_REGION_SEQLOC, slp);
+							}
+						}		
+					}
+					dmp->ms.Action_type=MS_ACTION_SELECT_FULL_SEQ;
+				}
+			}
+		}
+	}
+
+  /* if the mouse is located on one of the vertical bars, on top, that */
+  /* mark an alignment boundary */
+  else if (OnAlignmentBoundary(pt, p, dmp, &BlockIndex, &LeftBoundary, &Col, &HPos)) {
+    /* record the boundary and block that are being moved */
+    dmp->dsp->FromCol = Col;
+    dmp->dsp->BlockIndex = BlockIndex;
+    dmp->dsp->LeftBoundary = LeftBoundary;
+    /* record the column of the last drawn vertical bar */
+    dmp->dsp->SaveCol = Col;
+    dmp->ms.Action_type = MS_ACTION_SHIFT_BOUNDARY;
+    /* draw a dotted outline of the vertical bar */
+    ObjectRect(p, &rcP);
+    UDV_draw_vertical_bar(rcP, HPos, TRUE);
+    CrossCursor();
+  }
+
+	else{/*click outside "special" regions : deselect everything*/
+		if (dmp->MouseMode==DDV_MOUSEMODE_SELECT ||
+        dmp->MouseMode==DDV_MOUSEMODE_SELECT_ONE_ROW)
+			ObjMgrDeSelectAll ();
+			/*this line if for cn3d only*/
+            ObjMgrSendMsg(OM_MSG_MOUSEUP, dmp->MSA_d.entityID, 
+						dmp->MSA_d.itemID, OBJ_SEQALIGN);
+	}
+
+  if (dmp->bEditor) {
+    DDV_GreyOut(mWin_d, DDE_AtStartOfStack(dmp->dsp), DDE_AtEndOfStack(dmp->dsp));
+  }
+}
+
+
+static Boolean GetBlockAndAlignmentForCol(DdvMainPtr dmp, Int4 Col, Int4* pBlockIndex,
+                                          Boolean* pIsUnAligned, Int4* pOffset, Int4* pWidth) {
+/*****************************************************************************
+*  get the BlockIndex and Alignment status for Col.
+*****************************************************************************/
+  /* if Col is legal */
+  if ((Col >= 0) && (Col < dmp->MSA_d.pgp_l.LengthAli)) {
+    /* get the block or unaligned-region index */
+    if (DDE_IsColValid(&(dmp->MSA_d.pgp_l), Col, pBlockIndex, pIsUnAligned, pOffset, pWidth)) {
+      return(TRUE);
+    }
+  }
+  *pBlockIndex = -1;
+  *pIsUnAligned = TRUE;
+  return(FALSE);
+}
+
+
+static Boolean GetBlockAndAlignment(PoinT pt, PaneL p, DdvMainPtr dmp,
+                                    Int4* pBlockIndex, Boolean* pIsUnAligned,
+                                    Int4* pCol, Int4* pOffset, Int4* pWidth, RecT* rcP) {
+/*****************************************************************************
+*  get the BlockIndex and Alignment status for point pt.
+*****************************************************************************/
+  ObjectRect(p, rcP);
+  InsetRect(rcP,4,4);
+  DDV_AdjustDrawingRect(rcP, &(dmp->GrData.udv_font), dmp);
+  rcP->left += dmp->GrData.udv_panel.cxName + dmp->GrData.udv_scale.cxLeftScale;
+  /* if the point is in a valid spot */
+  if (PtInRect(pt, rcP)) {
+    ObjectRect(p, rcP);
+    *pCol = DDV_GetColNumberGivenMousePos(dmp, *rcP, pt);
+    /* and the column's legal */
+    if ((*pCol >= 0) && (*pCol < dmp->MSA_d.pgp_l.LengthAli)) {
+      /* get the block or unaligned-region index */
+      if (DDE_IsColValid(&(dmp->MSA_d.pgp_l), *pCol, pBlockIndex, pIsUnAligned, pOffset, pWidth)) {
+        return(TRUE);
+      }
+    }
+  }
+  *pCol=-1;
+  *pBlockIndex = -1;
+  *pIsUnAligned = TRUE;
+  return(FALSE);
+}
+
+
+static Boolean RectanglesAreSame(RecT rc1, RecT rc2) {
+/*****************************************************************************
+*  return TRUE if 2 rectangles are identical.
+*****************************************************************************/
+  if (rc1.left   != rc2.left)    return(FALSE);
+  if (rc1.right  != rc2.right)   return(FALSE);
+  if (rc1.top    != rc2.top)     return(FALSE);
+  if (rc1.bottom != rc2.bottom)  return(FALSE);
+  return(TRUE);
+}
+
+
+static void EraseOutline(PaneL p) {
+/*****************************************************************************
+*  erase the old outline of the region selected for highlighting.
+*****************************************************************************/
+  DdvMainPtr  dmp;
+  BaR         hsb, vsb;
+  Int4        HScroll, VScroll;
+
+  dmp = (DdvMainPtr) GetObjectExtra(p);
+	if (dmp==NULL) return;
+
+  hsb = GetSlateHScrollBar((SlatE) dmp->hWndDDV);
+  vsb = GetSlateVScrollBar((SlatE) dmp->hWndDDV);
+
+  /* save current scroll positions, set scroll positions to saved scroll positions */
+  HScroll = dmp->GrData.udv_hscrl.ScrollPos;
+  VScroll = dmp->GrData.udv_vscrl.ScrollPos;
+  SetValue(hsb, dmp->ms.old_HScroll);
+  SetValue(vsb, dmp->ms.old_VScroll);
+
+  /* erase the old rectangle */
+  InvertMode();
+  UDV_draw_rectangle(dmp->ms.outline, FALSE);
+
+  /* restore scroll positions */
+  SetValue(hsb, HScroll);
+  SetValue(vsb, VScroll);
+}
+
+
+static RecT DrawOutline(PaneL p, Int4 Line_num_start, Int4 Disp_coord_start,
+                        Int4 Line_num_stop, Int4 Disp_coord_stop, Boolean Draw) {
+/*****************************************************************************
+*  use current scroll postions.
+*****************************************************************************/
+  RecT        rcP2;
+  DdvMainPtr  dmp;
+
+  rcP2.left = rcP2.right = rcP2.top = rcP2.bottom = 0;
+
+  dmp = (DdvMainPtr) GetObjectExtra(p);
+	if (dmp==NULL) return(rcP2);
+
+  return(DrawOutlineGivenScroll(p,
+    Line_num_start, Disp_coord_start, Line_num_stop, Disp_coord_stop,
+    dmp->GrData.udv_vscrl.ScrollPos, dmp->GrData.udv_hscrl.ScrollPos, Draw));
+}
+
+
+static RecT DrawOutlineGivenScroll(PaneL p, Int4 Line_num_start, Int4 Disp_coord_start,
+                                   Int4 Line_num_stop, Int4 Disp_coord_stop, 
+                                   Int4 VScroll, Int4 HScroll, Boolean Draw) {
+/*****************************************************************************
+*  draw the outline of the region being selected for highlighting.
+*  Line_num_stop and Disp_coord_stop are for the current mouse position.
+*  Line_num_start and Disp_coord_start are for the first click position.
+*  if Draw is FALSE, just return the rectangle and don't draw it.
+*  Line_num's are 1-based.  Disp_coord's are 0-based.
+*  treat VScroll and HScroll as the current scroll positions.
+*  return rectangle that's drawn.
+*****************************************************************************/
+  RecT        rcP, rcP2;
+  DdvMainPtr  dmp;
+  Int4        Line_num_stop_save, Disp_coord_stop_save;
+
+  rcP2.left = rcP2.right = rcP2.top = rcP2.bottom = 0;
+  Line_num_stop_save = Line_num_stop;
+  Disp_coord_stop_save = Disp_coord_stop;
+  
+  dmp = (DdvMainPtr) GetObjectExtra(p);
+	if (dmp==NULL) return(rcP2);
+
+  if (Line_num_start > Line_num_stop) {
+    swap(&Line_num_start, &Line_num_stop);
+  }
+  if (Disp_coord_start > Disp_coord_stop) {
+    swap(&Disp_coord_start, &Disp_coord_stop);
+  }
+  if (Line_num_start < 1)
+    Line_num_start=1;
+  if (Line_num_stop > dmp->MSA_d.pgp_l.nBsp)
+    Line_num_stop=dmp->MSA_d.pgp_l.nBsp;
+  if (Disp_coord_start < 0)
+    Disp_coord_start=0;
+  if (Disp_coord_stop >= dmp->MSA_d.pgp_l.LengthAli)
+    Disp_coord_stop=dmp->MSA_d.pgp_l.LengthAli;
+
+  if (dmp->MouseMode==DDV_MOUSEMODE_SELECT || dmp->MouseMode==DDV_MOUSEMODE_SELECT_ONE_ROW) {
+    /* calculate new rectangle */
+    ObjectRect(p, &rcP);
+    rcP2.top =    DDV_GetVPixelPosGivenRowNumber(dmp, rcP, Line_num_start-1);
+    rcP2.bottom = DDV_GetVPixelPosGivenRowNumber(dmp, rcP, Line_num_stop-1);
+    rcP2.left =   DDV_GetHPixelPosGivenColNumber(dmp, rcP, Disp_coord_start);
+    rcP2.right =  DDV_GetHPixelPosGivenColNumber(dmp, rcP, Disp_coord_stop);
+    rcP2.top -=   dmp->GrData.udv_font.LineHeight;
+    rcP2.left -=  dmp->GrData.udv_font.ColWidth;
+    if (Draw) {
+      /* make clip region */
+	    InsetRect(&rcP,4,4);
+	    DDV_AdjustDrawingRect(&rcP,&(dmp->GrData.udv_font),dmp);
+	    rcP.left+=dmp->GrData.udv_panel.cxName+dmp->GrData.udv_scale.cxLeftScale;
+	    rcP.top+=3*dmp->GrData.udv_panel.cyScale/2;
+      rcP.bottom+=2; /* so bottom of rectangle not cut */
+      ClipRect(&rcP);
+      /* draw new rectangle */
+      UDV_draw_rectangle(rcP2, FALSE);
+      ResetClip();
+      /* save row and col for current mouse pos */
+      dmp->ms.last_row = Line_num_stop_save;
+      dmp->ms.last_col = Disp_coord_stop_save;
+    }
+  }
+  return(rcP2);
+}
+
+
+static Boolean OnAlignmentBoundary(PoinT pt, PaneL p, DdvMainPtr dmp,
+                                   Int4* pBlockIndex, Boolean* pLeftBoundary,
+                                   Int4* pCol, Int4* pHPos) {
+/*****************************************************************************
+*  check if point pt is on one of the vertical bars that mark
+*  alignment boundaries.  return TRUE if it is.
+*  whether it's TRUE or not, ...
+*  return BlockIndex indicating which aligned block,
+*  return LeftBoundary = TRUE if p is on a left boundary,
+*  return LeftBoundary = FALSE if p is on a right boundary.
+*  return Col; the display coordinate for the alignment boundary.
+*  return HPos; the horizontal pixel position of the boundary.
+*****************************************************************************/
+  RecT  rcP, rcBanner;
+  Int4  TopVPos, BotVPos, LeftHPos, RightHPos;
+  Int4  i, NumBlocks;
+
+  /* this only works in the editor */
+  if (!dmp->bEditor) return(FALSE);
+
+  /* make rectangle for banner across top.  make it extra wide */
+  ObjectRect(p, &rcP);
+  DDV_GetVPixelPosOfEmptySpace(dmp, rcP, &TopVPos, &BotVPos);
+  rcBanner = rcP;
+  rcBanner.left += dmp->GrData.udv_panel.cxName + dmp->GrData.udv_scale.cxLeftScale;
+  rcBanner.top =    TopVPos-4;
+  rcBanner.bottom = BotVPos+8;
+  rcBanner.left -= 4;
+
+  /* for each aligned block */
+  NumBlocks = DDE_GetNumBlocks(dmp->dsp->pEdit);
+  for (i=0; i<NumBlocks; i++) {
+    /* check if the pt is reasonably close to the left vertical bar */
+    *pCol = DDE_GetAlignStart(dmp->dsp->pEdit, i);
+    LeftHPos = DDV_GetHPixelPosGivenColNumber(dmp, rcP, *pCol);
+    LeftHPos -= dmp->GrData.udv_font.ColWidth;
+    if ((pt.x >= LeftHPos-5) && (pt.x <= LeftHPos+5)) {
+      *pBlockIndex = i;
+      *pLeftBoundary = TRUE;
+      *pHPos = LeftHPos;
+      if (PtInRect(pt, &rcBanner)) return(TRUE);
+      return(FALSE);
+    }
+    /* check if the pt is reasonably close to the right vertical bar */
+    *pCol = DDE_GetAlignStop(dmp->dsp->pEdit, i);
+    RightHPos = DDV_GetHPixelPosGivenColNumber(dmp, rcP, *pCol);
+    if ((pt.x >= RightHPos-5) && (pt.x <= RightHPos+5)) {
+      *pBlockIndex = i;
+      *pLeftBoundary = FALSE;
+      *pHPos = RightHPos;
+      if (PtInRect(pt, &rcBanner)) return(TRUE);
+      return(FALSE);
+    }
+  }
+  return(FALSE);
+}
+
+
+/*****************************************************************************
+
+Function: DDV_DragProc()
+
+Purpose: manage Mouse-Drag
+
+Parameters:	p; panel handle (currently unused)
+			pt; new position
+
+Return value: none
+
+*****************************************************************************/
+NLM_EXTERN void DDV_DragProc(PaneL p, PoinT pt)
+{
+DdvMainPtr 	dmp;
+RecT        rcP, rcP2;
+ParaGPtr    cur_pgp=NULL;
+Int4        Jump;
+Int4        Line_num, ParaGLine_num;/*to get the coordinates*/
+Int4        VPos, SavedVPos, from_col, to_col, from_row, to_row, old_VPos;
+Int4        HPos, SavedHPos, Col;
+Int4        Disp_coord_stop;
+Int4        Line_num_stop, BlockIndex, Offset, Width;
+BaR         vsb;
+Boolean     IsUnAligned;
+static Boolean  LineToErase=TRUE;
+
+	/*get the panel data*/
+	dmp = (DdvMainPtr) GetObjectExtra(p);
+	if (dmp==NULL) return;
+	
+	/*what is happening ?*/
+	switch(dmp->ms.Action_type){
+		case MS_ACTION_SELECT_SEQ:/*selection on a sequence*/
+			if (shftKey) break;
+			ObjectRect(p,&rcP);
+			/*get the ParaG list and look for the ParaG where the mouse is located*/
+			/*note : only implemented for DDV_DISP_HORZ type of display...*/
+			if (dmp->MSA_d.pgp_l.DisplayType==DDV_DISP_HORZ) {
+        /* get line num and col for current mouse position */
+        DDV_GetRowAndColGivenPt(dmp, rcP, pt, &Disp_coord_stop, &Line_num_stop);
+        /* force single row selection when needed */
+        if (dmp->MouseMode == DDV_MOUSEMODE_SELECT_ONE_ROW) Line_num_stop = dmp->ms.first_row;
+        /* erase the old rectangle */
+        InvertMode();
+        DrawOutline(p, dmp->ms.first_row, dmp->ms.first_col,
+                       dmp->ms.last_row,  dmp->ms.last_col, TRUE);
+        /* get display info */
+        DDV_GetCurrentDispRange(dmp->hWndDDV,&(dmp->GrData),
+          dmp->MSA_d.pgp_l.LengthAli,&from_col,&to_col,&from_row,&to_row);
+        /* draw the new rectangle */
+        CopyMode();
+        DrawOutline(p, dmp->ms.first_row, dmp->ms.first_col, 
+                       Line_num_stop,     Disp_coord_stop, TRUE);
+        /* display info about residues that mouse is over */
+        DDV_DispStatus(dmp, Line_num_stop, dmp->ms.first_col, Disp_coord_stop);
+      }
+
+      break;
+		case MS_ACTION_RESIZE_WIN:/*the user moves the 3D line located between 
+			name area and SeqAlign area*/
+			InvertMode();	
+			UDV_draw_double_cursor(dmp->ms.rcClip, dmp->ms.oldPos);
+			dmp->ms.newPos=pt;
+			UDV_draw_double_cursor(dmp->ms.rcClip, dmp->ms.newPos);
+ 			dmp->ms.oldPos=dmp->ms.newPos;
+			Update();
+			break;
+		case MS_ACTION_SELECT_FULL_SEQ:
+			break;
+    case MS_ACTION_MOVE_ROW:
+			ObjectRect(p,&rcP);
+      rcP2.left =   rcP.left;
+      rcP2.right =  rcP.left + dmp->GrData.udv_panel.cxName - 10;
+      rcP2.top =    rcP.top;
+      rcP2.bottom = rcP.bottom;
+      Line_num=DDV_GetRowGivenMousePos(dmp, &rcP, &pt,&ParaGLine_num);
+
+      DDV_GetCurrentDispRange(dmp->hWndDDV,&(dmp->GrData),
+        dmp->MSA_d.pgp_l.LengthAli,&from_col,&to_col,&from_row,&to_row);
+      vsb = GetSlateVScrollBar ((SlatE)dmp->hWndDDV);
+      old_VPos = GetBarValue(vsb);
+
+      if ((Line_num != -1) && (Line_num-1 >= from_row) && (Line_num-1 <= to_row)) {
+        /* scroll vertically */
+        Jump = ABS((Line_num-1) - dmp->dsp->SaveRow);
+        if (Line_num >= to_row) {
+          SetValue(vsb, old_VPos + Jump);
+        }
+        if (Line_num <= from_row+1) {
+          SetValue(vsb, old_VPos - Jump);
+        }
+        /* get new line number, erase last underline, draw new one */
+        SavedVPos = DDV_GetVPixelPosGivenRowNumber(dmp, rcP2, dmp->dsp->SaveRow);
+        if ((Line_num-1) <= dmp->dsp->FromRow) {
+          /* move before new row */
+          VPos = DDV_GetVPixelPosGivenRowNumber(dmp, rcP2, Line_num-2);
+          dmp->dsp->SaveRow = Line_num-2;
+        }
+        else {
+          /* move after new row */
+          VPos = DDV_GetVPixelPosGivenRowNumber(dmp, rcP2, Line_num-1);
+          dmp->dsp->SaveRow = Line_num-1;
+        }
+        if (LineToErase) {
+          InvertMode();
+          UDV_draw_horizontal_line(rcP2, SavedVPos);
+        }
+        LineToErase = TRUE;
+        UDV_draw_horizontal_line(rcP2, VPos);
+      }
+      else {
+        /* just one time, xor the horizontal line to turn it off */
+        if (LineToErase) {
+          InvertMode();
+          SavedVPos = DDV_GetVPixelPosGivenRowNumber(dmp, rcP2, dmp->dsp->SaveRow);
+          UDV_draw_horizontal_line(rcP2, SavedVPos);
+          LineToErase = FALSE;
+        }
+      }
+      break;
+    case MS_ACTION_SHIFT_ROW:
+			ObjectRect(p,&rcP);
+      Col = DDV_GetColNumberGivenMousePos(dmp, rcP, pt);
+      DDV_GetCurrentDispRange(dmp->hWndDDV,&(dmp->GrData),
+        dmp->MSA_d.pgp_l.LengthAli,&from_col,&to_col,&from_row,&to_row);
+      /* if we're still in a legal area */
+      if ((Col>=from_col) && (Col<=to_col) && PtInRect(pt, &rcP)) {
+        /* if a new box needs to be drawn */
+        if (dmp->dsp->SaveCol != Col) {
+          ObjectRect(p,&rcP);
+          SavedVPos = DDV_GetVPixelPosGivenRowNumber(dmp, rcP, dmp->dsp->SaveRow);
+          SavedHPos = DDV_GetHPixelPosGivenColNumber(dmp, rcP, dmp->dsp->SaveCol);
+          /* erase old box */
+          rcP2.left =    SavedHPos - dmp->GrData.udv_font.ColWidth;
+          rcP2.right =   SavedHPos;
+          rcP2.top =     SavedVPos - dmp->GrData.udv_font.LineHeight;
+          rcP2.bottom =  SavedVPos;
+          InvertMode();
+          UDV_draw_rectangle(rcP2, FALSE);
+          /* draw new box */
+          dmp->dsp->SaveCol = Col;
+          HPos = DDV_GetHPixelPosGivenColNumber(dmp, rcP, Col);
+          rcP2.left =    HPos - dmp->GrData.udv_font.ColWidth;
+          rcP2.right =   HPos;
+          rcP2.top =     SavedVPos - dmp->GrData.udv_font.LineHeight;
+          rcP2.bottom =  SavedVPos;
+          UDV_draw_rectangle(rcP2, FALSE);
+        }
+      }
+      break;
+    case MS_ACTION_SHIFT_BOUNDARY:
+      /* if we're still in a legit area */
+      ObjectRect(p, &rcP);
+      InsetRect(&rcP,4,4);
+      DDV_AdjustDrawingRect(&rcP,&(dmp->GrData.udv_font),dmp);
+      rcP.left += dmp->GrData.udv_panel.cxName + dmp->GrData.udv_scale.cxLeftScale;
+      if (PtInRect(pt, &rcP)) {
+        ObjectRect(p, &rcP);
+        /* get column of new vertical bar */
+        Col = DDV_GetColNumberGivenMousePos(dmp, rcP, pt);
+        /* if column has changed since vertical bar was last drawn */
+        if (Col != dmp->dsp->SaveCol) {
+          /* and the column's legal */
+          if ((Col >= 0) && (Col < dmp->MSA_d.pgp_l.LengthAli)) {
+            /* get horizontal pixel position of old column */
+            HPos = DDV_GetHPixelPosGivenColNumber(dmp, rcP, dmp->dsp->SaveCol);
+            /* adjust for drawing bar preceeding left boundary */
+            if (dmp->dsp->LeftBoundary) HPos -= dmp->GrData.udv_font.ColWidth;
+            /* erase old vertical bar */
+            InvertMode();
+            UDV_draw_vertical_bar(rcP, HPos, TRUE);
+            /* get horizontal pixel position of new column */
+            HPos = DDV_GetHPixelPosGivenColNumber(dmp, rcP, Col);
+            /* adjust for drawing bar preceeding left boundary */
+            if (dmp->dsp->LeftBoundary) HPos -= dmp->GrData.udv_font.ColWidth;
+            /* draw the new vertical bar */
+            UDV_draw_vertical_bar(rcP, HPos, TRUE);
+            /* save the column */
+            dmp->dsp->SaveCol = Col;
+          }
+        }
+      }
+      break;
+    case MS_ACTION_CREATE_BLOCK:
+      ObjectRect(p, &rcP);
+      InsetRect(&rcP,4,4);
+      DDV_AdjustDrawingRect(&rcP,&(dmp->GrData.udv_font),dmp);
+      rcP.left += dmp->GrData.udv_panel.cxName + dmp->GrData.udv_scale.cxLeftScale;
+      /* if we're still in a legit area */
+      if (PtInRect(pt, &rcP)) {
+        ObjectRect(p, &rcP);
+        Col = DDV_GetColNumberGivenMousePos(dmp, rcP, pt);
+        /* and the column has changed since vertical bar was last drawn */
+        if (Col != dmp->dsp->SaveCol) {
+          /* and the column's legal */
+          if ((Col >= 0) && (Col < dmp->MSA_d.pgp_l.LengthAli)) {
+            if (Col >= dmp->dsp->FromCol) {
+              /* get horizontal pixel position of old column */
+              HPos = DDV_GetHPixelPosGivenColNumber(dmp, rcP, dmp->dsp->SaveCol);
+              /* erase old vertical bar */
+              InvertMode();
+              UDV_draw_vertical_bar(rcP, HPos, TRUE);
+              /* get horizontal pixel position of new column */
+              HPos = DDV_GetHPixelPosGivenColNumber(dmp, rcP, Col);
+              /* draw the new vertical bar */
+              UDV_draw_vertical_bar(rcP, HPos, TRUE);
+              /* save the column */
+              dmp->dsp->SaveCol = Col;
+            }
+          }
+        }
+      }
+      break;
+    case MS_ACTION_SPLIT_BLOCK:
+      /* adjust x position so vertical bar jumps when mouse is on center of char */
+      pt.x -= dmp->GrData.udv_font.ColWidth/2;
+      /* get block, col, etc for new mouse position */
+      if (GetBlockAndAlignment(pt, p, dmp, &BlockIndex, &IsUnAligned, &Col, &Offset, &Width, &rcP)) {
+        /* if mouse col changed */
+        if (Col != dmp->SaveCol) {
+          /* get horizontal pixel position of old column */
+          HPos = DDV_GetHPixelPosGivenColNumber(dmp, rcP, dmp->SaveCol);
+          /* erase old vertical bar */
+          InvertMode();
+          UDV_draw_vertical_bar(rcP, HPos, FALSE);
+          /* get horizontal pixel position of new column */
+          HPos = DDV_GetHPixelPosGivenColNumber(dmp, rcP, Col);
+          /* draw the new vertical bar */
+          UDV_draw_vertical_bar(rcP, HPos, FALSE);
+          /* save the column */
+          dmp->SaveCol = Col;
+        }
+      }
+	}
+}
+
+/*****************************************************************************
+
+Function: DDV_ReleaseProc()
+
+Purpose: manage Mouse-Release
+
+Parameters:	p; panel handle (currently unused)
+			pt; new position
+
+Return value: none
+
+*****************************************************************************/
+NLM_EXTERN void DDV_ReleaseProc(PaneL p, PoinT pt)
+{
+WindoW 	       temport;
+DdvMainPtr 	   dmp;
+DdvMainWinPtr  dmwp;
+DDVUpdateMSGPtr dump;
+RecT         rcP, rcP2;
+ParaGPtr     cur_pgp=NULL;
+Int4         bsp_coord, SeqAlign_coord;
+Int4         Disp_coord, Line_num,ParaGLine_Num;/*to get the coordinates*/
+Uint1        uWhere; /*where the use clicked (seq, feat, name,...)*/
+Uint2        bsp_eID, bsp_iID;
+Int4         VPos, Shift, SavedVPos, SavedHPos, BlockIndex, NumBlocks;
+Boolean      IsUnAligned;
+MsaParaGPopListPtr  mpplp;
+SeqAlignPtr   sap;
+DDE_StackPtr  dsp;
+Int4          Offset, Width;
+BaR           hsb;
+RecT          rc;
+
+
+	/*get the panel data*/
+	dmp = (DdvMainPtr) GetObjectExtra(p);
+	if (dmp==NULL) return;
+
+    switch(dmp->ms.Action_type){
+		case MS_ACTION_SELECT_FULL_SEQ:
+            ObjectRect(p,&rcP);
+			Line_num=DDV_GetRowGivenMousePos(dmp,&rcP,&pt,&ParaGLine_Num);
+			if (Line_num!=(Int4)-1){
+                UDV_DecodeIdxFeat (dmp->MSA_d.pgp_l.entitiesTbl[ParaGLine_Num-1], 
+                    &bsp_eID,&bsp_iID);                    
+                ObjMgrSendMsg(OM_MSG_MOUSEUP, bsp_eID, bsp_iID, OBJ_BIOSEQ);
+			}
+			break;
+        case MS_ACTION_SELECT_SEQ:
+            /* erase outline */
+            InvertMode();
+            rc = DrawOutline(p, dmp->ms.first_row, dmp->ms.first_col,
+                                dmp->ms.last_row,   dmp->ms.last_col, TRUE);
+            CopyMode();
+            DDV_SelectRegion(dmp, pt, rc, dmp->ms.first_row, dmp->ms.last_row,
+                                          dmp->ms.first_col, dmp->ms.last_col);
+
+            ObjectRect(p,&rcP);
+            pt.y=dmp->ms.oldPos.y;
+            if (dmp->MSA_d.pgp_l.DisplayType==DDV_DISP_HORZ){            
+                if (DDV_GetCoordsGivenAClick(dmp,&rcP,&pt,
+                        &bsp_coord,&SeqAlign_coord,&Disp_coord,&Line_num,
+
+						&ParaGLine_Num,&uWhere,&cur_pgp)){
+					if (uWhere==PGP_REGION_SEQ){
+                        UDV_DecodeIdxFeat (dmp->MSA_d.pgp_l.entitiesTbl[ParaGLine_Num-1], 
+                            &bsp_eID,&bsp_iID);                    
+                        ObjMgrSendMsg(OM_MSG_MOUSEUP, bsp_eID, bsp_iID, OBJ_BIOSEQ);
+						/*send a OM_MSG_UPDATE message to move the caret (if needed)*/
+						if (dmp->MouseMode==DDV_MOUSEMODE_EDIT){
+							dump=(DDVUpdateMSGPtr)MemNew(sizeof(DDVUpdateMSG));
+							if (dump){
+								dmp->dci.new_row=Line_num;
+								dmp->dci.new_col=Disp_coord;
+								dump->type=UPDATE_TYPE_CARETPOS;
+								dump->data=NULL;
+								ObjMgrSendProcMsg(OM_MSG_UPDATE, bsp_eID, bsp_iID, OBJ_BIOSEQ,
+										0,0,(Pointer)dump);
+								MemFree(dump);
+							}
+						}
+                    }
+                } else {  /* send mouse up anyway */
+                    if(ParaGLine_Num > 0) {
+                        UDV_DecodeIdxFeat (dmp->MSA_d.pgp_l.entitiesTbl[ParaGLine_Num-1], 
+                            &bsp_eID,&bsp_iID);                    
+                        ObjMgrSendMsg(OM_MSG_MOUSEUP, bsp_eID, bsp_iID, OBJ_BIOSEQ);
+                    }
+                }
+            }
+			break;
+		case MS_ACTION_RESIZE_WIN:
+			temport=SavePort((WindoW)p);
+			Select(p);
+			InvertMode();	
+			UDV_draw_double_cursor(dmp->ms.rcClip,
+				dmp->ms.oldPos);
+			/*redraw panel with new 'cxName' value*/
+			if (PtInRect(dmp->ms.newPos,&dmp->ms.rcClip)){
+				RecT rc;
+
+				ObjectRect(p,&rc);
+				rc.left=0;/*for obscure reasons, not == 0*/
+				rc.top=0;
+				dmp->GrData.udv_panel.cxName=dmp->ms.newPos.x;
+				DDV_Resize_DDV(p,FALSE); /*DDV_SetupWin (p,FALSE,NULL); */
+				InvalRect(&rc);
+			}
+			RestorePort(temport);
+			break;
+    case MS_ACTION_MOVE_ROW:
+      ObjectRect(p, &rcP);
+      /* if the mouse is released in sequence name section */
+      if (pt.x<dmp->GrData.udv_panel.cxName &&
+          pt.y>(rcP.top+dmp->GrData.udv_panel.cyScale)){
+        /* get the line number where the mouse is released */
+        Line_num=DDV_GetRowGivenMousePos(dmp, &rcP, &pt,&ParaGLine_Num);
+        if (Line_num != -1) {
+          /* if the line number is valid */
+          if (dmp->dsp->FromRow != Line_num-1) {
+            /* move the saved row to this line number */
+            DDE_MoveRow(dmp->dsp, dmp->dsp->FromRow, Line_num-1, TRUE);
+            dmp->deri.curEditRow = Line_num-1;
+            DDV_ReDraw(dmp);
+          }
+          /* otherwise */
+          else {
+            /* since screen's not redrawn, turn off the last drawn horizontal line */
+            ObjectRect(p, &rcP);
+            rcP2.left =   rcP.left;
+            rcP2.right =  rcP.left + dmp->GrData.udv_panel.cxName - 10;
+            rcP2.top =    rcP.top;
+            rcP2.bottom = rcP.bottom;
+            VPos = DDV_GetVPixelPosGivenRowNumber(dmp, rcP2, dmp->dsp->SaveRow);
+            InvertMode();
+            UDV_draw_horizontal_line(rcP2, VPos);
+          }
+        }
+      }
+      ArrowCursor();
+      break;
+    case MS_ACTION_SHIFT_ROW:
+      /* shift row by diff between original col position and last position */
+      Shift = dmp->dsp->SaveCol - dmp->dsp->FromCol;
+      if (DDE_ShiftRow(dmp->dsp, dmp->dsp->SaveRow, Shift, TRUE, TRUE)) {
+        DDV_ReDraw(dmp);
+      }
+      else {
+        /* if no shift was done, erase the boxes */
+        ObjectRect(p,&rcP);
+        SavedVPos = DDV_GetVPixelPosGivenRowNumber(dmp, rcP, dmp->dsp->SaveRow);
+        SavedHPos = DDV_GetHPixelPosGivenColNumber(dmp, rcP, dmp->dsp->SaveCol);
+        rcP2.left =    SavedHPos - dmp->GrData.udv_font.ColWidth;
+        rcP2.right =   SavedHPos;
+        rcP2.top =     SavedVPos - dmp->GrData.udv_font.LineHeight;
+        rcP2.bottom =  SavedVPos;
+        InsetRect(&rcP2, -2, -2);
+        InvalRect(&rcP2);
+      }
+      ArrowCursor();
+      break;
+    case MS_ACTION_SHIFT_BOUNDARY:
+      /* shift boundary by diff between original col position and last position */
+      Shift = dmp->dsp->SaveCol - dmp->dsp->FromCol;
+      if (dmp->dsp->LeftBoundary) {
+        DDE_ShiftLeftBoundary(dmp->dsp, dmp->dsp->BlockIndex, Shift, TRUE);
+        DDV_ReDraw(dmp);
+      }
+      else {
+        DDE_ShiftRightBoundary(dmp->dsp, dmp->dsp->BlockIndex, Shift, TRUE);
+        DDV_ReDraw(dmp);
+      }
+      ArrowCursor();
+      break;
+    case MS_ACTION_CREATE_BLOCK:
+      DDE_CreateBlock(dmp->dsp, dmp->dsp->FromCol, dmp->dsp->SaveCol, TRUE);
+      dmp->MouseMode = dmp->SavedMouseMode;
+      DDV_ReDraw(dmp);
+      ArrowCursor();
+      break;
+    case MS_ACTION_SPLIT_BLOCK:
+      /* get block and alignment for last saved col */
+      /* also get offset into block and width of block */
+      GetBlockAndAlignmentForCol(dmp, dmp->SaveCol, &BlockIndex, &IsUnAligned, &Offset, &Width);
+      /* if col is in aligned region */
+      if (!IsUnAligned && (Offset < (Width-1))) {
+        /* create a stack for the block */
+        sap = ViewMgr_GetBeginIndexed(dmp->MSA_d.pgp_l.sap);
+        dmp->MSA_d.pgp_l.viewed_sap = dmp->MSA_d.pgp_l.sap;
+        mpplp = DDE_CreateDisplay(sap, BlockIndex, FALSE, &NumBlocks);
+        dsp = DDE_NewStack(mpplp);
+        DDE_MergeNodesLists(dsp->pEdit);
+        /* record which block is being edited, etc */
+        dsp->LaunchBlock = BlockIndex;
+        dsp->NumBlocks =   NumBlocks;
+        dsp->IsUnAligned = IsUnAligned;
+        /* shift right boundary of block left, to the split line */
+        DDE_ShiftRightBoundary(dsp, 0, -(Width-(Offset+1)), FALSE);
+        /* tell AlnMgr to save edits, don't redraw yet */
+        dmp->dsp = dsp;
+        DDV_SaveEdits(dmp, FALSE);
+        /* free stack for block.  create stack for unaligned region to right of block */
+        DDE_FreeStack(dsp);
+        sap = ViewMgr_GetBeginIndexed(dmp->MSA_d.pgp_l.sap);
+        dmp->MSA_d.pgp_l.viewed_sap = dmp->MSA_d.pgp_l.sap;
+        mpplp = DDE_CreateDisplay(sap, BlockIndex+1, TRUE, &NumBlocks);
+        dsp = DDE_NewStack(mpplp);
+        DDE_MergeNodesLists(dsp->pEdit);
+        /* create new block of part that was just unaligned */
+        DDE_CreateBlock(dsp, 0, (Width-(Offset+1)-1), FALSE);
+        /* tell AlnMgr to save edits, now redraw */
+        dmp->dsp = dsp;
+        DDV_SaveEdits(dmp, TRUE);
+        /* free remaining stack */
+        dsp = DDE_FreeStack(dsp);
+        dmp->dsp = dsp;
+        dmp->MouseMode = dmp->SavedMouseMode;
+      }
+      /* get rid of vertical bar */
+      else {
+        hsb = GetSlateHScrollBar((SlatE) dmp->hWndDDV);
+        DDV_ReDrawAtCol(dmp, GetBarValue(hsb), FALSE);
+      }
+	}	
+
+  ClearUDV_mouse_select(&(dmp->ms));
+	dmp->ms.Action_type=MS_ACTION_FEAT_NOTHING;
+	/*update InfoPanel*/
+	dmwp=(DdvMainWinPtr)GetObjectExtra(dmp->hParent);
+  if (dmp->bEditor) {
+    DDV_GreyOut(dmwp, DDE_AtStartOfStack(dmp->dsp), DDE_AtEndOfStack(dmp->dsp));
+  }
+	if (dmwp && dmp->MouseMode!=DDV_MOUSEMODE_EDIT)
+		SetTitle(dmwp->InfoPanel,"Ready !");
+
+  if (dmp->MouseMode != DDV_MOUSEMODE_MERGEBLOCKS2)
+    ArrowCursor();
+}
+
+/*****************************************************************************
+
+Function: DDV_HoldProc()
+
+Purpose: manage Mouse-Hold
+
+Parameters:	p; panel handle (currently unused)
+			pt; new position
+
+Return value: none
+
+*****************************************************************************/
+NLM_EXTERN void DDV_HoldProc(PaneL p, PoinT pt)
+{
+DdvMainPtr 	dmp;
+RecT        rcP;
+ParaGPtr    cur_pgp=NULL;
+Int4        Disp_coord_stop;
+Int4        Line_num_stop;
+Int4        from_col, to_col, from_row, to_row;
+Boolean     Scroll=FALSE;
+
+	/*get the panel data*/
+	dmp = (DdvMainPtr) GetObjectExtra(p);
+	if (dmp==NULL) return;
+
+	/*what is happening ?*/
+	switch(dmp->ms.Action_type){
+		case MS_ACTION_SELECT_SEQ:
+			if (shftKey) break;
+			ObjectRect(p,&rcP);
+			/*get the ParaG list and look for the ParaG where the mouse is located*/
+			/*note : only implemented for DDV_DISP_HORZ type of display...*/
+			if (dmp->MSA_d.pgp_l.DisplayType==DDV_DISP_HORZ) {
+        /* get line num and col for current mouse position */
+        DDV_GetRowAndColGivenPt(dmp, rcP, pt, &Disp_coord_stop, &Line_num_stop);
+        /* force single row selection when needed */
+        if (dmp->MouseMode == DDV_MOUSEMODE_SELECT_ONE_ROW) Line_num_stop = dmp->ms.first_row;
+        /* erase the old rectangle */
+        InvertMode();
+        DrawOutline(p, dmp->ms.first_row, dmp->ms.first_col,
+                       dmp->ms.last_row,  dmp->ms.last_col, TRUE);
+        /* get display info */
+        DDV_GetCurrentDispRange(dmp->hWndDDV,&(dmp->GrData),
+          dmp->MSA_d.pgp_l.LengthAli,&from_col,&to_col,&from_row,&to_row);
+        /* draw the new rectangle after scrolling */
+        DDV_AutoHScroll(dmp, Disp_coord_stop);
+        DDV_AutoVScroll(dmp, Line_num_stop);
+        CopyMode();
+        DrawOutline(p, dmp->ms.first_row, dmp->ms.first_col, 
+                       Line_num_stop,     Disp_coord_stop, TRUE);
+        /* display info about residues that mouse is over */
+        DDV_DispStatus(dmp, Line_num_stop, dmp->ms.first_col, Disp_coord_stop);
+      }
+      break;
+		case MS_ACTION_RESIZE_WIN:
+		case MS_ACTION_SELECT_FULL_SEQ:
+			break;
+	}/*end switch()*/
+}
+
+/*****************************************************************************
+
+Function: DDV_MoveCaretLR()
+
+Purpose: move the caret to the right or to the left
+
+Parameters:	
+
+Return value: none
+
+*****************************************************************************/
+static void DDV_MoveCaretLR(DdvMainPtr dmp,Int4 decal_Hscroll,
+	Boolean bMoveRight,BaR hsb,Int4 old_Hpos,Int4 from_col,Int4 to_col)
+{
+DDVUpdateMSGPtr dump;
+Uint2           bsp_eID, bsp_iID;
+Int4            shift, new_from_col, new_to_col;
+
+	dump=(DDVUpdateMSGPtr)MemNew(sizeof(DDVUpdateMSG));
+	if (dump){
+		/*get bsp IDs*/
+		UDV_DecodeIdxFeat(dmp->MSA_d.pgp_l.entitiesTbl[dmp->dci.new_row-1], 
+            	&bsp_eID,&bsp_iID);
+		/*save old position*/
+		dmp->dci.old_col=dmp->dci.new_col;
+		dmp->dci.old_row=dmp->dci.new_row;
+		/*update the position*/
+		if (bMoveRight)
+			dmp->dci.new_col+=decal_Hscroll;
+		else
+			dmp->dci.new_col-=decal_Hscroll;
+		if (dmp->dci.new_col<0){
+			dmp->dci.new_col=0;
+			Beep();
+			return;
+		}
+		if (dmp->dci.new_col>dmp->MSA_d.pgp_l.LengthAli-1){
+			dmp->dci.new_col=dmp->MSA_d.pgp_l.LengthAli-1;
+			Beep();
+			return;
+		}
+		/*auto-scroll the panel if needed*/
+    if (dmp->dci.new_col<=from_col){
+      shift = (to_col-from_col)/2;
+      new_from_col = from_col - shift;
+      new_to_col = to_col - shift;
+      if ((dmp->dci.new_col >= new_from_col) && (dmp->dci.new_col <= new_to_col)) {
+        /* shift left by 1/2 the window width */
+        SetValue(hsb,old_Hpos-shift);
+      }
+      else {
+        /* shifting by more than 1/2 the window width */
+        SetValue(hsb, dmp->dci.new_col);
+      }
+    }
+    if (dmp->dci.new_col>=to_col){
+      shift = (to_col-from_col)/2;
+      new_from_col = from_col + shift;
+      new_to_col = to_col + shift;
+      if ((dmp->dci.new_col >= new_from_col) && (dmp->dci.new_col <= new_to_col)) {
+        /* shift right by 1/2 the window width */
+        SetValue(hsb,old_Hpos+shift);
+      }
+      else {
+        /* shifting by more than 1/2 the window width */
+        SetValue(hsb, dmp->dci.new_col);
+      }
+    }
+		/*if ok, move the caret*/
+		dump->type=UPDATE_TYPE_CARETPOS;
+		dump->data=NULL;
+		ObjMgrSendProcMsg(OM_MSG_UPDATE, bsp_eID, bsp_iID, OBJ_BIOSEQ,
+				0,0,(Pointer)dump);
+		MemFree(dump);
+	}
+}
+
+/*****************************************************************************
+
+Function: DDV_MoveCaretUD()
+
+Purpose: move the caret up or down
+
+Parameters:	
+
+Return value: none
+
+*****************************************************************************/
+static void DDV_MoveCaretUD(DdvMainPtr dmp,Int4 decal_Vscroll,
+	Boolean bMoveDown,BaR vsb,Int4 old_Vpos,Int4 from_row,Int4 to_row)
+{
+DDVUpdateMSGPtr dump;
+Uint2           bsp_eID, bsp_iID;
+Int4            shift;
+
+	dump=(DDVUpdateMSGPtr)MemNew(sizeof(DDVUpdateMSG));
+	if (dump){
+		/*get bsp IDs*/
+		UDV_DecodeIdxFeat(dmp->MSA_d.pgp_l.entitiesTbl[dmp->dci.new_row-1], 
+            	&bsp_eID,&bsp_iID);
+		/*save old position*/
+		dmp->dci.old_row=dmp->dci.new_row;
+		dmp->dci.old_col=dmp->dci.new_col;
+		/*update the position*/
+		if (bMoveDown)
+			dmp->dci.new_row+=decal_Vscroll;
+		else
+			dmp->dci.new_row-=decal_Vscroll;
+
+		if (dmp->dci.new_row<1){
+			dmp->dci.new_row=1;
+      SetValue(vsb, 0);
+			Beep();
+      goto send_msg;
+		}
+		if (dmp->dci.new_row>dmp->MSA_d.pgp_l.nBsp){
+			dmp->dci.new_row=dmp->MSA_d.pgp_l.nBsp;
+      SetValue(vsb, dmp->MSA_d.pgp_l.nBsp);
+			Beep();
+      goto send_msg;
+		}
+
+		/*auto-scroll the panel if needed*/
+    if (ABS(decal_Vscroll) == 1) {
+		  if (dmp->dci.new_row<=from_row){
+        shift = (to_row-from_row)/2;
+        SetValue(vsb, old_Vpos-shift);
+		  }
+		  if (dmp->dci.new_row>=to_row-1){
+        shift = (to_row-from_row)/2;
+        SetValue(vsb, old_Vpos+shift);
+		  }
+    }
+    else {
+      if (bMoveDown) {
+        SetValue(vsb, old_Vpos+decal_Vscroll);
+      }
+      else {
+        SetValue(vsb, old_Vpos-decal_Vscroll);
+      }
+    }
+
+		/*if ok, move the caret*/
+send_msg:
+		dump->type=UPDATE_TYPE_CARETPOS;
+		dump->data=NULL;
+		ObjMgrSendProcMsg(OM_MSG_UPDATE, bsp_eID, bsp_iID, OBJ_BIOSEQ,
+				0,0,(Pointer)dump);
+		MemFree(dump);
+	}
+}
+
+/*****************************************************************************
+
+Function: DDV_KeyboardProc()
+
+Purpose: manage keyboard actions
+
+Parameters:	s; panel handle (DDV panel)
+			ch; key
+
+Return value: none
+
+*****************************************************************************/
+NLM_EXTERN void DDV_KeyboardProc (SlatE s, Char ch)
+{
+DdvMainWinPtr dmwp; /*main window*/
+DdvMainPtr dmp;     /*DDV panel associated data*/
+BaR        hsb,vsb; /*DDV' scroll bars*/
+Int4       old_Hpos,old_Vpos,/*scrolls positions*/
+           decal_Hscroll,decal_Vscroll,/*used to scroll DDV's panel*/
+           from_col,to_col,from_row,to_row,/*display size*/
+           bsp_pos, height;
+		   
+	if ( (int) ch == 0 ) return;
+	
+	/*get the panel data*/
+	dmp = (DdvMainPtr) GetObjectExtra(s);
+	if (dmp==NULL) return;
+	dmwp = (DdvMainWinPtr) GetObjectExtra(dmp->hParent);
+  if (dmwp == NULL) return;
+	
+	/*get scroll handles and data*/
+	hsb = GetSlateHScrollBar ((SlatE) dmp->hWndDDV);
+	old_Hpos=GetBarValue(hsb);
+	vsb = GetSlateVScrollBar ((SlatE) dmp->hWndDDV);
+	old_Vpos=GetBarValue(vsb);
+
+	/*get the display size*/
+	DDV_GetCurrentDispRange(dmp->hWndDDV,&(dmp->GrData),
+		dmp->MSA_d.pgp_l.LengthAli,&from_col,&to_col,&from_row,&to_row);
+	
+	/*if pressed, scroll panel by one 'panel' size*/
+	if (ctrlKey) {
+		decal_Hscroll=to_col-from_col;
+		decal_Vscroll=to_row-from_row;
+	}
+	else{
+		decal_Hscroll=1;
+		decal_Vscroll=1;
+	}
+
+	/*switch to one-bsed value because dmp->dci values 
+	  are one-based values*/
+	from_row++;to_row++;
+
+	switch ((int) TO_UPPER(ch)){
+    case NLM_PREV:
+      /* page-up -- scoll page up one page height */
+      height = (to_row-from_row) - 1;
+			if (dmp->MouseMode==DDV_MOUSEMODE_EDIT) {
+        DDV_MoveCaretUD(dmp, height, FALSE, vsb, old_Vpos, from_row, to_row);
+      }
+      else {
+        SetValue(vsb, old_Vpos - height);
+      }
+      break;
+    case NLM_NEXT:
+      /* page-down -- scoll page down one page height */
+      height = (to_row-from_row) - 1;
+			if (dmp->MouseMode==DDV_MOUSEMODE_EDIT) {
+				DDV_MoveCaretUD(dmp, height, TRUE, vsb, old_Vpos, from_row, to_row);
+      }
+      else {
+        SetValue(vsb, old_Vpos + height);
+      }
+      break;
+    case NLM_HOME:
+      /* for home key, move cursor to start of row */
+			if (dmp->MouseMode==DDV_MOUSEMODE_EDIT){
+        /* move caret left by current col pos */
+				DDV_MoveCaretLR(dmp, dmp->dci.new_col, FALSE, hsb, old_Hpos, from_col, to_col);
+      }
+      else {
+        SetValue(hsb, 0);
+      }
+      break;
+    case NLM_END:
+      /* for end key, move cursor to end of row */
+			if (dmp->MouseMode==DDV_MOUSEMODE_EDIT){
+        /* move caret right by diff between last col and current col */
+        DDV_MoveCaretLR(dmp, ((dmp->MSA_d.pgp_l.LengthAli-1) - dmp->dci.new_col), TRUE,
+                        hsb, old_Hpos, from_col, to_col);
+      }
+      else {
+        SetValue(hsb, dmp->MSA_d.pgp_l.LengthAli-1);
+      }
+      break;
+    case 0x1a:
+      /* for ctrl-z, undo the last edit */
+      if (DDE_Prev(dmp->dsp)) {
+        DDV_ReDraw(dmp);
+      }
+      break;
+    case 0x19:
+      /* for ctrl-y, redo the last undone edit */
+      if (DDE_Next(dmp->dsp)) {
+        DDV_ReDraw(dmp);
+      }
+      break;
+    case NLM_DEL:
+      /* delete key pressed -- remove a gap and leave carat in place */
+			if (dmp->MouseMode==DDV_MOUSEMODE_EDIT){
+        if (DDE_RemoveGap(dmp->dsp, dmp->dci.new_row-1, dmp->dci.new_col+1, TRUE)) {
+          DDV_ReDraw(dmp);
+        }
+      }
+      break;
+    case 0x08:
+      /* backspace key pressed -- remove gap to the left and move carat left */
+			if (dmp->MouseMode==DDV_MOUSEMODE_EDIT){
+        if (DDE_RemoveGap(dmp->dsp, dmp->dci.new_row-1, dmp->dci.new_col, TRUE)) {
+          DDV_ReDraw(dmp);
+        }
+      }
+		case NLM_LEFT:
+			/*move the caret ?*/
+			if (dmp->MouseMode==DDV_MOUSEMODE_EDIT){
+				decal_Hscroll=1;/*doesn't accept ctrlKey motions*/
+				DDV_MoveCaretLR(dmp,decal_Hscroll,FALSE,hsb,old_Hpos,
+					from_col,to_col);
+			}
+			/*scroll the panel*/
+			else{
+				SetValue(hsb,old_Hpos-decal_Hscroll);
+			}
+			break;
+    case 0x20:
+      /* space bar pressed -- insert a gap and move carat to the right */
+			if (dmp->MouseMode==DDV_MOUSEMODE_EDIT){
+        if (DDE_InsertGap(dmp->dsp, dmp->dci.new_row-1, dmp->dci.new_col+1, TRUE)) {
+          DDV_ReDraw(dmp);
+        }
+      }
+		case NLM_RIGHT:
+			/*move the caret ?*/
+			if (dmp->MouseMode==DDV_MOUSEMODE_EDIT){
+				decal_Hscroll=1;/*doesn't accept ctrlKey motions*/
+				DDV_MoveCaretLR(dmp,decal_Hscroll,TRUE,hsb,old_Hpos,
+					from_col,to_col);
+			}
+			/*scroll the panel*/
+			else {
+				SetValue(hsb,old_Hpos+decal_Hscroll);
+			}
+			break;
+		case NLM_UP:
+			/*move the caret ?*/
+			if (dmp->MouseMode==DDV_MOUSEMODE_EDIT){
+				decal_Vscroll=1;/*doesn't accept ctrlKey motions*/
+				DDV_MoveCaretUD(dmp,decal_Vscroll,FALSE,vsb,old_Vpos,
+					from_row,to_row);
+			}
+			/*scroll the panel*/
+			else{
+				SetValue(vsb,old_Vpos-decal_Vscroll);
+			}
+			break;
+		case NLM_DOWN:
+			/*move the caret ?*/
+			if (dmp->MouseMode==DDV_MOUSEMODE_EDIT){
+				decal_Vscroll=1;/*doesn't accept ctrlKey motions*/
+				DDV_MoveCaretUD(dmp,decal_Vscroll,TRUE,vsb,old_Vpos,
+					from_row,to_row);
+			}
+			/*scroll the panel*/
+			else{
+				SetValue(vsb,old_Vpos+decal_Vscroll);
+			}
+			break;
+		default:
+			Beep ();
+			break;
+	}
+  if (dmp->bEditor) {
+    DDV_GreyOut(dmwp, DDE_AtStartOfStack(dmp->dsp), DDE_AtEndOfStack(dmp->dsp));
+  }
+
+	/*update InfoPanel with position*/
+	if (dmwp && dmp->MouseMode==DDV_MOUSEMODE_EDIT){
+		Char szAccess[21];
+		DDV_GetSeqNameGivenRow(dmp->MSA_d.pgp_l.TableHead, dmp->dci.new_row,
+			szAccess);
+		bsp_pos=DDV_GetBspCoordGivenPgpList(
+			dmp->MSA_d.pgp_l.TableHead[dmp->dci.new_row-1],
+			dmp->dci.new_col);
+		if (bsp_pos!=(Int4)-1){
+			DDV_DispPositionInStatus(dmwp->InfoPanel, 
+				bsp_pos+1,dmp->dci.new_row,szAccess);
+					/*+1 : switch to one-based value*/
+		}
+	}
+}
+
+
+NLM_EXTERN void DDV_ReDrawAtCol(DdvMainPtr dmp, Int4 Col, Boolean DDE) {
+/*------------------------------------------
+*  resize, redraw.
+*------------------------------------------*/
+  DdvMainWinPtr  dmwp;
+  WindoW         temport;
+  RecT 	         rcP;
+  BaR            hsb;
+  Int4           NumBlocks;
+
+  if (DDE) {
+    MemCopy(&(dmp->MSA_d.pgp_l), dmp->dsp->pEdit->pPopList, sizeof(MsaParaGPopList));
+  }
+
+  DDV_InitColour_When_Start(dmp->MSA_d.pgp_l.sap,
+    &(dmp->MSA_d.pgp_l),&(dmp->Globals.colorp), FALSE);
+  /* recalculate window size */
+  DDV_WhatSize(dmp);
+  /* adjust horizontal scroll bar */
+  hsb = GetSlateHScrollBar((SlatE) dmp->hWndDDV);
+  DDV_UpdateHScrollVal(dmp->hWndDDV, FALSE, GetBarValue(hsb));
+
+  dmwp=(DdvMainWinPtr)GetObjectExtra(dmp->hParent);
+  temport=SavePort(dmwp->hWndDDV);
+  Select(dmwp->hWndDDV);
+  ObjectRect(dmwp->hWndDDV, &rcP);
+  InvalRect(&rcP);
+  if (Col >= 0) {
+    SetValue(hsb, Col);
+  }
+  Update();
+  RestorePort(temport);
+
+  if (DDE) {
+    /* decide about greying out undo and redo functions */
+    DDV_GreyOut(dmwp, DDE_AtStartOfStack(dmp->dsp), DDE_AtEndOfStack(dmp->dsp));
+
+    /* decide about greying out left/right/center functions */
+    NumBlocks = DDE_GetNumBlocks(dmp->dsp->pEdit);
+    if (NumBlocks == 0) {
+      Enable(dmwp->MainMenu.Justify);
+    }
+    else {
+      Disable(dmwp->MainMenu.Justify);
+    }
+  }
+
+ 	return;
+}
+
+
+NLM_EXTERN void DDV_ReDraw(DdvMainPtr dmp) {
+/*------------------------------------------
+*  resize, redraw.
+*------------------------------------------*/
+  /* give an illegal column so the column's not set */
+  /* specify that this redraw is for DDE */
+  DDV_ReDrawAtCol(dmp, -1, TRUE);
+}
+
+
+static void DDV_SelectRegion(DdvMainPtr dmp, PoinT pt, RecT rc,
+                             Int4 row_start, Int4 row_stop,
+                             Int4 col_start, Int4 col_stop) {
+/*----------------------------------------------------------------------------
+*  select from row_start to row_stop between columns col_start and col_stop.
+*  rows are 1-based, cols are 0-based.  why?  go figure.
+*  
+*----------------------------------------------------------------------------*/
+  Int4           row;
+  Uint1          uWhere;
+  ParaGPtr       pgp;
+
+  if (row_start > row_stop) swap(&row_start, &row_stop);
+  if (row_start < 1) row_start=1;
+  if (row_stop > dmp->MSA_d.pgp_l.nBsp) row_stop=dmp->MSA_d.pgp_l.nBsp;
+
+  for (row=row_start; row<=row_stop; row++) {
+    /* send message to select all intervening columns on this row */
+    pgp = DDV_GetPGPGivenRowAndCol(dmp, row, col_stop);
+    uWhere = DDV_GetRegionInParaG(pgp, row);
+    if (uWhere == PGP_REGION_SEQ) {
+      DDV_SendBSPSelectMsg(dmp, col_start, col_stop, row, TRUE);
+    }
+  }
+
+  /* redraw section that's been highlighted */
+/*
+  InsetRect(&rc, -4, -4);
+  InvalRect(&rc);
+  Update();
+*/
+}
diff --git a/ddv/ddvclick.h b/ddv/ddvclick.h
new file mode 100644
index 00000000..ec82166f
--- /dev/null
+++ b/ddv/ddvclick.h
@@ -0,0 +1,152 @@
+/*  $Id: ddvclick.h,v 1.10 2000/07/12 15:38:08 hurwitz Exp $
+* ===========================================================================
+*
+*                            PUBLIC DOMAIN NOTICE
+*            National Center for Biotechnology Information (NCBI)
+*
+*  This software/database is a "United States Government Work" under the
+*  terms of the United States Copyright Act.  It was written as part of
+*  the author's official duties as a United States Government employee and
+*  thus cannot be copyrighted.  This software/database is freely available
+*  to the public for use. The National Library of Medicine and the U.S.
+*  Government do not place any restriction on its use or reproduction.
+*  We would, however, appreciate having the NCBI and the author cited in
+*  any work or product based on this material
+*
+*  Although all reasonable efforts have been taken to ensure the accuracy
+*  and reliability of the software and data, the NLM and the U.S.
+*  Government do not and cannot warrant the performance or results that
+*  may be obtained by using this software or data. The NLM and the U.S.
+*  Government disclaim all warranties, express or implied, including
+*  warranties of performance, merchantability or fitness for any particular
+*  purpose.
+*
+* ===========================================================================
+*
+* File Name:  ddvclick.h
+*
+* Author:  Patrick Durand
+*
+* Version Creation Date:   09/20/99
+*
+* $Revision: 1.10 $
+*
+* File Description: 
+*
+* Modifications:
+* --------------------------------------------------------------------------
+* $Log: ddvclick.h,v $
+* Revision 1.10  2000/07/12 15:38:08  hurwitz
+* made rectangle select much faster.  it's almost working.
+*
+* Revision 1.9  2000/07/08 20:43:58  vakatov
+* Get all "#include" out of the 'extern "C" { }' scope;  other cleanup...
+*
+* Revision 1.8  2000/07/05 19:23:13  lewisg
+* add two panes to ddv, update msvc project files
+*
+* Revision 1.7  2000/07/05 18:42:16  hurwitz
+* added split block function to DDV
+*
+* Revision 1.6  2000/05/05 20:24:13  hurwitz
+* some bug fixes, also redraw proper block in DDE after a save operation that causes a merge of 2 blocks
+*
+* Revision 1.5  2000/05/04 22:43:38  hurwitz
+* don't launch DDE on top of DDV, change some wording, redraw DDE after save to AlnMgr
+*
+* Revision 1.4  2000/04/05 20:52:35  hurwitz
+* added GUI control for shifting left and right alignment boundaries
+*
+* Revision 1.3  1999/12/07 21:40:14  durand
+* add mouse modes menu and caret facility for the editor
+*
+* Revision 1.2  1999/10/29 14:15:39  durand
+* add simple mouse selection functions
+*
+* Revision 1.1  1999/09/30 14:10:25  durand
+* add ddv to toolkit
+*
+* Revision 1.2  1999/09/22 20:41:18  durand
+* add mouse-click and drag functions
+*
+* Revision 1.1  1999/09/21 14:20:00  durand
+* add basic mouse management functions
+*
+*
+*
+*
+* ==========================================================================
+*/
+
+#ifndef _DDVCLICK_
+#define _DDVCLICK_
+
+#include <ddvmain.h>
+
+#undef NLM_EXTERN
+#ifdef NLM_IMPORT
+#define NLM_EXTERN NLM_IMPORT
+#else
+#define NLM_EXTERN extern
+#endif
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/******************************************************************************
+
+	structures
+
+******************************************************************************/
+
+/******************************************************************************
+
+	defines
+
+******************************************************************************/
+/*identifiers of the regions within a ParaG*/
+#define PGP_REGION_NOWHERE ((Uint1)1)
+#define PGP_REGION_SEQ ((Uint1)2)
+#define PGP_REGION_FEAT ((Uint1)3)
+
+/******************************************************************************
+
+	Exported functions
+
+******************************************************************************/
+NLM_EXTERN void DDV_DispPositionInStatus(PrompT InfoPanel,Int4 bsp_pos,
+		Int4 line_num,CharPtr szSeqName);
+NLM_EXTERN void DDV_GetSeqNameGivenRow(ValNodePtr * ParaG_List, Int4 row_num,
+	CharPtr szSeqName);
+NLM_EXTERN void DDV_ClickProcUpper(PaneL p, PoinT pt);
+NLM_EXTERN void DDV_ClickProcLower(PaneL p, PoinT pt);
+NLM_EXTERN void DDV_ClickProc(PaneL p, PoinT pt);
+NLM_EXTERN void DDV_DragProc(PaneL p, PoinT pt);
+NLM_EXTERN void DDV_HoldProc(PaneL p, PoinT pt);
+NLM_EXTERN void DDV_ReleaseProc(PaneL p, PoinT pt);
+NLM_EXTERN void DDV_KeyboardProc (SlatE s, Char ch);
+NLM_EXTERN Int4 DDV_GetHPixelPosGivenColNumber(DdvMainPtr dmp, RecT rc, Int4 Col);
+NLM_EXTERN Int4 DDV_GetHPixelPosGivenColNumberAndScroll(DdvMainPtr dmp, RecT rc,
+                                                        Int4 Col, Int4 ScrollPos);
+NLM_EXTERN Int4 DDV_GetVPixelPosGivenRowNumber(DdvMainPtr dmp, RecT rc, Int4 Row);
+NLM_EXTERN Int4 DDV_GetVPixelPosGivenRowNumberAndScroll(DdvMainPtr dmp, RecT rc,
+                                                        Int4 Row, Int4 ScrollPos);
+NLM_EXTERN void DDV_GetVPixelPosOfEmptySpace(DdvMainPtr dmp, RecT rc, Int4* pTop, Int4* pBot);
+NLM_EXTERN Int4 DDV_GetColNumberGivenMousePos(DdvMainPtr dmp, RecT rc, PoinT pt);
+NLM_EXTERN void DDV_ReDraw(DdvMainPtr dmp);
+NLM_EXTERN void DDV_ReDrawAtCol(DdvMainPtr dmp, Int4 Col, Boolean DDE);
+
+#ifdef __cplusplus
+}
+#endif
+
+#undef NLM_EXTERN
+#ifdef NLM_EXPORT
+#define NLM_EXTERN NLM_EXPORT
+#else
+#define NLM_EXTERN
+#endif
+
+#endif /* ndef _DDVCLICK_ */
+
diff --git a/ddv/ddvcreate.c b/ddv/ddvcreate.c
new file mode 100644
index 00000000..6964e70f
--- /dev/null
+++ b/ddv/ddvcreate.c
@@ -0,0 +1,3439 @@
+/*  $Id: ddvcreate.c,v 1.66 2001/02/01 00:39:53 lewisg Exp $
+* ===========================================================================
+*
+*                            PUBLIC DOMAIN NOTICE
+*            National Center for Biotechnology Information (NCBI)
+*
+*  This software/database is a "United States Government Work" under the
+*  terms of the United States Copyright Act.  It was written as part of
+*  the author's official duties as a United States Government employee and
+*  thus cannot be copyrighted.  This software/database is freely available
+*  to the public for use. The National Library of Medicine and the U.S.
+*  Government do not place any restriction on its use or reproduction.
+*  We would, however, appreciate having the NCBI and the author cited in
+*  any work or product based on this material
+*
+*  Although all reasonable efforts have been taken to ensure the accuracy
+*  and reliability of the software and data, the NLM and the U.S.
+*  Government do not and cannot warrant the performance or results that
+*  may be obtained by using this software or data. The NLM and the U.S.
+*  Government disclaim all warranties, express or implied, including
+*  warranties of performance, merchantability or fitness for any particular
+*  purpose.
+*
+* ===========================================================================
+*
+* File Name:  ddvcreate.c
+*
+* Author:  Sarah Wheelan
+*
+* Version Creation Date:   08/99
+*
+* $Revision: 1.66 $
+*
+* File Description: 
+*
+* Modifications:
+* --------------------------------------------------------------------------
+* $Log: ddvcreate.c,v $
+* Revision 1.66  2001/02/01 00:39:53  lewisg
+* fix leak
+*
+* Revision 1.65  2001/01/29 20:35:49  hurwitz
+* make gap between aligned blocks optional
+*
+* Revision 1.64  2001/01/25 21:49:14  hurwitz
+* added option for extra gap char (tilde) between aligned blocks
+*
+* Revision 1.63  2001/01/19 22:05:40  wheelan
+* took out small spaces created by UABuildDescriptor
+*
+* Revision 1.62  2001/01/10 23:38:39  lewisg
+* fix seqid and various memory leaks
+*
+* Revision 1.61  2000/09/08 21:50:38  hurwitz
+* made DDV_ReadSeqBin public
+*
+* Revision 1.60  2000/09/06 17:41:26  shavirin
+* Fixed bug with printing gaps with discontinuous alignment.
+*
+* Revision 1.59  2000/08/25 18:55:27  shavirin
+* Changed layout - unaligned regions will be always in lower characters.
+*
+* Revision 1.58  2000/08/22 19:59:28  shavirin
+* Changed layout no.1 - it will be used for standalone blast with
+* decline-to-align parameter not = 0
+*
+* Revision 1.57  2000/07/19 18:46:19  bauer
+* Fixed bug in DDV_CreateDisplayFromIndex_EX
+*
+* Revision 1.56  2000/06/29 23:15:13  hurwitz
+* leave single space between aligned blocks with no unaligned sequence between them, no auto-merge of adjacent aligned blocks
+*
+* Revision 1.55  2000/06/22 20:56:52  hurwitz
+* assorted bug fixes
+*
+* Revision 1.54  2000/06/13 18:23:55  hurwitz
+* made ViewMgr_MakeMultiple routine, call this on each launch of DDE rather than launch of DDV
+*
+* Revision 1.53  2000/06/12 23:02:40  hurwitz
+* enable launch of DDE from Cn3D, swith from DDV_ComputeRuler to DDE_ReMakeRuler, get rid of styles option for DDE
+*
+* Revision 1.52  2000/06/08 20:04:38  hurwitz
+* made warning about converting to true multiple alignment into a Message window, and other small fixes
+*
+* Revision 1.51  2000/06/07 19:09:36  hurwitz
+* made DDE_ReMakeRuler work with linked list of ParaGs
+*
+* Revision 1.50  2000/05/10 16:17:00  hurwitz
+* can show tails for just 1 aligned block
+*
+* Revision 1.49  2000/05/08 13:16:00  wheelan
+* replaced segment-based counting with block-based counting
+*
+* Revision 1.48  2000/05/04 22:43:38  hurwitz
+* don't launch DDE on top of DDV, change some wording, redraw DDE after save to AlnMgr
+*
+* Revision 1.47  2000/05/03 19:34:38  wheelan
+* added fix for NULL alignments
+*
+* Revision 1.46  2000/05/03 14:51:02  thiessen
+* revert to ~ gap char for Cn3D
+*
+* Revision 1.45  2000/04/21 23:00:50  hurwitz
+* can launch DDE from DDV
+*
+* Revision 1.44  2000/04/19 19:08:23  hurwitz
+* problem with justification of flanking unaligned regions fixed
+*
+* Revision 1.43  2000/04/19 15:45:50  hurwitz
+* can create display for a block
+*
+* Revision 1.42  2000/04/06 17:59:50  durand
+* fixed a conflict between BLAST and DDV in the use of the function DDV_SetSTyle
+*
+* Revision 1.41  2000/04/04 19:08:00  durand
+* add new BLAST color schemas; fixed a bug in DDV_PopulateDisplayForDisc
+*
+* Revision 1.40  2000/03/31 21:33:07  durand
+* added new default color schemas for BLAST
+*
+* Revision 1.39  2000/03/28 21:20:07  shavirin
+* Adjusted for correct structure of BLAST location mask.
+*
+* Revision 1.38  2000/03/28 17:08:17  durand
+* removed debugging code lines
+*
+* Revision 1.37  2000/03/27 14:19:28  durand
+* fixed bugs in BLAST outputs
+*
+* Revision 1.36  2000/03/21 19:26:45  durand
+* adapt ddvcreate to be used by pgppop
+*
+* Revision 1.35  2000/03/20 13:46:23  durand
+* fixed a bug in BLAST functions; added DDV_BLAST_COLOR0 to produce a BLAST output without any layout
+*
+* Revision 1.34  2000/02/28 16:52:47  durand
+* wrote a new manager for unaligned regions
+*
+* Revision 1.33  2000/02/23 21:34:29  durand
+* allow custom display of gap characters
+*
+* Revision 1.32  2000/02/23 19:49:33  durand
+* use row number instead of SeqId for coloring
+*
+* Revision 1.31  2000/02/17 15:54:56  durand
+* use ~ for an unaligned gap and - for an aligned gap
+*
+* Revision 1.30  2000/02/15 22:40:57  lewisg
+* add ability to launch udv so that it colors by row, fixes to colormgr, track rows from viewmgr, fix visual c projects
+*
+* Revision 1.29  2000/02/14 16:49:33  durand
+* add new options for BLAST output
+*
+* Revision 1.28  2000/02/11 13:58:21  wheelan
+* bug fix for unaligned region of length 0 (Durand)
+*
+* Revision 1.27  2000/02/07 14:03:35  durand
+* replace BioseqUnlockById by BioseqUnlock
+*
+* Revision 1.26  2000/02/05 01:32:22  lewisg
+* add viewmgr, move place freeing is done in ddv, modify visual c++ projects
+*
+* Revision 1.25  2000/02/02 14:44:30  durand
+* added function to create data structure for block editor, fixed some bugs
+*
+* Revision 1.24  2000/01/26 13:38:54  durand
+* update the GUI for the editor. Add functions to create the data to be used by the editor
+*
+* Revision 1.23  1999/12/29 22:55:03  lewisg
+* get rid of seqalign id
+*
+* Revision 1.22  1999/12/20 20:20:41  lewisg
+* allow cn3d to do color and ddv to do case when both are running
+*
+* Revision 1.21  1999/12/20 14:45:37  durand
+* add new functions for the new BLAST outputs
+*
+* Revision 1.20  1999/12/08 22:42:17  durand
+* add the code to produce colored BLAST outputs
+*
+* Revision 1.19  1999/12/03 23:17:22  lewisg
+* Patrick's new global update msg, argument passing when launching ddv, experimental editing
+*
+* Revision 1.18  1999/12/03 18:24:08  durand
+* gapped regions are displayed using lower cases; BLAST outputs
+*
+* Revision 1.17  1999/12/03 13:23:08  durand
+* replace AlnMgrGetNumSeqs by AlnMgrGetNumRows
+*
+* Revision 1.16  1999/12/02 14:46:42  durand
+* fix a bug in UABuildDescriptor; problem with unaligned region of size 0
+*
+* Revision 1.15  1999/11/24 21:26:29  vakatov
+* Fixed for the C++ and/or MSVC DLL compilation
+*
+* Revision 1.14  1999/11/17 22:44:02  durand
+* speed up the selection manager for large SeqAlign
+*
+* Revision 1.13  1999/11/09 22:14:01  shavirin
+* Added parameter follower to the Blast score printing function
+*
+* Revision 1.12  1999/11/09 17:08:59  durand
+* transfer some functions from ddvgraph to ddvcreate, so that ddvcreate remains Vibrant free and can be compiled with BLAST
+*
+* Revision 1.11  1999/11/03 21:29:48  durand
+* add CTRL and SHFT keys for mouse selection. redesign the loader functions of DDV to properly register the message callbacks
+*
+* Revision 1.10  1999/10/29 14:15:40  durand
+* add simple mouse selection functions
+*
+* Revision 1.9  1999/10/22 20:12:47  durand
+* add Export command (text, HTML and Phylip formats)
+*
+* Revision 1.8  1999/10/22 14:57:25  durand
+* use AlnMgrIndexSingleChildSeqAlign to build BLAST output
+*
+* Revision 1.7  1999/10/22 13:17:19  durand
+* remove unreferenced variables to avoid warnings with Visual C
+*
+* Revision 1.6  1999/10/20 13:17:19  durand
+* add display for disc. SeqAlign tails
+*
+* Revision 1.5  1999/10/15 21:57:35  durand
+* add a UI for display options
+*
+* Revision 1.4  1999/10/12 15:01:29  lewisg
+* resolve confict with internal/ddv
+*
+* Revision 1.3  1999/10/07 13:36:08  wheelan
+* bug fixes -- AlnLengths were 1 too long
+*
+* Revision 1.2  1999/10/05 14:04:21  wheelan
+* made DDV_CreateDisplayFromIndex_2, which creates the display for discontinuous alignments; minor bug fixes
+*
+* Revision 1.1  1999/09/30 14:10:25  durand
+* add ddv to toolkit
+*
+* Revision 1.11  1999/09/30 13:38:09  durand
+* DDV_CreateDisplayFromIndex takes ParaG_Size as an argument
+*
+*
+*
+* ==========================================================================
+*/
+#include <ddvcreate.h>
+#include <pgppop.h>
+#include <udvseq.h>
+#include <tofasta.h>
+#include <sqnutils.h>
+
+typedef struct ddvdataforcolorfunc{
+	SeqIdPtr sip;
+	Int4     from;
+	Int4     to;
+	Int4     row;
+	Uint1    strand;
+	Boolean  IsUnAligned;
+	Uint1    style;
+	Uint1    rgb[3];
+	Uint1    UAstyle;
+	Uint1    UArgb[3];
+} DDVDataForColorFunc, PNTR DDVDataForColorFuncPtr;
+
+#define MAX_NCBIstdaa 26
+#define MAX_NCBI4na 17
+#define DDVCOL_DEFAULT 0
+#define DDVCOL_HOTPINK 1
+#define DDVCOL_MAGENTA 2
+#define DDVCOL_PURPLE 3
+#define DDVCOL_BLUE 4
+#define DDVCOL_SKY 5
+#define DDVCOL_CYAN 6
+#define DDVCOL_SEA 7
+#define DDVCOL_GREEN 8
+#define DDVCOL_YELLOW 9
+#define DDVCOL_GOLD 10
+#define DDVCOL_ORANGE 11
+#define DDVCOL_RED 12
+#define DDVCOL_PINK 13
+#define DDVCOL_PINKTINT 14
+#define DDVCOL_WHITE 15
+#define DDVCOL_BLACK 16
+#define DDVCOL_BLUETINT 17
+#define DDVCOL_GREENTINT 18
+#define DDVCOL_YELLOWTINT 19
+#define DDVCOL_GRAY 20
+#define DDVCOL_BROWN 21
+#define DDV_COLOR_MAX 33 
+ static Uint1 DDV_PaletteRGB[DDV_COLOR_MAX][3] =
+ {
+     /* Red  Grn Blue     Color     ColorID             Old Hex  New Hex */
+   255, 255, 255, /* default     0                 0xffffff - */ 
+   255,   0, 153, /* hotpink     1                 0xff1493 0xff0099 */
+   255,   0, 255, /* magenta     2                 0xff00ff - */
+   153,  51, 255, /* purple      3                 0x9b30ff 0x9933ff */
+     0,   0, 255, /* blue        4                 0x0000ff - */
+    00, 153, 255, /* sky         5                 0x1e90ff 0x0099ff */
+     0, 255, 255, /* cyan        6                 0x00ffff - */
+     0, 255, 153, /* sea         7                 0x00ff8f 0x00ff99 */
+     0, 192,   0, /* green       8                 0x00ff00 - */
+   255, 255,   0, /* yellow      9                 0xffff00 - */
+   255, 204,   0, /* gold       10                 0xffa500 0xffcc00 */
+   255, 102,   0, /* orange     11                 0xff4500 0xff6600 */
+   255,   0,   0, /* red        12                 0xff0000 - */
+   255, 153, 153, /* pink       13                 0xff7256 0xff9999 */
+   255, 204, 204, /* pinktint   14                 0xffaeb9 0xffcccc */
+   255, 255, 255, /* white      15                0xffffff  -*/
+     0,   0,   0, /* black      16                0x000000 - */
+   204, 204, 255, /* bluetint   17                0xb0e2ff - 0xccccff*/
+   153, 255, 153, /* greentint  18                0x9aff9a - 0x99ff99 */
+   255, 255, 153, /* yellowtint 19                0xffec8b - 0xffff99 */
+   102, 102, 102, /* gray       20                0x7d7d7d   0x666666 */
+   153, 102,  51, /* brown      21                0x8b5742   01x996633 */
+   255,   0,   0, /* perm colors 22: red          0xff0000 - */
+     0, 255,   0, /* perm colors 23: green        0x00ff00 - */
+   255,   0, 255, /* perm colors 24: magenta      0xff00ff - */
+    00, 153, 255, /* perm colors 25: sky          0x1e90ff 0x0099ff */
+   153,	 51, 255, /* perm colors 26: purple        0x9b30ff 0x9933ff */
+     0, 255,   0, /* SS colors 27: helix, green   0x00ff00 - */
+   255, 204,   0, /* SS colors 28: strand, gold   0xffa500 0xffcc00 */
+   255, 102,   0, /* SS colors 29: turn, orange   0xff4500 0xff6600 */
+     0, 255, 255, /* SS colors 30: coil, cyan     ox00ffff - */
+   255, 255,   0, /* highlight colors 31: yellow  0xffff00 - */
+     0,   0,   0 /* background colors 32: black  0x000000 - */
+ };
+Uint1 DDV_STD_AAColor[MAX_NCBIstdaa] =
+{DDVCOL_BROWN, /*-*/
+DDVCOL_GRAY,   /*A*/
+DDVCOL_ORANGE, /*B*/
+DDVCOL_PINK, /*C*/
+DDVCOL_RED,    /*D*/
+DDVCOL_RED,    /*E*/
+DDVCOL_PURPLE, /*F*/
+DDVCOL_GRAY,   /*G*/
+DDVCOL_BLUE,   /*H*/
+DDVCOL_GRAY,   /*I*/
+DDVCOL_BLUE,   /*K*/
+DDVCOL_GRAY,   /*L*/
+DDVCOL_PINK, /*M*/
+DDVCOL_CYAN,   /*N*/
+DDVCOL_MAGENTA,/*P*/
+DDVCOL_CYAN,   /*Q*/
+DDVCOL_BLUE,   /*R*/
+DDVCOL_GREEN,  /*S*/
+DDVCOL_GREEN,  /*T*/
+DDVCOL_GRAY,   /*V*/
+DDVCOL_PURPLE, /*W*/
+DDVCOL_GRAY,   /*X*/
+DDVCOL_PURPLE, /*Y*/
+DDVCOL_ORANGE, /*Z*/
+DDVCOL_GOLD,   /*U*/
+DDVCOL_HOTPINK /***/};
+
+Uint1 DDV_STD_NAColor[MAX_NCBI4na] = {
+DDVCOL_PINK,   /* gap */
+DDVCOL_GREEN,  /* A */
+DDVCOL_BLUE,   /* C */
+DDVCOL_CYAN,   /* A or C */
+DDVCOL_BLACK,  /* G */
+DDVCOL_CYAN,   /* G or A */
+DDVCOL_CYAN,   /* G or C */
+DDVCOL_PURPLE, /* G C or A */
+DDVCOL_RED,    /* T */
+DDVCOL_CYAN,   /* A or T */
+DDVCOL_CYAN,   /* T or C */
+DDVCOL_PURPLE, /* A C ot T */
+DDVCOL_CYAN,   /* G ot T */
+DDVCOL_PURPLE, /* G or A or T */
+DDVCOL_PURPLE, /* G T or C */
+DDVCOL_HOTPINK,/* G T A or C */
+DDVCOL_GRAY /*?, but MAX_NCBI4na==17, see mmdbapi2.h*/
+};
+
+extern void display_ParaG_content(MsaParaGPopListPtr mpplp,Int2 LineSize)
+{
+BioseqPtr bsp_debug=NULL;
+Char                    szBuf[15];
+ParaGPtr                pgp;
+MsaTxtDispPtr mtdp;
+ValNodePtr    vnp,vnp2;
+Uint4 j,k,size,sum;
+FILE *fp;
+Boolean bClose=TRUE;
+Int4 i;
+	if (LineSize<=50)/*just for the integrity of the function...*/
+		LineSize=ParaG_Size;
+		
+        fp=fopen("zpgplist.txt","w");
+        if (fp==NULL) {fp=stdout;bClose=FALSE;}
+        for(i=0;i<mpplp->nBsp;i++){
+                /*for each line (i.e. bioseq) */
+                vnp=mpplp->TableHead[i];
+                if (vnp) pgp=(ParaGPtr)(vnp->data.ptrvalue);
+                else pgp=NULL;
+                if(pgp){
+                        if (pgp->sip) bsp_debug=BioseqLockById(pgp->sip);
+                        else bsp_debug=NULL;
+                        if (bsp_debug){
+                                /*get the access code*/
+                                SeqIdWrite(bsp_debug->id, szBuf, PRINTID_TEXTID_ACCESSION, 14);
+                                fprintf(fp,"[%5u] %s , size: %d, IsAA :%d \n",
+                                        i,szBuf,BioseqGetLen(bsp_debug),
+                                        ISA_aa(bsp_debug->mol));
+                                BioseqUnlock(bsp_debug);
+                        }
+                        else StringCpy(szBuf,"unknown");
+                }
+                k=1;size=1;
+                while(vnp){
+                        pgp=(ParaGPtr)(vnp->data.ptrvalue);
+                        if (pgp){/*create the name table*/
+                                /*loop on the pgp*/
+                                fprintf(fp,"  ->ParaG[%d] , range (%7d..%7d):\n",k++,size,size+LineSize-1);
+                                size+=LineSize;
+                                vnp2=pgp->ptxtList;
+                                j=1;sum=0;
+                                while(vnp2){
+                                        mtdp=(MsaTxtDispPtr)vnp2->data.ptrvalue;
+                                        if (mtdp){
+                                        fprintf(fp,"    (%4u): range(%7d..%7d) (%2d), Gap: %2d, Strand(%d)\n",
+                                                j++,mtdp->from,mtdp->to,mtdp->to-mtdp->from+1,mtdp->IsGap,
+                                                mtdp->strand);
+                                        }
+										sum+=(mtdp->to-mtdp->from+1);
+                                        vnp2=vnp2->next;
+                                }
+								fprintf (fp,"            Total = %d.\n",sum);
+                        }
+                        vnp=vnp->next;
+                }
+                fprintf(fp,"\n");
+        }
+        if (bClose) fclose(fp);
+
+}
+
+static Boolean DDV_CreateDisplayFromIndex_1(SeqAlignPtr sap, MsaParaGPopListPtr mpplp, Int2 LineSize,
+		Int4 start,Int4 stop)
+{
+   AlnMsgPtr      amp;
+   Int4           i,from,to;
+   Boolean        more;
+   MsaTxtDispPtr  mtdp;
+   Int4           n;
+   ParaGPtr       pgp;
+   SeqIdPtr       sip;
+   ValNodePtr     vnp;
+   ValNodePtr     vnp_head;
+   ValNodePtr     PNTR vnp_list;  
+   ValNodePtr     vnp_para;
+   ValNodePtr     vnp_para_head;
+
+	if (LineSize<=50)/*just for the integrity of the function...*/
+		LineSize=ParaG_Size;
+		
+   amp = AlnMsgNew();
+   vnp_list = (ValNodePtr PNTR)MemNew((mpplp->nBsp)*sizeof(ValNodePtr));
+	if (start!=(Int4)-1){
+		from=start;
+	}
+	else{
+		from=0;
+	}
+	if (stop!=(Int4)-1){
+		to=stop+1;
+	}
+	else{
+		to=mpplp->LengthAli;
+	}
+
+   for (n = 1; n<=(mpplp->nBsp); n++)
+   {
+      vnp_para = vnp_para_head = NULL;
+      sip = AlnMgrGetNthSeqIdPtr(mpplp->sap, n);
+      for (i = from; i<to; i+=LineSize)
+      {
+         amp = AlnMsgReNew(amp);
+         pgp = (ParaGPtr)MemNew(sizeof(ParaG));
+         pgp->StartLine = n - 1;
+         pgp->nLines = 1;
+         pgp->StartLetter = amp->from_m = i;
+         if (i + LineSize >= to)
+            pgp->StopLetter = amp->to_m = to - 1;
+         else
+            pgp->StopLetter = amp->to_m = i + LineSize -1;
+         if(i == from) pgp->sip = sip;
+         else pgp->sip = SeqIdDup(sip);
+         pgp->ScaleStyle = SCALE_POS_NONE;
+         amp->which_bsq = NULL;
+         amp->row_num = n;
+         vnp = vnp_head = NULL;
+         amp->place = 0;
+         while (more = AlnMgrGetNextAlnBit(mpplp->sap, amp))
+         {
+            vnp = ValNodeAdd(&vnp);
+            if (!vnp_head)
+               vnp_head = vnp;
+            mtdp = (MsaTxtDispPtr)MemNew(sizeof(MsaTxtDisp));
+            mtdp->from = amp->from_b;
+            mtdp->to = amp->to_b;
+            mtdp->IsGap = (Boolean)(amp->gap);
+            if (mtdp->IsGap)
+               mtdp->TextStyle = MSA_TXT_STYLE_GAP;
+            else
+               mtdp->TextStyle = MSA_TXT_STYLE_SEQ;
+            mtdp->strand = amp->strand;
+			mtdp->IsUnAligned=FALSE;
+            vnp->data.ptrvalue = mtdp;
+         }
+         pgp->ptxtList = vnp_head;
+         vnp_para = ValNodeAdd(&vnp_para);
+         vnp_para->data.ptrvalue = pgp;
+         if (!vnp_para_head)
+            vnp_para_head = vnp_para;
+      }
+      vnp_list[n-1]=vnp_para_head;
+   }
+   mpplp->TableHead = vnp_list;
+   /*display_ParaG_content(mpplp,LineSize);*/
+   DDV_LocateParaG(mpplp->TableHead,mpplp->nBsp);
+   return TRUE;
+}
+
+
+static Boolean DDV_CreateDisplayFromIndex_2(SeqAlignPtr sap, MsaParaGPopListPtr mpplp, Int2 LineSize)
+{
+   AlnMsgPtr        amp;
+   Int4             i;
+   Boolean          more;
+   MsaTxtDispPtr    mtdp;
+   Int4             n;
+   ParaGPtr         pgp;
+
+
+   ValNodePtr       vnp;
+   ValNodePtr       vnp_head;
+   ValNodePtr       PNTR vnp_list;
+   ValNodePtr       vnp_para;
+   ValNodePtr       vnp_para_head;
+   Int4             PopulateTo;
+   Int4             ReportSpacer;
+   Int4             PlaceSpacer;
+   Int4             RealAlnLength;
+   SeqIdPtr         sip;
+   Boolean          last;
+
+
+   amp = AlnMsgNew();
+   vnp_list = (ValNodePtr PNTR)MemNew((mpplp->nBsp)*sizeof(ValNodePtr));
+   RealAlnLength = AlnMgrGetAlnLength(mpplp->sap, FALSE);
+   for (n = 1; n<=(mpplp->nBsp); n++)
+   {
+      vnp_para = vnp_para_head = NULL;
+      sip = AlnMgrGetNthSeqIdPtr(mpplp->sap, n);
+          ReportSpacer=0;
+          amp->to_m=-1;
+      amp = AlnMsgReNew(amp);
+      last = FALSE;
+      for (i = 0; i<mpplp->LengthAli; i+=LineSize)
+      {
+         amp->place = 0;
+         pgp = (ParaGPtr)MemNew(sizeof(ParaG));
+         pgp->StartLine = n - 1;
+         pgp->nLines = 1;
+         pgp->StartLetter = i;
+         if (i + LineSize >= mpplp->LengthAli)
+         {
+            last = TRUE;
+            pgp->StopLetter = mpplp->LengthAli;
+         }
+         else
+            pgp->StopLetter = i + LineSize -1;
+         if(i == 0) pgp->sip = sip;
+         else pgp->sip = SeqIdDup(sip);
+         pgp->ScaleStyle = SCALE_POS_NONE;
+         amp->which_master = 0;
+         if (amp->to_m != 0)
+                 amp->from_m = amp->to_m + 1 ;
+         else
+                 amp->from_m = 0;
+         amp->to_m = amp->from_m + LineSize -1;
+         amp->row_num = n;
+         if (amp->to_m > RealAlnLength)
+            amp->to_m = RealAlnLength - 1;
+         more = TRUE;
+         vnp = vnp_head = NULL;
+                 PopulateTo=0;
+                 PlaceSpacer=0;
+         while (amp->place == 0)
+         {
+            vnp = ValNodeAdd(&vnp);
+            if (!vnp_head)
+               vnp_head = vnp;
+            if (amp->send_space)
+            {
+               if (!last)
+                  amp->to_m=amp->to_m - PlaceSpacer;
+            }
+                        if (ReportSpacer){
+                           amp->to_m -=ReportSpacer;
+               mtdp = (MsaTxtDispPtr)MemNew(sizeof(MsaTxtDisp));
+               mtdp->from = pgp->StartLetter;
+               mtdp->to = mtdp->from+ReportSpacer-1;
+                           PopulateTo+=(ReportSpacer+1);
+                           ReportSpacer=0;
+               mtdp->IsGap = TRUE;
+               mtdp->TextStyle = MSA_TXT_STYLE_1;
+               vnp->data.ptrvalue = mtdp;
+               vnp = ValNodeAdd(&vnp);
+                        }
+            amp->send_space = FALSE;
+            more = AlnMgrGetNextAlnBit(mpplp->sap, amp);
+            mtdp = (MsaTxtDispPtr)MemNew(sizeof(MsaTxtDisp));
+            mtdp->from = amp->from_b;
+            mtdp->to = amp->to_b;
+            PopulateTo+=(amp->to_b-amp->from_b+1);
+                        mtdp->IsGap = (Boolean)(amp->gap);
+            if (mtdp->IsGap)
+               mtdp->TextStyle = MSA_TXT_STYLE_GAP;
+            else
+               mtdp->TextStyle = MSA_TXT_STYLE_SEQ;
+            mtdp->strand = amp->strand;
+            vnp->data.ptrvalue = mtdp;
+            if (amp->send_space)
+            {
+               vnp = ValNodeAdd(&vnp);
+               mtdp = (MsaTxtDispPtr)MemNew(sizeof(MsaTxtDisp));
+               mtdp->from = pgp->StartLetter+PopulateTo;
+               mtdp->to = mtdp->from+SPACER_TXT_BLANK-1;
+                           if (mtdp->to>pgp->StopLetter){
+                               ReportSpacer=mtdp->to-pgp->StopLetter;
+                               mtdp->to=pgp->StopLetter;
+               }
+                           else{
+                               ReportSpacer=0;
+                           }
+                           PlaceSpacer=SPACER_TXT_BLANK-ReportSpacer;
+                           PopulateTo+=(mtdp->to-mtdp->from+1);
+               mtdp->IsGap = TRUE;
+               mtdp->TextStyle = MSA_TXT_STYLE_1;
+				mtdp->IsUnAligned=FALSE;
+               vnp->data.ptrvalue = mtdp;
+            }
+         }
+         pgp->ptxtList = vnp_head;
+         vnp_para = ValNodeAdd(&vnp_para);
+         vnp_para->data.ptrvalue = pgp;
+         if (!vnp_para_head)
+            vnp_para_head = vnp_para;
+      }
+      vnp_list[n-1]=vnp_para_head;
+   }
+   mpplp->TableHead = vnp_list;
+   /*display_ParaG_content(mpplp,LineSize);*/
+   DDV_LocateParaG(mpplp->TableHead,mpplp->nBsp);
+   return TRUE;
+}
+
+
+NLM_EXTERN Boolean DDV_CreateDisplayFromIndex_EX(SeqAlignPtr sap, MsaParaGPopListPtr mpplp, 
+		Int2 LineSize, DDV_Disp_OptPtr ddop,Int4 start, Int4 stop) {
+/*******************************************************************************
+*  same as DDV_CreateDisplayFromIndex_EX2, but by default no extra gap char.
+*******************************************************************************/
+  return(DDV_CreateDisplayFromIndex_EX2(sap, mpplp, LineSize, ddop, start, stop, FALSE));
+}
+
+
+NLM_EXTERN Boolean DDV_CreateDisplayFromIndex_EX2(SeqAlignPtr sap, MsaParaGPopListPtr mpplp, 
+		Int2 LineSize, DDV_Disp_OptPtr ddop,Int4 start, Int4 stop, Boolean WantExtraGapChar)
+{
+   AMAlignIndexPtr  amaip;
+   AlnMsgPtr        amp;
+   Int4             i,from,to;
+   Boolean          more;
+   MsaTxtDispPtr    mtdp;
+   Int4             n;
+   ParaGPtr         pgp;
+
+
+   ValNodePtr       vnp;
+   ValNodePtr       vnp_head;
+   ValNodePtr       PNTR vnp_list;
+   ValNodePtr       vnp_para;
+   ValNodePtr       vnp_para_head;
+   Int4             PopulateTo;
+
+
+   SeqIdPtr         sip;
+   Boolean          last;
+
+	if (LineSize<=50)/*just for the integrity of the function...*/
+		LineSize=ParaG_Size;
+		
+   if (!sap)
+      return FALSE;
+   if (!AlnMgrIndexSeqAlign(sap))
+      return FALSE;
+   if (sap->saip->indextype == INDEX_PARENT)
+   {
+      amaip = (AMAlignIndexPtr)sap->saip;
+      if (sap->type == SAT_PARTIAL || 
+         (sap->type == SAT_MASTERSLAVE && (amaip->mstype == AM_SEGMENTED_MASTERSLAVE || 
+                                           amaip->mstype == AM_NULL ||
+                                           amaip->mstype == AM_MASTERSLAVE)))
+      {
+         return(DDV_CreateDisplay_DiscAlign2(sap,mpplp,LineSize,ddop,WantExtraGapChar));
+      } 
+      else if (sap->type == SAT_MASTERSLAVE && amaip->mstype == AM_MASTERSLAVE)
+      {
+         mpplp->sap = sap;
+         if (start==(Int4)-1 && stop==(Int4)-1)
+			 mpplp->LengthAli = AlnMgrGetAlnLength(mpplp->sap, FALSE);
+		else
+			mpplp->LengthAli=stop-start+1;
+         mpplp->nBsp = AlnMgrGetNumRows(mpplp->sap);
+         mpplp->DisplayType = DDV_DISP_HORZ;
+         if (!DDV_CreateDisplayFromIndex_1(sap, mpplp,LineSize,start,stop))
+            return FALSE;
+         else
+            return TRUE;
+      } else
+         mpplp->sap = (SeqAlignPtr)sap->segs;
+   } else 
+      mpplp->sap = sap;
+   mpplp->LengthAli = AlnMgrGetAlnLength(mpplp->sap, FALSE);
+   mpplp->nBsp = AlnMgrGetNumRows(mpplp->sap);
+   mpplp->DisplayType = DDV_DISP_HORZ;
+   amp = AlnMsgNew();
+   vnp_list = (ValNodePtr PNTR)MemNew((mpplp->nBsp)*sizeof(ValNodePtr));
+	if (start!=(Int4)-1){
+		from=start;
+	}
+	else{
+		from=0;
+	}
+	if (stop!=(Int4)-1){
+		to=stop+1;
+	}
+	else{
+		to=mpplp->LengthAli;
+	}
+   for (n = 1; n<=(mpplp->nBsp); n++)
+   {
+      vnp_para = vnp_para_head = NULL;
+      sip = AlnMgrGetNthSeqIdPtr(mpplp->sap, n);
+	  amp->to_m=-1;
+      amp = AlnMsgReNew(amp);
+      last = FALSE;
+      for (i = from; i<to; i+=LineSize)
+      {
+         amp->place = 0;
+         pgp = (ParaGPtr)MemNew(sizeof(ParaG));
+         pgp->StartLine = n - 1;
+         pgp->nLines = 1;
+         pgp->StartLetter = i;
+         if (i + LineSize >= to)
+         {
+            last = TRUE;
+            pgp->StopLetter = to;
+         }
+         else
+            pgp->StopLetter = i + LineSize -1;
+         if(i == from) pgp->sip = sip;
+         else pgp->sip = SeqIdDup(sip);
+         pgp->ScaleStyle = SCALE_POS_NONE;
+         amp->which_master = 0;
+         if (amp->to_m != 0)
+		 amp->from_m = amp->to_m + 1 ;
+         else
+                 amp->from_m = 0;
+	 amp->to_m = amp->from_m + LineSize -1;
+         amp->row_num = n;
+         if (amp->to_m >= to)
+            amp->to_m = to - 1;
+         more = TRUE;
+         vnp = vnp_head = NULL;
+		 PopulateTo=0;
+         while (more = AlnMgrGetNextAlnBit(mpplp->sap, amp))
+         {
+            vnp = ValNodeAdd(&vnp);
+            if (!vnp_head)
+               vnp_head = vnp;
+            mtdp = (MsaTxtDispPtr)MemNew(sizeof(MsaTxtDisp));
+            mtdp->from = amp->from_b;
+            mtdp->to = amp->to_b;
+			mtdp->IsGap = (Boolean)(amp->gap);
+            if (mtdp->IsGap)
+               mtdp->TextStyle = MSA_TXT_STYLE_GAP;
+            else
+               mtdp->TextStyle = MSA_TXT_STYLE_SEQ;
+            mtdp->strand = amp->strand;
+			mtdp->IsUnAligned=FALSE;
+            vnp->data.ptrvalue = mtdp;
+         }
+         pgp->ptxtList = vnp_head;
+         vnp_para = ValNodeAdd(&vnp_para);
+         vnp_para->data.ptrvalue = pgp;
+         if (!vnp_para_head)
+            vnp_para_head = vnp_para;
+      }
+      vnp_list[n-1]=vnp_para_head;
+   }
+   mpplp->TableHead = vnp_list;
+   /*display_ParaG_content(mpplp,LineSize);*/
+   DDV_LocateParaG(mpplp->TableHead,mpplp->nBsp);
+   return TRUE;
+}
+
+
+NLM_EXTERN Boolean DDV_CreateDisplayFromIndex(SeqAlignPtr sap, MsaParaGPopListPtr mpplp, 
+		Int2 LineSize, DDV_Disp_OptPtr ddop) {
+/*******************************************************************************
+*  same as DDV_CreateDisplayFromIndex2, but by default no extra gap char.
+*******************************************************************************/
+  return(DDV_CreateDisplayFromIndex2(sap, mpplp, LineSize, ddop, FALSE));
+}
+
+
+NLM_EXTERN Boolean DDV_CreateDisplayFromIndex2(SeqAlignPtr sap, MsaParaGPopListPtr mpplp, 
+		Int2 LineSize, DDV_Disp_OptPtr ddop, Boolean WantExtraGapChar)
+{
+	return(DDV_CreateDisplayFromIndex_EX2(sap,  mpplp, 
+		 LineSize,  ddop, (Int4) -1,  (Int4) -1, WantExtraGapChar));
+}
+
+
+static Boolean DDV_PopulateDisplayForDisc(SeqAlignPtr sap,MsaParaGPopListPtr mpplp,
+	Int4 nBsp,Int4 LineSize,DDV_Disp_OptPtr ddop,Int4 TotLength,ValNodePtr vnp_head,
+  Boolean OverrideDiscJustification, Boolean ForceLeft)
+{
+/*-------------------------------------------------------------
+  Added OverrideDiscJustification:
+  Set this true for single block alignment.  In that case,
+  the first unaligned region will be right-justified and
+  the second unaligned region will be left-justified.
+
+  Added ForceLeft:
+  Set this true for single unaligned region alignment.
+  In that case, the unaligned region will be left-aligned.
+-------------------------------------------------------------*/
+Int4            cumulpop,StartLetter,n,nPgp,from_bsp,to_bsp,MaxLength,
+                BspLength=0,BspStart,BspStop,AbsPos;
+Boolean         more,bFirstMtdp,bFirstPgp,IsGap;
+ValNodePtr      vnp,vnp2,vnp3,vnp_para,vnp_mtdp=NULL;
+ValNodePtr PNTR vnp_list;
+ParaGPtr        pgp;
+SeqIdPtr        sip;
+DescriDispPtr   ddp;
+MsaTxtDispPtr   mtdp_pgp;
+AlnMsgPtr       amp;
+UAMsgPtr        uamp;
+Uint1           strand = Seq_strand_unknown;
+Uint1           strand_tmp, Justification;
+Int4            PassCount;
+
+	/*now, use the previous descriptor to build the ParaG List*/
+	mpplp->sap=sap;
+	mpplp->nBsp = nBsp;
+	mpplp->LengthAli = TotLength;
+	mpplp->DisplayType = DDV_DISP_HORZ;
+	amp = AlnMsgNew();
+	vnp_list = (ValNodePtr PNTR)MemNew((mpplp->nBsp)*sizeof(ValNodePtr));
+	if (!vnp_list || !amp){
+		/*delete the descriptor*/
+		ValNodeFreeData(vnp_head);
+		return(FALSE);
+	}
+
+	cumulpop=0;
+	
+	/*loop on each sequence*/
+	for (n = 1; n<=(mpplp->nBsp); n++){
+		sip = AlnMgrGetNthSeqIdPtr(mpplp->sap, n);
+		/*for each sequence, use the descriptors to build the ParaG list*/
+		bFirstPgp=TRUE;
+		bFirstMtdp=TRUE;
+		StartLetter=0;AbsPos=0;/*disp coord*/
+		nPgp=0;
+		vnp=vnp_head;
+    PassCount = 0;
+		while(vnp){
+			ddp=(DescriDispPtr)vnp->data.ptrvalue;
+			if (ddp->TextStyle==MSA_TXT_STYLE_REG_ALIGN){/*aligned*/
+				/*initialize the amp struct for the current aligned region*/
+				amp = AlnMsgReNew(amp);
+				amp->place = 0;
+				amp->from_m = ddp->from;
+				amp->to_m=ddp->to;
+				amp->which_master=0;
+				amp->row_num=n;
+				amp->send_space = FALSE;
+				more=TRUE;
+				AlnMgrGetNextAlnBit(mpplp->sap, amp);
+				while (more){
+					/*list of TxT descriptors*/
+					mtdp_pgp = (MsaTxtDispPtr)MemNew(sizeof(MsaTxtDisp));
+					mtdp_pgp->IsGap = (Boolean)(amp->gap);
+					if (mtdp_pgp->IsGap){/*disp coord*/
+						mtdp_pgp->from=AbsPos;
+						mtdp_pgp->to=mtdp_pgp->from+(amp->to_b-amp->from_b);
+						mtdp_pgp->TextStyle = ddop->AGapStyle;
+					}
+					else{/*BSP coord*/
+						mtdp_pgp->from = amp->from_b;
+						mtdp_pgp->to = amp->to_b;
+						mtdp_pgp->TextStyle = MSA_TXT_STYLE_SEQ;
+					}
+					mtdp_pgp->strand = amp->strand;
+					mtdp_pgp->IsUnAligned=FALSE;
+					strand=amp->strand;
+					/*add the new node*/
+					if (bFirstMtdp){
+						vnp2=ValNodeAddPointer(NULL,0,(Pointer)mtdp_pgp);
+						vnp_mtdp=vnp2;
+						bFirstMtdp=FALSE;
+					}
+					else{
+						vnp2=ValNodeAddPointer(&vnp2,0,(Pointer)mtdp_pgp);
+					}
+					more=AlnMgrGetNextAlnBit(mpplp->sap, amp);
+					AbsPos+=(mtdp_pgp->to-mtdp_pgp->from+1);
+				}
+			}
+			else{/*unaligned*/
+				switch(ddop->DispDiscStyle){/*user's display choice*/
+					case MSA_TXT_STYLE_1:/*just put a little spacer*/
+						mtdp_pgp = (MsaTxtDispPtr)MemNew(sizeof(MsaTxtDisp));
+						mtdp_pgp->from = StartLetter;/*put DISP coord*/
+						mtdp_pgp->to = mtdp_pgp->from+(ddp->to-ddp->from);
+						mtdp_pgp->IsGap = TRUE;
+						mtdp_pgp->TextStyle = MSA_TXT_STYLE_1;
+						mtdp_pgp->strand = strand;
+						mtdp_pgp->IsUnAligned=TRUE;
+						/*add the new node*/
+						if (bFirstMtdp){
+							vnp2=ValNodeAddPointer(NULL,0,(Pointer)mtdp_pgp);
+							vnp_mtdp=vnp2;
+							bFirstMtdp=FALSE;
+						}
+						else{
+							vnp2=ValNodeAddPointer(&vnp2,0,(Pointer)mtdp_pgp);
+						}
+						break;
+					case MSA_TXT_STYLE_2:/*display the unaligned sequence*/
+						MaxLength=ddp->UAMaxlength;
+						
+						if (ddp->UAnum>0){/*within SAP*/
+							AlnMgrGetNthUnalignedForNthRow(sap, ddp->UAnum, n, &BspStart, 
+								&BspStop);
+						}
+						else{/*Tails of the SAP*/
+							if (AlnMgrGetNthRowTail(sap,n,
+								(Uint1)(ddp->UAnum==(Int4)-1 ? LEFT_TAIL : RIGHT_TAIL),
+								&BspStart,&BspStop,&strand_tmp)==FALSE){
+								BspStart=(Int4)-1;
+								BspStop=(Int4)-1;
+								BspLength=0;
+							}
+						
+						}
+												
+						if (BspStart!=(Int4)-1 && BspStop!=(Int4)-1){
+							BspLength=BspStop-BspStart+1;
+						}
+						/*init the analysis process of an UA region*/
+						switch(ddp->UAnum){
+							case (Int4)-1:/*left tail*/
+                Justification = ForceLeft ? DISP_JUST_LEFT : DISP_JUST_RIGHT;
+								uamp=UAMgrIntUAMsg(MaxLength,BspLength,BspStart,BspStop, 
+									ddp->from,ddp->to, Justification, strand);
+								break;
+							case (Int4)-2:/*right tail*/
+								uamp=UAMgrIntUAMsg(MaxLength,BspLength,BspStart,BspStop, 
+									ddp->from,ddp->to,DISP_JUST_LEFT, strand);
+								break;
+							default:/*within SAP*/
+                Justification = ddop->DiscJustification;
+                if (OverrideDiscJustification) {
+                  if (PassCount==0) {Justification = DISP_JUST_RIGHT;}
+                  if (PassCount==2) {Justification = DISP_JUST_LEFT;}
+                }
+								uamp=UAMgrIntUAMsg(MaxLength,BspLength,BspStart,BspStop, 
+									ddp->from,ddp->to, Justification, strand);
+								break;
+						}
+						/*analyse the content of the UA region*/
+						while(UAMgrGetNextUAbit(uamp, BspStart, BspStop)){
+							/*get data*/
+							UAMgrUAMsgGetInfo(uamp,&from_bsp,&to_bsp,&IsGap);
+							/*list of TxT descriptors*/
+							mtdp_pgp = (MsaTxtDispPtr)MemNew(sizeof(MsaTxtDisp));
+							mtdp_pgp->IsGap = IsGap;
+							if (mtdp_pgp->IsGap){/*disp coord*/
+								mtdp_pgp->TextStyle = ddop->UAGapStyle;
+								mtdp_pgp->from=AbsPos;
+								mtdp_pgp->to=mtdp_pgp->from+(to_bsp-from_bsp);
+							}
+							else{/*BSP coord*/
+								mtdp_pgp->from = from_bsp;
+								mtdp_pgp->to = to_bsp;
+								mtdp_pgp->TextStyle = MSA_TXT_STYLE_SEQ;
+							}
+							mtdp_pgp->strand = strand;
+							mtdp_pgp->IsUnAligned=TRUE;
+							/*add the new node*/
+							if (bFirstMtdp){
+								vnp2=ValNodeAddPointer(NULL,0,(Pointer)mtdp_pgp);
+								vnp_mtdp=vnp2;
+								bFirstMtdp=FALSE;
+							}
+							else{
+								vnp2=ValNodeAddPointer(&vnp2,0,(Pointer)mtdp_pgp);
+							}
+							AbsPos+=(mtdp_pgp->to-mtdp_pgp->from+1);
+						}
+						uamp=UAMgrDelUAMsg(&uamp);
+						break;
+				}
+			}
+			cumulpop+=(ddp->to-ddp->from+1);
+			StartLetter+=(ddp->to-ddp->from+1);
+			if (cumulpop==LineSize || vnp->next==NULL){
+				/*new ParaG*/
+				pgp=(ParaGPtr)MemNew(sizeof(ParaG));
+				pgp->StartLine=n-1;
+				pgp->nLines=1;
+				pgp->StartLetter=nPgp*LineSize;
+				pgp->StopLetter=_min_(pgp->StartLetter+LineSize-1,mpplp->LengthAli-1);
+				pgp->sip=SeqIdDup(sip);
+				pgp->ScaleStyle=SCALE_POS_NONE;
+				pgp->ptxtList=vnp_mtdp;
+				if (bFirstPgp){
+					vnp3=ValNodeAddPointer(NULL,0,(Pointer)pgp);
+					vnp_para=vnp3;
+					bFirstPgp=FALSE;
+				}
+				else{
+					vnp3=ValNodeAddPointer(&vnp3,0,(Pointer)pgp);
+				}
+				bFirstMtdp=TRUE;
+				cumulpop=0;
+				nPgp++;
+			}
+			vnp=vnp->next;
+      PassCount++;
+		}/*while() on the descriptor list*/
+		vnp_list[n-1]=vnp_para;
+        SeqIdFree(sip);
+	}/*for() on the bsp */
+	
+	/*delete the descriptor*/
+	ValNodeFreeData(vnp_head);
+
+	mpplp->TableHead = vnp_list;
+	/*just for debugging purpose*/
+	/*display_ParaG_content(mpplp,LineSize);*/
+	DDV_LocateParaG(mpplp->TableHead,mpplp->nBsp);
+	MemFree(amp);
+
+	return(TRUE);
+}
+
+NLM_EXTERN Boolean DDV_CreateDisplay_DiscAlign(SeqAlignPtr sap, 
+		MsaParaGPopListPtr mpplp, Int2 LineSize,DDV_Disp_OptPtr ddop) {
+/*******************************************************************************
+*  same as DDV_CreateDisplay_DiscAlign2, but by default no extra gap char.
+*******************************************************************************/
+  return(DDV_CreateDisplay_DiscAlign2(sap, mpplp, LineSize, ddop, FALSE));
+}
+
+
+/*******************************************************************************
+
+  Function : DDV_CreateDisplay_DiscAlign2()
+  
+  Purpose : create a display for a Disc. SeqAlign
+
+  Return value : FALSE if failure
+
+*******************************************************************************/
+NLM_EXTERN Boolean DDV_CreateDisplay_DiscAlign2(SeqAlignPtr sap, 
+		MsaParaGPopListPtr mpplp, Int2 LineSize,DDV_Disp_OptPtr ddop, Boolean WantExtraGapChar)
+{
+Int4 nBsp,TotLength;
+ValNodePtr vnp_head;
+
+	/*descriptor*/
+	nBsp = AlnMgrGetNumRows(sap);
+	vnp_head=UABuildDescriptor2(sap,nBsp,LineSize,ddop,&TotLength,
+		ddop->ShowLeftTail,ddop->ShowRightTail, WantExtraGapChar);
+	if (vnp_head==NULL)
+		return(FALSE);
+
+	/*build the display*/
+	return(DDV_PopulateDisplayForDisc(sap,mpplp,nBsp,LineSize,ddop,
+		TotLength,vnp_head, FALSE, FALSE));
+}
+
+/*******************************************************************************
+
+  Function : DDV_BuildDisp_BlockEditor()
+  
+  Purpose : create a display for a Disc. SeqAlign
+
+  Return value : FALSE if failure
+
+*******************************************************************************/
+NLM_EXTERN Boolean DDV_BuildDisp_BlockEditor(SeqAlignPtr sap, 
+		MsaParaGPopListPtr mpplp, Int4 block_num)
+{
+Int4 nBsp,TotLength;
+ValNodePtr vnp_head;
+DDV_Disp_Opt ddo;
+
+	/*descriptor*/
+	nBsp = AlnMgrGetNumRows(sap);
+	vnp_head=UABuildDescriptorForBlockEditor(sap,nBsp, 
+			block_num,LIMIT_EDITOR_SIZE,&TotLength);
+	
+	if (vnp_head==NULL)
+		return(FALSE);
+
+	DDV_InitDDESAPdispStyles(&ddo);
+	/*build the display*/
+	return(DDV_PopulateDisplayForDisc(sap,mpplp,nBsp,LIMIT_EDITOR_SIZE,&ddo,
+		TotLength,vnp_head, FALSE, FALSE));
+}
+
+/*******************************************************************************
+
+  Function : UABitDescrInit()
+  
+  Purpose : init a UABitDescr data block
+  
+  Return value : -
+
+*******************************************************************************/
+static void UABitDescrInit(UABitDescrPtr ubd,Int4 Start,Int4 Stop,Boolean IsGap)
+{
+	ubd->from=Start;
+	ubd->to=Stop;
+	ubd->IsGap=IsGap;
+}
+
+/*******************************************************************************
+
+  Function : UAMgrInitBitList()
+  
+  Purpose : init the descriptor of an UA region
+  
+  Return value : -
+
+*******************************************************************************/
+static void UAMgrInitBitList(UAMsgPtr uamp, Int4 MaxLength, Int4 BspLength,
+		Int4 BspStart,Int4 BspStop)
+{
+Int4 halfBspLengthSeqL,halfBspLengthSeqR,halfBspLengthDesc,start_middle,stop_middle;
+
+	/*just a gap*/
+	if (BspStart==(Int4)-1 && BspStop==(Int4)-1){
+		UABitDescrInit(&uamp->ubd[0],0,MaxLength-1,TRUE);
+		UABitDescrInit(&uamp->ubd[1],(Int4)-1,(Int4)-1,FALSE);
+		UABitDescrInit(&uamp->ubd[2],(Int4)-1,(Int4)-1,FALSE);
+		return;
+	}
+	/*only sequence*/
+	if (BspLength==MaxLength){
+		UABitDescrInit(&uamp->ubd[0],BspStart,BspStop,FALSE);
+		UABitDescrInit(&uamp->ubd[1],(Int4)-1,(Int4)-1,FALSE);
+		UABitDescrInit(&uamp->ubd[2],(Int4)-1,(Int4)-1,FALSE);
+		return;
+	}
+	/*additional data for DISP_JUST_CENTER and DISP_JUST_SPLIT*/
+	if (uamp->DispType==DISP_JUST_CENTER || uamp->DispType==DISP_JUST_SPLIT){
+		halfBspLengthSeqL=BspLength/2;
+		halfBspLengthSeqR=BspLength-halfBspLengthSeqL;
+		halfBspLengthDesc=MaxLength/2;
+		start_middle=halfBspLengthDesc-halfBspLengthSeqL;
+		stop_middle=start_middle+BspLength;
+	}
+
+	/*only one sequence letter and DISP_JUST_SPLIT : use DISP_JUST_LEFT*/
+	if (BspStart==BspStop && uamp->DispType==DISP_JUST_SPLIT){
+		uamp->DispType=DISP_JUST_LEFT;
+	}
+
+	switch(uamp->DispType){
+		case DISP_JUST_RIGHT:
+			UABitDescrInit(&uamp->ubd[0],0,MaxLength-BspLength-1,TRUE);
+			UABitDescrInit(&uamp->ubd[1],BspStart,BspStop,FALSE);
+			UABitDescrInit(&uamp->ubd[2],(Int4)-1,(Int4)-1,FALSE);
+			break;
+		case DISP_JUST_CENTER:
+			UABitDescrInit(&uamp->ubd[0],0,start_middle-1,TRUE);
+			UABitDescrInit(&uamp->ubd[1],BspStart,BspStop,FALSE);
+			UABitDescrInit(&uamp->ubd[2],stop_middle,MaxLength-1,TRUE);
+			break;
+		case DISP_JUST_SPLIT:
+			UABitDescrInit(&uamp->ubd[0],BspStart,BspStart+halfBspLengthSeqL-1,FALSE);
+			UABitDescrInit(&uamp->ubd[1],halfBspLengthSeqL,MaxLength-halfBspLengthSeqR-1,TRUE);
+			UABitDescrInit(&uamp->ubd[2],BspStart+halfBspLengthSeqL,BspStop,FALSE);
+			break;
+		case DISP_JUST_LEFT:
+			UABitDescrInit(&uamp->ubd[0],BspStart,BspStop,FALSE);
+			UABitDescrInit(&uamp->ubd[1],BspLength,MaxLength-1,TRUE);
+			UABitDescrInit(&uamp->ubd[2],(Int4)-1,(Int4)-1,FALSE);
+		default:
+			break;
+	}
+}
+
+
+/*******************************************************************************
+
+  Function : UAMgrIntUAMsg()
+  
+  Purpose : constructor for a struct UAMsg
+  
+  Note : from and to are in UnAligned region coord. system. Such a coord system
+         always starts at 0. Length = max length of the UA region
+		 
+  Return value : -
+
+*******************************************************************************/
+NLM_EXTERN UAMsgPtr UAMgrIntUAMsg( Int4 MaxLength, Int4 BspLength,
+		Int4 BspStart,Int4 BspStop,Int4 ddpFrom ,Int4 ddpTo , Uint1 DispType, Uint1 strand)
+{
+UAMsgPtr uamp=NULL;
+
+	uamp=(UAMsgPtr)MemNew(sizeof(UAMsg));
+	if (uamp){
+		uamp->DispType=DispType;
+		uamp->strand=strand;
+		uamp->from_a=uamp->currentPos=ddpFrom;
+		uamp->to_a=ddpTo;
+		UAMgrInitBitList(uamp,MaxLength,BspLength,BspStart,BspStop);
+	}
+	return(uamp);
+}
+
+/*******************************************************************************
+
+  Function : UAMgrDelUAMsg()
+  
+  Purpose : destructor for UAMsg structure
+    
+  Return value : -
+
+*******************************************************************************/
+NLM_EXTERN UAMsgPtr UAMgrDelUAMsg(UAMsgPtr PNTR uamp)
+{
+	if (*uamp)
+		MemFree(*uamp);
+	return(NULL);
+}
+
+/*******************************************************************************
+
+  Function : UAMgrUAMsgGetInfo()
+  
+  Purpose : query function for a UAMsg structure
+  
+  Note : from_bsp and to_bsp are in BSP coord system.
+    
+  Return value : -
+
+*******************************************************************************/
+NLM_EXTERN void UAMgrUAMsgGetInfo(UAMsgPtr uamp,Int4Ptr from_bsp, Int4Ptr to_bsp, 
+		BoolPtr IsGap)
+{
+	*from_bsp=uamp->from_r;
+	*to_bsp=uamp->to_r;
+	*IsGap=uamp->IsGap;
+}
+
+/*******************************************************************************
+
+  Function : UAMgrGetNextUAbit()
+  
+  Purpose : analytical function to retrieve information about an unaligned
+            region. uamp must be init. before entering this function.
+    
+*******************************************************************************/
+NLM_EXTERN Boolean UAMgrGetNextUAbit(UAMsgPtr uamp,Int4 BspStart,Int4 BspStop)
+{
+Uint1 i;
+Int4  from_a,to_a,cumul=0,diff,tmp;
+	
+	if (uamp->currentPos>uamp->to_a) return(FALSE);
+	for (i=0;i<3;i++){
+		if (uamp->ubd[i].from!=(Int4)-1 && uamp->ubd[i].to!=(Int4)-1){
+			if (uamp->ubd[i].IsGap){/*disp coord*/
+				from_a=uamp->ubd[i].from;
+				to_a=uamp->ubd[i].to;
+			}
+			else{/*switch bsp coord to disp coord*/
+				from_a=cumul;
+				to_a=uamp->ubd[i].to-uamp->ubd[i].from+cumul;
+			}
+			if (uamp->currentPos>=from_a && uamp->currentPos<=to_a){
+				if (uamp->ubd[i].IsGap)
+					uamp->from_r=uamp->currentPos;
+				else
+					uamp->from_r=uamp->ubd[i].from+uamp->currentPos-cumul;
+			}
+			else{
+				cumul+=(to_a-from_a+1);
+				continue;
+			}
+			if (uamp->to_a>=from_a && uamp->to_a<=to_a){
+				uamp->to_r=_min_(uamp->to_a,to_a);
+				if (!uamp->ubd[i].IsGap)
+					uamp->to_r+=uamp->ubd[i].from-cumul;
+			}
+			else{
+				uamp->to_r=uamp->ubd[i].to;
+			}
+			uamp->currentPos+=(uamp->to_r-uamp->from_r+1);
+			uamp->IsGap=uamp->ubd[i].IsGap;
+			break;
+		}
+	}
+
+	/*if minus strand (nuc. only); reverse the values*/
+	if (uamp->strand==Seq_strand_minus && !uamp->IsGap){
+		diff=uamp->to_r-uamp->from_r;
+		uamp->from_r=uamp->from_r+(BspStop-uamp->from_r)-(uamp->from_r-BspStart);
+		uamp->to_r=uamp->from_r-diff;
+		tmp=uamp->to_r;
+		uamp->to_r=uamp->from_r;
+		uamp->from_r=tmp;
+	}
+	
+	return(TRUE);
+}
+
+/*******************************************************************************
+
+  Function : DDV_BuildBspEntitiesTbl()
+  
+  Purpose : build a table of eID, iID of each Bioseq of a SeqAlign.
+    
+  Return value : a table of entities
+
+*******************************************************************************/
+NLM_EXTERN Uint4Ptr DDV_BuildBspEntitiesTbl(ValNodePtr PNTR TableHead,Int4 nBsp)
+{
+ValNodePtr vnp;
+ParaGPtr   pgp;
+BioseqPtr  bsp;
+Uint4Ptr    entitiesTbl;
+Uint2      bsp_eID,bsp_iID;
+Int4       i;
+
+	entitiesTbl=(Uint4Ptr)MemNew(nBsp*sizeof(Uint4));
+	if (!entitiesTbl) return(NULL);
+	
+	for (i=0;i<nBsp;i++){
+		vnp=TableHead[i];
+		if (vnp){
+			pgp=(ParaGPtr)vnp->data.ptrvalue;
+			
+			bsp=BioseqLockById(pgp->sip);
+			if (bsp){
+				bsp_eID=ObjMgrGetEntityIDForPointer((Pointer)bsp);
+				bsp_iID = GetItemIDGivenPointer (bsp_eID, 
+						OBJ_BIOSEQ, (Pointer) bsp);	
+				entitiesTbl[i]=UDV_EncodeIdxFeat(bsp_eID,bsp_iID);
+				BioseqUnlock(bsp);
+			}
+		}
+	}
+	return(entitiesTbl);
+}
+
+/*******************************************************************************
+
+  Function : DDV_BuildTailDescriptor()
+  
+  Purpose : build a descriptor for the unaligned left/right tails of a SeqAlign
+    
+  Return value : the descriptor (see also TotLength; total size of the tail)
+
+*******************************************************************************/
+NLM_EXTERN ValNodePtr DDV_BuildTailDescriptor(SeqAlignPtr sap, Int4 nBsp, 
+	Int2 LineSize,Uint1 which_tail,Int4Ptr TotLength,Int4Ptr cumulpop)
+{
+Int4            startcopy,stopcopy,pop,i,MaxLength,start,stop;
+Boolean         bError;
+ValNodePtr      vnp,vnp_head;
+DescriDispPtr   ddp;
+Uint1           strand;
+
+	vnp_head=NULL;
+	bError=FALSE;
+	MaxLength=0;
+	/*get the size of the left UA region*/
+	for(i=0;i<nBsp;i++){
+		if (AlnMgrGetNthRowTail(sap,i+1,which_tail,&start,&stop,&strand)){
+			if (start!=(Int4)-1 && stop!=(Int4)-1){
+				MaxLength=MAX(MaxLength,ABS(stop-start)+1);
+			}
+		}
+	}
+	/*build a descriptor node for that region, if needed*/
+	if (MaxLength>0){
+		startcopy=0;
+		stopcopy=MaxLength;
+		*TotLength+=(stopcopy-startcopy);/*to be used for the display coord. system*/
+
+		while(startcopy<stopcopy){
+			/*store data*/
+			pop=_min_(stopcopy-startcopy,LineSize-(*cumulpop));
+			ddp=(DescriDispPtr)MemNew(sizeof(DescriDisp));
+			if (ddp==NULL) {
+				bError=TRUE;break;
+			}
+			ddp->from=startcopy;/*use relative coord, i.e. UA coord system*/
+			ddp->to=ddp->from+pop-1;
+			ddp->TextStyle=MSA_TXT_STYLE_REG_UNALIGN;
+			if (which_tail==LEFT_TAIL)
+				ddp->UAnum=(Int4)-1;/*UA region number; -1 means LEFT TAIL*/
+			else
+				ddp->UAnum=(Int4)-2;/*UA region number; -2 means RIGHT TAIL*/
+			ddp->UAMaxlength=stopcopy;
+			/*create a new node*/
+			if (vnp_head==NULL) {
+				vnp_head=ValNodeAddPointer(NULL,0,(Pointer)ddp);
+				vnp=vnp_head;
+			}
+			else vnp=ValNodeAddPointer(&vnp,0,(Pointer)ddp);
+
+			if (!vnp){
+				bError=TRUE;
+				break;
+			}
+			(*cumulpop)+=pop;
+			if ((*cumulpop)==LineSize) (*cumulpop)=0;
+			startcopy+=pop;
+		}
+	}
+
+	if (bError){
+		vnp_head=ValNodeFreeData(vnp_head);
+	}
+	
+	return(vnp_head);
+}
+
+NLM_EXTERN ValNodePtr UABuildDescriptor(SeqAlignPtr sap, Int4 nBsp, Int2 LineSize,
+	DDV_Disp_OptPtr ddop, Int4Ptr TotLength,Boolean AddLeftUAPart,
+  Boolean AddRightUAPart) {
+/*******************************************************************************
+*  same as UABuildDescriptor2, but by default no extra gap char.
+*******************************************************************************/
+  return(UABuildDescriptor2(sap, nBsp, LineSize, ddop, TotLength,
+         AddLeftUAPart, AddRightUAPart, FALSE));
+}
+
+
+/*******************************************************************************
+
+  Function : UABuildDescriptor2()
+  
+  Purpose : build the descriptor of a SeqAlign. This function is ONLY designed 
+            for discontinuous SeqAlign. The descriptor is a valnodelist. For
+			each node, the field data.ptrvalue is of type MsaTxtDispPtr. It
+			contains inportant info : start-stop of either an aligned or unaligned
+			region. In the first case, SeqAlign coord system is used, otherwise
+			UA coord system is used (UA=UnAligned). The descriptor should then
+			be used as a guide to populate ParaG for the display. Note that this
+			descriptor is a "pre"-layout of the ParaG structure : some descriptor's
+			nodes put together = a ParaG in size.
+    
+  Return value : the descriptor (see also TotLength; total size of the SeqAlign,
+	  display coordinates)
+
+*******************************************************************************/
+NLM_EXTERN ValNodePtr UABuildDescriptor2(SeqAlignPtr sap, Int4 nBsp, Int2 LineSize,
+	DDV_Disp_OptPtr ddop, Int4Ptr TotLength,Boolean AddLeftUAPart,
+	Boolean AddRightUAPart, Boolean WantExtraGapChar)
+{
+Int4            length,r,cumulpop,StartLetter,startcopy,stopcopy,pop,UAnum;
+Boolean         bUnAligned,bError;
+ValNodePtr      vnp,vnp_head,vnp2;
+DescriDispPtr   ddp;
+
+
+	r=0;
+	cumulpop=0;
+	StartLetter=0;/*align coord*/
+	bError=FALSE;
+	vnp_head=NULL;
+	*TotLength=0;
+
+	/*build UnAligned left part, if needed*/
+	if (AddLeftUAPart && ddop->DispDiscStyle!=MSA_TXT_STYLE_1){
+		vnp_head=DDV_BuildTailDescriptor(sap,nBsp,LineSize,LEFT_TAIL,TotLength,
+			&cumulpop);
+		/*get the last node; will be used in the SAP loop (see below)*/
+		if (vnp_head){
+			vnp=vnp_head;
+			while(vnp->next){
+				vnp=vnp->next;
+			}
+		}
+	}
+
+	/*loop through each aligned and unaligned regions to build
+	a ValNode list of descriptors. These descriptors will be used to
+	generate the ParaG list*/
+	UAnum=0;
+	while(AlnMgrGetNextLengthBit(sap,&length,&r)){
+
+		startcopy=0;
+
+		if (length<=0){
+			bUnAligned=TRUE;
+			switch(ddop->DispDiscStyle){/*user's display choice*/
+				case MSA_TXT_STYLE_1:/*put a spacer between 2 align blocks*/
+					stopcopy=ddop->SpacerSize;
+					break;
+				case MSA_TXT_STYLE_2:/*put sequence between 2 align blocks*/
+					stopcopy=ABS(length);
+          /* give a small space no matter what */
+          /* took out small spaces SW 1/19/01 */
+          /* put it back in optionally, DIH, 1/25/01 */
+          if (WantExtraGapChar) {
+            if (stopcopy==0) stopcopy=1; 
+          }
+					break;
+			}
+			UAnum++;
+		}
+		else if (length>0) {
+			bUnAligned=FALSE;
+			stopcopy=length;
+		} 
+
+		*TotLength+=(stopcopy-startcopy);/*to be used for the display coord. system*/
+		
+		while(startcopy<stopcopy){
+			/*store data*/
+			pop=_min_(stopcopy-startcopy,LineSize-cumulpop);
+			ddp=(DescriDispPtr)MemNew(sizeof(DescriDisp));
+			if (ddp==NULL) {
+				bError=TRUE;break;
+			}
+			if (bUnAligned==FALSE){
+				ddp->from=StartLetter;/*use align coord*/
+				ddp->to=ddp->from+pop-1;
+				ddp->TextStyle=MSA_TXT_STYLE_REG_ALIGN;
+				StartLetter+=pop;
+			}
+			else{
+				ddp->from=startcopy;/*use relative coord, i.e. UA coord system*/
+				ddp->to=ddp->from+pop-1;
+				ddp->TextStyle=MSA_TXT_STYLE_REG_UNALIGN;
+				ddp->UAnum=UAnum;/*UA region number*/
+				ddp->UAMaxlength=stopcopy;
+			}			
+			/*create a new node*/
+			if (vnp_head==NULL) {
+				vnp_head=ValNodeAddPointer(NULL,0,(Pointer)ddp);
+				vnp=vnp_head;
+			}
+			else vnp=ValNodeAddPointer(&vnp,0,(Pointer)ddp);
+
+			if (!vnp){
+				bError=TRUE;
+				break;
+			}
+			cumulpop+=pop;
+			if (cumulpop==LineSize) cumulpop=0;
+			startcopy+=pop;
+		}
+		if (bError) break;
+	}
+
+	if (bError){
+		vnp_head=ValNodeFreeData(vnp_head);
+		goto erreur;
+	}
+
+	/*build UnAligned right part, if needed*/
+	if (AddRightUAPart && ddop->DispDiscStyle!=MSA_TXT_STYLE_1){
+		vnp2=DDV_BuildTailDescriptor(sap,nBsp,LineSize,RIGHT_TAIL,TotLength,
+			&cumulpop);
+		/*add vnp2 at the end of vnp_head*/
+		if (vnp2) {
+			vnp=vnp_head;
+			while(vnp->next){
+				vnp=vnp->next;
+			}
+			vnp->next=vnp2;
+		}
+	}
+
+/*debug only : print the content of the descriptor
+
+	vnp=vnp_head;
+	while(vnp){
+		ddp=(DescriDispPtr)vnp->data.ptrvalue;
+		printf("[%4i..%4i],%2i (%4i) ; ",ddp->from,ddp->to,ddp->TextStyle,
+			ddp->to-ddp->from+1);
+		if (ddp->TextStyle==MSA_TXT_STYLE_REG_UNALIGN){
+			printf("MaxLength = %i ; UAnum = %i\n",ddp->UAMaxlength,ddp->UAnum);
+		}
+		else{
+			printf("\n");
+		}
+		vnp=vnp->next;
+	}
+
+debug only - end*/
+
+erreur :
+	return(vnp_head);
+}
+
+/*******************************************************************************
+
+  Function : UABuildDescriptorForBlockEditor()
+  
+  Purpose : build the descriptor of a SeqAlign for the block editor; i.e. the 
+  		descriptor contains the information about one aligned block along with
+		its two adjacent unaligned regions. See also the 'purpose' fo the function 
+		UABuildDescriptor() above.
+    
+  Return value : the descriptor (see also TotLength; total size of the SeqAlign,
+	  display coordinates)
+
+*******************************************************************************/
+NLM_EXTERN ValNodePtr UABuildDescriptorForBlockEditor(SeqAlignPtr sap, Int4 nBsp, 
+	Int4 block_num,Int4 LineSize,Int4Ptr TotLength)
+{
+Int4            length,r,cumulpop,StartLetter,startcopy,stopcopy,pop,UAnum,nBlock,
+				blockNum;
+Boolean         bUnAligned,bError,bPopNow;
+ValNodePtr      vnp,vnp_head,vnp2;
+DescriDispPtr   ddp;
+
+
+	/*test if we have a Discontinuous SeqAlign*/
+	if (!AlnMgrIsSAPDiscAli(sap)) return(NULL);
+	
+	/*get the number of block(s)*/
+	nBlock=AlnMgrGetNumAlnBlocks(sap);
+	if (block_num<0 || block_num>nBlock-1){
+		return(NULL);
+	}
+	r=cumulpop=UAnum=blockNum=0;
+	StartLetter=0;/*align coord*/
+	bError=FALSE;
+	vnp_head=NULL;
+	*TotLength=0;
+	/*if the user wants to edit the first block (block_num==0), I have
+	to use a special function to create the left-side part of the 
+	descriptor*/
+	if (block_num==0){
+		vnp_head=DDV_BuildTailDescriptor(sap,nBsp,LIMIT_EDITOR_SIZE,
+			LEFT_TAIL,TotLength,&cumulpop);
+		if (vnp_head){
+			vnp=vnp_head;
+			while(vnp->next){
+				vnp=vnp->next;
+			}
+		}
+	}
+
+	while(AlnMgrGetNextLengthBit(sap,&length,&r)){
+
+		bPopNow=FALSE;
+		startcopy=0;
+
+		/*unaligned region ?*/
+		if (length<=0){
+			/*region adjacent to the block of interest ?*/
+			if (UAnum==block_num-1 || UAnum==block_num){
+				bUnAligned=TRUE;
+				stopcopy=ABS(length);
+				bPopNow=TRUE;
+			}
+			UAnum++;
+		}
+		else{/*aligned region*/
+			if (blockNum==block_num){
+				bUnAligned=FALSE;
+				stopcopy=length;
+				bPopNow=TRUE;
+			}
+			else{
+				StartLetter+=length;
+			}
+			blockNum++;
+		}
+		
+		if (!bPopNow) continue;
+		
+		*TotLength+=(stopcopy-startcopy);/*to be used for the display coord. system*/
+		
+		while(startcopy<stopcopy){
+			/*store data*/
+			pop=_min_(stopcopy-startcopy,LineSize-cumulpop);
+			ddp=(DescriDispPtr)MemNew(sizeof(DescriDisp));
+			if (ddp==NULL) {
+				bError=TRUE;break;
+			}
+			if (bUnAligned==FALSE){
+				ddp->from=StartLetter;/*use align coord*/
+				ddp->to=ddp->from+pop-1;
+				ddp->TextStyle=MSA_TXT_STYLE_REG_ALIGN;
+				StartLetter+=pop;
+			}
+			else{
+				ddp->from=startcopy;/*use relative coord, i.e. UA coord system*/
+				ddp->to=ddp->from+pop-1;
+				ddp->TextStyle=MSA_TXT_STYLE_REG_UNALIGN;
+				ddp->UAnum=UAnum;/*UA region number*/
+				ddp->UAMaxlength=stopcopy;
+			}			
+			/*create a new node*/
+			if (vnp_head==NULL) {
+				vnp_head=ValNodeAddPointer(NULL,0,(Pointer)ddp);
+				vnp=vnp_head;
+			}
+			else vnp=ValNodeAddPointer(&vnp,0,(Pointer)ddp);
+
+			if (!vnp){
+				bError=TRUE;
+				break;
+			}
+			cumulpop+=pop;
+			if (cumulpop==LineSize) cumulpop=0;
+			startcopy+=pop;
+		}
+		if (bError) break;
+	}
+
+	/*oups...*/
+	if (bError){
+		vnp_head=ValNodeFreeData(vnp_head);
+		goto erreur;
+	}
+
+	
+	/*if the user wants to edit the last block (block_num==nBlock-1), I have
+	to use a special function to create the right-side part of the 
+	descriptor*/
+	if (block_num==nBlock-1){
+		vnp2=DDV_BuildTailDescriptor(sap,nBsp,LIMIT_EDITOR_SIZE,
+			RIGHT_TAIL,TotLength,&cumulpop);
+		if (vnp2) {
+			vnp=vnp_head;
+			while(vnp->next){
+				vnp=vnp->next;
+			}
+			vnp->next=vnp2;
+		}
+	}
+
+erreur :
+	return(vnp_head);
+}
+
+/*******************************************************************************
+
+  Function : DDV_DumpSAPInAFile()
+  
+  Purpose : write an Indexed SeqALign in a file (use the code of the Population
+      Viewer).
+  
+  Return value : -
+
+*******************************************************************************/
+NLM_EXTERN void DDV_DumpSAPInAFile(MsaParaGPopListPtr mpplp,DDVOptionsBlockPtr dobp, 
+		FILE *hFile,Uint4 option,DDV_ColorGlobal * gclr)
+{
+ByteStorePtr    PNTR byteSpp;
+Int4Ptr PNTR    matrix  ;
+Int2            LineSize;
+
+	if (!mpplp || !hFile) return;
+	
+	/*get the optional data*/
+	if (dobp){
+		LineSize=dobp->LineSize;
+		byteSpp=dobp->byteSpp;
+		matrix=dobp->matrix;
+	}
+	else{
+		LineSize=ParaG_Size;
+		byteSpp=NULL;
+	}
+
+	/*do the display */
+	DDV_AffichageParaG(mpplp,0,0,mpplp->LengthAli-1,mpplp->LengthAli,0,option,
+		LineSize,hFile,byteSpp,matrix,gclr,NULL);
+
+}
+
+/*******************************************************************************
+
+  Function : DDV_DumpSAPInFastaFile()
+  
+  Purpose : write an Indexed SeqALign in a file (use FASTA format only).
+  
+  Return value : -
+
+*******************************************************************************/
+NLM_EXTERN void DDV_DumpSAPInFastaFile(MsaParaGPopListPtr mpplp,DDVOptionsBlockPtr dobp, 
+		FILE *fp,Boolean bPrintGap)
+{
+CharPtr    szBuf,szSeq;
+ParaGPtr   pgp;
+SeqIdPtr   sip;
+ValNodePtr vnp;
+BioseqPtr  bsp;
+Int4       i,j,n,LineSize,bspLength;
+Boolean    bFirst,IsAA;
+Char       letter;
+Char       DefLine[255];
+
+	if (!mpplp || !fp) return;
+
+	if (dobp){
+		LineSize=dobp->LineSize;
+	}
+	else{
+		LineSize=ParaG_Size;
+	}
+	
+	szBuf=(CharPtr)MemNew((LineSize+1)*sizeof(Char));
+	if (!szBuf) return;/*todo : error msg for the user*/
+	
+	for(i=0;i<mpplp->nBsp;i++){
+		vnp=mpplp->TableHead[i];
+		n=0;
+		bFirst=TRUE;
+		while(vnp){
+			pgp=(ParaGPtr)vnp->data.ptrvalue;
+			sip=SeqIdFindBest(pgp->sip,0);
+			if (sip==NULL) sip=pgp->sip;
+			bsp=BioseqLockById(sip);
+			if (!bsp) return;/*todo : error msg for the user*/
+			bspLength=BioseqGetLen(bsp);
+			IsAA=ISA_aa(bsp->mol);
+			if (bFirst){
+				FastaId(bsp,DefLine,254);
+				fprintf(fp,">%s ",DefLine);
+				CreateDefLine(NULL, bsp, DefLine, 254, 0,NULL, NULL);
+				fprintf(fp,"%s\n",DefLine);
+				bFirst=FALSE;
+			}
+			BioseqUnlock(bsp);
+			szSeq=(CharPtr)MemNew((pgp->StopLetter-pgp->StartLetter+2)*sizeof(Char));
+			if (!szSeq) return;/*todo : error msg for the user*/
+			DDV_GetSequenceFromParaG(pgp,&szSeq,bspLength,IsAA,NULL,NULL,NULL);
+			j=0;
+			while(szSeq[j]){
+				letter=szSeq[j++];
+				if (isalpha(letter)){
+					szBuf[n++]=letter;
+				}
+				else{
+					if (bPrintGap)
+						szBuf[n++]=letter;
+				}
+				if (n==LineSize){
+					szBuf[n]='\0';
+					fprintf(fp,"%s\n",szBuf);
+					n=0;
+				}
+			}
+			MemFree(szSeq);
+			vnp=vnp->next;
+			if (vnp==NULL && n!=0){
+				szBuf[n]='\0';
+				fprintf(fp,"%s\n",szBuf);
+			}
+		}
+	}
+	MemFree(szBuf);
+}
+
+/*******************************************************************************
+
+  Function : DDV_InitDefSAPdispStyles_BLAST()
+  
+  Purpose : set the default styles for SeqAligns.
+  
+  Return value : -
+
+*******************************************************************************/
+static void DDV_InitDefSAPdispStyles_BLAST(DDV_Disp_OptPtr ddop)
+{
+	/*use colors*/
+	ddop->bUseColors=FALSE;
+	/*disc SAP styles*/
+	ddop->ShowLeftTail=FALSE;
+	ddop->ShowRightTail=FALSE;
+	ddop->DispDiscStyle=MSA_TXT_STYLE_2;
+	ddop->SpacerSize=SPACER_TXT_BLANK;
+        ddop->DiscJustification=DISP_JUST_LEFT;
+
+	ddop->UAGapStyle=MSA_TXT_STYLE_UAGAP;
+	ddop->AGapStyle=MSA_TXT_STYLE_GAP;
+
+	/*ruler style*/
+	ddop->RulerStyle=RulerStyle_Continue_Start;
+
+}
+
+
+/*******************************************************************************
+
+  Function : DDV_DisplayNewBLAST()
+  
+  Purpose : build a default SeqAlign display for BLAST.
+  
+  Parameters : 	sap; SeqAlign
+				disp_format; display formats (see pgppop.h)
+				disp_data; for future implementation
+				fp; to send the output
+
+  NOTE : this function uses the alignmgr.[ch] instead of blocks.[ch]
+  
+  Return value : FALSE if failed 
+
+*******************************************************************************/
+static Boolean DDV_DisplayNewBLAST(SeqAlignPtr sap, ValNodePtr mask,
+		Int4Ptr PNTR matrix,Uint4 disp_format,Pointer disp_data,FILE *fp)
+{
+MsaParaGPopList mppl;/*contains the data for the display*/
+Int2            LineSize;
+DDVOptionsBlockPtr dobp;
+ByteStorePtr   PNTR byteSpp;
+DDV_ColorGlobal *layout;
+DDV_Disp_Opt   ddo;
+Boolean        bUseLayout;
+Uint1          what;
+
+	MemSet(&mppl,0,sizeof(MsaParaGPopList));
+	MemSet(&ddo,0,sizeof(DDV_Disp_Opt));
+	layout=NULL;
+
+	/*get the optional data*/
+	if (disp_data){
+		dobp=(DDVOptionsBlockPtr)disp_data;
+		LineSize=dobp->LineSize;
+		byteSpp=dobp->byteSpp;
+		bUseLayout=dobp->bUseLayout;
+		what=dobp->LayoutType;
+	}
+	else{
+		LineSize=ParaG_Size;
+		byteSpp=NULL;
+		bUseLayout=FALSE;
+	}
+
+	DDV_InitDefSAPdispStyles_BLAST(&ddo);
+	
+	/*build the indexed SeqAlign and the ParaG structure*/
+	DDV_CreateDisplayFromIndex(sap, &mppl, LineSize,&ddo);
+	
+	/*create the layout*/
+	if (bUseLayout){
+		layout = DDV_CreateColorGlobal(TRUE, (void *)sap);
+		if (layout){
+			if (dobp->LayoutType&DDV_USE_STDCLR){
+				DDV_InitColour_When_Start(sap,&mppl,&layout, FALSE);
+			}
+			if (dobp->LayoutType&DDV_USE_UALAYOUT || dobp->LayoutType&DDV_USE_NOMLAYOUT){
+				DDV_LayoutUAregion(sap,&mppl,&layout,
+					dobp->normlayout.rgb,dobp->normlayout.style,
+					dobp->UAlayout.rgb,dobp->UAlayout.style);
+			}
+			if (dobp->LayoutType&DDV_USE_ISOLAYOUT){
+				DDV_LayoutISOColors(layout,mppl.TableHead,mppl.nBsp,
+					0,TRUE,matrix,dobp->ISOlayout.clr_ident,
+					dobp->ISOlayout.clr_simil,dobp->ISOlayout.clr_other,
+					dobp->ISOlayout.sty_ident,
+					dobp->ISOlayout.sty_simil,dobp->ISOlayout.sty_other);
+			}
+			if (dobp->LayoutType&DDV_USE_GAPLAYOUT){
+				DDV_LayoutGap(layout,mppl.TableHead[0],mppl.TableHead[1],1,
+					dobp->GAPlayout.style,dobp->GAPlayout.rgb);
+				DDV_LayoutGap(layout,mppl.TableHead[1],mppl.TableHead[0],0,
+					dobp->GAPlayout.style,dobp->GAPlayout.rgb);
+			}
+			if (dobp->LayoutType&DDV_USE_MASKLAYOUT){
+				DDV_LayoutMaskRegions(layout,mppl.TableHead[0],mask,0,
+					dobp->MASKlayout.style,dobp->MASKlayout.rgb);
+			}
+		}
+	}
+	
+	/*do the display */
+	DDV_AffichageParaG(&mppl,0,0,mppl.LengthAli-1,mppl.LengthAli,0,disp_format,
+		LineSize,fp,byteSpp,matrix,layout,mask);
+
+	/*done... delete data*/
+	DDV_DeleteDisplayList(&mppl);
+	if (layout) DDV_DeleteColorGlobal(layout);
+
+	
+	return(TRUE);
+}
+
+/*******************************************************************************
+
+  Function : DDV_BlastGetColorSchemaZero()
+  
+  Purpose : BLAST color sheme 0 : standard b&w BLAST output
+  
+*******************************************************************************/
+static void DDV_BlastGetColorSchemaZero(DDVOptionsBlockPtr dobp)
+{
+	memset(dobp,0,sizeof(DDVOptionsBlock));
+	
+	dobp->bUseLayout=FALSE;
+}
+
+/*******************************************************************************
+
+  Function : DDV_BlastGetColorSchemaOne()
+  
+  Purpose : BLAST color sheme 1 :
+              - masked regions in lowe case,
+			  - everything else in upper case.
+  
+*******************************************************************************/
+static void DDV_BlastGetColorSchemaOne(DDVOptionsBlockPtr dobp)
+{
+    memset(dobp,0,sizeof(DDVOptionsBlock));
+    
+    dobp->bUseLayout=TRUE;
+    
+    /* dobp->LayoutType=DDV_USE_MASKLAYOUT|DDV_USE_NOMLAYOUT; */
+    
+    dobp->LayoutType=DDV_USE_UALAYOUT|DDV_USE_GAPLAYOUT;
+
+    dobp->UAlayout.style=DDV_TXTSTYLE_LOWERCASE;
+    dobp->GAPlayout.style=DDV_TXTSTYLE_LOWERCASE;
+    
+    /* dobp->MASKlayout.style=DDV_TXTSTYLE_LOWERCASE; */
+}
+
+/*******************************************************************************
+
+  Function : DDV_BlastGetColorSchemaTwo()
+  
+  Purpose : BLAST color sheme 2 :
+              - masked regions in lower case, gray letters,
+			  - UnAligned regions in italic,
+			  - everything else in upper case.
+  
+*******************************************************************************/
+static void DDV_BlastGetColorSchemaTwo(DDVOptionsBlockPtr dobp)
+{
+	memset(dobp,0,sizeof(DDVOptionsBlock));
+	
+	dobp->bUseLayout=TRUE;
+
+	dobp->LayoutType=DDV_USE_MASKLAYOUT|DDV_USE_NOMLAYOUT;
+	dobp->LayoutType|=DDV_USE_UALAYOUT;
+
+	dobp->UAlayout.style=DDV_TXTSTYLE_ITALIC|DDV_TXTSTYLE_LOWERCASE;
+	dobp->normlayout.style=DDV_TXTSTYLE_BOLD;
+
+	dobp->MASKlayout.style=DDV_TXTSTYLE_LOWERCASE|DDV_TXTSTYLE_COLOR;
+	dobp->MASKlayout.rgb[0]=102;
+	dobp->MASKlayout.rgb[1]=102;
+	dobp->MASKlayout.rgb[2]=102;
+}
+
+/*******************************************************************************
+
+  Function : DDV_BlastGetColorSchemaThree()
+  
+  Purpose : BLAST color sheme 3 :
+              - masked regions in lower case, gray letters,
+			  - UnAligned regions in italic,
+			  - Identity/Similarity colors
+			  - everything else in upper case.
+  
+*******************************************************************************/
+static void DDV_BlastGetColorSchemaThree(DDVOptionsBlockPtr dobp)
+{
+	memset(dobp,0,sizeof(DDVOptionsBlock));
+	
+	dobp->bUseLayout=TRUE;
+
+	dobp->LayoutType=DDV_USE_MASKLAYOUT;
+	dobp->LayoutType|=DDV_USE_UALAYOUT;
+	dobp->LayoutType|=DDV_USE_ISOLAYOUT;
+
+	dobp->UAlayout.style=DDV_TXTSTYLE_ITALIC|DDV_TXTSTYLE_LOWERCASE;
+
+	dobp->MASKlayout.style=DDV_TXTSTYLE_LOWERCASE;/*|DDV_TXTSTYLE_COLOR;
+	dobp->MASKlayout.rgb[0]=102;
+	dobp->MASKlayout.rgb[1]=102;
+	dobp->MASKlayout.rgb[2]=102;
+*/
+	dobp->ISOlayout.clr_ident=DDVCOL_ORANGE;
+	dobp->ISOlayout.clr_simil=DDVCOL_BLUE;
+	dobp->ISOlayout.clr_other=DDVCOL_BLACK;
+}
+
+/*******************************************************************************
+
+  Function : DDV_BlastGetColorSchemaFour()
+  
+  Purpose : BLAST color sheme 4 = BLAST color schema 3 but with different colors
+  
+*******************************************************************************/
+static void DDV_BlastGetColorSchemaFour(DDVOptionsBlockPtr dobp)
+{
+	memset(dobp,0,sizeof(DDVOptionsBlock));
+	
+	dobp->bUseLayout=TRUE;
+
+	dobp->LayoutType=DDV_USE_MASKLAYOUT;
+	dobp->LayoutType|=DDV_USE_UALAYOUT;
+	dobp->LayoutType|=DDV_USE_ISOLAYOUT;
+
+	dobp->UAlayout.style=DDV_TXTSTYLE_ITALIC|DDV_TXTSTYLE_LOWERCASE;
+
+	dobp->MASKlayout.style=DDV_TXTSTYLE_LOWERCASE|DDV_TXTSTYLE_COLOR;
+	dobp->MASKlayout.rgb[0]=102;
+	dobp->MASKlayout.rgb[1]=102;
+	dobp->MASKlayout.rgb[2]=102;
+
+	dobp->ISOlayout.clr_ident=DDVCOL_BLUE;
+	dobp->ISOlayout.clr_simil=DDVCOL_BROWN;
+	dobp->ISOlayout.clr_other=DDVCOL_RED;
+}
+
+/*******************************************************************************
+
+  Function : DDV_BlastGetColorSchemaFive()
+  
+  Purpose : BLAST color sheme 5 = BLAST color schema 3 but with different colors
+  
+*******************************************************************************/
+static void DDV_BlastGetColorSchemaFive(DDVOptionsBlockPtr dobp)
+{
+	memset(dobp,0,sizeof(DDVOptionsBlock));
+	
+	dobp->bUseLayout=TRUE;
+
+	dobp->LayoutType=DDV_USE_MASKLAYOUT;
+	dobp->LayoutType|=DDV_USE_UALAYOUT;
+	dobp->LayoutType|=DDV_USE_ISOLAYOUT;
+
+	dobp->UAlayout.style=DDV_TXTSTYLE_ITALIC|DDV_TXTSTYLE_LOWERCASE;
+
+	dobp->MASKlayout.style=DDV_TXTSTYLE_LOWERCASE|DDV_TXTSTYLE_COLOR;
+	dobp->MASKlayout.rgb[0]=102;
+	dobp->MASKlayout.rgb[1]=102;
+	dobp->MASKlayout.rgb[2]=102;
+
+	dobp->ISOlayout.clr_ident=DDVCOL_RED;
+	dobp->ISOlayout.clr_simil=DDVCOL_BLUE;
+	dobp->ISOlayout.clr_other=DDVCOL_BLACK;
+}
+
+/*******************************************************************************
+
+  Function : DDV_BlastGetColorSchemaSix()
+  
+  Purpose : BLAST color sheme 6 = BLAST color schema 3 but with different colors
+  
+*******************************************************************************/
+static void DDV_BlastGetColorSchemaSix(DDVOptionsBlockPtr dobp)
+{
+	memset(dobp,0,sizeof(DDVOptionsBlock));
+	
+	dobp->bUseLayout=TRUE;
+
+	dobp->LayoutType=DDV_USE_MASKLAYOUT;
+	dobp->LayoutType|=DDV_USE_UALAYOUT;
+	dobp->LayoutType|=DDV_USE_ISOLAYOUT;
+
+	dobp->UAlayout.style=DDV_TXTSTYLE_ITALIC|DDV_TXTSTYLE_LOWERCASE;
+
+	dobp->MASKlayout.style=DDV_TXTSTYLE_LOWERCASE;/*|DDV_TXTSTYLE_COLOR;
+	dobp->MASKlayout.rgb[0]=102;
+	dobp->MASKlayout.rgb[1]=102;
+	dobp->MASKlayout.rgb[2]=102;
+*/
+	dobp->ISOlayout.clr_ident=DDVCOL_ORANGE;
+	dobp->ISOlayout.clr_simil=DDVCOL_BLUE;
+	dobp->ISOlayout.clr_other=DDVCOL_BLACK;
+
+	dobp->ISOlayout.sty_ident=DDV_TXTSTYLE_BOLD;
+}
+
+/*******************************************************************************
+
+  Function : DDV_DisplayBlastPairList()
+  
+  Purpose : function to display a BLAST output.
+  
+  Parameters : 	sap; seqalign
+			    mask; list of masked regions in the query
+				fp; output file;
+				is_na; TRUE means nuc sequence
+				tx_option; some display options
+				ColorSchema; one of the available color schemes
+				
+  Return value : FALSE if failure
+
+*******************************************************************************/
+NLM_EXTERN Boolean DDV_DisplayBlastPairList(SeqAlignPtr sap, ValNodePtr mask,
+	FILE *fp, Boolean is_na, Uint4 tx_option,Uint1 ColorSchema)
+{
+    DDVOptionsBlock dob;
+    SeqAlignPtr     sap4;
+    SeqIdPtr        new_id = NULL, old_id = NULL;    
+    Int4Ptr PNTR    matrix;
+    Uint4           option,i;
+    Boolean         bRet, follower= FALSE;
+    
+    if (!sap || !fp) 
+        return(FALSE);
+    
+    /*get the matrix*/
+    if (is_na == FALSE){
+        matrix=load_default_matrix();
+        if (!matrix)
+            return(FALSE);
+    } else {
+        matrix=NULL;
+    }
+    
+    memset(&dob, '\0', sizeof(DDVOptionsBlock));
+    
+    /*init display format*/
+    option =VIEW_FULLSEQ;
+
+    if (ColorSchema==DDV_BLAST_COLOR0 || ColorSchema==DDV_BLAST_COLOR1)    
+        option|=DISP_FULL_TXT;
+    else
+        option|=DISP_FULL_HTML;
+
+    option|=DISP_BSP_COORD;
+    option|=SEQNAME_BLAST_STD;
+    option|=DISP_NOLINKONNAME;
+    option|=DISP_BLAST_STD;
+    option|=DISPE_COLOR;
+    
+    /*get the color scheme layout*/
+    /*note that the following functions will set to 0 the entire dob structure, before
+      filling in its content with the layout information. All subsequent init. of dob
+      should be done after the following switch()*/
+    switch(ColorSchema){
+    case DDV_BLAST_COLOR0:
+        option|=DISP_BLAST_MIDLINE;
+        DDV_BlastGetColorSchemaZero(&dob);
+        break;
+    case DDV_BLAST_COLOR1:
+        option|=DISP_BLAST_MIDLINE;
+        DDV_BlastGetColorSchemaOne(&dob);
+        break;
+    case DDV_BLAST_COLOR2:
+        option|=DISP_BLAST_MIDLINE;
+        DDV_BlastGetColorSchemaTwo(&dob);
+        break;
+    case DDV_BLAST_COLOR3:
+        DDV_BlastGetColorSchemaThree(&dob);
+        break;
+    case DDV_BLAST_COLOR4:
+        DDV_BlastGetColorSchemaFour(&dob);
+        break;
+    case DDV_BLAST_COLOR5:
+        DDV_BlastGetColorSchemaFive(&dob);
+        break;
+    case DDV_BLAST_COLOR6:
+        DDV_BlastGetColorSchemaSix(&dob);
+        break;
+    }
+    
+    dob.LineSize=(Int2)60;
+    dob.matrix=matrix;
+    bRet=TRUE;
+    sap4=sap;
+    
+    while(sap4) {
+        /*build the Index*/
+        if (sap4->segtype == SAS_DISC){
+            if (!sap4 || !AlnMgrIndexSingleSeqAlign(sap4)){
+                bRet=FALSE;
+                break;
+            }
+        }
+        else{
+            if (!sap4 || !AlnMgrIndexSingleChildSeqAlign(sap4)){
+                bRet=FALSE;
+                break;
+            }
+        }
+        
+        if (option&DISP_FULL_HTML){
+            fprintf(fp,"<pre>\n");
+        }
+        /* Attempt to print score for the alignment */
+        new_id = TxGetSubjectIdFromSeqAlign(sap4);
+        if(old_id != NULL) {
+            if(SeqIdMatch(new_id, old_id))
+                follower = TRUE;
+        }
+        
+        /*separator*/
+        if (option&DISP_FULL_HTML)
+            fprintf(fp,"<HR WIDTH=\"400\">");
+        
+        old_id = new_id;
+        if(!FormatScoreFromSeqAlign(sap4, tx_option, fp, matrix, follower)){
+            bRet=FALSE;
+            break;
+        }
+        follower = FALSE;
+        if (option&DISP_FULL_HTML){
+            fprintf(fp,"</pre>\n");
+        }
+        
+        /*display a SeqAlign*/
+        if (!DDV_DisplayNewBLAST(sap4, mask, matrix, option, (Pointer) &dob, fp)){
+            bRet=FALSE;
+            break;
+        }
+        sap4 = sap4->next;
+    }
+    
+    if (matrix){
+        for(i = 0; i<TX_MATRIX_SIZE; ++i)
+            MemFree(matrix[i]);
+        MemFree(matrix);
+    } 
+    
+    return(bRet);
+	
+}
+
+/*******************************************************************************
+
+  Function : DDV_DisplayBlastSAP()
+  
+  Purpose : test function to display a BLAST output.
+  
+  Parameters : 	sap; seqalign
+			    mask; list of masked regions in the query
+				fo; output file;
+				is_na; TRUE means nuc sequence
+				tx_option; some display options
+				
+  Return value : -
+
+*******************************************************************************/
+static Boolean DDV_DisplayBlastSAP(SeqAlignPtr sap, ValNodePtr mask,
+	FILE *fp, Boolean is_na, Uint4 tx_option)
+{
+DDVOptionsBlock dob;
+SeqAlignPtr     sap4;
+SeqIdPtr        new_id = NULL, old_id = NULL;    
+Int4Ptr PNTR    matrix;
+Uint4           option,i;
+Boolean         bRet, follower= FALSE;
+
+    if (!sap || !fp) 
+        return(FALSE);
+    
+	/*get the matrix*/
+    if (is_na == FALSE){
+        matrix=load_default_matrix();
+        if (!matrix)
+            return(FALSE);
+    } else {
+        matrix=NULL;
+    }
+    
+    /*init display format*/
+    option =VIEW_FULLSEQ;
+    option|=DISP_FULL_HTML;
+    option|=DISP_BSP_COORD;
+    option|=SEQNAME_BLAST_STD;
+    option|=DISP_BLAST_STD;
+	option|=DISP_BLAST_MIDLINE;
+    option|=DISPE_COLOR;
+    dob.LineSize=(Int2)60;
+    dob.matrix=matrix;
+	
+    bRet=TRUE;
+    sap4=sap;
+    while(sap4) {
+        /*build the Index*/
+        if (sap4->segtype == SAS_DISC){
+            if (!sap4 || !AlnMgrIndexSingleSeqAlign(sap4)){
+                bRet=FALSE;
+                break;
+            }
+            dob.bUseLayout=TRUE;
+        }
+        else{
+            if (!sap4 || !AlnMgrIndexSingleChildSeqAlign(sap4)){
+                bRet=FALSE;
+                break;
+            }
+            dob.bUseLayout=TRUE;
+        }
+		
+		/*set the layout type, if needed*/
+		if (dob.bUseLayout){
+			/*basic layout*/
+			dob.LayoutType=DDV_USE_UALAYOUT;
+			dob.LayoutType|=DDV_USE_GAPLAYOUT;
+			dob.LayoutType|=DDV_USE_MASKLAYOUT;
+			/*dob.LayoutType|=DDV_USE_ISOLAYOUT;*/
+			/*ext. layout*/
+			dob.UAlayout.style=DDV_TXTSTYLE_LOWERCASE;
+			dob.UAlayout.style|=DDV_TXTSTYLE_ITALIC;
+			dob.UAlayout.style|=DDV_TXTSTYLE_COLOR;
+			dob.UAlayout.rgb[0]=255;
+			dob.UAlayout.rgb[1]=0;
+			dob.UAlayout.rgb[2]=0;
+			dob.GAPlayout.style=DDV_TXTSTYLE_LOWERCASE;
+			dob.GAPlayout.style|=DDV_TXTSTYLE_ITALIC;
+			dob.GAPlayout.style|=DDV_TXTSTYLE_COLOR;
+			dob.GAPlayout.rgb[0]=255;
+			dob.GAPlayout.rgb[1]=0;
+			dob.GAPlayout.rgb[2]=0;
+			dob.MASKlayout.style=DDV_TXTSTYLE_BOLD;
+			dob.MASKlayout.style|=DDV_TXTSTYLE_UNDERLINE;
+			dob.ISOlayout.clr_ident=DDVCOL_ORANGE;
+			dob.ISOlayout.clr_simil=DDVCOL_SKY;
+			dob.ISOlayout.clr_other=DDVCOL_BLACK;
+		}
+					
+        if (option&DISP_FULL_HTML){
+			fprintf(fp,"<pre>\n");
+		}
+        /* Attempt to print score for the alignment */
+        new_id = TxGetSubjectIdFromSeqAlign(sap4);
+        if(old_id != NULL) {
+            if(SeqIdMatch(new_id, old_id))
+                follower = TRUE;
+        }
+		
+		/*separator*/
+		fprintf(fp,"<HR WIDTH=\"400\">");
+        old_id = new_id;
+        if(!FormatScoreFromSeqAlign(sap4, tx_option, fp, matrix, follower)){
+            bRet=FALSE;
+            break;
+        }
+        follower = FALSE;
+        if (option&DISP_FULL_HTML){
+			fprintf(fp,"</pre>\n");
+		}
+
+        /*display a SeqAlign*/
+		if (!DDV_DisplayNewBLAST(sap4, mask, matrix, option, (Pointer) &dob, fp)){
+            bRet=FALSE;
+            break;
+        }
+        sap4 = sap4->next;
+    }
+    
+    if (matrix){
+        for(i = 0; i<TX_MATRIX_SIZE; ++i)
+            MemFree(matrix[i]);
+        MemFree(matrix);
+    } 
+    
+    return(bRet);
+}
+/*******************************************************************************
+
+  Function : DDV_InitDefSAPdispStyles()
+  
+  Purpose : set the default styles for SeqAligns.
+  
+  Return value : -
+
+*******************************************************************************/
+NLM_EXTERN void DDV_InitDefSAPdispStyles(DDV_Disp_OptPtr ddop)
+{
+	/*use colors*/
+	ddop->bUseColors=TRUE;
+	/*disc SAP styles*/
+	ddop->ShowLeftTail=FALSE;
+	ddop->ShowRightTail=FALSE;
+	ddop->DispDiscStyle=MSA_TXT_STYLE_1;
+	ddop->SpacerSize=SPACER_TXT_BLANK;
+    ddop->DiscJustification=DISP_JUST_CENTER;
+	ddop->UAGapStyle=MSA_TXT_STYLE_UAGAP;
+	ddop->AGapStyle=MSA_TXT_STYLE_GAP;
+
+	/*ruler style*/
+	ddop->RulerStyle=RulerStyle_Continue_Start;
+}
+
+/*******************************************************************************
+
+  Function : DDV_InitCn3DSAPdispStyles()
+  
+  Purpose : set the styles for Cn3D SeqAligns.
+  
+  Return value : -
+
+*******************************************************************************/
+NLM_EXTERN void DDV_InitCn3DSAPdispStyles(DDV_Disp_OptPtr ddop)
+{
+	/*use colors*/
+	ddop->bUseColors=TRUE;
+	/*disc SAP styles*/
+	ddop->ShowLeftTail=TRUE;
+	ddop->ShowRightTail=TRUE;
+	ddop->DispDiscStyle=MSA_TXT_STYLE_2;
+	ddop->SpacerSize=0;
+    ddop->DiscJustification=DISP_JUST_SPLIT;
+    ddop->UAGapStyle=MSA_TXT_STYLE_UAGAP; /* use different unaligned gap chars ('~') */
+	ddop->AGapStyle=MSA_TXT_STYLE_GAP;
+
+	/*ruler style*/
+	ddop->RulerStyle=RulerStyle_Continue_Start;
+}
+
+/*******************************************************************************
+
+  Function : DDV_InitDDESAPdispStyles()
+  
+  Purpose : set the styles for DDE (i.e. DDV used as an editor).
+  
+  Return value : -
+
+*******************************************************************************/
+NLM_EXTERN void DDV_InitDDESAPdispStyles(DDV_Disp_OptPtr ddop)
+{
+	/*use colors*/
+	ddop->bUseColors=TRUE;
+	/*disc SAP styles*/
+	ddop->ShowLeftTail=TRUE;
+	ddop->ShowRightTail=TRUE;
+	ddop->DispDiscStyle=MSA_TXT_STYLE_2;
+	ddop->SpacerSize=0;
+    ddop->DiscJustification=DISP_JUST_LEFT;
+	ddop->UAGapStyle=MSA_TXT_STYLE_UAGAP;
+	ddop->AGapStyle=MSA_TXT_STYLE_GAP;
+
+	/*ruler style*/
+	ddop->RulerStyle=RulerStyle_Continue_Start;
+}
+
+/*******************************************************************************
+
+  Function : DDV_ReadSeqBin()
+  
+  Purpose : read a sequence using Seq_code_ncbistdaa or Seq_code_ncbi4na
+    
+  Return value : the sequence 
+
+*******************************************************************************/
+NLM_EXTERN Uint1Ptr DDV_ReadSeqBin (SeqIdPtr sip, Int4 from, Int4 to, 
+                                    Boolean IsProt,Int2 len,Uint1 strand)
+{
+SeqLocPtr  slp;
+SeqPortPtr spp;
+Uint1Ptr    btr;
+Uint1	   residue;
+Uint2	   i=0;
+
+	/*from always < than to*/
+	slp = SeqLocIntNew (from, to, strand, sip);
+	if (!slp) return(NULL);
+	spp = SeqPortNewByLoc (slp, (Uint1)(IsProt==TRUE ? Seq_code_ncbistdaa 
+			: Seq_code_ncbi4na));
+	if (spp != NULL) {
+		btr = (Uint1Ptr) MemNew (len * sizeof(Uint1));
+		if (!btr) return(NULL);
+		while ((residue = SeqPortGetResidue(spp)) != SEQPORT_EOF) {
+			if (IS_residue(residue)) {
+				btr[i] = residue;
+				i++;
+			}
+		}
+		/*SeqPortRead(spp, btr, len);*/
+		SeqPortFree (spp);
+	}   
+	SeqLocFree (slp);
+	return btr;
+}
+
+/*******************************************************************************
+
+  Function : DDV_SetStyle()
+  
+  Purpose : set the layout of a single letter 
+  
+  Return value : -.
+
+*******************************************************************************/
+static void DDV_SetStyle(DDV_ColorCell * dccp,Uint1 style, Uint1 *rgb,
+	Boolean bAllowReset)
+{
+	if (style&DDV_TXTSTYLE_ITALIC){
+		dccp->UseItalic=TRUE;
+	}
+    else if (bAllowReset){
+			dccp->UseItalic=FALSE;
+	}
+	
+	if (style&DDV_TXTSTYLE_BOLD){
+		dccp->UseBold=TRUE;
+	}
+    else if (bAllowReset){
+		dccp->UseBold=FALSE;
+	}
+	
+	if (style&DDV_TXTSTYLE_UNDERLINE){
+		dccp->UseUnderline=TRUE;
+	}
+	else if (bAllowReset){
+    	dccp->UseUnderline=FALSE;
+	}
+	
+	if (style&DDV_TXTSTYLE_LOWERCASE){
+		dccp->LowerCase=TRUE;
+	}
+	else if(bAllowReset) {
+    	dccp->LowerCase=FALSE;
+	}
+	
+	if (style&DDV_TXTSTYLE_COLOR && rgb){
+		dccp->rgb[0]=rgb[0];
+		dccp->rgb[1]=rgb[1];
+		dccp->rgb[2]=rgb[2];
+	}
+}
+
+/*******************************************************************************
+
+  Function : DDV_SetStd_AA_UA_ClrEx()
+  
+  Purpose : set the standard colours for a nuc or prot sequence; 
+     or the same function can be used to layout UnAligned regions
+
+  Note: For performance issue this function set up the layout of
+		 both aligned and unaligned regions at the same time
+    
+  Return value : -
+
+*******************************************************************************/
+#define read_buf_size 3000
+static void DDV_SetStd_AA_UA_ClrEx(DDV_ColorGlobal *pColorGlobal, void *pData,
+                                DDV_Range *pRange,Uint1 what)
+{
+DDVDataForColorFuncPtr ddfcfp;
+BioseqPtr              bsp;
+Int4                   bsp_length,i,from,to,limit;
+Boolean                IsAA;
+Int4                   dp;
+Uint1Ptr               SeqBuf;
+Int2                   len;
+Uint1                  idx;
+DDV_ColorCell *        dccp;
+
+	ddfcfp=(DDVDataForColorFuncPtr)pData;
+	
+	if (!ddfcfp) return;
+	
+	/*get bioseq size and type */
+	bsp=BioseqLockById(ddfcfp->sip);
+	if (bsp){
+		bsp_length=bsp->length;
+		IsAA=ISA_aa(bsp->mol);
+		BioseqUnlock(bsp);
+	}
+	else return;
+
+
+	/*compute the ends of the bioseq's region we want to analyse*/
+	if (ddfcfp->from!=(Int4)-1)
+		from=ddfcfp->from;
+	else
+		from=0;
+
+	if (ddfcfp->to!=(Int4)-1)
+		limit=ddfcfp->to;
+	else
+		limit=bsp_length-1;
+
+	to=from+read_buf_size-1;
+	if (to>limit) to=limit;
+
+	/*read the sequence by chunk of 'read_buf_size' letters*/
+	while(TRUE){
+		len=(Int2)(to-from+1);
+		/*get a sequence chunck ; from is always < than to*/
+		SeqBuf=DDV_ReadSeqBin (ddfcfp->sip, from, to, IsAA,len,ddfcfp->strand);
+		if (SeqBuf){/*scan each letter and get the appropriate colour*/
+			for(i=0;i<len;i++){
+				/*compute the correct position; depend on the strand*/
+				if (ddfcfp->strand==Seq_strand_minus)
+					dp=to-i;
+				else
+					dp=from+i;
+				/*first, query Color Manager*/
+                dccp=DDV_GetColor(pColorGlobal,NULL,ddfcfp->row+1,dp);
+                if (!dccp) return;
+                if(what & DDV_USE_STDCLR) {
+                    if (IsAA) 
+                        idx=DDV_STD_AAColor[*(SeqBuf+i)];/*AA*/
+                    else
+                        idx=DDV_STD_NAColor[*(SeqBuf+i)];/*NA*/
+                    
+                    if (ddfcfp->IsUnAligned)
+						DDV_SetStyle(dccp,ddfcfp->UAstyle,DDV_PaletteRGB[idx],TRUE);
+                    else 
+						DDV_SetStyle(dccp,ddfcfp->style,DDV_PaletteRGB[idx],TRUE);
+                }
+                else if(what & DDV_USE_UALAYOUT) {
+                    if (ddfcfp->IsUnAligned)
+						DDV_SetStyle(dccp,ddfcfp->UAstyle,ddfcfp->UArgb,TRUE);
+                    else 
+						DDV_SetStyle(dccp,ddfcfp->style,DDV_PaletteRGB[DDVCOL_BLACK],TRUE);
+                }				
+                /*set the colour*/
+                DDV_SetColor(pColorGlobal, NULL, ddfcfp->row+1, dp, dccp);
+            }
+            MemFree(SeqBuf);
+        }
+		
+		/*compute the next chunk*/		
+		from+=read_buf_size;
+		to+=read_buf_size;
+		if (to>limit) to=limit;
+		/*end ?*/
+		if (from>limit) break;
+	}
+
+}
+
+
+/*******************************************************************************
+
+  Function : DDV_InitColourSAP()
+  
+  Purpose : init the colours for each Bsp of a SeqAlign
+  
+  Parameters : sap; a (indexed) SeqAlign
+  		global colour data struct (see ddvcolor.[ch] in api)
+        NoColor; don't color the bsp's, but do change the case.
+		
+  Note : usually, this function is called when DDV loads a SeqAlign
+         For performance issue this function set up the layout of
+		 both aligned and unaligned regions at the same time
+  
+  Return value : FALSE is failure.
+
+*******************************************************************************/
+static Boolean DDV_InitColourSAP(SeqAlignPtr sap,MsaParaGPopListPtr mpplp,
+	DDV_ColorGlobal * * gclr,Uint1 what,Uint1 * pRGB,Uint1 style,
+	Uint1 * pUARGB,Uint1 UAstyle)
+{
+DDVDataForColorFunc  ddfcf;
+SeqIdPtr             sip;
+ValNodePtr           vnp,vnp2;
+ParaGPtr             pgp;
+MsaTxtDispPtr        mtdp;
+Int4                 n;
+
+    if (!sap)
+    return (FALSE);
+
+    if (!(*gclr)){
+        *gclr = DDV_CreateColorGlobal(FALSE, (void *) sap);
+        if (!(*gclr))
+            return(FALSE);
+    }
+
+    for(n=0;n<mpplp->nBsp;n++){
+        vnp=mpplp->TableHead[n];
+        while(vnp){
+            pgp=(ParaGPtr)vnp->data.ptrvalue;
+            if (pgp){
+                vnp2=pgp->ptxtList;
+                sip=pgp->sip;
+                while(vnp2){
+                    mtdp = (MsaTxtDispPtr)vnp2->data.ptrvalue;
+                    if(mtdp && mtdp->TextStyle==MSA_TXT_STYLE_SEQ){
+                        ddfcf.sip=sip;
+                        ddfcf.from=mtdp->from;
+                        ddfcf.to=mtdp->to;
+                        ddfcf.row=n;
+                        ddfcf.strand=mtdp->strand;
+                        ddfcf.IsUnAligned=mtdp->IsUnAligned;
+                        ddfcf.style=style;
+                        ddfcf.UAstyle=UAstyle;
+                        if (pRGB){
+                            ddfcf.rgb[0]=pRGB[0];
+                            ddfcf.rgb[1]=pRGB[1];
+                            ddfcf.rgb[2]=pRGB[2];
+                        }
+                        else{
+                            ddfcf.rgb[0]=0;
+                            ddfcf.rgb[1]=0;
+                            ddfcf.rgb[2]=0;
+                        }
+                        if (pUARGB){
+                            ddfcf.UArgb[0]=pUARGB[0];
+                            ddfcf.UArgb[1]=pUARGB[1];
+                            ddfcf.UArgb[2]=pUARGB[2];
+                        }
+                        else{
+                            ddfcf.UArgb[0]=0;
+                            ddfcf.UArgb[1]=0;
+                            ddfcf.UArgb[2]=0;
+                        }
+                        DDV_SetStd_AA_UA_ClrEx(*gclr, (Pointer)&ddfcf, NULL, what);
+                    }
+                    vnp2=vnp2->next;
+                }
+            }
+            vnp=vnp->next;
+        }
+    }
+    return(TRUE);
+}
+
+/*******************************************************************************
+
+  Function : DDV_InitColour_When_Start()
+  
+  Purpose : standard init function for Vibrant DDV ; see DDV_InitColourSAP()
+  
+*******************************************************************************/
+NLM_EXTERN Boolean DDV_InitColour_When_Start(SeqAlignPtr sap,MsaParaGPopListPtr mpplp,
+	DDV_ColorGlobal * * gclr, Boolean NoColor)
+{
+    if(NoColor) 
+		return(DDV_InitColourSAP(sap,mpplp,gclr,DDV_USE_STDCLR,NULL,0,NULL,0));
+    else 
+		return(DDV_InitColourSAP(sap,mpplp,gclr,DDV_USE_STDCLR,NULL,
+        	DDV_TXTSTYLE_COLOR,NULL,DDV_TXTSTYLE_COLOR|DDV_TXTSTYLE_LOWERCASE));
+}
+
+/*******************************************************************************
+
+  Function : DDV_LayoutUAregion()
+  
+  Purpose : set a layout for UnAligned regions; see DDV_InitColourSAP()
+  
+*******************************************************************************/
+NLM_EXTERN Boolean DDV_LayoutUAregion(SeqAlignPtr sap,MsaParaGPopListPtr mpplp,
+	DDV_ColorGlobal * * gclr,Uint1 * pRGB,Uint1 style,Uint1 * pUARGB,Uint1 UAstyle)
+{
+	return(DDV_InitColourSAP(sap,mpplp,gclr,DDV_USE_UALAYOUT,pRGB,style,pUARGB,UAstyle));
+}
+
+
+/*******************************************************************************
+
+  Function : UDV_BigEncodeIdxFeat4()
+  
+  Purpose : encode two Uint4 into one Uint8
+  
+*******************************************************************************/
+static Uint8 UDV_BigEncodeIdxFeat4 (Uint4 val1,Uint4 val2)
+{
+Uint4 index_g[2];
+	
+	index_g[0]=val1;
+	index_g[1]=val2;
+	
+	return *((Uint8Ptr) index_g);
+	
+}
+
+/*******************************************************************************
+
+  Function : UDV_BigEncodeIdxFeat4()
+  
+  Purpose : decode one Uint8 into two Uint4
+  
+*******************************************************************************/
+static void  UDV_BigDecodeIdxFeat4 (Uint8 index_g, Uint4Ptr val1, Uint4Ptr val2)
+{
+Uint4Ptr  index_g2;
+
+	index_g2 = (Uint4Ptr) (&index_g);
+	if (val1) *val1 = (Uint4) index_g2 [0];
+	if (val2) *val2 = (Uint4) index_g2 [1];
+}
+
+/*******************************************************************************
+
+  Function : DDV_GetGapCoord()
+  
+  Purpose : get the list of gaps given a ParaG.
+  
+  Return value : -.
+
+*******************************************************************************/
+static void DDV_GetGapCoord(ParaGPtr pgp,ValNodePtr PNTR gap_list)
+{
+ValNodePtr    vnp;
+MsaTxtDispPtr mtdp;
+
+	if (!pgp) return;
+	vnp=pgp->ptxtList;
+	while(vnp){
+		mtdp=(MsaTxtDispPtr)vnp->data.ptrvalue;
+		if (mtdp){
+			if(mtdp->IsGap && (mtdp->TextStyle==MSA_TXT_STYLE_GAP || 
+				mtdp->TextStyle==MSA_TXT_STYLE_2)){
+				ValNodeAddBigInt(gap_list,0,
+					UDV_BigEncodeIdxFeat4 ((Uint4)mtdp->from,(Uint4)mtdp->to));
+			}
+		}
+		vnp=vnp->next;
+	}
+}
+
+/*******************************************************************************
+
+  Function : DDV_AllGapInLowerCase()
+  
+  Purpose : analyse sequences by pair and switch to lower case all residues
+            "aligned" with a gap.
+  
+  Return value : -.
+
+*******************************************************************************/
+NLM_EXTERN void DDV_LayoutGap(DDV_ColorGlobal *pcg,ValNodePtr vnp_seq1,
+		ValNodePtr vnp_seq2,Int4 row2,Uint1 style,Uint1 *rgb)
+{
+DDV_ColorCell * dccp;
+ValNodePtr      vnp1,vnp2,vnp3,vnp4;
+ParaGPtr        pgp1,pgp2;
+Uint4           i,from,to;/*display coord.*/
+Int4            bsp_coord;
+DDV_ColorCell   dcc;
+
+	if (pcg==NULL || vnp_seq1==NULL || vnp_seq2==NULL) return;
+	/*scan the first sequence to modify the second*/
+	vnp1=vnp_seq1;
+	vnp2=vnp_seq2;
+	vnp3=NULL;
+	while(vnp1){
+		/*is there a gap in the vnp1 ParaG*/
+		pgp1=(ParaGPtr)vnp1->data.ptrvalue;
+		pgp2=(ParaGPtr)vnp2->data.ptrvalue;
+		DDV_GetGapCoord(pgp1,&vnp3);
+		if (vnp3){
+			vnp4=vnp3;
+			while(vnp4){
+				UDV_BigDecodeIdxFeat4((Uint8)vnp4->data.bigintvalue, 
+					&from, &to);
+				to++;
+				for (i=from;i<to;i++){
+					bsp_coord=(Int4)DDV_GetBspCoordGivenDispCoord(pgp2,(Int4)i);
+					if (bsp_coord>=0){
+						dccp=DDV_GetColor(pcg,NULL,row2+1,bsp_coord);
+						if (dccp){/*if there is already a color, just
+						  update the required parameter*/
+							DDV_SetStyle(dccp,style,rgb,FALSE);
+							DDV_SetColor(pcg,NULL,row2+1,bsp_coord,dccp);
+						}
+						else{/*otherwise, set up a new layout for that letter*/
+							memset(&dcc,0,sizeof(DDV_ColorCell));
+							DDV_SetStyle(&dcc,style,rgb,FALSE);
+							DDV_SetColor(pcg, NULL, row2+1, bsp_coord, &dcc);
+						}
+					}
+				}
+				vnp4=vnp4->next;
+			}
+		}
+		vnp1=vnp1->next;
+		vnp2=vnp2->next;
+		if (vnp3) 
+			vnp3=ValNodeFree(vnp3);
+	}
+}
+
+/*******************************************************************************
+
+  Function : DDV_LayoutMaskRegions()
+  
+  Purpose : layout the masked regions of a sequence (usually the query sequence
+       of BLAST).
+  
+  Return value : -.
+
+*******************************************************************************/
+NLM_EXTERN void DDV_LayoutMaskRegions(DDV_ColorGlobal *pcg,
+	ValNodePtr vnp_query,ValNodePtr mask,Int4 row,Uint1 style,Uint1 *rgb)
+{
+    DDV_ColorCell * dccp;
+    ValNodePtr      vnp;
+    SeqLocPtr       slp;
+    Int4            i,bsp_start,bsp_stop,mask_start,mask_stop,scan_from,
+        scan_to;
+    DDV_ColorCell   dcc;
+    
+    if (pcg==NULL || vnp_query==NULL || mask==NULL) return;
+    
+    /*get sequence range*/
+    UDV_GetBspRangeinPGPList(vnp_query,&bsp_start,&bsp_stop);
+    
+    /*scan the mask list*/
+    vnp=mask;
+    while(vnp) {
+        slp=(SeqLocPtr)vnp->data.ptrvalue;
+        
+        if(slp == NULL) 
+            return;
+        
+        if(slp->choice == SEQLOC_PACKED_INT)
+            slp = slp->data.ptrvalue;
+        else if (slp->choice != SEQLOC_INT)
+            return;
+        
+        while(slp) {
+
+            if(slp->choice != SEQLOC_INT) {
+                slp = slp->next;
+                continue;
+            }
+            
+            mask_start=SeqLocStart(slp);
+            mask_stop=SeqLocStop(slp);
+            
+            /*check if the masked region is in the bsp range*/
+            if (mask_stop>=bsp_start && mask_start<=bsp_stop){
+                scan_from=_max_(mask_start,bsp_start);
+                scan_to=_min_(mask_stop,bsp_stop)+1;
+                for(i=scan_from;i<scan_to;i++) {
+                    dccp=DDV_GetColor(pcg,NULL,row+1,i);
+                    if (dccp){/*if there is already a color, just
+                                update the LowerCase parameter*/
+                        DDV_SetStyle(dccp,style,rgb,FALSE);
+                        DDV_SetColor(pcg,NULL,row+1,i,dccp);
+                    } else{/*otherwies, set a new layout for that letter*/
+                        memset(&dcc,0,sizeof(DDV_ColorCell));
+                        DDV_SetStyle(&dcc,style,rgb,FALSE);
+                        DDV_SetColor(pcg, NULL, row+1, i, &dcc);
+                    }
+                }
+            }
+            slp = slp->next;
+        }
+        vnp=vnp->next;
+    }
+}
+
+/*******************************************************************************
+
+  Function : DDV_SetISOClr()
+  
+  Purpose : layout the colors for ident/simil/other (I/S/O).
+  
+*******************************************************************************/
+static void DDV_SetISOClr(DDV_ColorGlobal * pcg, ParaGPtr pgp,Int4 disp_coord, 
+		Int4 row, Uint1 idx,Uint1 sty)
+{					
+DDV_ColorCell * dccp;
+DDV_ColorCell   dcc;
+Int4            bsp_coord;
+
+	bsp_coord=DDV_GetBspCoordGivenDispCoord(pgp,disp_coord);
+	if (bsp_coord>=0){
+		dccp=DDV_GetColor(pcg,NULL,row+1,bsp_coord);
+		if (dccp){/*if there is already a color, just
+		  update the required parameter*/
+			dccp->rgb[0]=DDV_PaletteRGB[idx][0];
+			dccp->rgb[1]=DDV_PaletteRGB[idx][1];
+			dccp->rgb[2]=DDV_PaletteRGB[idx][2];
+			DDV_SetStyle(dccp,sty,NULL,FALSE);
+			DDV_SetColor(pcg,NULL,row+1,bsp_coord,dccp);
+		}
+		else{/*otherwise, set up a new layout for that letter*/
+			memset(&dcc,0,sizeof(DDV_ColorCell));
+			dcc.rgb[0]=DDV_PaletteRGB[idx][0];
+			dcc.rgb[1]=DDV_PaletteRGB[idx][1];
+			dcc.rgb[2]=DDV_PaletteRGB[idx][2];
+			DDV_SetStyle(&dcc,sty,NULL,FALSE);
+			DDV_SetColor(pcg, NULL, row+1, bsp_coord, &dcc);
+		}
+	}
+}
+
+/*******************************************************************************
+
+  Function : DDV_LayoutIdentColors()
+  
+  Purpose : layout the colors for ident/simil/other (I/S/O).
+  
+  Return value : -.
+
+*******************************************************************************/
+NLM_EXTERN void DDV_LayoutISOColors(DDV_ColorGlobal *pcg,ValNodePtr * row_list,Int4 nRow,
+	Int4 Master,Boolean bSetMaster,Int4Ptr * matrix,Uint1 IdentClr,Uint1 SimilClr,
+	Uint1 OtherClr,Uint1 IdentSty,Uint1 SimilSty,Uint1 OtherSty)
+{
+ValNodePtr * row;
+ValNodePtr vnp;
+ParaGPtr  pgpQuery,pgpSubject;
+CharPtr   szQuery,szComp;
+BioseqPtr bsp;
+Boolean   IsAA;
+Int4      i,j,len,bspLength;
+Uint1     idx,sty;
+
+	row=(ValNodePtr *)MemNew(nRow*sizeof(ValNodePtr));
+	if (!row) return;
+	for (i=0;i<nRow;i++){
+		row[i]=row_list[i];
+	}
+
+	vnp=row_list[Master];
+	while(vnp){
+		/*get the master sequence*/
+		pgpQuery=(ParaGPtr)vnp->data.ptrvalue;
+		szQuery=(CharPtr)MemNew((pgpQuery->StopLetter-pgpQuery->StartLetter+3)*sizeof(Char));
+		if (!szQuery) goto error;
+		bsp=BioseqLockById(pgpQuery->sip);
+		if (!bsp) goto error;
+		bspLength=BioseqGetLen(bsp);
+		IsAA=ISA_aa(bsp->mol);
+		BioseqUnlock(bsp);
+		if (!DDV_GetSequenceFromParaG(pgpQuery,&szQuery,bspLength,IsAA,NULL,
+				NULL,NULL)) goto error;
+		/*lopp on each row, get the sequence, set the colors*/
+		for (i=0;i<nRow;i++){
+			if (i==Master) continue;
+			pgpSubject=(ParaGPtr)row[i]->data.ptrvalue;
+			szComp=DDV_GetBLASTCompLine_3(szQuery,pgpSubject,matrix);
+			if (szComp){
+				len=StringLen(szComp)+1;
+				for (j=0;j<len;j++){
+					if (isalpha(szComp[j]) || szComp[j]=='|'){
+						idx=IdentClr;
+						sty=IdentSty;
+					}
+					else if (szComp[j]=='+'){
+						idx=SimilClr;
+						sty=SimilSty;
+					}
+					else{
+						idx=OtherClr;
+						sty=OtherSty;
+					}
+					DDV_SetISOClr(pcg,pgpSubject,pgpSubject->StartLetter+j,i,idx,sty);
+					if (bSetMaster)
+						DDV_SetISOClr(pcg,pgpQuery,pgpQuery->StartLetter+j,0,idx,sty);
+				}
+				MemFree(szComp);
+			}
+			row[i]=row[i]->next;
+		}
+		szQuery=MemFree(szQuery);
+		vnp=vnp->next;
+	}
+error:
+
+	MemFree(row);
+	if (szQuery) MemFree(szQuery);
+}
+
+
+NLM_EXTERN MsaParaGPopListPtr DDE_CreateDisplayForBlock(SeqAlignPtr sap, Int4 BlockIndex) {
+/*----------------------------------------------------------------------------
+*  allocate and fill the paragraphs for displaying 1 block of a
+*  sequence alignment, plus the flanking unaligned regions.
+*  BlockIndex is a 0-based block count.
+*
+*  This function works by making a linked-list of 3 DescriDisp's:
+*  head --> node1 --> node2 --> node3
+*            ||        ||        ||
+*            \/        \/        \/
+*         unaligned  aligned  unaligned
+*
+*  This is a descriptor for the display.  This descriptor is passed
+*  to DDV_PopulateDisplayForDisc to create the paragraphs.
+*  Each node is easy to construct:
+*
+*
+*                           Aligned (A)                UnAligned (UA)
+*                           -----------                --------------
+*  from:                SeqAlign coords                             0
+*  to:                     "       "                         length-1
+*  TextStyle:   MSA_TXT_STYLE_REG_ALIGN     MSA_TXT_STYLE_REG_UNALIGN
+*  UAnum:                             0             (explained below)
+*  UAMaxLength:                       0                        length
+*
+*
+*  UAnum, for unaligned regions, is determined as shown here:
+*
+*  BlockIndex:               0                1                2
+*               |<--UA-->|<--A-->|<--UA-->|<--A-->|<--UA-->|<--A-->|<--UA-->|
+*  UAnum:           -1                1                2               -2
+*  where -1 and -2 are for the LEFT_TAIL and RIGHT_TAIL, respectively.
+*
+*
+*  return a pointer to the paragraph list.
+*  return NULL for unsuccessful completion.
+*---------------------------------------------------------------------------*/
+  ValNodePtr          head = NULL;
+  DescriDispPtr       ddp1, ddp2, ddp3;
+  Int4                i, NumRows, NumBlocks, Size, SaveSize, start, stop;
+  Int4                TotalLength=0;
+  Uint1               strand=Seq_strand_unknown;
+  DDV_Disp_Opt        DisplayOptions;
+  MsaParaGPopListPtr  pPopList;
+
+  /* index the seq align */
+/*  if (!AlnMgrIndexSeqAlign(sap)) {
+    return(NULL);
+  } */
+
+  NumRows = AlnMgrGetNumRows(sap);
+  NumBlocks = AlnMgrGetNumAlnBlocks(sap);
+  if ((BlockIndex < 0) || (BlockIndex >= NumBlocks)) {
+    return(NULL);
+  }
+
+  /* figure out the length of the unaligned region preceeding the block */
+  SaveSize = 0;
+  for (i=0; i<NumRows; i++) {
+    if (BlockIndex == 0) {
+      AlnMgrGetNthRowTail(sap, i+1, LEFT_TAIL, &start, &stop, &strand);
+    }
+    else {
+      AlnMgrGetNthUnalignedForNthRow(sap, BlockIndex, i+1, &start, &stop);
+    }
+    if ((start == -1) && (stop == -1)) {Size = 0;}
+    else                               {Size = (stop-start)+1;}
+    if (Size > SaveSize) {SaveSize = Size;}
+  }
+  TotalLength += SaveSize;
+
+  /* make a node for this region */
+  ddp1 = MemNew(sizeof(DescriDisp));
+  ddp1->from = 0;
+  ddp1->to = SaveSize - 1;
+  ddp1->TextStyle = MSA_TXT_STYLE_REG_UNALIGN;
+  /* set UAnum to -1 for LEFT_TAIL */
+  ddp1->UAnum = (BlockIndex == 0) ? -1 : BlockIndex;
+  ddp1->UAMaxlength = SaveSize;
+  ddp1->strand = strand;
+  ddp1->IsGap = FALSE;
+
+  /* add it to the linked list */
+  ValNodeAddPointer(&head, 0, ddp1);
+
+  /* make node for aligned block and add it to linked list */
+  AlnMgrGetNthBlockRange(sap, BlockIndex+1, &start, &stop);
+  ddp2 = MemNew(sizeof(DescriDisp));
+  ddp2->from = start;
+  ddp2->to = stop;
+  ddp2->TextStyle = MSA_TXT_STYLE_REG_ALIGN;
+  ddp2->UAnum = 0;
+  ddp2->UAMaxlength = 0;
+  ddp2->strand = strand;
+  ddp2->IsGap = FALSE;
+  ValNodeAddPointer(&head, 0, ddp2);
+  TotalLength += (stop - start) + 1;
+
+  /* figure out the length of the unaligned region following the block */
+  SaveSize = 0;
+  for (i=0; i<NumRows; i++) {
+    if (BlockIndex == (NumBlocks-1)) {
+      AlnMgrGetNthRowTail(sap, i+1, RIGHT_TAIL, &start, &stop, &strand);
+    }
+    else {
+      AlnMgrGetNthUnalignedForNthRow(sap, BlockIndex+1, i+1, &start, &stop);
+    }
+    if ((start == -1) && (stop == -1)) {Size = 0;}
+    else                               {Size = (stop-start)+1;}
+    if (Size > SaveSize) {SaveSize = Size;}
+  }
+  TotalLength += SaveSize;
+
+  /* make a node for this region */
+  ddp3 = MemNew(sizeof(DescriDisp));
+  ddp3->from = 0;
+  ddp3->to = SaveSize - 1;
+  ddp3->TextStyle = MSA_TXT_STYLE_REG_UNALIGN;
+  /* set UAnum to -2 for RIGHT_TAIL */
+  ddp3->UAnum = (BlockIndex == (NumBlocks-1)) ? -2 : BlockIndex + 1;
+  ddp3->UAMaxlength = SaveSize;
+  ddp3->strand = strand;
+  ddp3->IsGap = FALSE;
+
+  /* add it to the linked list */
+  ValNodeAddPointer(&head, 0, ddp3);
+
+  /* create the paragraphs from the descriptor */
+  pPopList = MemNew(sizeof(MsaParaGPopList));
+  DDV_InitDDESAPdispStyles(&DisplayOptions);
+  if (DDV_PopulateDisplayForDisc(sap, pPopList, NumRows, TotalLength+10,
+                                 &DisplayOptions, TotalLength, head, TRUE, FALSE)) {
+    return(pPopList);
+  }
+  else {
+    return(NULL);
+  }
+}
+
+
+NLM_EXTERN MsaParaGPopListPtr DDE_CreateDisplayForUnAligned(SeqAlignPtr sap, Int4 UAIndex) {
+/*----------------------------------------------------------------------------
+*  allocate and fill the paragraphs for displaying 1 unaligned
+*  region of a sequence alignment.  UAIndex is a 0-based count.
+*  (UA = unaligned)
+*
+*  This function works by making a linked-list of just 1 DescriDisp.
+*  This is a descriptor for the display.  This descriptor is passed
+*  to DDV_PopulateDisplayForDisc to create the paragraphs.
+*
+*  Each node is easy to construct:
+*
+*                             UnAligned (UA)
+*                ---------------------------
+*  from:                                   0
+*  to:                              length-1
+*  TextStyle:      MSA_TXT_STYLE_REG_UNALIGN
+*  UAnum:                  (explained below)
+*  UAMaxLength:                       length
+*
+*  UAnum is determined as shown here:
+*
+*  UAIndex:           0                1                2                3
+*                |<--UA-->|<--A-->|<--UA-->|<--A-->|<--UA-->|<--A-->|<--UA-->|
+*  UAnum:            -1                1                2               -2
+*  where -1 and -2 are for the LEFT_TAIL and RIGHT_TAIL, respectively.
+*
+*  return a pointer to the paragraph list.
+*  return NULL for unsuccessful completion.
+*---------------------------------------------------------------------------*/
+  ValNodePtr          head = NULL;
+  DescriDispPtr       ddp1;
+  Int4                NumRows, NumBlocks;
+  Int4                i, Size, SaveSize, start, stop;
+  Int4                TotalLength=0;
+  Uint1               strand=Seq_strand_unknown;
+  DDV_Disp_Opt        DisplayOptions;
+  MsaParaGPopListPtr  pPopList;
+
+  /* index the seq align */
+/*  if (!AlnMgrIndexSeqAlign(sap)) {
+    return(NULL);
+  } */
+
+  NumRows = AlnMgrGetNumRows(sap);
+  NumBlocks = AlnMgrGetNumAlnBlocks(sap);
+  if ((UAIndex < 0) || (UAIndex > NumBlocks)) {
+    return(NULL);
+  }
+
+  /* figure out the length of the unaligned region preceeding the block */
+  SaveSize = 0;
+  for (i=0; i<NumRows; i++) {
+    if (UAIndex == 0) {
+      AlnMgrGetNthRowTail(sap, i+1, LEFT_TAIL, &start, &stop, &strand);
+    }
+    else if (UAIndex == NumBlocks) {
+      AlnMgrGetNthRowTail(sap, i+1, RIGHT_TAIL, &start, &stop, &strand);
+    }
+    else {
+      AlnMgrGetNthUnalignedForNthRow(sap, UAIndex, i+1, &start, &stop);
+    }
+    if ((start == -1) && (stop == -1)) {Size = 0;}
+    else                               {Size = (stop-start)+1;}
+    if (Size > SaveSize) {SaveSize = Size;}
+  }
+  TotalLength += SaveSize;
+
+  /* make a node for this region */
+  ddp1 = MemNew(sizeof(DescriDisp));
+  ddp1->from = 0;
+  ddp1->to = SaveSize - 1;
+  ddp1->TextStyle = MSA_TXT_STYLE_REG_UNALIGN;
+  /* set UAnum to -1 for LEFT_TAIL, -2 for RIGHT_TAIL, or UAIndex */
+  if (UAIndex == 0)              {ddp1->UAnum = -1;}
+  else if (UAIndex == NumBlocks) {ddp1->UAnum = -2;}
+  else                           {ddp1->UAnum = UAIndex;}
+  ddp1->UAMaxlength = SaveSize;
+  ddp1->strand = strand;
+  ddp1->IsGap = FALSE;
+
+  /* add it to the linked list */
+  ValNodeAddPointer(&head, 0, ddp1);
+
+  /* create the paragraphs from the descriptor */
+  pPopList = MemNew(sizeof(MsaParaGPopList));
+  DDV_InitDDESAPdispStyles(&DisplayOptions);
+  if (DDV_PopulateDisplayForDisc(sap, pPopList, NumRows, TotalLength+10,
+                                 &DisplayOptions, TotalLength, head, FALSE, TRUE)) {
+    return(pPopList);
+  }
+  else {
+    return(NULL);
+  }
+}
+
+
+NLM_EXTERN MsaParaGPopListPtr DDE_CreateDisplay(SeqAlignPtr sap, Int4 BlockIndex,
+                                                Boolean IsUnAligned, Int4* pNumBlocks) {
+/*----------------------------------------------------------------------------
+*  build display, ruler, entitiesTbl for either an
+*  unaligned region or an aligned block
+*---------------------------------------------------------------------------*/
+  MsaParaGPopListPtr  mpplp;
+  Int4                from=-1, to;
+ 
+  if (IsUnAligned) {
+    mpplp = DDE_CreateDisplayForUnAligned(sap, BlockIndex);
+    *pNumBlocks = 0;
+  }
+  else {
+    mpplp = DDE_CreateDisplayForBlock(sap, BlockIndex);
+    *pNumBlocks = 1;
+    /* get the first align index of block */
+    AlnMgrGetNthBlockRange(sap, BlockIndex+1, &from, &to);
+  }
+  ASSERT(mpplp != NULL);
+
+  mpplp->entitiesTbl = DDV_BuildBspEntitiesTbl(mpplp->TableHead, mpplp->nBsp);
+  ASSERT(mpplp->entitiesTbl != NULL);
+
+  mpplp->RulerDescr = DDE_ReMakeRuler(mpplp, FALSE, from);
+  return(mpplp);
+}
+
diff --git a/ddv/ddvcreate.h b/ddv/ddvcreate.h
new file mode 100644
index 00000000..dc94153b
--- /dev/null
+++ b/ddv/ddvcreate.h
@@ -0,0 +1,303 @@
+/*  $Id: ddvcreate.h,v 1.31 2001/01/29 20:35:49 hurwitz Exp $
+* ===========================================================================
+*
+*                            PUBLIC DOMAIN NOTICE
+*            National Center for Biotechnology Information (NCBI)
+*
+*  This software/database is a "United States Government Work" under the
+*  terms of the United States Copyright Act.  It was written as part of
+*  the author's official duties as a United States Government employee and
+*  thus cannot be copyrighted.  This software/database is freely available
+*  to the public for use. The National Library of Medicine and the U.S.
+*  Government do not place any restriction on its use or reproduction.
+*  We would, however, appreciate having the NCBI and the author cited in
+*  any work or product based on this material
+*
+*  Although all reasonable efforts have been taken to ensure the accuracy
+*  and reliability of the software and data, the NLM and the U.S.
+*  Government do not and cannot warrant the performance or results that
+*  may be obtained by using this software or data. The NLM and the U.S.
+*  Government disclaim all warranties, express or implied, including
+*  warranties of performance, merchantability or fitness for any particular
+*  purpose.
+*
+* ===========================================================================
+*
+* File Name:  ddvcreate.h
+*
+* Author:  Sarah Wheelan
+*
+* Version Creation Date:   08/99
+*
+* $Revision: 1.31 $
+*
+* File Description: 
+*
+* Modifications:
+* --------------------------------------------------------------------------
+* $Log: ddvcreate.h,v $
+* Revision 1.31  2001/01/29 20:35:49  hurwitz
+* make gap between aligned blocks optional
+*
+* Revision 1.30  2001/01/25 21:49:14  hurwitz
+* added option for extra gap char (tilde) between aligned blocks
+*
+* Revision 1.29  2000/09/08 21:50:39  hurwitz
+* made DDV_ReadSeqBin public
+*
+* Revision 1.28  2000/05/04 22:43:38  hurwitz
+* don't launch DDE on top of DDV, change some wording, redraw DDE after save to AlnMgr
+*
+* Revision 1.27  2000/04/21 23:00:50  hurwitz
+* can launch DDE from DDV
+*
+* Revision 1.26  2000/04/19 15:45:50  hurwitz
+* can create display for a block
+*
+* Revision 1.25  2000/03/31 21:33:07  durand
+* added new default color schemas for BLAST
+*
+* Revision 1.24  2000/03/28 13:33:27  durand
+* moved DDV_Disp_Opt data structure to pgppop.h
+*
+* Revision 1.23  2000/03/21 19:26:45  durand
+* adapt ddvcreate to be used by pgppop
+*
+* Revision 1.22  2000/03/20 13:46:23  durand
+* fixed a bug in BLAST functions; added DDV_BLAST_COLOR0 to produce a BLAST output without any layout
+*
+* Revision 1.21  2000/02/28 16:52:47  durand
+* wrote a new manager for unaligned regions
+*
+* Revision 1.20  2000/02/23 21:34:29  durand
+* allow custom display of gap characters
+*
+* Revision 1.19  2000/02/23 19:49:33  durand
+* use row number instead of SeqId for coloring
+*
+* Revision 1.18  2000/02/14 16:49:34  durand
+* add new options for BLAST output
+*
+* Revision 1.17  2000/02/02 14:44:31  durand
+* added function to create data structure for block editor, fixed some bugs
+*
+* Revision 1.16  2000/01/26 13:38:55  durand
+* update the GUI for the editor. Add functions to create the data to be used by the editor
+*
+* Revision 1.15  1999/12/20 20:20:41  lewisg
+* allow cn3d to do color and ddv to do case when both are running
+*
+* Revision 1.14  1999/12/20 14:45:37  durand
+* add new functions for the new BLAST outputs
+*
+* Revision 1.13  1999/12/08 22:42:17  durand
+* add the code to produce colored BLAST outputs
+*
+* Revision 1.12  1999/12/03 23:17:22  lewisg
+* Patrick's new global update msg, argument passing when launching ddv, experimental editing
+*
+* Revision 1.11  1999/12/03 15:11:49  durand
+* add DDV_AllGapInLowerCase declaration
+*
+* Revision 1.10  1999/11/24 21:26:30  vakatov
+* Fixed for the C++ and/or MSVC DLL compilation
+*
+* Revision 1.9  1999/11/17 22:43:57  durand
+* speed up the selection manager for large SeqAlign
+*
+* Revision 1.8  1999/11/09 17:08:59  durand
+* transfer some functions from ddvgraph to ddvcreate, so that ddvcreate remains Vibrant free and can be compiled with BLAST
+*
+* Revision 1.7  1999/11/03 21:29:48  durand
+* add CTRL and SHFT keys for mouse selection. redesign the loader functions of DDV to properly register the message callbacks
+*
+* Revision 1.6  1999/10/29 14:15:40  durand
+* add simple mouse selection functions
+*
+* Revision 1.5  1999/10/22 20:12:47  durand
+* add Export command (text, HTML and Phylip formats)
+*
+* Revision 1.4  1999/10/20 13:17:19  durand
+* add display for disc. SeqAlign tails
+*
+* Revision 1.3  1999/10/15 21:57:36  durand
+* add a UI for display options
+*
+* Revision 1.2  1999/10/12 15:01:29  lewisg
+* resolve confict with internal/ddv
+*
+* Revision 1.1  1999/09/30 14:10:26  durand
+* add ddv to toolkit
+*
+* Revision 1.5  1999/09/30 13:38:09  durand
+* DDV_CreateDisplayFromIndex takes ParaG_Size as an argument
+*
+*
+*
+* ==========================================================================
+*/
+#ifndef _DDVCREATE_
+#define _DDVCREATE_
+
+#include <ncbi.h>
+#include <alignmgr.h>
+#include <udvseq.h>
+#include <pgppop.h>
+#include <udvdef.h>
+#include <ddvcreate.h>
+
+#undef NLM_EXTERN
+#ifdef NLM_IMPORT
+#define NLM_EXTERN NLM_IMPORT
+#else
+#define NLM_EXTERN extern
+#endif
+
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+
+/*******************************************************************************
+
+  structure
+
+*******************************************************************************/
+typedef struct uabitdescr{
+	Int4    from;
+	Int4    to;
+	Boolean IsGap;
+} UABitDescr, PNTR UABitDescrPtr;
+
+typedef struct uamsg{ /*UnAligned Messaging structure*/
+	Int4    from_a; /*asked coord.*/
+	Int4    to_a;
+	Int4    from_r; /*returned coord.*/
+	Int4    to_r;
+	Int4    currentPos;
+	Uint1   DispType;
+	Uint1   strand;
+	Boolean IsGap;
+	UABitDescr ubd[3];
+} UAMsg, PNTR UAMsgPtr;
+
+typedef struct descridisp {
+        Int4            from;
+        Int4            to;
+        Int4            UAnum;
+        Int4            UAMaxlength;
+        Boolean         IsGap;
+        Uint1           TextStyle;
+        Uint1           strand;
+} DescriDisp, PNTR DescriDispPtr;
+
+/*******************************************************************************
+
+  defines
+
+*******************************************************************************/
+#define RulerStyle_One_Start      ((Uint1)1)
+#define RulerStyle_Continue_Start ((Uint1)2)
+
+/*size limit of a seqalign for edition (number of columns)*/
+#define LIMIT_EDITOR_SIZE 10000
+
+#define DDV_BLAST_COLOR0 0
+#define DDV_BLAST_COLOR1 1
+#define DDV_BLAST_COLOR2 2
+#define DDV_BLAST_COLOR3 3
+#define DDV_BLAST_COLOR4 4
+#define DDV_BLAST_COLOR5 5
+#define DDV_BLAST_COLOR6 6
+
+/*******************************************************************************
+
+  functions
+
+*******************************************************************************/
+NLM_EXTERN Boolean DDV_CreateDisplayFromIndex(SeqAlignPtr sap, MsaParaGPopListPtr mpplp, 
+		Int2 LineSize, DDV_Disp_OptPtr ddop);
+NLM_EXTERN Boolean DDV_CreateDisplayFromIndex2(SeqAlignPtr sap, MsaParaGPopListPtr mpplp, 
+		Int2 LineSize, DDV_Disp_OptPtr ddop, Boolean WantExtraGapChar);
+
+NLM_EXTERN Boolean DDV_CreateDisplayFromIndex_EX(SeqAlignPtr sap, MsaParaGPopListPtr mpplp, 
+		Int2 LineSize, DDV_Disp_OptPtr ddop,Int4 start, Int4 stop);
+NLM_EXTERN Boolean DDV_CreateDisplayFromIndex_EX2(SeqAlignPtr sap, MsaParaGPopListPtr mpplp, 
+		Int2 LineSize, DDV_Disp_OptPtr ddop,Int4 start, Int4 stop, Boolean WantExtraGapChar);
+
+NLM_EXTERN Boolean DDV_CreateDisplay_DiscAlign(SeqAlignPtr sap, 
+		MsaParaGPopListPtr mpplp, Int2 LineSize,DDV_Disp_OptPtr ddop);
+NLM_EXTERN Boolean DDV_CreateDisplay_DiscAlign2(SeqAlignPtr sap, 
+		MsaParaGPopListPtr mpplp, Int2 LineSize,DDV_Disp_OptPtr ddop, Boolean WantExtraGapChar);
+
+NLM_EXTERN Boolean DDV_BuildDisp_BlockEditor(SeqAlignPtr sap, 
+		MsaParaGPopListPtr mpplp, Int4 block_num);
+NLM_EXTERN UAMsgPtr UAMgrIntUAMsg( Int4 MaxLength, Int4 BspLength,
+		Int4 BspStart,Int4 BspStop, Int4 ddpFrom, Int4 ddpTo,Uint1 DispType, Uint1 strand);
+NLM_EXTERN UAMsgPtr UAMgrDelUAMsg(UAMsgPtr PNTR uamp);
+NLM_EXTERN void UAMgrUAMsgGetInfo(UAMsgPtr uamp,Int4Ptr from_bsp, Int4Ptr to_bsp, 
+		BoolPtr IsGap);
+NLM_EXTERN Boolean UAMgrGetNextUAbit(UAMsgPtr uamp,Int4 BspStart,Int4 BspStop);
+
+NLM_EXTERN ValNodePtr UABuildDescriptor(SeqAlignPtr sap, Int4 nBsp, Int2 LineSize,
+	DDV_Disp_OptPtr ddop, Int4Ptr TotLength,Boolean AddLeftUAPart,
+	Boolean AddRightUAPart);
+NLM_EXTERN ValNodePtr UABuildDescriptor2(SeqAlignPtr sap, Int4 nBsp, Int2 LineSize,
+	DDV_Disp_OptPtr ddop, Int4Ptr TotLength,Boolean AddLeftUAPart,
+	Boolean AddRightUAPart, Boolean WantExtraGapChar);
+
+NLM_EXTERN ValNodePtr UABuildDescriptorForBlockEditor(SeqAlignPtr sap, Int4 nBsp, 
+	Int4 block_num,Int4 LineSize,Int4Ptr TotLength);
+NLM_EXTERN ValNodePtr DDV_BuildTailDescriptor(SeqAlignPtr sap, Int4 nBsp, Int2 LineSize,
+	Uint1 which_tail,Int4Ptr TotLength,Int4Ptr cumulpop);
+NLM_EXTERN void DDV_InitDefSAPdispStyles(DDV_Disp_OptPtr ddop);
+NLM_EXTERN void DDV_InitCn3DSAPdispStyles(DDV_Disp_OptPtr ddop);
+NLM_EXTERN void DDV_InitDDESAPdispStyles(DDV_Disp_OptPtr ddop);
+NLM_EXTERN Uint4Ptr DDV_BuildBspEntitiesTbl(ValNodePtr PNTR TableHead,Int4 nBsp);
+NLM_EXTERN Uint1Ptr DDV_ReadSeqBin (SeqIdPtr sip, Int4 from, Int4 to, 
+                                    Boolean IsProt,Int2 len,Uint1 strand);
+
+/*export functions*/
+NLM_EXTERN void DDV_DumpSAPInAFile(MsaParaGPopListPtr mpplp,DDVOptionsBlockPtr dobp, 
+		FILE *hFile,Uint4 option, DDV_ColorGlobal *gclr);
+NLM_EXTERN void DDV_DumpSAPInFastaFile(MsaParaGPopListPtr mpplp,DDVOptionsBlockPtr dobp, 
+		FILE *hFile,Boolean bPrintGap);
+
+/*BLAST stuffs; function to build new outputs*/
+NLM_EXTERN Boolean DDV_DisplayBlastPairList(SeqAlignPtr sap, ValNodePtr mask,
+	FILE *fp, Boolean is_na, Uint4 tx_option,Uint1 ColorScheme);
+
+/*layout manager stuff*/
+NLM_EXTERN Boolean DDV_InitColour_When_Start(SeqAlignPtr sap,MsaParaGPopListPtr mpplp,
+	DDV_ColorGlobal * * gclr, Boolean NoColor);
+NLM_EXTERN Boolean DDV_LayoutUAregion(SeqAlignPtr sap,MsaParaGPopListPtr mpplp,
+	DDV_ColorGlobal * * gclr,Uint1 * pRGB,Uint1 style,Uint1 * pUARGB,
+	Uint1 UAstyle);
+NLM_EXTERN void DDV_LayoutGap(DDV_ColorGlobal *pcg,ValNodePtr vnp_seq1,
+		ValNodePtr vnp_seq2,Int4 row2,Uint1 style,Uint1 *rgb);
+NLM_EXTERN void DDV_LayoutMaskRegions(DDV_ColorGlobal *pcg,
+	ValNodePtr vnp_query,ValNodePtr mask,Int4 row,Uint1 style,Uint1 *rgb);
+NLM_EXTERN void DDV_LayoutISOColors(DDV_ColorGlobal *pcg,ValNodePtr * row_list,Int4 nRow,
+	Int4 Master,Boolean bSetMaster,Int4Ptr * matrix,Uint1 IdentClr,Uint1 SimilClr,
+	Uint1 OtherClr,Uint1 IdentSty,Uint1 SimilSty,Uint1 OtherSty);
+
+/* create display for a single aligned block or an unaligned region */
+NLM_EXTERN MsaParaGPopListPtr DDE_CreateDisplayForBlock(SeqAlignPtr sap, Int4 BlockIndex);
+NLM_EXTERN MsaParaGPopListPtr DDE_CreateDisplayForUnAligned(SeqAlignPtr sap, Int4 UAIndex);
+NLM_EXTERN MsaParaGPopListPtr DDE_CreateDisplay(SeqAlignPtr sap, Int4 BlockIndex,
+                                                Boolean IsUnAligned, Int4* pNumBlocks);
+
+#ifdef __cplusplus
+}
+#endif
+
+#undef NLM_EXTERN
+#ifdef NLM_EXPORT
+#define NLM_EXTERN NLM_EXPORT
+#else
+#define NLM_EXTERN
+#endif
+
+#endif /* ndef _DDVCREATE_ */
+
diff --git a/ddv/ddvgraph.c b/ddv/ddvgraph.c
new file mode 100644
index 00000000..cfba0802
--- /dev/null
+++ b/ddv/ddvgraph.c
@@ -0,0 +1,1349 @@
+/*  $Id: ddvgraph.c,v 1.40 2001/04/27 20:12:46 juran Exp $
+* ===========================================================================
+*
+*                            PUBLIC DOMAIN NOTICE
+*            National Center for Biotechnology Information (NCBI)
+*
+*  This software/database is a "United States Government Work" under the
+*  terms of the United States Copyright Act.  It was written as part of
+*  the author's official duties as a United States Government employee and
+*  thus cannot be copyrighted.  This software/database is freely available
+*  to the public for use. The National Library of Medicine and the U.S.
+*  Government do not place any restriction on its use or reproduction.
+*  We would, however, appreciate having the NCBI and the author cited in
+*  any work or product based on this material
+*
+*  Although all reasonable efforts have been taken to ensure the accuracy
+*  and reliability of the software and data, the NLM and the U.S.
+*  Government do not and cannot warrant the performance or results that
+*  may be obtained by using this software or data. The NLM and the U.S.
+*  Government disclaim all warranties, express or implied, including
+*  warranties of performance, merchantability or fitness for any particular
+*  purpose.
+*
+* ===========================================================================
+*
+* File Name:  ddvgraph.c
+*
+* Author:  Patrick Durand
+*
+* Version Creation Date:   06/19/99
+*
+* $Revision: 1.40 $
+*
+* File Description: graphic engine of DeuxD-Viewer (DDV)
+*
+* Modifications:
+* --------------------------------------------------------------------------
+* $Log: ddvgraph.c,v $
+* Revision 1.40  2001/04/27 20:12:46  juran
+* Heed warnings:  Make functions static.
Block out 'dead code' (functions that aren't called anywhere in ncbi).
+*
+* Revision 1.39  2000/07/24 22:00:08  hurwitz
+* fixed bug that 1/2 characters were displayed sometimes
+*
+* Revision 1.38  2000/07/19 19:04:01  hurwitz
+* fixed bug that was causing overwrite of numbering over tick marks in DDE
+*
+* Revision 1.37  2000/07/07 22:43:55  lewisg
+* interface tweaks
+*
+* Revision 1.36  2000/07/07 22:31:14  lewisg
+* interface tweaks
+*
+* Revision 1.35  2000/05/16 19:43:00  hurwitz
+* grey out create block, delete block, undo, and redo as needed
+*
+* Revision 1.34  2000/05/09 22:24:06  hurwitz
+* extend ruler to cover tails even when there's only 1 aligned block in the alignment
+*
+* Revision 1.33  2000/05/09 19:53:17  hurwitz
+* extended ruler to cover tails
+*
+* Revision 1.32  2000/04/26 21:54:27  hurwitz
+* added save function to tell AlnMgr about edits made in DDE
+*
+* Revision 1.31  2000/04/05 20:52:35  hurwitz
+* added GUI control for shifting left and right alignment boundaries
+*
+* Revision 1.30  2000/03/29 23:57:04  hurwitz
+* temporary fix for DDE use before it's initialized
+*
+* Revision 1.29  2000/03/29 20:02:48  hurwitz
+* keep track of master during move row operations
+*
+* Revision 1.28  2000/03/24 20:34:59  lewisg
+* add blast from file, bug fixes, get rid of redundant code, etc.
+*
+* Revision 1.27  2000/02/23 19:49:33  durand
+* use row number instead of SeqId for coloring
+*
+* Revision 1.26  2000/02/15 15:31:46  lewisg
+* move DDVRulerDescr to pgppop
+*
+* Revision 1.25  2000/02/08 17:18:40  hurwitz
+* don't use char* szEditSeq
+*
+* Revision 1.24  2000/02/07 14:03:35  durand
+* replace BioseqUnlockById by BioseqUnlock
+*
+* Revision 1.23  2000/02/04 16:05:40  durand
+* add click action to select a row
+*
+* Revision 1.22  2000/02/03 15:56:47  hurwitz
+* added constructor and destructor for DDVRulerDescrPtr
+*
+* Revision 1.21  2000/02/02 14:44:31  durand
+* added function to create data structure for block editor, fixed some bugs
+*
+* Revision 1.20  2000/01/26 13:38:54  durand
+* update the GUI for the editor. Add functions to create the data to be used by the editor
+*
+* Revision 1.19  2000/01/24 16:11:13  lewisg
+* speed up seqid comparison in color manager, make fast windows version of SetColor()
+*
+* Revision 1.18  2000/01/10 15:09:46  durand
+* Use Entrez instead of ID1
+*
+* Revision 1.17  2000/01/05 21:11:14  durand
+* update mouse click actions and DrawSequence function for a better use from ddv and cn3d
+*
+* Revision 1.16  1999/12/29 22:55:03  lewisg
+* get rid of seqalign id
+*
+* Revision 1.15  1999/12/07 21:40:14  durand
+* add mouse modes menu and caret facility for the editor
+*
+* Revision 1.14  1999/11/29 15:26:25  durand
+* designed a new GUI to fix problems under MacOS, Linux and SGI
+*
+* Revision 1.13  1999/11/23 17:34:33  lewisg
+* SavePort added to redraw
+*
+* Revision 1.12  1999/11/18 14:37:14  durand
+* avoid flashing sequence during selection
+*
+* Revision 1.11  1999/11/09 17:09:00  durand
+* transfer some functions from ddvgraph to ddvcreate, so that ddvcreate remains Vibrant free and can be compiled with BLAST
+*
+* Revision 1.10  1999/11/03 21:29:49  durand
+* add CTRL and SHFT keys for mouse selection. redesign the loader functions of DDV to properly register the message callbacks
+*
+* Revision 1.9  1999/10/29 14:15:38  durand
+* add simple mouse selection functions
+*
+* Revision 1.8  1999/10/21 13:12:12  durand
+* fix a problem in panel draw callback
+*
+* Revision 1.7  1999/10/20 13:17:18  durand
+* add display for disc. SeqAlign tails
+*
+* Revision 1.5  1999/10/18 17:20:56  durand
+* fix a bug in the bsp coord mapping for minus strand
+*
+* Revision 1.4  1999/10/15 21:57:36  durand
+* add a UI for display options
+*
+* Revision 1.3  1999/10/12 15:01:29  lewisg
+* resolve confict with internal/ddv
+*
+* Revision 1.2  1999/10/02 15:11:21  durand
+* update the code to reuse more functions from UDV
+*
+* Revision 1.1  1999/09/30 14:10:26  durand
+* add ddv to toolkit
+*
+* Revision 1.16  1999/09/22 20:40:20  durand
+* update the drawing procedure to deal with discontinuous seqalign
+*
+* Revision 1.15  1999/09/22 13:17:15  wheelan
+* Changed DDV_InitColour_When_Start to use new AlnMgrGetNextNthSeqRange function (better for discontinuous)
+*
+* Revision 1.14  1999/09/20 13:39:04  durand
+* replace totsaps by alnsaps (new AlignMgr stuff)
+*
+* Revision 1.13  1999/09/16 13:07:07  durand
+* DDV is able to display bioseq coords along with seqalign coords
+*
+* Revision 1.11  1999/09/09 21:54:23  durand
+* create a display for disconitnuous SeqAlign
+*
+* Revision 1.10  1999/09/01 23:02:59  lewisg
+* binary search in color functions
+*
+* Revision 1.9  1999/08/06 14:32:18  wheelan
+* changes to support new alignmgr function names
+*
+* Revision 1.8  1999/08/04 18:01:47  wheelan
+* changes to support new seqalign indexing
+*
+* Revision 1.7  1999/07/22 15:25:27  durand
+* improve DDV_DrawSequence function
+*
+* Revision 1.6  1999/07/20 14:58:00  durand
+* use the Color Manager to display colored MSA
+*
+* Revision 1.5  1999/07/06 19:02:21  durand
+* update DDV_GetSequenceFromParaG
+*
+* Revision 1.4  1999/06/30 14:57:23  durand
+* update DDV loader functions
+*
+* Revision 1.3  1999/06/28 22:07:18  durand
+* add loader functions and clean the code with Lint and Purify
+*
+* Revision 1.2  1999/06/19 18:36:44  durand
+* update display procedure
+*
+* Revision 1.1  1999/06/19 17:21:05  durand
+* add Vibrant DDV code
+*
+*
+*
+* ==========================================================================
+*/
+
+#include <ncbi.h>
+#include <vibrant.h>
+#include <udviewer.h>
+#include <udvseq.h>
+#include <ddvcolor.h>
+#include <ddvmain.h>
+#include <ddvgraph.h>
+#include <ddvclick.h>
+#include <pgppop.h>
+#include <alignmgr.h>
+#include <ddvcreate.h>
+
+#undef WANTDEADCODE
+
+static void DDV_DrawAlignmentBoundaries(PaneL p, DdvMainPtr dmp);
+
+/*******************************************************************************
+
+  Function : DDV_ReorderParaG()
+  
+  Purpose : reorder ParaG positions after style change(s)
+    
+  Return value : -
+
+*******************************************************************************/
+#ifdef WANTDEADCODE
+static void DDV_ReorderParaG(ValNodePtr PNTR TableHead, Int4 nRow)
+{
+Int4       Startline=0,i,nLines;
+ParaGPtr   pgp;
+ValNodePtr vnp;
+
+	for(i=0;i<nRow;i++){
+		vnp=TableHead[i];
+		pgp=(ParaGPtr)vnp->data.ptrvalue;
+		if (pgp->ScaleStyle==SCALE_POS_TOP)
+			nLines++;
+		nLines=1;
+		while(vnp){
+			pgp=(ParaGPtr)vnp->data.ptrvalue;
+			pgp->StartLine=Startline;
+			pgp->nLines=nLines;
+			vnp=vnp->next;
+		}
+		Startline+=nLines;
+	}
+}
+#endif
+
+/*******************************************************************************
+
+  Function : DDV_ChangeRulerStyleForSeq()
+  
+  Purpose : change the ruler style for a row in the alignment; ie for a Seq.
+    
+  Return value : -
+
+*******************************************************************************/
+#ifdef WANTDEADCODE
+static void DDV_ChangeRulerStyleForSeq(ValNodePtr PNTR TableHead,Int4 nRow,
+		Uint1 RulerStyle)
+{
+ParaGPtr   pgp;
+ValNodePtr vnp;
+
+	vnp=TableHead[nRow];
+	while(vnp){
+		pgp=(ParaGPtr)vnp->data.ptrvalue;
+		pgp->ScaleStyle=RulerStyle;
+		vnp=vnp->next;
+	}
+}
+#endif
+
+/*******************************************************************************
+
+  Function : DDV_InvalRegion()
+  
+  Purpose : invalidate a specific region of DDV panel
+
+  Note : disp_from,disp_to,disp_row are display coordinates. 
+         disp_from,disp_to are zero-based. 
+         disp_row is one-based  
+		 
+  Return value : the sequence 
+
+*******************************************************************************/
+extern void DDV_InvalRegion(PaneL hWndDDV,UnDViewerGraphDataPtr GrData,
+		Int4 disp_from,Int4 disp_to,Int4 disp_row,Boolean IsSelect)
+{
+DdvMainPtr dmp;
+RecT       rcP,rc;
+Int2       from_x,to_x,from_y,to_y;
+WindoW     temport;
+
+	dmp = (DdvMainPtr) GetObjectExtra(hWndDDV);
+	if (dmp==NULL) return;
+
+	/*convert disp coord to pixel positions*/
+		/*left of the first letter in the range*/
+	from_x=(Int2)((disp_from-GrData->udv_hscrl.ScrollPos)*GrData->udv_font.ColWidth);
+		/*right of the last letter in the range*/
+	to_x=(Int2)((disp_to-GrData->udv_hscrl.ScrollPos+1)*GrData->udv_font.ColWidth);
+		/*just above the row*/
+	from_y=(Int2)((disp_row-GrData->udv_vscrl.ScrollPos-1)*GrData->udv_font.LineHeight);
+		/*just below the row*/
+	to_y=(Int2)(from_y+2*GrData->udv_font.LineHeight);
+
+	/*adjust the values according to the PaneL RecT position*/
+		/*panel size*/
+    temport=SavePort(ParentWindow(hWndDDV));
+    Select(hWndDDV);
+	ObjectRect(hWndDDV,&rcP);
+	InsetRect(&rcP,4,4);
+		/*drawing region:*/
+	DDV_AdjustDrawingRect(&rcP,&(GrData->udv_font),dmp);
+	
+	rcP.left+=GrData->udv_panel.cxName+GrData->udv_scale.cxLeftScale;
+	rcP.top+=3*GrData->udv_panel.cyScale/2;
+	from_x+=rcP.left-1;
+	to_x+=rcP.left;
+	from_y+=rcP.top+1;
+	to_y+=rcP.top;
+
+	rc.left=from_x-2;
+	rc.top=from_y-2;
+	rc.right=to_x+2;
+	rc.bottom=to_y+2;
+
+	/*InvalRect(&rc);*/
+	/*DDV_DrawPanelContent_H (hWndDDV,dmp,&rc,IsSelect);*/
+
+	if (!IsSelect){
+		/*printf("invalRect\n");*/
+		InvalRect(&rc);
+	}
+	else{
+		DDV_DrawPanelContent_H (hWndDDV,dmp,&rc,IsSelect);
+	}
+/*	Update();*/
+    RestorePort(temport);
+}
+
+/*******************************************************************************
+
+  Function : DDV_GetBspRangeInSeg()
+  
+  Purpose : scan a segment and get the region of a Bsp in the SeqAlign
+    
+  Return value : the sequence 
+
+*******************************************************************************/
+
+#ifdef WANTDEADCODE
+static void DDV_GetBspRangeInSeg(SegmentPtr segp,Int4Ptr start,Int4Ptr stop)
+{
+SegmentPtr segp2;
+Int4       from,to;
+
+	if (!segp) return;
+	from=INT4_MAX;
+	to=INT4_MIN;
+	segp2=segp;
+	while(segp2){
+		if (segp2->gap==0) {
+			from=MIN(from,segp2->from);
+			to=MAX(to,segp2->to);
+		}
+		segp2=segp2->bsp_next;
+	}
+	*start=from;
+	*stop=to;
+}
+#endif
+
+
+/*******************************************************************************
+
+  Function : DDV_GetCurrentDispRange()
+  
+  Purpose : compute the size (row/col) of the DDV panel
+  
+  Return value : see arguments (zero-based values)
+
+*******************************************************************************/
+extern void DDV_GetCurrentDispRange(PaneL hWndDDV,UnDViewerGraphDataPtr GrData,
+		Int4 LengthAli,Int4Ptr from_col,Int4Ptr to_col,Int4Ptr from_row,
+		Int4Ptr to_row)
+{
+
+  RecT        rcP;
+  DdvMainPtr  dmp;
+
+  dmp = (DdvMainPtr) GetObjectExtra(hWndDDV);
+	if (dmp==NULL) return;
+
+	/*panel size*/
+	ObjectRect(hWndDDV,&rcP);
+	InsetRect(&rcP,4,4);
+
+	/*drawing region:*/
+	DDV_AdjustDrawingRect(&rcP,&(GrData->udv_font),dmp);
+	
+	rcP.left+=GrData->udv_panel.cxName+GrData->udv_scale.cxLeftScale;
+	rcP.top+=GrData->udv_panel.cyScale;
+	
+	*from_col=0;
+	*to_col=(rcP.right-rcP.left)/GrData->udv_font.ColWidth-1;
+	*from_col+=GrData->udv_hscrl.ScrollPos;
+	*to_col+=GrData->udv_hscrl.ScrollPos;
+	if (*to_col>LengthAli) *to_col=LengthAli-1;
+	if (*from_col>LengthAli) *from_col=LengthAli-1;
+	*from_row=0;
+	*to_row=(rcP.bottom-rcP.top)/GrData->udv_font.LineHeight-1;
+	*from_row+=GrData->udv_vscrl.ScrollPos;
+	*to_row+=GrData->udv_vscrl.ScrollPos;
+	if (*from_row>(GrData->udv_panel.nTotLines-1)) *from_row=GrData->udv_panel.nTotLines-1;
+	if (*to_row>(GrData->udv_panel.nTotLines-1)) *to_row=GrData->udv_panel.nTotLines-1;
+
+}
+
+/*******************************************************************************
+
+  Function : DDV_GetRulerForEditor()
+  
+  Purpose : create the ruler for the editor. This new descriptor is created
+      using the descriptor of the viewer.
+
+  Return value : an allocated data block ready for use by the editor. Null if
+  failure
+
+*******************************************************************************/
+NLM_EXTERN ValNodePtr DDV_GetRulerForEditor(ValNodePtr descr_head,Int4 from_disp,
+		Int4 to_disp)
+{
+DDVRulerDescrPtr drdp,prev_drdp,new_drdp;
+ValNodePtr  vnp2,vnp3,vnpDesc;
+Int4     cumulDecr,drdp_size,beginCopy,endCopy,drdp_start_ali;
+Boolean  bPop;
+
+	cumulDecr=0;
+	vnpDesc=NULL;
+	prev_drdp=NULL;
+	
+	for(vnp2=descr_head;vnp2!=NULL;vnp2=vnp2->next){
+		drdp=(DDVRulerDescrPtr)vnp2->data.ptrvalue;
+		drdp_size=drdp->disp_stop-drdp->disp_start+1;
+
+		/*not yet in the region of interest ?*/
+		if (drdp->disp_stop<from_disp) {
+			cumulDecr+=drdp_size;
+			continue;
+		}
+		
+		beginCopy=_max_(from_disp,drdp->disp_start);
+		endCopy=_min_(drdp->disp_stop,to_disp);
+
+		if (drdp->bUnAligned==FALSE)
+			drdp_start_ali=drdp->align_start+(beginCopy-drdp->disp_start);
+		else
+			drdp_start_ali=(Int4)-1;
+		/*in order to merge nodes of same type, i keep track of
+		the previous populated drdp node. Same style==yes, then
+		just extend to the right the previous node*/
+		if (prev_drdp){
+			if (prev_drdp->bUnAligned==drdp->bUnAligned){
+				prev_drdp->disp_stop=endCopy;
+				bPop=TRUE;
+			}
+			else{
+				bPop=FALSE;
+			}
+		}
+		else{
+			bPop=FALSE;
+		}
+		if (!bPop){
+			new_drdp=(DDVRulerDescrPtr)MemNew(sizeof(DDVRulerDescr));
+			if (!new_drdp) goto erreur;
+			
+			new_drdp->disp_start=beginCopy;
+			new_drdp->disp_stop=endCopy;
+			new_drdp->align_start=drdp_start_ali;
+			new_drdp->bUnAligned=drdp->bUnAligned;
+			if (!vnpDesc){
+				vnp3=ValNodeAddPointer(&vnpDesc,0,(Pointer)new_drdp);
+			}
+			else{
+				vnp3=ValNodeAddPointer(&vnp3,0,(Pointer)new_drdp);
+			}
+			prev_drdp=new_drdp;
+		}
+		if (drdp->disp_stop>=to_disp) break;
+		cumulDecr+=drdp_size;
+	}
+
+	return(vnpDesc);
+erreur:
+	if (vnpDesc)
+		ValNodeFreeData(vnpDesc);
+	return(NULL);
+}
+
+
+/*******************************************************************************
+
+  Function : DDV_ComputeRuler()
+  
+  Purpose : compute the Ruler descriptor (usefull for discontinuous align)
+  
+  Parameters : 
+  
+  Return value : a list of RUler descriptor
+
+*******************************************************************************/
+extern ValNodePtr DDV_ComputeRuler(SeqAlignPtr sap,DDV_Disp_OptPtr ddop)
+{
+
+DDVRulerDescrPtr drdp;
+ValNodePtr       vnp=NULL,vnp_head=NULL;
+Int4             disp_start=0,length,TotAliLength=0,r=0;
+Boolean          bUnAligned;
+
+  /* make ruler for LEFT_TAIL */
+  if ((ddop->DispDiscStyle == MSA_TXT_STYLE_2) && (ddop->ShowLeftTail)) {
+    length = AlnMgrGetMaxTailLength(sap, LEFT_TAIL);
+    if (length) {
+	    drdp=(DDVRulerDescrPtr)MemNew(sizeof(DDVRulerDescr));
+	    drdp->disp_start=disp_start;
+	    drdp->disp_stop=disp_start+length-1;
+	    drdp->bUnAligned=TRUE;
+      drdp->align_start = -1;
+      disp_start += length;
+	    vnp_head=ValNodeAddPointer(NULL,0,(Pointer)drdp);
+	    vnp=vnp_head;
+    }
+  }
+
+  if (AlnMgrIsSAPDiscAli(sap)){
+    /* make ruler for multiple blocks */
+		while(AlnMgrGetNextLengthBit(sap,&length,&r)){
+			if (length<0){
+				bUnAligned=TRUE;
+				switch(ddop->DispDiscStyle){/*user's display choice*/
+					case MSA_TXT_STYLE_1:
+						length=ddop->SpacerSize;
+						break;
+					case MSA_TXT_STYLE_2:
+						length=ABS(length);
+						break;
+				}
+			}
+			else{
+				bUnAligned=FALSE;
+			}
+
+			drdp=(DDVRulerDescrPtr)MemNew(sizeof(DDVRulerDescr));
+			drdp->disp_start=disp_start;
+			drdp->disp_stop=disp_start+length-1;
+			drdp->bUnAligned=bUnAligned;
+			
+			if (bUnAligned==FALSE)
+				drdp->align_start=TotAliLength;/*SeqAlign Coord*/
+			else
+				drdp->align_start=-1;/*drdp->disp_start;*//*Disp Coord*/
+
+			if (!vnp_head){
+				vnp_head=ValNodeAddPointer(NULL,0,(Pointer)drdp);
+				vnp=vnp_head;
+			}
+			else{
+				vnp=ValNodeAddPointer(&vnp,0,(Pointer)drdp);
+			}
+			disp_start+=length;
+			if (bUnAligned==FALSE) 
+				TotAliLength+=length;
+		}
+	}
+
+  else if (sap->type == SAT_MASTERSLAVE){
+    /* make ruler for a single block */
+		drdp=(DDVRulerDescrPtr)MemNew(sizeof(DDVRulerDescr));
+		drdp->disp_start=disp_start;
+		length=AlnMgrGetAlnLength(sap,FALSE);
+		drdp->disp_stop=disp_start+length-1;
+    drdp->bUnAligned = FALSE;
+		drdp->align_start=0;
+		if (!vnp_head){
+			vnp_head=ValNodeAddPointer(NULL,0,(Pointer)drdp);
+			vnp=vnp_head;
+		}
+		else{
+			vnp=ValNodeAddPointer(&vnp,0,(Pointer)drdp);
+		}
+	}
+
+  /* make ruler for RIGHT_TAIL */
+  if ((ddop->DispDiscStyle == MSA_TXT_STYLE_2) && (ddop->ShowRightTail)) {
+    length = AlnMgrGetMaxTailLength(sap, RIGHT_TAIL);
+    if (length) {
+	    drdp=(DDVRulerDescrPtr)MemNew(sizeof(DDVRulerDescr));
+	    drdp->disp_start=disp_start;
+	    drdp->disp_stop=disp_start+length-1;
+	    drdp->bUnAligned=TRUE;
+      drdp->align_start = -1;
+      disp_start += length;
+	    vnp = ValNodeAddPointer(&vnp,0,(Pointer)drdp);
+    }
+  }
+
+	return(vnp_head);
+}
+
+/*******************************************************************************
+
+  Function : DDV_DrawSequenceName()
+  
+  Purpose : draw the name of the sequence (left column of the DDV panel)
+  
+  Parameters : GrData; graphical data (font size, etc)
+				ScaleStyle;style of the ParaG scale
+				top, left; coord to start the draw
+  
+  Return value : none
+
+*******************************************************************************/
+static void  DDV_DrawSequenceName(UnDViewerGraphDataPtr GrData,ParaGPtr pgp,
+	Int2 top,Int2 left,Int4 cur_row,Int4 CurEditRow,Int4 CurMasterRow)
+{
+SeqIdPtr  sip = NULL;
+RecT      rc;
+Int2      x,y,decal=1,size;/*text position/size*/
+Char      szAccess[21];
+BioseqPtr bsp;
+
+	/*get a name*/	
+    bsp = BioseqLockById(pgp->sip);
+    if(bsp) {
+        sip = SeqIdFindBestAccession(bsp->id);
+        BioseqUnlock(bsp);
+    }
+	if (!sip)
+		sip = SeqIdFindBest(pgp->sip, 0);
+	SeqIdWrite(sip, szAccess,PRINTID_TEXTID_ACCESSION, 20);   
+
+	/*compute position*/
+	if (pgp->ScaleStyle==SCALE_POS_TOP) decal++;
+	
+	/*draw name*/
+	size=StringWidth(szAccess);
+	x=left/*-GrData->udv_scale.cxLeftScale*/-size;
+	y=top+decal*GrData->udv_font.LineHeight;
+	MoveTo(x,y);
+	if (cur_row==CurEditRow){
+		Magenta();
+	}
+	PaintString (szAccess);
+	if (cur_row==CurMasterRow){
+		Blue();
+		MoveTo(x,y);
+		LineTo(x+size,y);
+	}
+	/*draw a little box (for selection a full sequence)*/
+	left+=GrData->udv_font.cxChar;
+	top+=GrData->udv_font.cxChar/2;
+	LoadRect(&rc,left,top,left+GrData->udv_font.cxChar,
+		top+GrData->udv_font.cxChar);	
+	Blue();
+	PaintOval(&rc);
+	Black();
+}
+
+
+/*****************************************************************************
+
+Function: DDV_DrawSequence()
+
+Purpose: draw a sequence within a ParaG 
+
+Return value: -
+
+*****************************************************************************/
+static void DDV_DrawSequence(UnDViewerGraphDataPtr GrData,ParaGPtr pgp,
+		DDV_ColorGlobal *pColorGlobal,SeqIdPtr sip,RectPtr rc_pgp,
+		CharPtr szSeq,Int4 from,Int4 to,Uint1 ScaleStyle,
+		Int2 leftDecal,Uint1 strand,Boolean bUseColors,ValNodePtr vnp_bsp,
+		Int4 row,Boolean bSelect)
+{
+DDV_ColorCell *dclrp,*highlighClr;
+Int4            dp;
+Uint4           old_colour,new_colour,hlClr;
+Int2            decal=1,i,x,y,pos=0;
+Boolean         isAlpha,bSelected,bGoTo;
+RecT            rcSel;
+	
+	if (!szSeq) return;	
+	
+	/*scale or not... to be or not to be ?*/
+	if (ScaleStyle==SCALE_POS_TOP) decal++;
+	
+	/*compute the first letter's coordinate*/
+	x=rc_pgp->left+leftDecal-GrData->udv_font.cxChar/2;
+	y=rc_pgp->top+decal*GrData->udv_font.LineHeight;
+
+	i=from;/*if from!=0, means we don't draw the entire ParaG*/
+	to++;
+
+	/*get the selection(s)*/
+	
+	if (pColorGlobal){/*use color*/
+		old_colour=new_colour=GetColorRGB(0,0,0);
+	    highlighClr =
+    	    DDV_SearchColorCellbyName(pColorGlobal->pvnSpecialColors, "Highlight");
+		if (highlighClr)
+			hlClr = GetColorRGB (highlighClr->rgb[0], highlighClr->rgb[1],highlighClr->rgb[2]);
+		else 
+			hlClr = GetColorRGB (255,255,0);
+		while(szSeq[i] && i<to){
+			/*if a letter, get the color*/
+			if (szSeq[i]!=' '){
+				if (isalpha(szSeq[i])){
+					isAlpha=TRUE;
+					dp=DDV_GetBspCoordGivenDispCoord(pgp,pgp->StartLetter+i);
+					bSelected=DDV_IsLetterSelected(vnp_bsp,dp);
+					if (dp==(Int4)-1)
+						dclrp=NULL;
+					else
+						dclrp=DDV_GetColor(pColorGlobal,NULL, row+1, dp);
+
+					if(bUseColors){
+						if (dclrp) 
+							new_colour=GetColorRGB(dclrp->rgb[0],dclrp->rgb[1],dclrp->rgb[2]);
+						else
+							new_colour=GetColorRGB(0,0,0);
+					}
+				}
+				else {
+					bSelected=FALSE;
+					isAlpha=FALSE;
+					new_colour=GetColorRGB(0,0,0);
+				}
+				if (GrData->GotoLetter==pgp->StartLetter+i){
+					bGoTo=TRUE;bSelected=TRUE;
+				}
+				else{
+					bGoTo=FALSE;
+				}
+				if (bSelected){
+					if (bGoTo==FALSE){
+						if (bSelect) 
+#ifdef WIN_MSWIN
+                            Nlm_SetColorEx(hlClr);
+#else
+                            Nlm_SetColor(hlClr);
+#endif
+						else White();
+					}
+					else{
+						Red();
+					}
+					rcSel.left=x-2;
+					rcSel.top=y-GrData->udv_font.LineHeight;
+					rcSel.bottom=y;
+					rcSel.right=rcSel.left+GrData->udv_font.ColWidth;
+					PaintRect(&rcSel);
+					/*FrameRect(&rcSel);*/
+				}
+				if ((bUseColors && new_colour!=old_colour) || bSelected) {
+#ifdef WIN_MSWIN
+                    Nlm_SetColorEx(new_colour);
+#else
+                    Nlm_SetColor(new_colour);
+#endif
+					old_colour=new_colour;
+				}
+				MoveTo(x,y);
+				if (isAlpha && dclrp)
+					PaintChar((dclrp->LowerCase ? TO_LOWER(szSeq[i]) : szSeq[i]));
+				else
+					PaintChar(szSeq[i]);
+			}
+			i++;
+			x+=GrData->udv_font.ColWidth;
+		}
+	}
+	else{/*B&W display mode*/
+		Black();
+		while(szSeq[i] && i<to){
+			/*if a letter, get the color*/
+			if (szSeq[i]!=' '){
+				MoveTo(x,y);
+				PaintChar(szSeq[i]);
+			}
+			i++;
+			x+=GrData->udv_font.ColWidth;
+		}
+	}
+	
+	Black();
+}
+
+/*****************************************************************************
+
+Function: DDV_DrawParaG()
+
+Purpose: draw a ParaG given from, to (seqalign coord) and a position (rc_pgp) 
+
+Return value: -
+
+*****************************************************************************/
+static void DDV_DrawParaG(RectPtr rc_pgp,ParaGPtr pgp,Int4 from,Int4 to,
+			UnDViewerGraphDataPtr GrData,DDV_ColorGlobal *pColorGlobal,
+			DDV_Disp_OptPtr ddop,ValNodePtr vnp_bsp,Int4 row,Boolean bSelect)
+{
+CharPtr   szSeq;
+BioseqPtr bsp;
+SeqIdPtr  sip;
+Int4      bspLength,bsp_start,bsp_stop,from_pgp,to_pgp;
+Int2 decal,diff;
+Boolean   IsAA;
+Uint1     strand;
+MsaTxtDispPtr    mtdp;
+ValNodePtr vnp;
+
+	/*get some bsp info*/	
+	/*sip=SeqIdFindBest(pgp->sip,0);
+	if (sip==NULL)*/
+	sip=pgp->sip;
+	bsp=BioseqLockById(sip);
+	if (!bsp) return;
+	bspLength=BioseqGetLen(bsp);
+	IsAA=ISA_aa(bsp->mol);
+	BioseqUnlock(bsp);
+
+	szSeq=(CharPtr)MemNew((pgp->StopLetter-pgp->StartLetter+2)*sizeof(Char));
+	/*get a sequence to draw*/
+	DDV_GetSequenceFromParaG(pgp,&szSeq,bspLength,IsAA,&strand,&bsp_start,&bsp_stop);
+	
+	if (pgp->ScaleStyle==SCALE_POS_TOP){
+		vnp=pgp->ptxtList;
+		decal=0;
+		while(vnp){
+			mtdp=(MsaTxtDispPtr)vnp->data.ptrvalue;
+			diff=(Int2)(mtdp->to-mtdp->from+1);
+			if (mtdp->TextStyle == MSA_TXT_STYLE_SEQ){
+				UDV_Draw_scale(
+					GrData,
+					FALSE,
+					FALSE,
+					pgp->ScaleStyle,
+					(Int4)decal,
+					(Int4)decal+diff,
+					rc_pgp,
+					(Int2)(GrData->udv_font.ColWidth/2)+
+					(Int2)(decal*GrData->udv_font.ColWidth),
+					bspLength,
+					mtdp->from,
+					FALSE,
+					GrData->udv_font.ColWidth,(Uint4)DDV_DISP_HORZ);
+			}
+			decal+=diff;
+			vnp=vnp->next;
+		}
+	}
+	
+	if (szSeq){/*draw the sequence*/
+		from_pgp=_max_(pgp->StartLetter,from);
+		to_pgp=_min_(pgp->StopLetter,to);
+		DDV_DrawSequence(GrData,
+			pgp,
+			pColorGlobal,
+			sip,
+			rc_pgp,
+			szSeq,
+			from_pgp-pgp->StartLetter,
+			to_pgp-pgp->StartLetter,
+			pgp->ScaleStyle,
+			(Int2)(GrData->udv_font.ColWidth/2+
+			(Int2)(from_pgp-pgp->StartLetter)*GrData->udv_font.ColWidth),
+			strand,
+			ddop->bUseColors,
+			vnp_bsp,
+			row,
+			bSelect);
+		if (pgp->szEditSeq==NULL)/*viewer deletes allocated char array*/
+			MemFree(szSeq);
+	}
+}
+
+/*****************************************************************************
+
+Function: DDV_ComputeColWidth()
+
+Purpose: compute the width of a single column 
+
+Return value: the height
+
+*****************************************************************************/
+extern Int2 DDV_ComputeColWidth(Int2 cxChar)
+{
+	return(cxChar+2);
+}
+
+/*******************************************************************************
+
+  Function : DDV_AdjustDrawingRect()
+  
+  Purpose :  adjust the Panel Rect using the size of a letter ; in that way,
+             I get a RecT where it's possible to avoid the display of half letters
+			 (on the borders of the RecT).
+  
+  Parameters :	rcP;panel RecT
+  				udv_font; font information
+    
+  Return value : none
+
+*******************************************************************************/
+extern void	DDV_AdjustDrawingRect(RecT * rcP, UDVFontDataPtr udv_font, DdvMainPtr dmp)
+{	
+  Int4  temp;
+
+	rcP->left=(rcP->left/udv_font->ColWidth)*udv_font->ColWidth + udv_font->ColWidth;
+
+/*	rcP->right=(rcP->right/udv_font->ColWidth)*udv_font->ColWidth-2; */
+  /* bug fix, DIH, 7/24/00 */
+  temp = rcP->right - (dmp->GrData.udv_panel.cxName + dmp->GrData.udv_scale.cxLeftScale);
+  temp = (temp/udv_font->ColWidth)*udv_font->ColWidth - 2;
+  rcP->right = temp + (dmp->GrData.udv_panel.cxName + dmp->GrData.udv_scale.cxLeftScale);
+
+	rcP->top=(rcP->top/udv_font->LineHeight)*udv_font->LineHeight + udv_font->LineHeight;
+	rcP->bottom=(rcP->bottom/udv_font->LineHeight)*udv_font->LineHeight;
+}
+
+
+/*******************************************************************************
+
+  Function : DDV_DrawPanelContent_H()
+  
+  Purpose :  draw the panel of DDV viewer (case 1: full horz display)
+  
+  Parameters :	p;handle of the panel
+  				dmp; main data block
+    
+  Return value : none
+
+*******************************************************************************/
+extern void  DDV_DrawPanelContent_H (PaneL p,DdvMainPtr dmp,RecT PNTR MyUpdateRect,
+	Boolean bSelect)
+{
+ParaGPtr     pgp,/*ParaG data*/
+             first_pgp;/*used to get info from the first pgp of a row*/
+ValNodePtr   vnp,/*used to scan ParaGand Ruler Descriptor*/
+             vnp_pgp,/*used to get info from the first pgp of a row*/
+			 vnp_bsp=NULL;/*selected region(s) of one bioseq*/
+SelStructPtr ssp;/*used to get the selected region(s)*/
+BioseqPtr    bsp;
+Int4         i,/*just for a loop*/
+             from_row,/*first row to draw*/
+	         to_row,/*the last row to draw*/
+	         top_offset=0,/*offset from top (pixel)*/
+	         left_offset,/*offset from right (pixel)*/
+	         from_col,/*draw column from_col...*/
+	         to_col,/*...to column to_col*/
+	         from_pgp,/*within a ParaG, draw 'from'... */
+	         to_pgp,/*... 'to'*/
+	         nLinesDraw,/*number of lines drawn*/
+	         nColsDraw,/*number of col. drawn*/
+	         nTotRow,/*total number of row to draw*/
+	         start_i=0,/*first ParaG to draw*/
+           start_ruler,/*beginning of the display ruler*/
+           curMasterRow;
+RecT         rcP;/*size of the DDV panel*/
+RecT         rcD;/*size of the drawing panel*/
+RecT         rcI;/*size of the invalidated rect*/
+RecT         rc_pgp;/*location of a ParaG on the Panel*/
+Int2         length_pgp,/* i.e. 'length' letters to draw*/
+             x,y;/*caret position (edit mode only)*/
+Uint2        bsp_eID,/*...*/
+			 bsp_iID;/*... identifiers of a bioseq in the SeqAlign*/
+Boolean      bNotDrawCol;
+DdvMainWinPtr   mWin_d;
+DDVRulerDescrPtr drdp;	
+	
+	if (dmp->hParent){
+		mWin_d=(DdvMainWinPtr)GetObjectExtra(dmp->hParent);
+        if (mWin_d->Show_logo){
+            UDV_Logo_onDraw(p);
+            return;
+        }
+	}
+
+	/*some checks before a core dump...*/
+	if (!dmp->MSA_d.pgp_l.TableHead) return;
+	
+	/*restrict panel drawing area: 'add' little margins*/
+  ObjectRect((Handle) p, &rcP);
+  InsetRect(&rcP,4,4);
+
+	/*3D border to resize the cxName field*/
+	LtGray();
+	
+	MoveTo((Int2)(dmp->GrData.udv_panel.cxName-1),rcP.top);
+	LineTo((Int2)(dmp->GrData.udv_panel.cxName-1),rcP.bottom);
+
+	LtGray();
+	MoveTo((Int2)(dmp->GrData.udv_panel.cxName+1),rcP.top);
+	LineTo((Int2)(dmp->GrData.udv_panel.cxName+1),rcP.bottom);
+	LtGray();
+	MoveTo((Int2)(dmp->GrData.udv_panel.cxName+2),rcP.top);
+	LineTo((Int2)(dmp->GrData.udv_panel.cxName+2),rcP.bottom);
+
+	Black();
+	MoveTo((Int2)(dmp->GrData.udv_panel.cxName+3),rcP.top);
+	LineTo((Int2)(dmp->GrData.udv_panel.cxName+3),rcP.bottom);
+
+	/*drawing region:*/
+	DDV_AdjustDrawingRect(&rcP,&(dmp->GrData.udv_font),dmp);
+
+  /* debugging */
+/*  UDV_draw_rectangle(rcP, TRUE); */
+	
+	rcD=rcI=rcP;
+	rcP.left+=dmp->GrData.udv_panel.cxName+dmp->GrData.udv_scale.cxLeftScale;
+	top_offset=dmp->GrData.udv_vscrl.ScrollPos*dmp->GrData.udv_font.LineHeight;
+	left_offset=dmp->GrData.udv_hscrl.ScrollPos*dmp->GrData.udv_font.ColWidth;
+
+	/*set the font*/
+	SelectFont(dmp->GrData.udv_font.hFnt);
+	
+	rcD=rcP;
+	ClipRect(&rcD);
+	/*display the master numerical ruler*/
+	from_col=dmp->GrData.udv_hscrl.ScrollPos;
+	to_col=dmp->GrData.udv_hscrl.ScrollPos+dmp->GrData.udv_hscrl.ScrollPage;
+	if (to_col==0) to_col=dmp->MSA_d.pgp_l.LengthAli;
+	if (to_col>dmp->MSA_d.pgp_l.LengthAli) to_col=dmp->MSA_d.pgp_l.LengthAli;
+	rcD.top+=dmp->GrData.udv_panel.cyScale/2;
+
+	/*get the first node of the Ruler descriptor, then get the start value*/
+	drdp=(DDVRulerDescrPtr)dmp->MSA_d.pgp_l.RulerDescr->data.ptrvalue;
+	start_ruler=drdp->disp_start;
+	UDV_Draw_scale(
+		&dmp->GrData,
+		dmp->GrData.udv_scale.ShowMajorTick,
+		dmp->GrData.udv_scale.ShowMMinorTick,
+		(Uint1)dmp->GrData.udv_scale.ScalePosition,
+		from_col+start_ruler,
+		to_col+start_ruler,
+		&rcD,
+		(Int2)(dmp->GrData.udv_font.ColWidth/2)+
+		(Int2)((from_col-dmp->GrData.udv_hscrl.ScrollPos)*
+		dmp->GrData.udv_font.ColWidth),
+		dmp->MSA_d.pgp_l.LengthAli+start_ruler-1,
+		from_col+start_ruler,
+		FALSE,
+		dmp->GrData.udv_font.ColWidth,(Uint4)DDV_DISP_HORZ);
+
+	/*go at the bottom of the scale*/
+	ResetClip();
+
+	rcP.top+=3*dmp->GrData.udv_panel.cyScale/2;
+	rcD=rcP;
+	rcD.left=rcI.left;
+	
+	/*compute the region to draw (invalidate rect only)*/
+	from_col=(MyUpdateRect->left-rcP.left)/dmp->GrData.udv_font.ColWidth-2;
+	to_col=(MyUpdateRect->right-rcP.left)/dmp->GrData.udv_font.ColWidth+2;
+	if (from_col<0 && to_col<0) bNotDrawCol=TRUE;
+	else bNotDrawCol=FALSE;
+	if (from_col<0) from_col=0;
+	if (to_col<0) to_col=0;
+	from_col+=dmp->GrData.udv_hscrl.ScrollPos;
+	to_col+=dmp->GrData.udv_hscrl.ScrollPos;
+	if (to_col>dmp->MSA_d.pgp_l.LengthAli) to_col=dmp->MSA_d.pgp_l.LengthAli;
+	if (from_col>dmp->MSA_d.pgp_l.LengthAli) from_col=dmp->MSA_d.pgp_l.LengthAli;
+	from_row=(MyUpdateRect->top-rcP.top)/dmp->GrData.udv_font.LineHeight-1;
+	to_row=(MyUpdateRect->bottom-rcP.top)/dmp->GrData.udv_font.LineHeight+1;
+	if (from_row<0 && to_row<0) return;		
+	if (from_row<0) from_row=0;
+	if (to_row<0) to_row=0;
+	from_row+=dmp->GrData.udv_vscrl.ScrollPos;
+	to_row+=dmp->GrData.udv_vscrl.ScrollPos;
+	if (from_row>dmp->GrData.udv_panel.nTotLines) from_row=dmp->GrData.udv_panel.nTotLines;
+	if (to_row>dmp->GrData.udv_panel.nTotLines) to_row=dmp->GrData.udv_panel.nTotLines;
+	nTotRow=to_row-from_row;
+
+	/*find the first ParaG to draw*/
+	for(i=0;i<dmp->MSA_d.pgp_l.nBsp;i++){
+		if (!(pgp=(ParaGPtr)(dmp->MSA_d.pgp_l.TableHead[i]->data.ptrvalue))) continue;
+		if ((pgp->StartLine<=to_row)&&((pgp->StartLine+pgp->nLines)>=from_row)){
+			start_i=i;break;
+		}
+	}
+
+	ClipRect(&rcD);
+
+  /* get the row of the master */
+  if (dmp->dsp == NULL) {
+    curMasterRow = 0;
+  }
+  else {
+    curMasterRow = DDE_GetIndexOfMaster(dmp->dsp);
+  }
+
+	/*draw the names*/
+  nLinesDraw=0;
+	for(i=start_i;i<dmp->MSA_d.pgp_l.nBsp;i++){
+		if (!(pgp=(ParaGPtr)(dmp->MSA_d.pgp_l.TableHead[i]->data.ptrvalue))) continue;
+		if ((pgp->StartLine<=to_row)&&(pgp->StartLine>=from_row)){
+			nLinesDraw+=pgp->nLines;
+			DDV_DrawSequenceName(&dmp->GrData,pgp,
+				(Int2)(pgp->StartLine*dmp->GrData.udv_font.LineHeight-
+				top_offset+rcP.top),
+				(Int2)(dmp->GrData.udv_panel.cxName-3),
+				i, dmp->deri.curEditRow, curMasterRow);
+		}
+		else nLinesDraw+=pgp->nLines;
+		if (nLinesDraw>to_row) break;
+	}
+	ResetClip();
+
+	if (bNotDrawCol) return;
+
+	ClipRect(&rcP);
+	nLinesDraw=0;
+	/*get the selection(s)*/
+	
+	ssp=ObjMgrGetSelected();
+	
+	/*draw ParaG*/
+	for(i=start_i;i<dmp->MSA_d.pgp_l.nBsp;i++){/*draw line by line...*/
+		if (!(pgp=(ParaGPtr)(dmp->MSA_d.pgp_l.TableHead[i]->data.ptrvalue))) continue;
+		nColsDraw=0;
+		if (vnp_bsp){
+			vnp_bsp=ValNodeFree(vnp_bsp);
+		}
+		/*for each line, get the selected region(s)*/
+		if (ssp!=NULL){
+			vnp_pgp=dmp->MSA_d.pgp_l.TableHead[i];
+			first_pgp=(ParaGPtr)(vnp_pgp->data.ptrvalue);
+			if (first_pgp){
+				bsp=BioseqLockById(first_pgp->sip);
+				if (bsp){
+					bsp_eID=ObjMgrGetEntityIDForPointer((Pointer)bsp);
+					bsp_iID = GetItemIDGivenPointer (bsp_eID, 
+							OBJ_BIOSEQ, (Pointer) bsp);	
+					if (bsp_eID!=0 && bsp_iID!=0){
+						vnp_bsp=DDV_GetSelectedRegions(ssp,bsp_eID,bsp_iID);
+					}
+					BioseqUnlock(bsp);
+				}
+			}
+		}
+		/*...col. by col.*/
+		for(vnp=dmp->MSA_d.pgp_l.TableHead[i];vnp!=NULL;vnp=vnp->next){
+			if (!(pgp=(ParaGPtr)(vnp->data.ptrvalue))) continue;
+			if ((pgp->StartLetter>=from_col && pgp->StartLetter<=to_col)||
+					(pgp->StopLetter>=from_col && pgp->StopLetter<=to_col)||
+					(pgp->StartLetter<=from_col && pgp->StopLetter>=to_col)){
+				
+				from_pgp=pgp->StartLetter;
+				to_pgp=pgp->StopLetter;
+				
+				length_pgp=to_pgp-from_pgp+1;/*+1 to surround the last letter*/
+				rc_pgp.top=(Int2)(pgp->StartLine*dmp->GrData.udv_font.LineHeight-
+						top_offset+rcP.top);
+				rc_pgp.bottom=(Int2)(rc_pgp.top+pgp->nLines*
+						dmp->GrData.udv_font.LineHeight);
+				rc_pgp.left=(Int2)(from_pgp*dmp->GrData.udv_font.ColWidth-
+						left_offset+rcP.left);
+				rc_pgp.right=(Int2)(rc_pgp.left+length_pgp*
+						dmp->GrData.udv_font.ColWidth);
+				/*highlight a goto position ?*/
+				if (dmp->dtd.row==i+1 && dmp->dtd.col!=0){
+					dmp->GrData.GotoLetter=dmp->dtd.col-1;
+				}
+				else{
+					dmp->GrData.GotoLetter=(Int4)-1;
+				}
+				DDV_DrawParaG(&rc_pgp,pgp,from_col,to_col,&dmp->GrData,
+					dmp->Globals.colorp,&(dmp->ddo),vnp_bsp,i,bSelect);
+			}
+			else{
+				nColsDraw+=(pgp->StopLetter-pgp->StartLetter);
+			}
+			if(nColsDraw>to_col)break;
+		}
+		nLinesDraw+=pgp->nLines;
+		if (nLinesDraw>nTotRow) break;
+	}
+	/*display the caret; edit mode only*/
+	if (dmp->MouseMode==DDV_MOUSEMODE_EDIT){
+		x=(Int2)(dmp->dci.new_col*dmp->GrData.udv_font.ColWidth-
+						left_offset+rcP.left);
+		y=(Int2)(dmp->dci.new_row*dmp->GrData.udv_font.LineHeight-
+						top_offset+rcP.top)-1;
+		Red();
+		MoveTo(x+dmp->GrData.udv_font.ColWidth,y);
+		LineTo(x+dmp->GrData.udv_font.ColWidth,
+			y-dmp->GrData.udv_font.LineHeight/2);
+		MoveTo(x+dmp->GrData.udv_font.ColWidth-1,y);
+		LineTo(x+dmp->GrData.udv_font.ColWidth-1,
+			y-dmp->GrData.udv_font.LineHeight/2);
+		MoveTo(x+dmp->GrData.udv_font.ColWidth/2,y+1);
+		LineTo(x+3*dmp->GrData.udv_font.ColWidth/2,y+1);
+		MoveTo(x+dmp->GrData.udv_font.ColWidth/2,y+2);
+		LineTo(x+3*dmp->GrData.udv_font.ColWidth/2,y+2);
+		Black();
+	}
+	ResetClip();
+
+  if (dmp->bEditor) {
+    /* this is for allowing edits of the alignment boundaries */
+    DDV_DrawAlignmentBoundaries(p, dmp);
+  }
+
+	return;
+}
+
+static void DDV_DrawAlignmentBoundaries(PaneL p, DdvMainPtr dmp) {
+/*******************************************************************************
+  draw vertical bars at the top of the panel showing the alignment
+  boundaries, and horizontal lines connecting them.
+*******************************************************************************/
+  Int4  LeftHPos, RightHPos;
+  Int4  TopVPos, BotVPos;
+  Int4  i, NumBlocks;
+  RecT  rcP, rcBanner;
+  DdvMainWinPtr  mWin_d;
+
+  ObjectRect(p, &rcP);
+  DDV_GetVPixelPosOfEmptySpace(dmp, rcP, &TopVPos, &BotVPos);
+  rcBanner = rcP;
+  rcBanner.left += dmp->GrData.udv_panel.cxName + dmp->GrData.udv_scale.cxLeftScale;
+  rcBanner.top =    TopVPos;
+  rcBanner.bottom = BotVPos;
+  rcBanner.left -= 4;
+  ClipRect(&rcBanner);
+  EraseRect(&rcBanner);
+
+  /* for each aligned block, draw a semi-rectangle on top of it */
+  NumBlocks = DDE_GetNumBlocks(dmp->dsp->pEdit);
+  for (i=0; i<NumBlocks; i++) {
+    LeftHPos = DDV_GetHPixelPosGivenColNumber(dmp, rcP, DDE_GetAlignStart(dmp->dsp->pEdit, i));
+    LeftHPos -= dmp->GrData.udv_font.ColWidth;
+    RightHPos = DDV_GetHPixelPosGivenColNumber(dmp, rcP, DDE_GetAlignStop(dmp->dsp->pEdit, i));
+    UDV_draw_vertical_bar(rcBanner, LeftHPos, FALSE);
+    UDV_draw_vertical_bar(rcBanner, RightHPos, FALSE);
+    UDV_draw_horizontal_bar(TopVPos, LeftHPos, RightHPos);
+  }
+
+  ResetClip();
+
+  /* grey out either "create block" or "delete block" option */
+  if (dmp->hParent){
+	  mWin_d = (DdvMainWinPtr) GetObjectExtra(dmp->hParent);
+    if (NumBlocks == 0) {
+      Disable(mWin_d->MainMenu.DeleteBlock);
+       Enable(mWin_d->MainMenu.CreateBlock);
+    }
+    else {
+       Enable(mWin_d->MainMenu.DeleteBlock);
+      Disable(mWin_d->MainMenu.CreateBlock);
+    }
+  }
+
+}
+
+
+extern void DDV_GreyOut(DdvMainWinPtr mWin_d, Boolean Start, Boolean End) {
+/*******************************************************************************
+  grey out "undo" if Start is TRUE.
+  grey out "redo" if End is TRUE.
+*******************************************************************************/
+  if (Start) { Disable(mWin_d->MainMenu.Prev); }
+  else       {  Enable(mWin_d->MainMenu.Prev); }
+  if (End)   { Disable(mWin_d->MainMenu.Next); }
+  else       {  Enable(mWin_d->MainMenu.Next); }
+}
+
+
+/*******************************************************************************
+
+  Function : DDV_DrawPanelContent_V()
+  
+  Purpose :  draw the panel of DDV viewer (case 2: full vert display)
+  
+  Parameters :	p;handle of the panel
+  				dmp; main data block
+    
+  Return value : none
+
+*******************************************************************************/
+static void  DDV_DrawPanelContent_V (PaneL p,DdvMainPtr dmp)
+{/*not yet implemented*/
+	return;
+}
+
+/*******************************************************************************
+
+  Function : DDV_DrawPanelContent()
+  
+  Purpose :  draw the panel of DDV viewer
+  
+  Parameters :	p;handle of the panel
+  				dmp; main data block
+    
+  Return value : none
+
+*******************************************************************************/
+extern void  DDV_DrawPanelContent (PaneL p,DdvMainPtr dmp)
+{
+	if (dmp->MSA_d.pgp_l.DisplayType==DDV_DISP_HORZ) 
+		DDV_DrawPanelContent_H (p,dmp,&updateRect,TRUE);
+	else 
+		DDV_DrawPanelContent_V (p,dmp);
+	return;
+}
+
+/*******************************************************************************
+
+  Function : DDV_DrawViewer()
+  
+  Purpose :  callback for the viewer panel
+  
+  Parameters :	handle of the panel
+    
+  Return value : none
+
+*******************************************************************************/
+extern void  DDV_DrawViewer (PaneL p)
+{
+
+DdvMainPtr 	dmp;
+
+	/*get the application data*/
+	dmp = (DdvMainPtr) GetObjectExtra(p);
+	if (dmp==NULL) return;
+
+	if (dmp->MSA_d.pgp_l.DisplayType==DDV_DISP_HORZ) 
+		DDV_DrawPanelContent_H (p,dmp,&updateRect,TRUE);
+	else 
+		DDV_DrawPanelContent_V (p,dmp);
+}
diff --git a/ddv/ddvgraph.h b/ddv/ddvgraph.h
new file mode 100644
index 00000000..46d019a2
--- /dev/null
+++ b/ddv/ddvgraph.h
@@ -0,0 +1,171 @@
+/*  $Id: ddvgraph.h,v 1.14 2000/07/24 22:00:08 hurwitz Exp $
+* ===========================================================================
+*
+*                            PUBLIC DOMAIN NOTICE
+*            National Center for Biotechnology Information (NCBI)
+*
+*  This software/database is a "United States Government Work" under the
+*  terms of the United States Copyright Act.  It was written as part of
+*  the author's official duties as a United States Government employee and
+*  thus cannot be copyrighted.  This software/database is freely available
+*  to the public for use. The National Library of Medicine and the U.S.
+*  Government do not place any restriction on its use or reproduction.
+*  We would, however, appreciate having the NCBI and the author cited in
+*  any work or product based on this material
+*
+*  Although all reasonable efforts have been taken to ensure the accuracy
+*  and reliability of the software and data, the NLM and the U.S.
+*  Government do not and cannot warrant the performance or results that
+*  may be obtained by using this software or data. The NLM and the U.S.
+*  Government disclaim all warranties, express or implied, including
+*  warranties of performance, merchantability or fitness for any particular
+*  purpose.
+*
+* ===========================================================================
+*
+* File Name:  ddvgraph.h
+*
+* Author:  Patrick Durand
+*
+* Version Creation Date:   06/19/99
+*
+* $Revision: 1.14 $
+*
+* File Description: 
+*
+* Modifications:
+* --------------------------------------------------------------------------
+* $Log: ddvgraph.h,v $
+* Revision 1.14  2000/07/24 22:00:08  hurwitz
+* fixed bug that 1/2 characters were displayed sometimes
+*
+* Revision 1.13  2000/07/08 20:43:58  vakatov
+* Get all "#include" out of the 'extern "C" { }' scope;  other cleanup...
+*
+* Revision 1.12  2000/05/16 19:43:01  hurwitz
+* grey out create block, delete block, undo, and redo as needed
+*
+* Revision 1.11  2000/02/15 15:31:47  lewisg
+* move DDVRulerDescr to pgppop
+*
+* Revision 1.10  2000/02/03 15:56:47  hurwitz
+* added constructor and destructor for DDVRulerDescrPtr
+*
+* Revision 1.9  2000/01/26 13:38:54  durand
+* update the GUI for the editor. Add functions to create the data to be used by the editor
+*
+* Revision 1.8  1999/11/18 14:37:15  durand
+* avoid flashing sequence during selection
+*
+* Revision 1.7  1999/11/09 17:09:00  durand
+* transfer some functions from ddvgraph to ddvcreate, so that ddvcreate remains Vibrant free and can be compiled with BLAST
+*
+* Revision 1.6  1999/11/03 21:29:49  durand
+* add CTRL and SHFT keys for mouse selection. redesign the loader functions of DDV to properly register the message callbacks
+*
+* Revision 1.5  1999/10/29 14:15:39  durand
+* add simple mouse selection functions
+*
+* Revision 1.4  1999/10/20 13:17:18  durand
+* add display for disc. SeqAlign tails
+*
+* Revision 1.3  1999/10/15 21:57:36  durand
+* add a UI for display options
+*
+* Revision 1.2  1999/10/12 15:07:52  durand
+* resolve problems with CVS
+*
+* Revision 1.1  1999/09/30 14:10:27  durand
+* add ddv to toolkit
+*
+* Revision 1.7  1999/09/22 20:40:20  durand
+* update the drawing procedure to deal with discontinuous seqalign
+*
+* Revision 1.6  1999/09/09 21:54:24  durand
+* create a display for disconitnuous SeqAlign
+*
+* Revision 1.5  1999/08/04 18:01:51  wheelan
+* changes to support new seqalign indexing
+*
+* Revision 1.4  1999/07/27 13:11:44  durand
+* transfer defines to udvdef.h
+*
+* Revision 1.3  1999/07/20 14:58:01  durand
+* use the Color Manager to display colored MSA
+*
+* Revision 1.2  1999/06/21 20:33:28  durand
+* add display type
+*
+* Revision 1.1  1999/06/19 17:21:07  durand
+* add Vibrant DDV code
+*
+*
+*
+* ==========================================================================
+*/
+
+#ifndef _DDVGRAPH_
+#define _DDVGRAPH_
+
+#include <udviewer.h>
+#include <udvdef.h>
+#include <ddvmain.h>
+#include <ddvcolor.h>
+
+#undef NLM_EXTERN
+#ifdef NLM_IMPORT
+#define NLM_EXTERN NLM_IMPORT
+#else
+#define NLM_EXTERN extern
+#endif
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/******************************************************************************
+
+	structures
+
+******************************************************************************/
+
+/******************************************************************************
+
+	defines
+
+******************************************************************************/
+
+/******************************************************************************
+
+	Exported functions
+
+******************************************************************************/
+
+extern Int2 DDV_ComputeColWidth(Int2 cxChar);
+extern void  DDV_DrawPanelContent (PaneL p,DdvMainPtr dmp);
+extern void  DDV_DrawViewer (PaneL p);
+extern void DDV_InvalRegion(PaneL hWndDDV,UnDViewerGraphDataPtr GrData,
+		Int4 disp_from,Int4 disp_to,Int4 disp_row,Boolean IsSelect);
+extern void DDV_GetCurrentDispRange(PaneL hWndDDV,UnDViewerGraphDataPtr GrData,
+		Int4 LengthAli,Int4Ptr from_col,Int4Ptr to_col,Int4Ptr from_row,
+		Int4Ptr to_row);
+NLM_EXTERN ValNodePtr DDV_GetRulerForEditor(ValNodePtr descr_head,Int4 from_disp,
+		Int4 to_disp);
+extern ValNodePtr DDV_ComputeRuler(SeqAlignPtr sap,DDV_Disp_OptPtr ddop);
+extern void	DDV_AdjustDrawingRect(RecT * rcP,UDVFontDataPtr udv_font, DdvMainPtr dmp);
+extern void DDV_DrawPanelContent_H (PaneL p,DdvMainPtr dmp,RecT PNTR MyUpdateRect,
+		Boolean bSelect);
+extern void DDV_GreyOut(DdvMainWinPtr mWin_d, Boolean Start, Boolean End);
+
+#ifdef __cplusplus
+}
+#endif
+
+#undef NLM_EXTERN
+#ifdef NLM_EXPORT
+#define NLM_EXTERN NLM_EXPORT
+#else
+#define NLM_EXTERN
+#endif
+
+#endif /* ndef _DDVGRAPH_ */
diff --git a/ddv/ddvlib.dsp b/ddv/ddvlib.dsp
new file mode 100644
index 00000000..d9146111
--- /dev/null
+++ b/ddv/ddvlib.dsp
@@ -0,0 +1,126 @@
+# Microsoft Developer Studio Project File - Name="ddvlib" - Package Owner=<4>
+# Microsoft Developer Studio Generated Build File, Format Version 6.00
+# ** DO NOT EDIT **
+
+# TARGTYPE "Win32 (x86) Static Library" 0x0104
+
+CFG=ddvlib - Win32 Release
+!MESSAGE This is not a valid makefile. To build this project using NMAKE,
+!MESSAGE use the Export Makefile command and run
+!MESSAGE 
+!MESSAGE NMAKE /f "ddvlib.mak".
+!MESSAGE 
+!MESSAGE You can specify a configuration when running NMAKE
+!MESSAGE by defining the macro CFG on the command line. For example:
+!MESSAGE 
+!MESSAGE NMAKE /f "ddvlib.mak" CFG="ddvlib - Win32 Release"
+!MESSAGE 
+!MESSAGE Possible choices for configuration are:
+!MESSAGE 
+!MESSAGE "ddvlib - Win32 Debug" (based on "Win32 (x86) Static Library")
+!MESSAGE "ddvlib - Win32 Release" (based on "Win32 (x86) Static Library")
+!MESSAGE 
+
+# Begin Project
+# PROP AllowPerConfigDependencies 0
+# PROP Scc_ProjName ""
+# PROP Scc_LocalPath ""
+CPP=cl.exe
+RSC=rc.exe
+
+!IF  "$(CFG)" == "ddvlib - Win32 Debug"
+
+# PROP BASE Use_MFC 0
+# PROP BASE Use_Debug_Libraries 1
+# PROP BASE Output_Dir "ddvlib___Win32_Debug"
+# PROP BASE Intermediate_Dir "ddvlib___Win32_Debug"
+# PROP BASE Target_Dir ""
+# PROP Use_MFC 0
+# PROP Use_Debug_Libraries 1
+# PROP Output_Dir "ddvlib___Win32_Debug"
+# PROP Intermediate_Dir "ddvlib___Win32_Debug"
+# PROP Target_Dir ""
+# ADD BASE CPP /nologo /W3 /Gm /GX /ZI /Od /D "WIN32" /D "_DEBUG" /D "_MBCS" /D "_LIB" /YX /FD /GZ /c
+# ADD CPP /nologo /W2 /Gm /GX /ZI /Od /I ".." /I "..\ddv" /I "..\cn3d" /I "..\access" /I "..\asnstat" /I "..\connect\lbapi" /I "..\connect" /I "..\asnlib" /I "..\vibrant" /I "..\biostruc" /I "..\object" /I "..\api" /I "..\cdromlib" /I "..\desktop" /I "..\tools" /I "..\corelib" /I "..\network\taxon1\common" /I "..\network\vibnet" /I "..\network\entrez\client" /I "..\network\nsclilib" /I "..\network\medarch\client" /I "..\network\id1arch" /I "..\network\taxon1\taxon2" /I "..\network\blast3\client" /D "WIN32" /D "_DEBUG" /D "_MBCS" /D "_LIB" /YX /FD /GZ /c
+# SUBTRACT CPP /Fr
+# ADD BASE RSC /l 0x409 /d "_DEBUG"
+# ADD RSC /l 0x409 /d "_DEBUG"
+BSC32=bscmake.exe
+# ADD BASE BSC32 /nologo
+# ADD BSC32 /nologo
+LIB32=link.exe -lib
+# ADD BASE LIB32 /nologo
+# ADD LIB32 /nologo
+
+!ELSEIF  "$(CFG)" == "ddvlib - Win32 Release"
+
+# PROP BASE Use_MFC 0
+# PROP BASE Use_Debug_Libraries 1
+# PROP BASE Output_Dir "ddvlib___Win32_Release"
+# PROP BASE Intermediate_Dir "ddvlib___Win32_Release"
+# PROP BASE Target_Dir ""
+# PROP Use_MFC 0
+# PROP Use_Debug_Libraries 1
+# PROP Output_Dir "ddvlib___Win32_Release"
+# PROP Intermediate_Dir "ddvlib___Win32_Release"
+# PROP Target_Dir ""
+# ADD BASE CPP /nologo /W2 /Gm /GX /ZI /Od /I ".." /I "..\ddv" /I "..\cn3d" /I "..\access" /I "..\asnstat" /I "..\connect\lbapi" /I "..\connect" /I "..\asnlib" /I "..\vibrant" /I "..\biostruc" /I "..\object" /I "..\api" /I "..\cdromlib" /I "..\desktop" /I "..\tools" /I "..\corelib" /I "..\network\taxon1\common" /I "..\network\vibnet" /I "..\network\entrez\client" /I "..\network\nsclilib" /I "..\network\medarch\client" /I "..\network\id1arch" /I "..\network\taxon1\taxon2" /I "..\network\blast3\client" /D "WIN32" /D "_DEBUG" /D "_MBCS" /D "_LIB" /YX /FD /GZ /c
+# SUBTRACT BASE CPP /Fr
+# ADD CPP /nologo /W2 /Gm /GX /Zi /I ".." /I "..\ddv" /I "..\cn3d" /I "..\access" /I "..\asnstat" /I "..\connect\lbapi" /I "..\connect" /I "..\asnlib" /I "..\vibrant" /I "..\biostruc" /I "..\object" /I "..\api" /I "..\cdromlib" /I "..\desktop" /I "..\tools" /I "..\corelib" /I "..\network\taxon1\common" /I "..\network\vibnet" /I "..\network\entrez\client" /I "..\network\nsclilib" /I "..\network\medarch\client" /I "..\network\id1arch" /I "..\network\taxon1\taxon2" /I "..\network\blast3\client" /D "_LIB" /D "WIN32" /D "_MBCS" /YX /FD /c
+# ADD BASE RSC /l 0x409 /d "_DEBUG"
+# ADD RSC /l 0x409
+BSC32=bscmake.exe
+# ADD BASE BSC32 /nologo
+# ADD BSC32 /nologo
+LIB32=link.exe -lib
+# ADD BASE LIB32 /nologo
+# ADD LIB32 /nologo
+
+!ENDIF 
+
+# Begin Target
+
+# Name "ddvlib - Win32 Debug"
+# Name "ddvlib - Win32 Release"
+# Begin Group "Source Files"
+
+# PROP Default_Filter "cpp;c;cxx;rc;def;r;odl;idl;hpj;bat"
+# Begin Source File
+
+SOURCE=.\ddvclick.c
+# End Source File
+# Begin Source File
+
+SOURCE=.\ddvgraph.c
+# End Source File
+# Begin Source File
+
+SOURCE=.\ddvopen.c
+# End Source File
+# Begin Source File
+
+SOURCE=.\ddvpanel.c
+# End Source File
+# End Group
+# Begin Group "Header Files"
+
+# PROP Default_Filter "h;hpp;hxx;hm;inl"
+# Begin Source File
+
+SOURCE=.\ddvclick.h
+# End Source File
+# Begin Source File
+
+SOURCE=.\ddvgraph.h
+# End Source File
+# Begin Source File
+
+SOURCE=.\ddvopen.h
+# End Source File
+# Begin Source File
+
+SOURCE=.\ddvpanel.h
+# End Source File
+# End Group
+# End Target
+# End Project
diff --git a/ddv/ddvmain.c b/ddv/ddvmain.c
new file mode 100644
index 00000000..d2ee2443
--- /dev/null
+++ b/ddv/ddvmain.c
@@ -0,0 +1,447 @@
+/*  $Id: ddvmain.c,v 1.26 2000/07/17 13:32:33 lewisg Exp $
+* ===========================================================================
+*
+*                            PUBLIC DOMAIN NOTICE
+*            National Center for Biotechnology Information (NCBI)
+*
+*  This software/database is a "United States Government Work" under the
+*  terms of the United States Copyright Act.  It was written as part of
+*  the author's official duties as a United States Government employee and
+*  thus cannot be copyrighted.  This software/database is freely available
+*  to the public for use. The National Library of Medicine and the U.S.
+*  Government do not place any restriction on its use or reproduction.
+*  We would, however, appreciate having the NCBI and the author cited in
+*  any work or product based on this material
+*
+*  Although all reasonable efforts have been taken to ensure the accuracy
+*  and reliability of the software and data, the NLM and the U.S.
+*  Government do not and cannot warrant the performance or results that
+*  may be obtained by using this software or data. The NLM and the U.S.
+*  Government disclaim all warranties, express or implied, including
+*  warranties of performance, merchantability or fitness for any particular
+*  purpose.
+*
+* ===========================================================================
+*
+* File Name:  ddvmain.c
+*
+* Author:  Patrick Durand
+*
+* Version Creation Date:   06/19/99
+*
+* $Revision: 1.26 $
+*
+* File Description: starter module of DeuxD-Viewer (DDV). Onlu use to
+* start DDV as a standalone software.
+*
+* Modifications:
+* --------------------------------------------------------------------------
+* $Log: ddvmain.c,v $
+* Revision 1.26  2000/07/17 13:32:33  lewisg
+* move DDV_args out of the library
+*
+* Revision 1.25  2000/07/17 12:38:53  kans
+* DDV_myargs is extern in header, instantiated in ddvpanel.c, since it is accessed from that library file
+*
+* Revision 1.24  2000/07/14 22:24:55  lewisg
+* fix scroll, click, visual c++ build bugs.  add command line arg parse to ddv
+*
+* Revision 1.23  2000/07/05 19:23:13  lewisg
+* add two panes to ddv, update msvc project files
+*
+* Revision 1.22  2000/06/06 14:44:16  hurwitz
+* fixed bug that SetAppProperty(dde_nogaps)
+*
+* Revision 1.21  2000/05/31 23:07:26  hurwitz
+* made NoGaps a runtime parameter, fixed bug with vertical scroll of show/hide list, save edits query is not performed if nothing to save
+*
+* Revision 1.20  2000/04/21 23:00:50  hurwitz
+* can launch DDE from DDV
+*
+* Revision 1.19  2000/04/17 13:30:43  durand
+* removed g_hParent and unused functions DDV_LaunchAlignViewer and DDV_LaunchAlignEditor
+*
+* Revision 1.18  2000/03/30 21:58:06  durand
+* made standalone DDV a viewer, not the editor
+*
+* Revision 1.17  2000/03/21 14:22:42  durand
+* fixed a problem with menus setup
+*
+* Revision 1.16  2000/03/16 18:38:38  durand
+* fixed the starter function for the GUI
+*
+* Revision 1.15  2000/02/04 16:05:41  durand
+* add click action to select a row
+*
+* Revision 1.14  2000/02/02 14:44:32  durand
+* added function to create data structure for block editor, fixed some bugs
+*
+* Revision 1.13  2000/01/26 13:38:55  durand
+* update the GUI for the editor. Add functions to create the data to be used by the editor
+*
+* Revision 1.12  2000/01/11 15:29:48  durand
+* add a cast to use EntrezSeqEntryGet instead of ID1SeqEntryGet
+*
+* Revision 1.11  2000/01/11 15:05:23  durand
+* remove network stuff
+*
+* Revision 1.10  2000/01/10 15:09:46  durand
+* Use Entrez instead of ID1
+*
+* Revision 1.9  2000/01/05 21:11:14  durand
+* update mouse click actions and DrawSequence function for a better use from ddv and cn3d
+*
+* Revision 1.8  1999/12/03 23:17:23  lewisg
+* Patrick's new global update msg, argument passing when launching ddv, experimental editing
+*
+* Revision 1.7  1999/11/29 15:26:25  durand
+* designed a new GUI to fix problems under MacOS, Linux and SGI
+*
+* Revision 1.6  1999/11/04 22:11:38  durand
+* add the Desktop to DDV. Add a better set of cleanup functions when closing DDV. Before creating color tables, try to get them from the SeqAlign
+*
+* Revision 1.5  1999/10/29 14:15:40  durand
+* add simple mouse selection functions
+*
+* Revision 1.4  1999/10/23 21:20:45  lewisg
+* move g_hParent to ddvopen.c
+*
+* Revision 1.3  1999/10/23 14:54:33  durand
+* resolve external symbol g_hParent
+*
+* Revision 1.2  1999/10/22 14:19:43  durand
+* update the code for the startup functions of DDV drawing panel
+*
+* Revision 1.1  1999/09/30 14:10:27  durand
+* add ddv to toolkit
+*
+* Revision 1.7  1999/09/23 19:06:50  lewisg
+* increase maxtemp number of cached sequences
+*
+* Revision 1.6  1999/09/23 17:44:32  lewisg
+* increase maxtemp number of cached sequences
+*
+* Revision 1.5  1999/07/01 15:28:28  durand
+* validate function loaders of DDV
+*
+* Revision 1.2  1999/06/28 22:07:18  durand
+* add loader functions and clean the code with Lint and Purify
+*
+* Revision 1.1  1999/06/19 17:21:05  durand
+* add Vibrant DDV code
+*
+*
+*
+* ==========================================================================
+*/
+
+#include <ncbi.h>
+#include <accentr.h>
+#include <udviewer.h>
+#include <ddvopen.h>
+#include <ddvmain.h>
+#include <ddvpanel.h>
+#include <vibrant.h>
+#include <netcnfg.h>
+
+extern Args DDV_myargs[NUMARGS] = {
+ /*0*/ { "Gaps allowed",  "T", NULL, NULL, TRUE, 'g', ARG_BOOLEAN, 0.0,0,NULL},
+ /*1*/ { "Allow Edits", "T", NULL, NULL, TRUE , 'e', ARG_BOOLEAN, 0.0,0,NULL},
+};
+
+/*******************************************************************************
+
+  Function : DDV_ConfigAccepted()
+  
+  Purpose : Entrez Network COnfiguration Dialog Box; accept a new config
+  
+  Return value : none 
+
+*******************************************************************************/
+static void DDV_ConfigAccepted(void)
+{
+    SetAppParam("DDV", "SETTINGS", "NETWORKAVAILABLE", "TRUE");
+    Message(MSG_OK, "Setting will take affect when you restart DDV");
+}
+
+/*******************************************************************************
+
+  Function : DDV_ConfigAccepted()
+  
+  Purpose : Entrez Network COnfiguration Dialog Box; close dlg without modif.
+  
+  Return value : none 
+
+*******************************************************************************/
+static void DDV_ConfigCancelled(void)
+{
+}
+
+/*******************************************************************************
+
+  Function : DDV_ConfigTurnedOff()
+  
+  Purpose : Entrez Network COnfiguration Dialog Box; cancel Entrez connection
+  
+  Return value : none 
+
+*******************************************************************************/
+static void DDV_ConfigTurnedOff(void)
+{
+    SetAppParam("DDV", "SETTINGS", "NETWORKAVAILABLE", "FALSE");
+    Message(MSG_OK, "Setting will take affect when you restart DDV");
+}
+
+/*******************************************************************************
+
+  Function : DDV_ConfigNetwork()
+  
+  Purpose : call the Entrez Network COnfiguration Dialog Box
+  
+  Return value : none 
+
+*******************************************************************************/
+static void DDV_ConfigNetwork(IteM i)
+{
+DdvMainWinPtr      dmwp;
+WindoW             hParent;
+
+	/*get main data block*/
+	hParent=(WindoW)ParentWindow(i);
+	if (!hParent) return;
+	dmwp=(DdvMainWinPtr)GetObjectExtra(hParent);
+
+    if (dmwp->UseNetwork) ShowNetConfigForm(NULL,
+        NULL, DDV_ConfigAccepted, DDV_ConfigCancelled, DDV_ConfigTurnedOff, TRUE);
+    else ShowNetConfigForm(NULL, NULL, DDV_ConfigAccepted, DDV_ConfigCancelled,
+                      DDV_ConfigTurnedOff, FALSE);
+}
+
+/*******************************************************************************
+
+  Function : DDV_StartEntrez()
+  
+  Purpose :  start connection to Entrez Server.
+  				    
+  Return value : -
+
+*******************************************************************************/
+static Boolean DDV_StartEntrez(Boolean UseNetwork)
+{
+Boolean bRet;
+
+	bRet=FALSE;
+	
+    if (!UseNetwork) {
+		bRet=FALSE; 
+	}
+	else{
+    	if (!EntrezIsInited()) {
+        	if(EntrezBioseqFetchEnable(szAppName, FALSE)) {
+            	if (EntrezInit(szAppName, TRUE, NULL)) 
+					bRet=TRUE;
+				else
+					bRet=FALSE;
+        	}
+			else {
+				bRet=FALSE;
+			}
+    	}
+		else{
+			bRet=TRUE;
+		}
+	}
+	return(bRet);
+}
+
+
+/*****************************************************************************
+
+Function: DDV_UseNetwork()
+
+Purpose:  Determines if DDV should use the network
+  
+Returns:  TRUE if yes
+
+*****************************************************************************/
+static Boolean DDV_UseNetwork(void)
+{
+Char str[64];
+
+    if (GetAppParam
+        ("DDV", "SETTINGS", "NETWORKAVAILABLE", NULL, str, sizeof(str))) {
+        if (StringICmp(str, "TRUE") == 0) return TRUE;
+    }
+    return FALSE;
+}
+
+/*******************************************************************************
+
+  Function : DDV_StartMainWin_Master()
+  
+  Purpose : start DDV main window as a standalone application. Never use this 
+  	function for other purpose. If you want to start DDV as a slave, take a
+	look at the functions below.
+  
+  Parameters : 	mWin_d; main program data
+  				ldp; logo data
+
+  Return value : handle to the DDV main window
+
+*******************************************************************************/
+static WindoW DDV_StartMainWin_Master(DdvMainWinPtr mWin_d,UDVLogoDataPtr ldp)
+{
+Int2	Margins;
+WindoW	w; 
+Boolean bRet;
+	
+	/*main window*/
+	Margins=10*stdCharWidth;
+
+	w=DocumentWindow(Margins,Margins ,-10,-10, 
+			szAppName, 
+			DDV_WinMainProgQuit,
+			DDV_WinMainResize);
+
+	if (w==NULL){
+		Message (MSG_ERROR, "Viewer creation failed.");
+		return(NULL);
+	}
+	
+	SetObjectExtra (w, (Pointer)mWin_d, (FreeProc)DDV_WinMainCleanup);
+	SetAppProperty("UDVLogoData",(Pointer)ldp);	
+
+	mWin_d->hWndMain=w;
+	/*this is an autonomous viewer*/
+	mWin_d->AutonomeViewer=TRUE;
+
+	/*use the Network ?*/
+	mWin_d->UseNetwork=TRUE;/*DDV_UseNetwork();*/
+
+	bRet=DDV_CreateViewerPanel(w,mWin_d,NULL,FALSE); /*FALSE for viewer */
+	if (!bRet) return(NULL);
+
+	/*init logo_panel*/
+	LogoFontCreate(&ldp->f1,&ldp->f2,&ldp->f3);
+	StringCpy(ldp->szTitle,"DDV");
+	StringCpy(ldp->szDesc,", a MSA viewer/editor");
+	mWin_d->Show_logo=TRUE;
+
+	/*set the function to get a gi over the network*/
+	mWin_d->fetchSepProc=(UdvFetchSeqEntryProc)EntrezSeqEntryGet;
+	mWin_d->NetCfgMenuProc=DDV_ConfigNetwork;
+	mWin_d->NetStartProc=DDV_StartEntrez;
+		
+	return(w);
+}
+
+/*******************************************************************************
+
+  Function : Main()
+  
+  Purpose : Entry point of the software 
+  
+  Parameters : 
+  
+  Return value : 
+
+*******************************************************************************/
+
+Int2 Main(void)
+{
+UDVLogoDataPtr	ldp;
+Boolean 		UseNetwork;
+WindoW			w; 
+DdvMainWinPtr   mWin_d;/*main window data*/
+ObjMgrPtr omp = NULL;
+Boolean  NoGaps;
+
+	if ( !Nlm_GetArgsSilent("DDV 1.0", NUMARGS, DDV_myargs) ) return 1;
+	
+	ErrSetMessageLevel(SEV_WARNING);
+	ErrSetOptFlags(EO_SHOW_CODES);
+	ErrSetOptFlags(EO_XLATE_CODES);
+		
+	/*init some important stuffs*/
+	UseLocalAsnloadDataAndErrMsg();
+
+	if (! AllObjLoad()){
+		Message (MSG_ERROR, "AsnObjLoad() failed.");
+		return(1);
+	}
+
+	if (! SubmitAsnLoad()){
+		Message (MSG_ERROR, "SeqSubmitLoad() failed.");
+		return(1);
+	}
+
+	if (!SeqCodeSetLoad ()){
+		Message (MSG_ERROR, "SeqCodeSetLoad () failed.");
+		return(1);
+	}
+
+	if (!GeneticCodeTableLoad()){
+		Message (MSG_ERROR, "GeneticCodeTableLoad() failed.");
+		return(1);
+	}
+
+	if (!FeatDefSetLoad()){
+		Message (MSG_ERROR, "FeatDefSeqLoad() failed.");
+		return(1);
+	}
+
+	/*init data blocks*/
+	mWin_d=(DdvMainWinPtr)MemNew(sizeof(DdvMainWin));
+	if (!mWin_d){
+		Message (MSG_ERROR, "Viewer creation failed.");
+		return(1);
+	}
+
+  /* look for "nogaps" runtime parameter */
+    NoGaps = (Boolean)DDV_myargs[0].intvalue;
+    SetAppProperty("dde_nogaps",(void*)&NoGaps);
+
+    mWin_d->EditAllowed = (Boolean)DDV_myargs[1].intvalue;
+	
+	/*init data blocks*/
+	ldp=(UDVLogoDataPtr)MemNew(sizeof(UDVLogoData));
+	if (ldp){
+		MemSet(ldp,0,sizeof(UDVLogoData));
+	}
+	else{
+		Message (MSG_ERROR, "Viewer creation failed.");
+		return(1);
+	}
+
+	/*OBjMgr Callback Function declaration*/
+/*	REG_DDV_AUTO_EDIT; */
+	REG_DDV_AUTO_VIEW;
+	REGISTER_UDV_AUTONOMOUS;
+    REG_DDV_SLA_EDIT;
+	
+    /* increment maximum # of objects held in memory */
+    omp = ObjMgrWriteLock();
+    if(omp != NULL ) omp->maxtemp = DDV_MAXTEMP;
+    ObjMgrUnlock();
+
+	w=DDV_StartMainWin_Master(mWin_d,ldp);
+	if (w==NULL) goto fin;
+	
+	ProcessUpdatesFirst(FALSE);
+	UseNetwork=mWin_d->UseNetwork;
+
+	/*display main window*/
+	RealizeWindow(w);
+	Show(w);
+
+	/*enter loop events*/
+	ProcessEvents();
+fin:
+	/*close network connection, if needed*/
+	if (UseNetwork && EntrezIsInited()) EntrezBioseqFetchDisable();
+	/*clean up*/
+	if (ldp) MemFree(ldp);
+	RemoveAppProperty("UDVLogoData");	
+	return(0);
+}
+
diff --git a/ddv/ddvmain.h b/ddv/ddvmain.h
new file mode 100644
index 00000000..ecb22d90
--- /dev/null
+++ b/ddv/ddvmain.h
@@ -0,0 +1,398 @@
+/*  $Id: ddvmain.h,v 1.44 2000/07/17 13:32:33 lewisg Exp $
+* ===========================================================================
+*
+*                            PUBLIC DOMAIN NOTICE
+*            National Center for Biotechnology Information (NCBI)
+*
+*  This software/database is a "United States Government Work" under the
+*  terms of the United States Copyright Act.  It was written as part of
+*  the author's official duties as a United States Government employee and
+*  thus cannot be copyrighted.  This software/database is freely available
+*  to the public for use. The National Library of Medicine and the U.S.
+*  Government do not place any restriction on its use or reproduction.
+*  We would, however, appreciate having the NCBI and the author cited in
+*  any work or product based on this material
+*
+*  Although all reasonable efforts have been taken to ensure the accuracy
+*  and reliability of the software and data, the NLM and the U.S.
+*  Government do not and cannot warrant the performance or results that
+*  may be obtained by using this software or data. The NLM and the U.S.
+*  Government disclaim all warranties, express or implied, including
+*  warranties of performance, merchantability or fitness for any particular
+*  purpose.
+*
+* ===========================================================================
+*
+* File Name:  ddvmain.h
+*
+* Author:  Patrick Durand
+*
+* Version Creation Date:   06/19/99
+*
+* $Revision: 1.44 $
+*
+* File Description: 
+*
+* Modifications:
+* --------------------------------------------------------------------------
+* $Log: ddvmain.h,v $
+* Revision 1.44  2000/07/17 13:32:33  lewisg
+* move DDV_args out of the library
+*
+* Revision 1.43  2000/07/17 12:38:53  kans
+* DDV_myargs is extern in header, instantiated in ddvpanel.c, since it is accessed from that library file
+*
+* Revision 1.42  2000/07/14 22:24:56  lewisg
+* fix scroll, click, visual c++ build bugs.  add command line arg parse to ddv
+*
+* Revision 1.41  2000/07/12 22:22:42  hurwitz
+* added delete block to DDV
+*
+* Revision 1.40  2000/07/10 14:38:07  lewisg
+* move seqalign and sequentry data from window to panels
+*
+* Revision 1.39  2000/07/08 20:43:58  vakatov
+* Get all "#include" out of the 'extern "C" { }' scope;  other cleanup...
+*
+* Revision 1.38  2000/07/05 19:23:13  lewisg
+* add two panes to ddv, update msvc project files
+*
+* Revision 1.37  2000/07/05 18:42:16  hurwitz
+* added split block function to DDV
+*
+* Revision 1.36  2000/06/30 22:31:51  hurwitz
+* added merge block function for DDV
+*
+* Revision 1.35  2000/06/27 20:46:38  hurwitz
+* fixed bugs with select rectangle, added select row option
+*
+* Revision 1.34  2000/06/15 17:33:18  hurwitz
+* used view seqAlignPtr to get original (bug fix), and started working on left/right/center justify for DDE
+*
+* Revision 1.33  2000/05/19 13:48:31  hurwitz
+* made a version of DDE that doesn't allow aligned gaps, changed wording for adding new rows
+*
+* Revision 1.32  2000/05/15 23:39:34  lewisg
+* shred cblast, add menu items for gapped/ungapped, fix pdbheaders
+*
+* Revision 1.31  2000/04/26 21:54:27  hurwitz
+* added save function to tell AlnMgr about edits made in DDE
+*
+* Revision 1.30  2000/04/21 23:00:50  hurwitz
+* can launch DDE from DDV
+*
+* Revision 1.29  2000/04/18 19:50:24  lewisg
+* add deselect menu item
+*
+* Revision 1.28  2000/04/17 13:30:43  durand
+* removed g_hParent and unused functions DDV_LaunchAlignViewer and DDV_LaunchAlignEditor
+*
+* Revision 1.27  2000/04/10 21:41:26  lewisg
+* move alignment menus into ddv, udv from cn3d
+*
+* Revision 1.26  2000/04/10 20:58:42  hurwitz
+* added GUI controls for DeleteBlock in DDE
+*
+* Revision 1.25  2000/04/07 16:21:08  hurwitz
+* made delete block faster, added delete block to edit menu
+*
+* Revision 1.24  2000/03/27 22:15:05  lewisg
+* add show/hide row dialog
+*
+* Revision 1.23  2000/03/25 00:22:09  hurwitz
+* put DDE_StackPtr in DDV_Main, add to stack inside DDE api's, added insert char, delete char, home and end keyboard control
+*
+* Revision 1.22  2000/03/14 22:08:21  hurwitz
+* undo and redo working properly, restore-original function added
+*
+* Revision 1.21  2000/03/10 23:01:43  hurwitz
+* added undo and redo functions, first pass
+*
+* Revision 1.20  2000/03/06 22:45:58  hurwitz
+* can shift right boundary of an aligned block left and right, DDVRuler updates added
+*
+* Revision 1.19  2000/03/01 22:49:41  lewisg
+* import bioseq, neatlyindex, get rid of dead code
+*
+* Revision 1.18  2000/02/04 16:05:41  durand
+* add click action to select a row
+*
+* Revision 1.17  2000/01/26 13:38:55  durand
+* update the GUI for the editor. Add functions to create the data to be used by the editor
+*
+* Revision 1.16  2000/01/12 21:52:17  durand
+* add import function; update menus when DDV is loaded from Cn3D
+*
+* Revision 1.15  2000/01/11 15:05:23  durand
+* remove network stuff
+*
+* Revision 1.14  2000/01/10 15:09:45  durand
+* Use Entrez instead of ID1
+*
+* Revision 1.13  1999/12/20 20:20:41  lewisg
+* allow cn3d to do color and ddv to do case when both are running
+*
+* Revision 1.12  1999/12/07 21:40:14  durand
+* add mouse modes menu and caret facility for the editor
+*
+* Revision 1.11  1999/12/03 23:17:23  lewisg
+* Patrick's new global update msg, argument passing when launching ddv, experimental editing
+*
+* Revision 1.10  1999/11/29 15:26:25  durand
+* designed a new GUI to fix problems under MacOS, Linux and SGI
+*
+* Revision 1.9  1999/11/09 17:09:00  durand
+* transfer some functions from ddvgraph to ddvcreate, so that ddvcreate remains Vibrant free and can be compiled with BLAST
+*
+* Revision 1.8  1999/11/03 21:29:48  durand
+* add CTRL and SHFT keys for mouse selection. redesign the loader functions of DDV to properly register the message callbacks
+*
+* Revision 1.7  1999/10/29 14:15:40  durand
+* add simple mouse selection functions
+*
+* Revision 1.6  1999/10/23 14:54:34  durand
+* resolve external symbol g_hParent
+*
+* Revision 1.5  1999/10/22 20:12:47  durand
+* add Export command (text, HTML and Phylip formats)
+*
+* Revision 1.4  1999/10/22 14:19:43  durand
+* update the code for the startup functions of DDV drawing panel
+*
+* Revision 1.3  1999/10/20 13:17:19  durand
+* add display for disc. SeqAlign tails
+*
+* Revision 1.2  1999/10/15 21:57:36  durand
+* add a UI for display options
+*
+* Revision 1.1  1999/09/30 14:10:27  durand
+* add ddv to toolkit
+*
+* Revision 1.7  1999/09/23 19:06:50  lewisg
+* increase maxtemp number of cached sequences
+*
+* Revision 1.6  1999/09/21 14:19:08  durand
+* add mouse click management layout
+*
+* Revision 1.5  1999/09/09 21:55:07  durand
+* instantiate the Fle|Close command of DDV
+*
+* Revision 1.4  1999/07/20 14:58:01  durand
+* use the Color Manager to display colored MSA
+*
+* Revision 1.3  1999/06/30 14:57:21  durand
+* update DDV loader functions
+*
+* Revision 1.2  1999/06/28 22:07:21  durand
+* add loader functions and clean the code with Lint and Purify
+*
+* Revision 1.1  1999/06/19 17:21:07  durand
+* add Vibrant DDV code
+*
+*
+*
+* ==========================================================================
+*/
+
+#ifndef _DDVMAIN_
+#define _DDVMAIN_
+
+#include <ncbi.h>
+#include <vibrant.h>
+#include <ddvopen.h>
+#include <pgppop.h>
+#include <ddvcolor.h>
+#include <ddvcreate.h>
+
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+
+/******************************************************************************
+
+	ERROR / Information messages from DDV_OPEN module 
+
+******************************************************************************/
+#define DVV_MSG_M_OK 1
+
+/******************************************************************************
+
+	defines
+
+******************************************************************************/
+
+/* maximum number of sequences to hold in memory */
+#define DDV_MAXTEMP 500 
+/*caret style */
+#define DDV_CARET_BAR 1
+/*mouse mode*/
+#define DDV_MOUSEMODE_QUERY           0
+#define DDV_MOUSEMODE_SELECT          1
+#define DDV_MOUSEMODE_EDIT            2
+#define DDV_MOUSEMODE_CREATEBLOCK     3
+#define DDV_MOUSEMODE_LAUNCHEDITOR    4
+#define DDV_MOUSEMODE_SELECT_ONE_ROW  5
+#define DDV_MOUSEMODE_MERGEBLOCKS1    6
+#define DDV_MOUSEMODE_MERGEBLOCKS2    7
+#define DDV_MOUSEMODE_SPLITBLOCK      8
+#define DDV_MOUSEMODE_DELETEBLOCK     9
+
+/*timer control*/
+#define DDV_SET_TIMER 1
+#define DDV_TEST_TIMER 2
+/*action associated with the timer*/
+#define DDV_INVAL_REGION 1
+#define DDV_NOTHING 2
+
+/******************************************************************************
+
+	Data structures
+
+******************************************************************************/
+/*used to display the caret (editor mode only)*/
+typedef struct ddvcaretinfo{
+	Int4  old_row;/*zero-based values; display coordinates*/
+	Int4  old_col;
+	Int4  new_row;/*zero-based values; display coordinates*/
+	Int4  new_col;
+	Uint1 style; /*see DDV_CARET_* defines */
+} DDVCaretInfo, PNTR DDVCaretInfoPtr;
+
+/*used to remember the selected row (editor mode only)*/
+typedef struct ddveditrowinfo{
+	Int4  curEditRow;/*zero-based values; row for applying delete, move*/
+	Int4  curMasterRow;/*zero-based values; this row is the master*/
+} DDVEditRowInfo, PNTR DDVEditRowInfoPtr;
+
+typedef struct ddv_global{
+	DDV_ColorGlobal * colorp;
+} DDV_Global, PNTR DDV_GlobalPtr;
+
+typedef struct ddvmenu {
+	/*file menu*/
+	MenU File;
+	IteM FileOpen;/*open file command*/
+	IteM EntrezOpen;/*open from ID1 command*/
+	IteM FileClose;/*close file command*/
+  IteM SaveEdits;/* save changes made in editor*/
+	IteM FileExport;/*export a seqalign*/
+    IteM ImportSeq;/* import a sequence */
+    IteM ImportNucSeqAlign;/* import a nuc SeqAlign */
+    IteM ImportProtSeqAlign;/* import a prot SeqAlign */
+    IteM Hide;/* show/hide dialog */
+	IteM QuitViewer;/*close the viewer*/
+	/*Edit menu*/
+	MenU Edit;
+	IteM DeleteRow;
+	IteM MoveRowLeft;
+	IteM MoveRowRight;
+  IteM LeftBoundaryLeft;
+  IteM LeftBoundaryRight;
+  IteM RightBoundaryLeft;
+  IteM RightBoundaryRight;
+  IteM DeleteBlock;
+  IteM CreateBlock;
+  IteM Prev;
+  IteM Next;
+  IteM Orig;
+    /*Align menu */
+    MenU Align;
+    MenU AddRow;
+    MenU FromFile;
+    MenU FromNet;
+    IteM Deselect;
+    IteM BlastFile;
+    IteM BlastNet;
+	/*Options menu*/
+	MenU Options;
+	IteM DispStyles;/*display styles*/
+	ChoicE MouseMode;/*mouse mode (query, selection, edit)*/
+    ChoicE Justify;/*justify (left, right, center)*/
+    IteM ShowLowerPanel;
+	IteM ConfigNet;/*Entrez Network Conf. dlg*/
+  IteM LaunchEditor;
+  IteM MergeBlocks;
+  IteM SplitBlock;
+  IteM DeleteDDVBlock;
+	} DdvMenu, PNTR DdvMenuPtr;
+
+typedef struct ddvmsadata {
+	MsaParaGPopList pgp_l;/*ParaG list*/
+	Uint2			entityID;/*currently displayed SeqAlign*/
+	Uint2			itemID;/*  */
+	} DdvMSAData, PNTR DdvMSADataPtr;
+
+typedef struct ddvmainwin {
+	Boolean UseNetwork;
+		/*main win menu*/
+	DdvMenu	MainMenu;/*menu command list*/
+	ButtoN  gotoBtn;
+	TexT    gotoValRow;
+	TexT    gotoValCol;
+	GrouP   StatusGroup;
+	GrouP   StatusGroupLower;
+	Boolean	Show_logo;
+	FonT	f1;	/*tree fonts used to display the software logo*/
+	FonT	f2;
+	FonT	f3;
+		/*viewer data used only when AutonomeViewer is TRUE */
+	Boolean	AutonomeViewer;/*viewer is standalone ?*/
+	WindoW	hWndMain;/*handle to the main window*/
+	PaneL   hWndDDV;/*handle of the current DDV panel*/
+    PaneL   hUpperPanel;/*handle of the upper DDV panel (the multiple)*/
+    PaneL   hLowerPanel;/*handle of the DDV panel (the pairwise) */
+	PrompT   InfoPanel;
+	PrompT   UpperInfoPanel;
+	PrompT   LowerInfoPanel;
+		/*use to open a file*/
+	UdvFetchSeqEntryProc  fetchSepProc;/*function to get a gi over the Network*/
+	Nlm_ItmActnProc   NetCfgMenuProc;
+	StartNetworkProc  NetStartProc;
+    Boolean EditAllowed;  /* editing is allowed */
+	}DdvMainWin,PNTR DdvMainWinPtr;
+
+typedef struct ddvtimerdata {
+	Int4 col;/*one-based; disp coord*/
+	Int4 row;/*one-based; disp coord*/
+	Int2 delay;
+	Uint1 status;
+	Uint1 action;
+}DdvTimerData, PNTR DdvTimerDataPtr;
+
+typedef struct ddvmain {
+    WindoW             hParent;
+    PaneL              hWndDDV;/*panel's handle*/
+    UnDViewerGraphData GrData;/*graphical data*/
+    DdvMSAData         MSA_d;/*data to display*/
+    DDV_Global         Globals;/*shared color data, among others*/
+    UDV_mouse_select   ms;/*mouse selection info*/
+    DDV_Disp_Opt       ddo;
+    DDVCaretInfo       dci;/*caret position and style (editor only)*/
+    DDVEditRowInfo     deri;/*some rows info to apply edit commands*/
+    DdvTimerData       dtd;/*last goto position*/
+    Uint1              MouseMode;
+    Uint1              SavedMouseMode;
+    Uint2              userkey;
+    Uint2              procid;
+    Uint2              proctype;
+    Int4               MasterViewer;/*the viewer launching ddv*/
+    Boolean	           bEditor;/*true if use DDV with editor functions*/
+    DDE_StackPtr       dsp;/*data for editor*/
+    Int4               BlockIndex;/*the first block of merge 2 blocks*/
+    Int4               SaveCol;/*col where split line is drawn*/
+    		/*SAP list when open a File or fetch an DB entry*/
+	ValNodePtr		vnp_ali;/*SeqAlign List*/
+	DdvOpenData        dod;/*what is open in DDV*/	
+	} DdvMain, PNTR DdvMainPtr;
+
+#define NUMARGS 2
+extern Args DDV_myargs[NUMARGS];
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* ndef _DDVMAIN_ */
+
diff --git a/ddv/ddvopen.c b/ddv/ddvopen.c
new file mode 100644
index 00000000..7cebf215
--- /dev/null
+++ b/ddv/ddvopen.c
@@ -0,0 +1,3441 @@
+/*  $Id: ddvopen.c,v 1.96 2001/04/26 16:41:20 juran Exp $
+* ===========================================================================
+*
+*                            PUBLIC DOMAIN NOTICE
+*            National Center for Biotechnology Information (NCBI)
+*
+*  This software/database is a "United States Government Work" under the
+*  terms of the United States Copyright Act.  It was written as part of
+*  the author's official duties as a United States Government employee and
+*  thus cannot be copyrighted.  This software/database is freely available
+*  to the public for use. The National Library of Medicine and the U.S.
+*  Government do not place any restriction on its use or reproduction.
+*  We would, however, appreciate having the NCBI and the author cited in
+*  any work or product based on this material
+*
+*  Although all reasonable efforts have been taken to ensure the accuracy
+*  and reliability of the software and data, the NLM and the U.S.
+*  Government do not and cannot warrant the performance or results that
+*  may be obtained by using this software or data. The NLM and the U.S.
+*  Government disclaim all warranties, express or implied, including
+*  warranties of performance, merchantability or fitness for any particular
+*  purpose.
+*
+* ===========================================================================
+*
+* File Name:  ddvopen.c
+*
+* Author:  Patrick Durand
+*
+* Version Creation Date:   06/19/99
+*
+* $Revision: 1.96 $
+*
+* File Description: code to open a SeqAlign (file & Net) and code of the
+* message callback for DeuxD-Viewer (DDV).
+*
+* Modifications:
+* --------------------------------------------------------------------------
+* $Log: ddvopen.c,v $
+* Revision 1.96  2001/04/26 16:41:20  juran
+* Squelch warnings.
+*
+* Revision 1.95  2000/07/17 17:46:48  hurwitz
+* made it so show/hide dialog only updates view when ok is clicked
+*
+* Revision 1.94  2000/07/14 22:24:56  lewisg
+* fix scroll, click, visual c++ build bugs.  add command line arg parse to ddv
+*
+* Revision 1.92  2000/07/05 19:23:13  lewisg
+* add two panes to ddv, update msvc project files
+*
+* Revision 1.91  2000/06/16 14:57:03  lewisg
+* move entrez calls out of desktop
+*
+* Revision 1.90  2000/06/15 17:33:18  hurwitz
+* used view seqAlignPtr to get original (bug fix), and started working on left/right/center justify for DDE
+*
+* Revision 1.89  2000/06/15 16:01:07  hurwitz
+* rewrote section that calls ViewMgr_Attach when SeqAlign is not editable but IBMable
+*
+* Revision 1.88  2000/06/13 18:23:55  hurwitz
+* made ViewMgr_MakeMultiple routine, call this on each launch of DDE rather than launch of DDV
+*
+* Revision 1.87  2000/06/12 23:02:40  hurwitz
+* enable launch of DDE from Cn3D, swith from DDV_ComputeRuler to DDE_ReMakeRuler, get rid of styles option for DDE
+*
+* Revision 1.86  2000/06/08 20:04:38  hurwitz
+* made warning about converting to true multiple alignment into a Message window, and other small fixes
+*
+* Revision 1.85  2000/06/07 19:09:36  hurwitz
+* made DDE_ReMakeRuler work with linked list of ParaGs
+*
+* Revision 1.84  2000/06/06 14:44:16  hurwitz
+* fixed bug that SetAppProperty(dde_nogaps)
+*
+* Revision 1.83  2000/06/02 19:57:03  hurwitz
+* added a query dialog when converting from pairwise multiple to true multiple, bug fix of double freeing of a seqAlignPtr
+*
+* Revision 1.82  2000/06/01 14:40:08  hurwitz
+* temp fix: when DDV is launched as slave, don't allow aligned gaps
+*
+* Revision 1.81  2000/05/31 23:07:26  hurwitz
+* made NoGaps a runtime parameter, fixed bug with vertical scroll of show/hide list, save edits query is not performed if nothing to save
+*
+* Revision 1.80  2000/05/24 21:43:00  hurwitz
+* getting hide/show rows to work with DDV and DDE together
+*
+* Revision 1.79  2000/05/23 22:00:14  hurwitz
+* working on launch of DDE from DDV
+*
+* Revision 1.78  2000/05/15 23:39:34  lewisg
+* shred cblast, add menu items for gapped/ungapped, fix pdbheaders
+*
+* Revision 1.77  2000/05/15 22:00:36  hurwitz
+* put save-edits query into DDV_SlaveQuit where it belongs
+*
+* Revision 1.76  2000/05/12 21:18:13  hurwitz
+* added window asking if user wants to save unsaved edits for dde
+*
+* Revision 1.75  2000/05/12 16:15:25  hurwitz
+* reverted to not doing IntersectOnMaster for DDE, now determined by call to ViewMgr_Attach
+*
+* Revision 1.74  2000/05/11 16:28:44  wheelan
+* made DDV_ShredAln NLM_EXTERN
+*
+* Revision 1.73  2000/05/10 22:03:29  thiessen
+* temporary fix for CN3D_[TRIM,SHRED] not defined
+*
+* Revision 1.72  2000/05/10 16:47:25  wheelan
+* added CN3D_SHRED and CN3D_TRIM options; added ddv_shred_aln
+*
+* Revision 1.71  2000/05/09 14:21:54  wheelan
+* added ddv_truncate_overlaps
+*
+* Revision 1.70  2000/05/08 16:29:27  wheelan
+* change to ungapped BLAST
+*
+* Revision 1.69  2000/05/04 22:43:38  hurwitz
+* don't launch DDE on top of DDV, change some wording, redraw DDE after save to AlnMgr
+*
+* Revision 1.68  2000/05/03 17:48:30  hurwitz
+* keep DDV in same column when DDE does a save
+*
+* Revision 1.67  2000/05/03 16:16:51  hurwitz
+* fixed bug fix from yesterday
+*
+* Revision 1.66  2000/05/02 19:50:38  hurwitz
+* fixed some bugs with launching DDE from DDV, added new alnMgr fn for positioning DDE on proper column
+*
+* Revision 1.65  2000/04/28 14:43:37  hurwitz
+* send message to DDV after edits in DDE are accepted by AlnMgr
+*
+* Revision 1.64  2000/04/27 22:21:58  lewisg
+* misc bugs/features
+*
+* Revision 1.63  2000/04/27 19:57:59  hurwitz
+* scroll to aligned block on launch of DDE
+*
+* Revision 1.62  2000/04/27 13:33:41  durand
+* SpacerSize min value fixed to 1; update view when SpacerSize is changed
+*
+* Revision 1.61  2000/04/21 23:00:50  hurwitz
+* can launch DDE from DDV
+*
+* Revision 1.60  2000/04/20 23:27:43  lewisg
+* misc bug fixes
+*
+* Revision 1.59  2000/04/19 15:45:50  hurwitz
+* can create display for a block
+*
+* Revision 1.58  2000/04/17 13:30:43  durand
+* removed g_hParent and unused functions DDV_LaunchAlignViewer and DDV_LaunchAlignEditor
+*
+* Revision 1.57  2000/04/11 14:08:33  durand
+* removed a debug line
+*
+* Revision 1.56  2000/04/10 20:33:40  lewisg
+* fix show/hide for blast multiple, make blast multiple API generic
+*
+* Revision 1.55  2000/04/10 19:53:14  durand
+* allowed ddv to display NULL SeqAlign
+*
+* Revision 1.54  2000/04/08 00:37:32  lewisg
+* multiple seqentries, NEWSEQ message, etc.
+*
+* Revision 1.53  2000/04/07 15:03:08  durand
+* added use of UPDATE_TYPE_NEWSEQ; DDV now rebuilt EntitiesTable after an update msg
+*
+* Revision 1.52  2000/04/04 17:51:54  lewisg
+* fix various seq import bugs
+*
+* Revision 1.51  2000/03/29 23:38:06  lewisg
+* hide/show, fixes to saving and opening
+*
+* Revision 1.50  2000/03/29 19:26:10  lewisg
+* use blast2seqs instead of bandalign
+*
+* Revision 1.49  2000/03/27 22:15:06  lewisg
+* add show/hide row dialog
+*
+* Revision 1.48  2000/03/27 18:07:48  hurwitz
+* page up and page down working, give panel focus on launch
+*
+* Revision 1.47  2000/03/24 20:34:58  lewisg
+* add blast from file, bug fixes, get rid of redundant code, etc.
+*
+* Revision 1.46  2000/03/22 20:31:34  durand
+* added system menus for slave DDV
+*
+* Revision 1.45  2000/03/21 14:21:46  durand
+* fixed a problem with menus setup
+*
+* Revision 1.44  2000/03/20 19:26:53  kans
+* need to create menus before other window contents - Mac menu bar for windows is actually in content area
+*
+* Revision 1.43  2000/03/16 14:11:59  durand
+* set corretly mouse mode menu
+*
+* Revision 1.42  2000/03/02 21:11:06  lewisg
+* use bandalign for import sequence, make standalone ddv use viewmgr, make dialogs modal, send color update
+*
+* Revision 1.41  2000/03/02 15:43:10  durand
+* use MovableModalWindow for dialog boxes
+*
+* Revision 1.40  2000/03/01 22:49:41  lewisg
+* import bioseq, neatlyindex, get rid of dead code
+*
+* Revision 1.39  2000/02/28 20:15:32  durand
+* if DDV is started from Cn3D, DDV doesn't set up anymore letters layout
+*
+* Revision 1.38  2000/02/15 22:40:57  lewisg
+* add ability to launch udv so that it colors by row, fixes to colormgr, track rows from viewmgr, fix visual c projects
+*
+* Revision 1.37  2000/02/07 21:14:08  durand
+* added a generic answer to Update messages
+*
+* Revision 1.36  2000/02/07 14:03:35  durand
+* replace BioseqUnlockById by BioseqUnlock
+*
+* Revision 1.35  2000/02/05 01:32:22  lewisg
+* add viewmgr, move place freeing is done in ddv, modify visual c++ projects
+*
+* Revision 1.34  2000/02/04 16:05:40  durand
+* add click action to select a row
+*
+* Revision 1.33  2000/02/02 14:44:32  durand
+* added function to create data structure for block editor, fixed some bugs
+*
+* Revision 1.32  2000/01/26 13:38:53  durand
+* update the GUI for the editor. Add functions to create the data to be used by the editor
+*
+* Revision 1.31  2000/01/18 22:49:16  lewisg
+* send OM_MSG_FLUSH to ddv/udv, tweak CPK coloration, misc bugs
+*
+* Revision 1.30  2000/01/12 21:52:16  durand
+* add import function; update menus when DDV is loaded from Cn3D
+*
+* Revision 1.29  2000/01/11 15:05:23  durand
+* remove network stuff
+*
+* Revision 1.28  2000/01/10 15:09:46  durand
+* Use Entrez instead of ID1
+*
+* Revision 1.27  2000/01/05 21:11:14  durand
+* update mouse click actions and DrawSequence function for a better use from ddv and cn3d
+*
+* Revision 1.26  1999/12/30 21:08:45  lewisg
+* bioseq import dialog
+*
+* Revision 1.25  1999/12/30 13:45:50  beloslyu
+* fix comment
+*
+* Revision 1.24  1999/12/29 22:55:03  lewisg
+* get rid of seqalign id
+*
+* Revision 1.23  1999/12/23 19:22:06  durand
+* modify default options for DDV when loaded from Cn3D
+*
+* Revision 1.22  1999/12/21 15:27:24  durand
+* avoid to quit Cn3D when closing DDV
+*
+* Revision 1.21  1999/12/20 20:20:41  lewisg
+* allow cn3d to do color and ddv to do case when both are running
+*
+* Revision 1.20  1999/12/07 21:40:13  durand
+* add mouse modes menu and caret facility for the editor
+*
+* Revision 1.19  1999/12/06 16:19:19  durand
+* add GoTo facility to DDV
+*
+* Revision 1.18  1999/12/03 23:17:23  lewisg
+* Patrick's new global update msg, argument passing when launching ddv, experimental editing
+*
+* Revision 1.17  1999/11/30 18:19:47  durand
+* fix a problem with function declaration DDV_CloseData
+*
+* Revision 1.16  1999/11/29 15:26:26  durand
+* designed a new GUI to fix problems under MacOS, Linux and SGI
+*
+* Revision 1.15  1999/11/17 22:43:58  durand
+* speed up the selection manager for large SeqAlign
+*
+* Revision 1.14  1999/11/09 17:09:00  durand
+* transfer some functions from ddvgraph to ddvcreate, so that ddvcreate remains Vibrant free and can be compiled with BLAST
+*
+* Revision 1.13  1999/11/04 22:11:38  durand
+* add the Desktop to DDV. Add a better set of cleanup functions when closing DDV. Before creating color tables, try to get them from the SeqAlign
+*
+* Revision 1.12  1999/11/03 21:29:47  durand
+* add CTRL and SHFT keys for mouse selection. redesign the loader functions of DDV to properly register the message callbacks
+*
+* Revision 1.11  1999/10/29 19:04:21  durand
+* move DDVUpdateMSG in objmgr.h
+*
+* Revision 1.10  1999/10/29 14:15:39  durand
+* add simple mouse selection functions
+*
+* Revision 1.9  1999/10/23 21:20:45  lewisg
+* move g_hParent to ddvopen.c
+*
+* Revision 1.8  1999/10/23 14:54:34  durand
+* resolve external symbol g_hParent
+*
+* Revision 1.7  1999/10/22 14:19:43  durand
+* update the code for the startup functions of DDV drawing panel
+*
+* Revision 1.6  1999/10/20 18:37:31  lewisg
+* add messagefunc for slave mode
+*
+* Revision 1.5  1999/10/20 13:17:18  durand
+* add display for disc. SeqAlign tails
+*
+* Revision 1.4  1999/10/16 15:02:25  durand
+* fixes due to toolkit build failed
+*
+* Revision 1.3  1999/10/15 21:57:36  durand
+* add a UI for display options
+*
+* Revision 1.2  1999/10/12 15:01:29  lewisg
+* resolve confict with internal/ddv
+*
+* Revision 1.1  1999/09/30 14:10:28  durand
+* add ddv to toolkit
+*
+* Revision 1.14  1999/09/30 13:38:10  durand
+* DDV_CreateDisplayFromIndex takes ParaG_Size as an argument
+*
+* Revision 1.13  1999/09/16 13:07:52  durand
+* add File|Close and File|Open|Network commands
+*
+* Revision 1.12  1999/09/09 21:55:06  durand
+* instantiate the Fle|Close command of DDV
+*
+* Revision 1.11  1999/09/02 17:36:07  durand
+* reconcile ddvopen.c
+*
+* Revision 1.10  1999/08/19 17:15:27  wheelan
+* added messages to indicate timing of index building vs color tables
+*
+* Revision 1.9  1999/08/04 18:02:12  wheelan
+* changes to support new seqalign indexing
+*
+* Revision 1.8  1999/07/29 12:43:07  durand
+* update DDV_GetAndCheckSeqAlign
+*
+* Revision 1.7  1999/07/20 17:18:23  durand
+* update DDV_GetAndCheckSeqAlign for PopSet Viewer
+*
+* Revision 1.6  1999/07/20 14:58:01  durand
+* use the Color Manager to display colored MSA
+*
+* Revision 1.5  1999/07/01 15:28:29  durand
+* validate function loaders of DDV
+*
+* Revision 1.2  1999/06/28 22:07:19  durand
+* add loader functions and clean the code with Lint and Purify
+*
+* Revision 1.1  1999/06/19 17:21:05  durand
+* add Vibrant DDV code
+*
+*
+*
+* ==========================================================================
+*/
+
+#include <ncbi.h>
+#include <vibrant.h>
+#include <salfiles.h>
+#include <pgppop.h>
+#include <udviewer.h>
+#include <ddvopen.h>
+#include <ddvpanel.h>
+#include <ddvmain.h>
+#include <ddvgraph.h>
+#include <ddvcreate.h>
+#include <objmgr.h>
+#include <gather.h>
+#include <ddvcolor.h>
+#include <samutil.h>
+#include <blast.h>
+#include <viewmgr.h>
+#include <actutils.h>
+
+/*extern WindoW g_hParent = NULL;*/
+static void DDV_RegisterMsgFuncOnBsp(Uint2 bsp_eID,DdvMainPtr dmp);
+
+static void DDV_Convert(ButtoN g);
+static void DDV_NoConvert(ButtoN g);
+
+/*local struct used only by the Download sequence dialog box*/
+	typedef struct ddvnetopen {
+		WindoW 			hWndMain;	/*main window*/
+		TexT			Entry;		/*Entrez entry*/
+		PopuP			AccessType;	/*database type*/
+		ButtoN  		ok;			/*ok button*/
+		UDVMainMenuPtr 	mmp;		/*main menu*/
+	} DDVNetOpen, PNTR DDVNetOpenPtr;
+
+
+/*******************************************************************************
+
+  Function : DDV_GetSelectedRegions()
+  
+  Purpose :  get the selected region(s) of one bioseq.
+  
+  Parameters :	om_ssp;list of selected regions (usually this field points to
+                  ObjMgr data)
+				bsp_eID,bsp_iID; bioseq identifiers.
+				    
+  Return value : list of selected regions on the bioseq bsp_eID,bsp_iID
+
+*******************************************************************************/
+extern ValNodePtr DDV_GetSelectedRegions(SelStructPtr om_ssp, Uint2 bsp_eID,
+	Uint2 bsp_iID)
+{
+SelStructPtr ssp;
+SeqLocPtr    slp,slp2;
+ValNodePtr   bsp_vnp=NULL,vnp;
+
+	if (om_ssp==NULL || bsp_eID==0 || bsp_iID==0) return(NULL);
+
+	ssp=om_ssp;
+	
+	while(ssp){
+		if (ssp->entityID==bsp_eID && ssp->itemID==bsp_iID && 
+			ssp->itemtype==OBJ_BIOSEQ && ssp->regiontype==OM_REGION_SEQLOC){
+			slp=(SeqLocPtr)ssp->region;
+			while(slp){
+				slp2=slp->next;
+				slp->next=NULL;
+				if (!bsp_vnp){
+					vnp=ValNodeAddPointer(NULL,0,(Pointer)slp);
+					if (!vnp) return(NULL);
+					bsp_vnp=vnp;
+				}
+				else{
+					vnp=ValNodeAddPointer(&vnp,0,(Pointer)slp);
+					if (!vnp){
+						if (bsp_vnp) ValNodeFree(bsp_vnp);
+						return(NULL);
+					}
+				}
+				slp->next=slp2;
+				slp=slp->next;
+			}
+		}
+		ssp=ssp->next;
+	}
+	return(bsp_vnp);
+}
+
+/*******************************************************************************
+
+  Function : DDV_IsLetterSelected()
+  
+  Purpose : check if a bsp_pos is selected (vnp_bsp is usually built with 
+      DDV_GetSelectedRegions() function)
+  
+  Return value : TRUE if bsp_pos is selected
+
+*******************************************************************************/
+extern Boolean DDV_IsLetterSelected(ValNodePtr vnp_bsp, Int4 bsp_pos)
+{
+Boolean    bSelected=FALSE;
+ValNodePtr vnp;
+SeqLocPtr  slp;
+Int4 bsp_start,bsp_stop;
+	if (vnp_bsp==NULL || bsp_pos==(Int4)-1) return(FALSE);
+
+	vnp=vnp_bsp;
+
+	while(vnp){
+		slp=(SeqLocPtr)vnp->data.ptrvalue;
+		bsp_start=SeqLocStart(slp);
+		bsp_stop=SeqLocStop(slp);
+		if (bsp_pos>=bsp_start && bsp_pos<=bsp_stop){
+			bSelected=TRUE;
+			break;
+		}
+		vnp=vnp->next;
+	}
+	
+	return(bSelected);
+}
+
+/*******************************************************************************
+
+  Function : DDV_CheckBSPEntitiesInPgp()
+  
+  Purpose : check if entityID,itemID Object is in the current paragraph
+  
+  Return value : TRUE if success
+
+*******************************************************************************/
+/*static Boolean DDV_CheckBSPEntities(Uint4Ptr entitiesTbl,Int4 nRowBsp,
+	Int4 nBsp,Uint2 eID,Uint2 iID)
+{
+Uint2     bsp_eID,bsp_iID;
+Int4      i;
+Boolean   bRet=FALSE;
+
+	for (i=0;i<nBsp;i++){
+		UDV_DecodeIdxFeat (entitiesTbl[i], &bsp_eID,&bsp_iID);
+	}
+	bsp=BioseqLockById(pgp->sip);
+	if (bsp){
+		bsp_eID=ObjMgrGetEntityIDForPointer((Pointer)bsp);
+		bsp_iID = GetItemIDGivenPointer (bsp_eID, 
+				OBJ_BIOSEQ, (Pointer) bsp);	
+	
+		if (bsp_eID==eID && bsp_iID==iID) bRet=TRUE;
+		BioseqUnlock(bsp);
+	}
+	return(bRet);
+}
+*/
+/*******************************************************************************
+
+  Function : DDV_CheckBSPEntitiesInDisplay()
+  
+  Purpose : check if entityID,itemID Object is in the current DDV display
+  
+  Return value : TRUE if object found
+
+*******************************************************************************/
+static Boolean DDV_CheckBSPEntitiesInDisplay(MsaParaGPopListPtr mpplp,
+		Uint2 entityID,Uint2 itemID)
+{
+Uint2     bsp_eID,bsp_iID;
+Int4      i;
+Boolean   bRet=FALSE;
+
+	/*scan the ParaG list to find the Bioseq*/
+	for (i=0;i<mpplp->nBsp;i++){
+		UDV_DecodeIdxFeat (mpplp->entitiesTbl[i], &bsp_eID,&bsp_iID);
+		if (bsp_eID==entityID && bsp_iID==itemID) {
+			bRet=TRUE;
+			break;
+		}
+	}
+	return(bRet);
+}
+
+/*******************************************************************************
+
+  Function : DDV_GetBspListGivenIDs()
+  
+  Purpose : analyse the ParaG struct and get a list of row(s) containing the
+         BSP identified by eID and iID
+  
+  Return value : list of row number (one-based values)
+
+*******************************************************************************/
+static Int4Ptr DDV_GetBspListGivenIDs(MsaParaGPopListPtr mpplp,
+		Uint2 entityID,Uint2 itemID,Int4Ptr nFound)
+{
+Int4       i;
+Int4Ptr    pList=NULL;
+Uint2     bsp_eID,bsp_iID;
+
+	*nFound=0;
+	
+	/*scan the ParaG list to find all the ref. of the Bioseq
+	(entityID,itemID) in the ParaG list*/
+	for (i=0;i<mpplp->nBsp;i++){
+		UDV_DecodeIdxFeat (mpplp->entitiesTbl[i], &bsp_eID,&bsp_iID);
+		if (bsp_eID==entityID && bsp_iID==itemID) {
+			if (!pList){
+				pList=(Int4Ptr)MemNew(sizeof(Int4));
+			}
+			else{
+				pList=(Int4Ptr)MemExtend((void *)pList, 
+					((*nFound)+1)*sizeof(Int4), (*nFound)*sizeof(Int4));
+			}
+			if (!pList) {*nFound=0;return(NULL);}
+
+
+			pList[*nFound]=i+1;
+			(*nFound)++;
+		}
+
+	}
+	return(pList);
+}
+
+/*******************************************************************************
+
+  Function : DDV_MSG_SELECT()
+  
+  Purpose : manage OM_MSG_SELECT & OM_MSG_DESELECT message
+  
+  Return value : OM_MSG_RET_OK if success
+
+*******************************************************************************/
+static Int2 DDV_MSG_SELECT(OMMsgStructPtr ommsp,Boolean IsSelectMsg)
+{
+DdvMainPtr    dmp;  /*DDV panel data*/
+OMUserDataPtr omudp;/*user data set when registering DDV panel*/
+Int4Ptr       bsp_List=NULL;
+ParaGPtr      pgp;
+
+Boolean       bRet;
+SeqLocPtr     slp;
+Int4          from_col,to_col,from_row,to_row,bsp_start,bsp_stop,nBspInstances=0,i,
+              row_num;
+
+	omudp = (OMUserDataPtr)(ommsp->omuserdata);
+	if (omudp == NULL) return(OM_MSG_RET_ERROR);
+
+	dmp=(DdvMainPtr)omudp->userdata.ptrvalue;
+	if (dmp == NULL) return(OM_MSG_RET_ERROR);
+
+	if (ommsp->itemtype != OBJ_BIOSEQ) return(OM_MSG_RET_OK);
+	if (ommsp->regiontype!=OM_REGION_SEQLOC) return(OM_MSG_RET_OK);
+
+	/*Am I concern by that Bioseq ?*/
+	bRet=DDV_CheckBSPEntitiesInDisplay(&(dmp->MSA_d.pgp_l),ommsp->entityID,
+		ommsp->itemID);
+	
+	if (bRet==FALSE) return(OM_MSG_RET_OK);  /* some other viewer */
+	
+	/*get the disp coord range*/
+	DDV_GetCurrentDispRange(dmp->hWndDDV,&(dmp->GrData),dmp->MSA_d.pgp_l.LengthAli,
+			&from_col,&to_col,&from_row,&to_row);
+
+	/*get the occurence(s) (row(s) #) for that bioseq*/
+	bsp_List=DDV_GetBspListGivenIDs(&(dmp->MSA_d.pgp_l),ommsp->entityID,
+		ommsp->itemID,&nBspInstances);
+
+	if (bsp_List==NULL || nBspInstances==0) return(OM_MSG_RET_ERROR);
+
+	/*scan the SeqLoc list to figure out if it's currently on the screen*/
+	slp=(SeqLocPtr)ommsp->region;
+	while(slp){/*for each SeqLoc, I try to see what region(s) has (have) to be
+		uptdated*/
+		for(i=0;i<nBspInstances;i++){
+			row_num=bsp_List[i]-1;
+			bsp_start=DDV_GetDispCoordGivenBspCoord(dmp->MSA_d.pgp_l.TableHead[row_num],
+				SeqLocStart(slp));
+			bsp_stop=DDV_GetDispCoordGivenBspCoord(dmp->MSA_d.pgp_l.TableHead[row_num],
+				SeqLocStop(slp));
+			if (bsp_start!=(Int4)-1 && bsp_stop!=(Int4)-1){
+				pgp=(ParaGPtr)(dmp->MSA_d.pgp_l.TableHead[row_num]->data.ptrvalue);
+
+				row_num=pgp->StartLine+
+
+						(pgp->ScaleStyle==SCALE_POS_NONE ? (Int4)0 : (Int4)1);
+
+				DDV_InvalRegion(dmp->hWndDDV,&(dmp->GrData),
+					_max_(bsp_start,from_col),_min_(bsp_stop,to_col),
+					row_num,IsSelectMsg);
+
+			}
+		}
+		slp=slp->next;
+	}
+	return(OM_MSG_RET_OK);
+}
+
+/*******************************************************************************
+
+  Function : DDV_MSG_UPDATE_CaretPos()
+  
+  Purpose : update the position of the caret (edit mode only)
+  
+  Return value : OM_MSG_RET_OK if success
+
+*******************************************************************************/
+static Int2 DDV_MSG_UPDATE_CaretPos(OMMsgStructPtr ommsp)
+{
+DdvMainPtr    dmp;  /*DDV panel data*/
+OMUserDataPtr omudp;/*user data set when registering DDV panel*/
+Boolean       bRet;
+Int4          from_col,to_col,from_row,to_row;
+
+	omudp = (OMUserDataPtr)(ommsp->omuserdata);
+	if (omudp == NULL) return(OM_MSG_RET_ERROR);
+
+	dmp=(DdvMainPtr)omudp->userdata.ptrvalue;
+	if (dmp == NULL) return(OM_MSG_RET_ERROR);
+	
+	/*Am I concern by that Bioseq ?*/
+	bRet=DDV_CheckBSPEntitiesInDisplay(&(dmp->MSA_d.pgp_l),ommsp->entityID,
+		ommsp->itemID);
+	
+	if (bRet==FALSE) return(OM_MSG_RET_ERROR);
+	
+	/*get the disp coord range*/
+	DDV_GetCurrentDispRange(dmp->hWndDDV,&(dmp->GrData),dmp->MSA_d.pgp_l.LengthAli,
+			&from_col,&to_col,&from_row,&to_row);
+	
+	/*switch to one-bsed value because dmp->dci values are one-based values*/
+	from_row++;
+	to_row++;
+	/*hide the caret from old coordinates*/
+	if (dmp->dci.old_col>=from_col && dmp->dci.old_col<=to_col &&
+		dmp->dci.old_row>=from_row && dmp->dci.old_row<=to_row){
+		DDV_InvalRegion(dmp->hWndDDV,&(dmp->GrData),
+			dmp->dci.old_col,dmp->dci.old_col+1,
+			dmp->dci.old_row,FALSE);
+	}
+	/*show caret on new coordinates*/
+	if (dmp->dci.new_col>=from_col && dmp->dci.new_col<=to_col &&
+		dmp->dci.new_row>=from_row && dmp->dci.new_row<=to_row){
+		DDV_InvalRegion(dmp->hWndDDV,&(dmp->GrData),
+			dmp->dci.new_col,dmp->dci.new_col+1,
+			dmp->dci.new_row,FALSE);
+	}
+    return(OM_MSG_RET_OK);
+}
+
+/*******************************************************************************
+
+  Function : DDV_MSG_UPDATE_DelBSP()
+  
+  Purpose : rebuilt a display after deletion of one BSP
+  
+  Return value : OM_MSG_RET_OK if success
+
+*******************************************************************************/
+static Int2 DDV_MSG_UPDATE_DelBSP(OMMsgStructPtr ommsp)
+{
+DdvMainPtr    dmp;  /*DDV panel data*/
+OMUserDataPtr omudp;/*user data set when registering DDV panel*/
+
+	omudp = (OMUserDataPtr)(ommsp->omuserdata);
+	if (omudp == NULL) return(OM_MSG_RET_ERROR);
+
+	dmp=(DdvMainPtr)omudp->userdata.ptrvalue;
+	if (dmp == NULL) return(OM_MSG_RET_ERROR);
+	
+    /*delete the current display*/
+	if (dmp->MSA_d.pgp_l.TableHead) 
+		DDV_DeleteDisplayList(&dmp->MSA_d.pgp_l);
+	if (dmp->MSA_d.pgp_l.RulerDescr) 
+		ValNodeFreeData(dmp->MSA_d.pgp_l.RulerDescr);
+	if (dmp->MSA_d.pgp_l.entitiesTbl) 
+		MemFree(dmp->MSA_d.pgp_l.entitiesTbl);
+	dmp->MSA_d.pgp_l.TableHead=NULL;
+	dmp->MSA_d.pgp_l.RulerDescr=NULL;
+	/*rebuild a new one*/
+	if (!DDV_CreateDisplayFromIndex(dmp->MSA_d.pgp_l.sap,
+		&(dmp->MSA_d.pgp_l),ParaG_Size,&(dmp->ddo))) 
+		return(OM_MSG_RET_ERROR);
+
+	dmp->MSA_d.pgp_l.entitiesTbl=
+		DDV_BuildBspEntitiesTbl(dmp->MSA_d.pgp_l.TableHead,
+			dmp->MSA_d.pgp_l.nBsp);
+	if (!dmp->MSA_d.pgp_l.entitiesTbl)
+		return(OM_MSG_RET_ERROR);	
+	/*build the Master Ruler descriptor*/
+/*	dmp->MSA_d.pgp_l.RulerDescr=DDV_ComputeRuler(dmp->MSA_d.pgp_l.sap,&(dmp->ddo)); */
+  dmp->MSA_d.pgp_l.RulerDescr = DDE_ReMakeRuler(&(dmp->MSA_d.pgp_l), FALSE, 0);
+
+	/*delete old tables*/
+    if(dmp->MasterViewer != SAMVIEWCN3D) {
+        DDV_ClearColor(dmp->Globals.colorp);
+        /*build new tables*/
+        if (!DDV_InitColour_When_Start(dmp->MSA_d.pgp_l.sap,
+            &(dmp->MSA_d.pgp_l),&(dmp->Globals.colorp), FALSE)){
+            dmp->ddo.bUseColors=FALSE;
+        }
+    }
+    
+    DDV_SortPGPLineNum(dmp->MSA_d.pgp_l.TableHead,dmp->MSA_d.pgp_l.nBsp);
+	DDV_WhatSize(dmp);
+	/* DDV_SetupWin(dmp->hWndDDV,TRUE,NULL); */
+    DDV_Resize_DDV(dmp->hWndDDV,TRUE); 
+	Update();
+
+    return(OM_MSG_RET_OK);
+}
+/*******************************************************************************
+
+  Function : DDV_MSG_UPDATE_ViewMgr()
+  
+  Purpose : rebuild a display after update message from the ViewMgr
+  
+  Return value : OM_MSG_RET_OK if success
+
+*******************************************************************************/
+static Int2 DDV_MSG_UPDATE_ViewMgr(OMMsgStructPtr ommsp)
+{
+DdvMainPtr    dmp;  /*DDV panel data*/
+OMUserDataPtr omudp;/*user data set when registering DDV panel*/
+BaR           hsb;
+Int4          HPos;
+
+	omudp = (OMUserDataPtr)(ommsp->omuserdata);
+	if (omudp == NULL) return(OM_MSG_RET_ERROR);
+
+	dmp=(DdvMainPtr)omudp->userdata.ptrvalue;
+	if (dmp == NULL) return(OM_MSG_RET_ERROR);
+
+  if (dmp->bEditor) return(OM_MSG_RET_OK);
+	
+  /* get the current column */
+  hsb = GetSlateHScrollBar((SlatE) dmp->hWndDDV);
+  HPos = GetBarValue(hsb);
+  
+  /*delete the current display*/
+	if (dmp->MSA_d.pgp_l.TableHead) 
+		DDV_DeleteDisplayList(&dmp->MSA_d.pgp_l);
+	if (dmp->MSA_d.pgp_l.RulerDescr) 
+		ValNodeFreeData(dmp->MSA_d.pgp_l.RulerDescr);
+	if (dmp->MSA_d.pgp_l.entitiesTbl) 
+		MemFree(dmp->MSA_d.pgp_l.entitiesTbl);
+	dmp->MSA_d.pgp_l.TableHead=NULL;
+	dmp->MSA_d.pgp_l.RulerDescr=NULL;
+	/*rebuild a new one*/
+	if (!DDV_CreateDisplayFromIndex(dmp->MSA_d.pgp_l.sap,
+		&(dmp->MSA_d.pgp_l),ParaG_Size,&(dmp->ddo))) 
+		return(OM_MSG_RET_ERROR);
+
+	dmp->MSA_d.pgp_l.entitiesTbl=
+		DDV_BuildBspEntitiesTbl(dmp->MSA_d.pgp_l.TableHead,
+			dmp->MSA_d.pgp_l.nBsp);
+	if (!dmp->MSA_d.pgp_l.entitiesTbl)
+		return(OM_MSG_RET_ERROR);
+
+	/* build the Master Ruler descriptor */
+  /* Patrick's ComputeRuler isn't working right, so I substituted mine -- Dave H. */
+  /* dmp->MSA_d.pgp_l.RulerDescr=DDV_ComputeRuler(dmp->MSA_d.pgp_l.sap,&(dmp->ddo)); */
+  dmp->MSA_d.pgp_l.RulerDescr = DDE_ReMakeRuler(&(dmp->MSA_d.pgp_l), FALSE, 0);
+
+	/*delete old tables*/
+    if(dmp->MasterViewer != SAMVIEWCN3D) {
+        DDV_ClearColor(dmp->Globals.colorp);
+        /*build new tables*/
+        if (!DDV_InitColour_When_Start(dmp->MSA_d.pgp_l.sap,
+            &(dmp->MSA_d.pgp_l),&(dmp->Globals.colorp), FALSE)){
+            dmp->ddo.bUseColors=FALSE;
+        }
+    }
+    
+  DDV_SortPGPLineNum(dmp->MSA_d.pgp_l.TableHead,dmp->MSA_d.pgp_l.nBsp);
+	DDV_WhatSize(dmp);
+	DDV_Resize_DDV(dmp->hWndDDV,TRUE); /* DDV_SetupWin(dmp->hWndDDV,TRUE,NULL); */
+
+  /* put col back to where it was */
+  SetValue(hsb, HPos);
+
+	Update();
+
+    return(OM_MSG_RET_OK);
+}
+
+/*******************************************************************************
+
+  Function : DDV_MSG_UPDATE_Layout()
+  
+  Purpose : manage the OM_MSG_UPDATE message
+  
+  Return value : OM_MSG_RET_OK if success
+
+*******************************************************************************/
+static Int2 DDV_MSG_UPDATE_Layout(PaneL hWndDDV, DDVUpdateLayoutDataPtr dumdp)
+{
+DdvMainPtr  dmp;
+Int4        j;
+Boolean     bResetScrolls=FALSE,
+			bRebuildDisplay=FALSE,
+			bSwitchColors=FALSE,
+			bUpdateColors=FALSE;
+Uint1       oldSpacerSize;
+
+	if (!hWndDDV || !dumdp)
+		return(OM_MSG_RET_OK);
+	
+	dmp = (DdvMainPtr) GetObjectExtra(hWndDDV);
+	
+	if (!dmp)
+		return(OM_MSG_RET_OK);
+
+	if (!Visible(hWndDDV))
+		return(OM_MSG_RET_OK);
+	
+	oldSpacerSize=dmp->ddo.SpacerSize;
+	dmp->ddo.SpacerSize=dumdp->SpacerSize;
+
+	/*rebuild the display, if needed*/	
+	if ((dmp->ddo.DispDiscStyle!=dumdp->DispDiscStyle) ||
+		(oldSpacerSize!=dumdp->SpacerSize) ||
+		(dmp->ddo.DiscJustification!=dumdp->DiscJustification) ||
+		(dmp->ddo.ShowLeftTail!=dumdp->ShowLeftTail)||
+		(dmp->ddo.ShowRightTail!=dumdp->ShowRightTail)){
+		
+		if((dmp->ddo.ShowLeftTail!=dumdp->ShowLeftTail)||
+			(dmp->ddo.ShowRightTail!=dumdp->ShowRightTail)||
+			(dmp->ddo.DispDiscStyle!=dumdp->DispDiscStyle)){
+			bUpdateColors=TRUE;
+		}
+		/*update the styles*/
+		dmp->ddo.DispDiscStyle=dumdp->DispDiscStyle;
+		dmp->ddo.DiscJustification=dumdp->DiscJustification;
+		dmp->ddo.ShowLeftTail=dumdp->ShowLeftTail;
+		dmp->ddo.ShowRightTail=dumdp->ShowRightTail;
+		
+		/*delete the current display*/
+		if (dmp->MSA_d.pgp_l.TableHead) 
+			DDV_DeleteDisplayList(&dmp->MSA_d.pgp_l);
+		if (dmp->MSA_d.pgp_l.RulerDescr) 
+			ValNodeFreeData(dmp->MSA_d.pgp_l.RulerDescr);
+		if (dmp->MSA_d.pgp_l.entitiesTbl) 
+			MemFree(dmp->MSA_d.pgp_l.entitiesTbl);
+
+		dmp->MSA_d.pgp_l.TableHead=NULL;
+		dmp->MSA_d.pgp_l.RulerDescr=NULL;
+		/*rebuild a new one*/
+		if (!DDV_CreateDisplayFromIndex(dmp->MSA_d.pgp_l.sap,
+			&(dmp->MSA_d.pgp_l),ParaG_Size,&(dmp->ddo))) 
+			return(OM_MSG_RET_ERROR);
+
+		dmp->MSA_d.pgp_l.entitiesTbl=
+			DDV_BuildBspEntitiesTbl(dmp->MSA_d.pgp_l.TableHead,
+				dmp->MSA_d.pgp_l.nBsp);
+		if (!dmp->MSA_d.pgp_l.entitiesTbl)
+			return(OM_MSG_RET_ERROR);	
+		/*build the Master Ruler descriptor*/
+/*		dmp->MSA_d.pgp_l.RulerDescr=DDV_ComputeRuler(dmp->MSA_d.pgp_l.sap,&(dmp->ddo));  */
+    dmp->MSA_d.pgp_l.RulerDescr = DDE_ReMakeRuler(&(dmp->MSA_d.pgp_l), FALSE, 0);
+
+		/*init the colours*/
+		if(bUpdateColors){
+            if(dmp->MasterViewer != SAMVIEWCN3D ) {
+                /*delete old tables*/
+                DDV_ClearColor(dmp->Globals.colorp);
+                /*build new tables*/
+                if (!DDV_InitColour_When_Start(dmp->MSA_d.pgp_l.sap,
+                    &(dmp->MSA_d.pgp_l),&(dmp->Globals.colorp),FALSE)){
+                    dmp->ddo.bUseColors=FALSE;
+                }
+            }
+        }
+        bResetScrolls=TRUE;
+		bRebuildDisplay=TRUE;
+	}
+
+	/*set the ruler styles*/
+	if(dumdp->nSeq && dumdp->SeqList){
+		for(j=0;j<dumdp->nSeq;j++){
+			switch(dumdp->RulerStyle){
+				case SCALE_POS_TOP:
+					DDV_SetRulerAttribInPGP(dmp->MSA_d.pgp_l.TableHead[dumdp->SeqList[j]-1], 
+							SCALE_POS_TOP);
+					break;
+				case SCALE_POS_NONE:
+					DDV_SetRulerAttribInPGP(dmp->MSA_d.pgp_l.TableHead[dumdp->SeqList[j]-1], 
+							SCALE_POS_NONE);
+					break;
+				default:
+					DDV_SetRulerAttribInPGP(dmp->MSA_d.pgp_l.TableHead[dumdp->SeqList[j]-1], 
+							SCALE_POS_NONE);
+					break;
+			}			
+		}
+		bRebuildDisplay=TRUE;
+	}
+
+	/*colors*/
+	if(dmp->ddo.bUseColors!=dumdp->bUseColors){
+		dmp->ddo.bUseColors=dumdp->bUseColors;
+		bSwitchColors=TRUE;
+	}
+
+	/*redraw if needed*/
+	if (bRebuildDisplay){
+	    DDV_SortPGPLineNum(dmp->MSA_d.pgp_l.TableHead,dmp->MSA_d.pgp_l.nBsp);
+	    DDV_WhatSize(dmp);
+	    DDV_Resize_DDV(hWndDDV,bResetScrolls); /* DDV_SetupWin(hWndDDV,bResetScrolls,NULL);*/
+	    Update();
+	}
+	else if (bSwitchColors){
+		RecT   rcP;
+		WindoW temport;
+		
+		temport=SavePort(ParentWindow(hWndDDV));
+		Select(hWndDDV);
+		
+		ObjectRect(hWndDDV,&rcP);
+		InvalRect(&rcP);
+		RestorePort(temport);
+		/*Update();*/
+	}
+
+
+	return(OM_MSG_RET_OK);
+}
+
+/*******************************************************************************
+
+  Function : DDV_MSG_FLUSH()
+  
+  Purpose : kill the viewer in response to a OM_MSG_FLUSH message
+  
+  Return value : OM_MSG_RET_OK if success
+
+*******************************************************************************/
+static Int2 DDV_MSG_FLUSH(OMMsgStructPtr ommsp)
+{
+DdvMainPtr    dmp;  /*DDV panel data*/
+OMUserDataPtr omudp;/*user data set when registering DDV panel*/
+/*ParaGPtr pgp;
+BioseqPtr bsp;
+Int4 i;
+Uint2 bsp_eID;*/
+
+
+	omudp = (OMUserDataPtr)(ommsp->omuserdata);
+	if (omudp == NULL) return(OM_MSG_RET_ERROR);
+
+	dmp=(DdvMainPtr)omudp->userdata.ptrvalue;
+	if (dmp == NULL) return(OM_MSG_RET_ERROR);
+	
+    if (dmp->MSA_d.entityID==ommsp->entityID &&
+        ((dmp->MSA_d.itemID==ommsp->itemID && ommsp->itemtype==OBJ_SEQALIGN)
+        ||(ommsp->itemID == 0 && ommsp->itemtype==0))){
+        Remove(dmp->hParent);
+        DDV_CleanupDDVPdata_g(dmp);
+       /* for(i=0;i<dmp->MSA_d.pgp_l.nBsp;i++){
+            pgp=(ParaGPtr)(dmp->MSA_d.pgp_l.TableHead[i]->data.ptrvalue);
+            bsp=BioseqLockById(pgp->sip);
+            if (bsp != NULL){
+                bsp_eID=ObjMgrGetEntityIDForPointer((Pointer)bsp);
+                BioseqUnlock(bsp);
+                if (bsp_eID>0 && bsp_eID!=dmp->MSA_d.entityID){
+                    ObjMgrFreeUserData(bsp_eID,dmp->procid,dmp->proctype,dmp->userkey);
+                }
+            }
+        }
+        
+        ObjMgrFreeUserData(dmp->MSA_d.entityID,dmp->procid,dmp->proctype,dmp->userkey);*/
+    }
+	return(OM_MSG_RET_OK);
+}
+
+/*******************************************************************************
+
+  Function : DDV_SimpleUpdateAnswer()
+  
+  Purpose : simple answer to an Update Msg; just redraw the window
+  
+  Parameters : see Toolkit
+  
+  Return value : see Toolkit 
+
+*******************************************************************************/
+static void DDV_SimpleUpdateAnswer(OMMsgStructPtr ommsp)
+{		            
+RecT   rcP;
+WindoW temport;
+DdvMainPtr    dmp;  /*DDV panel data*/
+OMUserDataPtr omudp;/*user data set when registering DDV panel*/
+
+	omudp = (OMUserDataPtr)(ommsp->omuserdata);
+	if (omudp == NULL) return;
+
+	dmp=(DdvMainPtr)omudp->userdata.ptrvalue;
+	if (dmp == NULL) return;
+	
+	temport=SavePort(ParentWindow(dmp->hWndDDV));
+	Select(dmp->hWndDDV);
+	
+	ObjectRect(dmp->hWndDDV,&rcP);
+	InvalRect(&rcP);
+	RestorePort(temport);
+}
+
+/*******************************************************************************
+
+  Function : DDV_UpdateRegMsgFunc()
+  
+  Purpose : register a MsgCallback in response to an OM_MSG_UPDATE, after 
+          SeqImport
+  
+*******************************************************************************/
+static void DDV_UpdateRegMsgFunc(OMMsgStructPtr ommsp,Uint2 bsp_eID)
+{
+DdvMainPtr    dmp;  /*DDV panel data*/
+OMUserDataPtr omudp;/*user data set when registering DDV panel*/
+
+	omudp = (OMUserDataPtr)(ommsp->omuserdata);
+	if (omudp == NULL) return;
+
+	dmp=(DdvMainPtr)omudp->userdata.ptrvalue;
+	if (dmp == NULL) return;
+
+	DDV_RegisterMsgFuncOnBsp(bsp_eID,dmp);		
+}
+
+/*******************************************************************************
+
+  Function : DDV_OM_MsgFunc()
+  
+  Purpose : ObjMgr message loop of the DDV viewer/editor
+  
+  Parameters : see Toolkit
+  
+  Return value : see Toolkit 
+
+*******************************************************************************/
+static Int2 LIBCALLBACK DDV_OM_MsgFunc (OMMsgStructPtr ommsp)
+{
+Int2 nRet=OM_MSG_RET_OK;
+  
+	switch (ommsp->message)
+	{
+		case OM_MSG_DEL:
+			break;
+		case OM_MSG_CREATE:
+			break;
+		case OM_MSG_UPDATE:{
+			DDVUpdateMSGPtr        dump;
+			
+			dump = (DDVUpdateMSGPtr)(ommsp->procmsgdata);
+			
+			/*generic UPDATE msg*/
+			if (!dump){
+				DDV_SimpleUpdateAnswer(ommsp);
+				break;
+			}
+
+			/*specific UPDATE msg*/
+            switch(dump->type){
+                case UPDATE_TYPE_LAYOUT:{
+                    DDVUpdateLayoutDataPtr dumdp;
+                
+                    dumdp=(DDVUpdateLayoutDataPtr)dump->data;
+                
+                    if (!dumdp)
+                        break;
+                
+                    nRet=DDV_MSG_UPDATE_Layout(dumdp->ddv_panel,dumdp);
+                    break;
+                }
+                case UPDATE_TYPE_EDIT_DELBSP:
+                    nRet=DDV_MSG_UPDATE_DelBSP(ommsp);
+                    break;
+                case UPDATE_TYPE_VIEWMGR:
+                    nRet=DDV_MSG_UPDATE_ViewMgr(ommsp);
+                    break;
+				case UPDATE_TYPE_CARETPOS:
+					nRet=DDV_MSG_UPDATE_CaretPos(ommsp);
+					break;
+                case UPDATE_TYPE_NEWSEQ:
+					if (dump->data)
+						DDV_UpdateRegMsgFunc(ommsp,*((Uint2 *)dump->data));
+					break;
+				default :
+					DDV_SimpleUpdateAnswer(ommsp);
+            }
+			
+			break;
+		}
+		case OM_MSG_SELECT:
+			nRet=DDV_MSG_SELECT(ommsp,TRUE);
+			break;
+		case OM_MSG_DESELECT:
+			nRet=DDV_MSG_SELECT(ommsp,FALSE);
+			break;
+		case OM_MSG_CACHED:
+			break;
+		case OM_MSG_UNCACHED:
+			break;
+		case OM_MSG_TO_CLIPBOARD:
+			break;
+		case OM_MSG_SETCOLOR:
+			break;
+		case OM_MSG_FLUSH:
+			DDV_MSG_FLUSH(ommsp);
+			break;
+		default:
+			break;
+	}
+
+	return (nRet);
+}
+
+/*******************************************************************************
+
+  Function : DDV_RegisterMsgFuncOnBsp()
+  
+  Purpose : register a MsgFunc for a bsp. 
+  
+*******************************************************************************/
+static void DDV_RegisterMsgFuncOnBsp(Uint2 bsp_eID,DdvMainPtr dmp)
+{
+OMUserDataPtr omudp;
+
+	if (bsp_eID==0 || dmp==NULL) return;
+	
+    omudp = ObjMgrAddUserData (bsp_eID,dmp->procid,dmp->proctype,dmp->userkey);
+    if (omudp != NULL) {
+    	omudp->messagefunc = DDV_OM_MsgFunc;
+		omudp->userdata.ptrvalue = (Pointer)dmp;
+	}
+}
+
+/*******************************************************************************
+
+  Function : DDV_RegMsgFuncForBsp()
+  
+  Purpose : given the display data structure (nBsp & TableHead), register a
+            MsgFunc callback for each bioseq of a SeqAlign.
+  
+  Parameters : TableHead; entry point of the display data structure (ParaG list)
+			   nBsp; number of sequences in the SeqAlign
+			   master_eID; entityID of the object containing the SeqAlign
+			   procID; identifier of the viewer (usually DDV)
+			   userkey; userkey of the viewer (usually DDV)
+			   
+  Return value : -
+
+*******************************************************************************/
+static void DDV_RegMsgFuncForBsp(ValNodePtr PNTR TableHead,DdvMainPtr dmp,Int4 nBsp, 
+	Uint2 master_eID, Uint2 procID, Uint2 procType, Uint2 userkey)
+{
+OMUserDataPtr omudp,omudp_tmp;
+ParaGPtr      pgp;
+BioseqPtr     bsp;
+Int4          i;
+Boolean       bFound;
+Uint2         bsp_eID;
+
+	if (!TableHead || nBsp==0 || master_eID==0 || procID==0 
+		|| procType==0 ||userkey==0) return;
+		
+	for(i=0;i<nBsp;i++){
+		pgp=(ParaGPtr)(dmp->MSA_d.pgp_l.TableHead[i]->data.ptrvalue);
+		bsp=BioseqLockById(pgp->sip);
+		if (bsp){
+			bsp_eID=ObjMgrGetEntityIDForPointer((Pointer)bsp);
+			if (bsp_eID>0 && bsp_eID!=master_eID){
+				omudp=ObjMgrGetUserData(bsp_eID,procID,procType,userkey);
+				if (omudp){
+					/*scan the user data associated with that bioseq and try to
+					find if a Msg Func is already attached for DDV*/
+					omudp_tmp=omudp;
+					bFound=FALSE;
+					while(omudp_tmp){
+						if (omudp_tmp->procid==procID && 
+							omudp_tmp->proctype==procType && 
+							omudp_tmp->userkey==userkey && 
+							omudp_tmp->messagefunc==DDV_OM_MsgFunc){
+							
+							bFound=TRUE;
+							break;
+						}
+						omudp_tmp=omudp_tmp->next;
+					}
+				}
+				else{/*add the Msg Callaback and DDV main data block to the bioseq*/
+					bFound=FALSE;
+				}
+				if (bFound==FALSE){
+					DDV_RegisterMsgFuncOnBsp(bsp_eID,dmp);
+				}
+			}
+			BioseqUnlock(bsp);
+		}
+	}
+}
+
+static void DDV_Convert(ButtoN g) {
+/*----------------------------------------------------------------------------
+*  just need to quit the pop-up window
+*---------------------------------------------------------------------------*/
+  WindoW  hDialog;
+
+	hDialog = (WindoW)ParentWindow(g);
+	if (!hDialog) return;
+	Remove(hDialog);
+  return;
+}
+
+
+static void DDV_NoConvert(ButtoN g) {
+/*----------------------------------------------------------------------------
+*  quit the pop-up window and close the file
+*---------------------------------------------------------------------------*/
+  WindoW         hDialog;
+  DdvMainPtr     dmp;
+
+	hDialog = (WindoW)ParentWindow(g);
+	if (!hDialog) return;
+	Remove(hDialog);
+
+  dmp = (DdvMainPtr) GetObjectExtra(hDialog);
+  DDV_FileCloseIt(dmp->hParent);
+  return;
+}
+
+
+/*******************************************************************************
+
+  Function : DDV_StartPanel_Slave()
+  
+  Purpose : start DDV main window as a slave module: init 'dmp' data structure
+  			(if needed), create the DDV panel, prepare a display from 'sap'.
+  
+  Parameters : 	sap; pointer to a SeqAlign
+  				input_entityID,input_itemID; identity of the SeqAlign
+  				dmp; main data of DDV. May be NULL
+				hParent; parent window for DDV. Must not be NULL
+  				bSetAppProp; if TRUE, use SetAppProperty().
+				bInitGraph; if TRUE, initialize the graphical data for DDV
+				bEditor; if TRUE, start the editor mode. Otherwise, a simple
+						viewer will ba started
+                rcPp; the RecT that defines the size of the panel.  can be NULL.
+						
+  Note :  This function assumes that DDV will be placed inside an existing 
+     parent window provided by the host application.
+	 
+  Return value : handle to the DDV panel
+
+*******************************************************************************/
+static Boolean DDV_StartPanel_Slave(DdvMainPtr dmp, SeqAlignPtr sap,
+		Uint2* pInput_entityID, Uint2* pInput_itemID, Boolean bEditor)
+{
+DDV_ColorGlobal * dcgp;
+MsaParaGPopListPtr  mpplp;
+BaR  hsb;
+Int4  HPos, Col, IsEditable;
+DdvMainWinPtr  mWin_d;
+Boolean*   pNoGaps;
+Boolean    NoGaps;
+char       Str[1024];
+MsgAnswer  Answer;
+Boolean    Attached = FALSE;
+  
+  WatchCursor();
+
+  if (!dmp->bEditor) {
+    mWin_d = (DdvMainWinPtr) GetObjectExtra(dmp->hParent);
+    Enable(mWin_d->MainMenu.LaunchEditor);
+    IsEditable = AlnMgrIsEditable(sap);
+    if (!IsEditable) {
+      if (AlnMgrIsIBMable(sap)) {
+        Str[0] = 0;
+        StringCat(Str, "This file is a multiple pairwise alignment.\n");
+        StringCat(Str, "To edit this file, it needs to be converted\n");
+        StringCat(Str, "to a true multiple alignment.\n");
+        StringCat(Str, "Should it be converted?");
+        mWin_d->Show_logo=TRUE;
+        Answer = Message(MSG_YN, "%s", Str);
+        mWin_d->Show_logo=FALSE;
+        if (Answer == ANS_YES) {
+          if (ViewMgr_Attach(sap, TRUE, TRUE, *pInput_entityID, *pInput_itemID) < 1)
+            return (FALSE);
+          Attached = TRUE;
+        }
+        else {
+          Disable(mWin_d->MainMenu.LaunchEditor);
+        }
+      }
+    }
+    else if (IsEditable == AM_EDITGAPS) {
+      pNoGaps = (Boolean*) GetAppProperty("dde_nogaps");
+      if (pNoGaps == NULL) NoGaps = TRUE;
+      else NoGaps = *pNoGaps;
+      if (NoGaps) {
+        Str[0] = 0;
+        StringCat(Str, "This alignment can't be edited\n");
+        StringCat(Str, "because it has aligned gaps\n");
+        StringCat(Str, "and DDV is running in NoGaps mode");
+        Message(MSG_OK, "%s", Str);
+        Disable(mWin_d->MainMenu.LaunchEditor);
+      }
+    }
+  }
+
+  if (!Attached) {
+    if (ViewMgr_Attach(sap, FALSE, FALSE, *pInput_entityID, *pInput_itemID) < 1)
+      return (FALSE);
+  }
+	
+	/*if we have a NULL SeqAlign, switch the display style to show
+	the sequences, not a spacer*/
+	if (AlnMgrIsSAPNULL(sap)){
+		dmp->ddo.DispDiscStyle=MSA_TXT_STYLE_2;
+		dmp->ddo.SpacerSize=SPACER_TXT_BLANK;
+    	dmp->ddo.DiscJustification=DISP_JUST_LEFT;
+	}
+
+  if (bEditor) {
+    dmp->dsp = (DDE_StackPtr) GetAppProperty("ddeinterndata");
+    if (dmp->dsp == NULL) {return(FALSE);}
+    mpplp = dmp->dsp->pEdit->pPopList;
+    /* copy paragraphs from DDE_Stack into the ones that are displayed */
+    MemCopy(&(dmp->MSA_d.pgp_l),mpplp,sizeof(MsaParaGPopList));
+  }
+  else {
+	  if (!DDV_CreateDisplayFromIndex(sap,&(dmp->MSA_d.pgp_l),ParaG_Size,
+		  &(dmp->ddo))) return(FALSE);
+	  dmp->MSA_d.pgp_l.entitiesTbl=
+		  DDV_BuildBspEntitiesTbl(dmp->MSA_d.pgp_l.TableHead,
+		  dmp->MSA_d.pgp_l.nBsp);
+	  if (!dmp->MSA_d.pgp_l.entitiesTbl) return(FALSE);
+	  /*build the Master Ruler descriptor*/
+/*	  dmp->MSA_d.pgp_l.RulerDescr=DDV_ComputeRuler(sap,&(dmp->ddo));  */
+    dmp->MSA_d.pgp_l.RulerDescr = DDE_ReMakeRuler(&(dmp->MSA_d.pgp_l), FALSE, 0);
+  }
+
+	dmp->MSA_d.entityID=*pInput_entityID;
+	dmp->MSA_d.itemID=*pInput_itemID;
+
+/*
+#if defined(_DEBUG_DDE)
+{
+  MsaParaGPopListPtr  mpplp;
+  mpplp = DDV_CreateDataForEditor(&(dmp->MSA_d.pgp_l), 0, dmp->MSA_d.pgp_l.LengthAli-1);
+	MemCopy(&(dmp->MSA_d.pgp_l),mpplp,sizeof(MsaParaGPopList));
+  dmp->dsp = DDE_NewStack(mpplp);
+}
+#endif
+*/
+
+	/*get the color stuff from the sap object. Usually I can do that
+	when DDV is loaded from Cn3D*/
+	dcgp=DDV_GetColorGlobal((Pointer) sap);
+
+	/*init the colours*/
+	if (dcgp==NULL){
+		if (!DDV_InitColour_When_Start(dmp->MSA_d.pgp_l.sap,&(dmp->MSA_d.pgp_l),
+			&(dmp->Globals.colorp),FALSE)){
+			dmp->ddo.bUseColors=FALSE;
+		}
+	}
+    else dmp->Globals.colorp = dcgp;        
+
+	/*set the initial position of the caret (edit mode)*/
+	dmp->dci.old_row=1;
+	dmp->dci.new_row=1;
+	dmp->dci.old_col=0;
+	dmp->dci.new_col=0;
+	
+
+	/*relation between align size and display type; compute nTotLines for example*/
+	DDV_WhatSize(dmp);
+
+	ArrowCursor();
+	DDV_Resize_DDV(dmp->hWndDDV,TRUE); /*DDV_SetupWin (dmp->hWndDDV,TRUE,NULL); */
+	/*Update();*/
+
+  CaptureSlateFocus((SlatE)dmp->hWndDDV);
+
+  /* scroll display horizontally so aligned region is shown at position 5 */
+  if (DDE_GetNumBlocks2(&(dmp->MSA_d.pgp_l))) {
+    hsb = GetSlateHScrollBar((SlatE) dmp->hWndDDV);
+    HPos = GetBarValue(hsb);
+    if (bEditor) {
+      Col = DDE_GetAlignStart(dmp->dsp->pEdit, 0);
+    }
+    else {
+      Col = 0;
+      if (dmp->ddo.ShowLeftTail) {
+        Col = AlnMgrGetMaxTailLength(sap, LEFT_TAIL);
+      }
+    }
+    SetValue(hsb, HPos+Col-5);
+  }
+
+  /* only enable left/right/center justify for an unaligned region in the editor */
+  if (bEditor) {
+    mWin_d = (DdvMainWinPtr) GetObjectExtra(dmp->hParent);
+    if (dmp->dsp->IsUnAligned) {
+      Enable(mWin_d->MainMenu.Justify);
+    }
+    else {
+      Disable(mWin_d->MainMenu.Justify);
+    }
+  }
+
+	return(TRUE);
+}
+
+
+/*******************************************************************************
+
+  Function : DDV_ObjRegMasterDDV()
+  
+  Purpose : call by ObjMgr to start DDV panel
+  
+  Parameters : see Toolkit
+  
+  Note : this callback is only used by the standalone DDV. Never use this
+         callback for other purpose.
+  
+  Return value : see Toolkit 
+
+*******************************************************************************/
+static Int2 DDV_ObjRegMasterDDV (Pointer data,Boolean bEditor)
+{
+OMProcControlPtr    ompcp;
+SeqAlignPtr			sap=NULL;
+OMUserDataPtr       omudp;
+DdvMainPtr          dmp;
+
+	/*retrieve data*/
+	ompcp = (OMProcControlPtr) data;
+
+	if (ompcp == NULL || ompcp->proc == NULL) {
+		ErrPostEx (SEV_ERROR, 0, 0, "Data NULL [1]");
+		return OM_MSG_RET_ERROR;
+	}
+	/*only accept a SeqALign*/
+	switch (ompcp->input_itemtype) {
+		case OBJ_SEQALIGN :
+			sap = (SeqAlignPtr) ompcp->input_data;
+			break;
+		default :
+			return OM_MSG_RET_ERROR;
+	}
+	/*oups... nothing to deal with*/
+	if (sap == NULL) {
+		ErrPostEx (SEV_ERROR, 0, 0, "Data NULL [2]");
+		return OM_MSG_RET_ERROR;
+	}
+	
+	dmp = (DdvMainPtr) GetAppProperty("ddvinterndata");
+	if (!dmp) goto error;
+	if (!DDV_StartPanel_Slave(dmp, sap, &ompcp->input_entityID,
+		&ompcp->input_itemID, bEditor)) goto error;
+	
+	
+	/*attach a Msg Func on the current seqalign*/
+	dmp->userkey=OMGetNextUserKey();
+	dmp->procid=ompcp->proc->procid;
+	dmp->proctype=ompcp->proc->proctype;
+    omudp = ObjMgrAddUserData (ompcp->input_entityID, ompcp->proc->procid, 
+		(bEditor==TRUE ? OMPROC_EDIT : OMPROC_VIEW),dmp->userkey);
+    if (omudp == NULL) 
+		goto error;
+    omudp->messagefunc =  DDV_OM_MsgFunc;
+	omudp->userdata.ptrvalue = (Pointer)dmp;
+
+	/*attach a Msg Func on each Bioseq of the current seqalign*/
+	DDV_RegMsgFuncForBsp(dmp->MSA_d.pgp_l.TableHead,dmp,dmp->MSA_d.pgp_l.nBsp, 
+		ompcp->input_entityID, dmp->procid,dmp->proctype,dmp->userkey);
+
+	DDV_EnableGotoTBItems(dmp->hParent,TRUE);
+	return(OM_MSG_RET_DONE);
+
+error:
+	/*show the logo window*/
+	/*mWin_d->Show_logo=TRUE;*/
+	Update ();
+	ArrowCursor();
+	return(OM_MSG_RET_ERROR);
+}
+
+/*******************************************************************************
+
+  Function : DDV_ObjRegMasterEditDDV()
+  
+  Purpose : call by ObjMgr to start DDV as a standalone editor
+  
+  Parameters : see Toolkit
+  
+  Return value : see Toolkit 
+
+*******************************************************************************/
+extern Int2 LIBCALLBACK DDV_ObjRegMasterEditDDV (Pointer data)
+{
+	return(DDV_ObjRegMasterDDV(data,TRUE));
+}
+
+/*******************************************************************************
+
+  Function : DDV_ObjRegMasterViewDDV()
+  
+  Purpose : call by ObjMgr to start DDV as a standalone viewer
+  
+  Parameters : see Toolkit
+  
+  Return value : see Toolkit 
+
+*******************************************************************************/
+extern Int2 LIBCALLBACK DDV_ObjRegMasterViewDDV (Pointer data)
+{
+	return(DDV_ObjRegMasterDDV(data,FALSE));
+}
+
+
+/*******************************************************************************
+
+  Function : DDV_ObjRegSlaveDDV()
+  
+  Purpose : call by DDV_ObjRegSlaveEditDDV() & DDV_ObjRegSlaveViewDDV(), below
+  
+*******************************************************************************/
+static Int2 DDV_ObjRegSlaveDDV(Pointer data,Boolean bEditor)
+{
+OMProcControlPtr    ompcp;
+SeqAlignPtr			sap=NULL;
+WindoW              hParent=NULL;
+DdvMainWinPtr 		mWin_d;
+OMUserDataPtr       omudp = NULL;
+DdvMainPtr          dmp;
+SAM_ViewGlobal      *vgp;
+
+
+	/*retrieve data*/
+	ompcp = (OMProcControlPtr) data;
+    if (ompcp == NULL || ompcp->proc == NULL) {
+		ErrPostEx (SEV_ERROR, 0, 0, "Data NULL [1]");
+		return OM_MSG_RET_ERROR;
+	}
+
+	/*only accept a SeqALign*/
+	switch (ompcp->input_itemtype) {
+		case OBJ_SEQALIGN :
+			sap = (SeqAlignPtr) ompcp->input_data;
+			break;
+		default :
+			return OM_MSG_RET_ERROR;
+	}
+
+	/*oups... nothing to deal with*/
+	if (sap == NULL) {
+		ErrPostEx (SEV_ERROR, 0, 0, "Data NULL [2]");
+		return OM_MSG_RET_ERROR;
+	}
+        
+	/*start the slave module*/
+    /* get parameters from launching program */
+    vgp = GetAppProperty(SAM_ViewString);
+    if(vgp == NULL) hParent=DDV_StartMainWin_Slave(NULL,bEditor);
+    else hParent=DDV_StartMainWin_Slave(vgp,bEditor);
+
+	if (hParent){
+		RealizeWindow(hParent);
+        Show(hParent);
+        mWin_d=(DdvMainWinPtr)GetObjectExtra(hParent);
+        dmp = (DdvMainPtr) GetObjectExtra(mWin_d->hWndDDV);
+        if(vgp != NULL) dmp->MasterViewer = vgp->MasterViewer;
+
+        if(dmp->MasterViewer == SAMVIEWCN3D) {
+            mWin_d->UseNetwork = TRUE;
+            mWin_d->NetStartProc = vgp->NetStartProc;
+        }
+        
+        if (!DDV_StartPanel_Slave(dmp, sap, &ompcp->input_entityID,
+            &ompcp->input_itemID, bEditor)) 
+            goto error;
+        
+		/*when the user will close DDV, DDV won't delete any data excepts
+		its internal data structure*/
+		dmp->dod.choice=DDV_OPENTYPE_NOTRESP;
+		
+		/*attach a Msg Func on the current seqalign*/
+		dmp->userkey=OMGetNextUserKey();
+		dmp->procid=ompcp->proc->procid;
+		dmp->proctype=ompcp->proc->proctype;
+    	omudp = ObjMgrAddUserData (ompcp->input_entityID, ompcp->proc->procid, 
+			(bEditor==TRUE ? OMPROC_EDIT : OMPROC_VIEW),dmp->userkey);
+    	if (omudp == NULL) 
+			goto error;
+    	omudp->messagefunc =  DDV_OM_MsgFunc;
+		omudp->userdata.ptrvalue = (Pointer)dmp;
+		/*attach a Msg Func on each Bioseq of the current seqalign*/
+		DDV_RegMsgFuncForBsp(dmp->MSA_d.pgp_l.TableHead,dmp,dmp->MSA_d.pgp_l.nBsp, 
+			ompcp->input_entityID, dmp->procid,dmp->proctype,dmp->userkey);
+		DDV_EnableGotoTBItems(hParent,TRUE);
+	} 
+	else {
+		goto error;
+	}
+	
+	return(OM_MSG_RET_DONE);
+
+error:
+	if (hParent) Remove(hParent);
+	return(OM_MSG_RET_ERROR);
+}
+
+/*******************************************************************************
+
+  Function : DDV_ObjRegSlaveEditDDV()
+  
+  Purpose : call by ObjMgr to start DDV as a slave, editor mode on a SeqAlign
+  
+  Parameters : see Toolkit
+  
+  Return value : see Toolkit 
+
+*******************************************************************************/
+extern Int2 LIBCALLBACK DDV_ObjRegSlaveEditDDV (Pointer data)
+{
+	return(DDV_ObjRegSlaveDDV(data,TRUE));
+}
+
+/*******************************************************************************
+
+  Function : DDV_ObjRegSlaveViewDDV()
+  
+  Purpose : call by ObjMgr to start DDV as a slave, editor mode on a SeqAlign
+  
+  Parameters : see Toolkit
+  
+  Return value : see Toolkit 
+
+*******************************************************************************/
+extern Int2 LIBCALLBACK DDV_ObjRegSlaveViewDDV (Pointer data)
+{
+	return(DDV_ObjRegSlaveDDV(data,FALSE));
+}
+
+/*******************************************************************************
+
+  Function : DDV_GetAndCheckSeqAlign()
+  
+  Purpose : given a file OR a GI OR a SeqEntry , retrieve SeqAlign(s) 
+  
+  Parameters :  fp; a handle of an open file
+  				gi; a GI numger
+				sep2; a SeqEntry
+				fetchSepProc; fetch procedure of the user (only if GI!=0)
+				
+  Return value : a list of nodes. For each node, data.intvalue is an entityID
+           of a SeqAlign 
+
+*******************************************************************************/
+extern ValNodePtr DDV_GetAndCheckSeqAlign(FILE *fp,Int4 gi,SeqEntryPtr sep2,
+	UdvFetchSeqEntryProc fetchSepProc,DdvOpenDataPtr dodp,Uint2Ptr entityID)
+{
+SeqEntryPtr sep=NULL;
+ValNodePtr  head = NULL,vnp_ali=NULL;
+Pointer     dataptr=NULL;
+Uint2       datatype=0;
+Uint2		nRet=DVV_MSG_M_OK;
+
+	*entityID=0;
+	if (fp!=NULL){/*open a file*/
+		/*Read the file (it can contain several objects)*/
+		while ((dataptr = ReadAsnFastaOrFlatFile (fp, &datatype, NULL, FALSE, 
+			FALSE, TRUE, FALSE)) != NULL) {
+				ValNodeAddPointer (&head, datatype, dataptr);
+		}
+		/*scan the first node of the head list*/
+		datatype = head->choice;
+		dataptr = head->data.ptrvalue;
+        *entityID=ObjMgrRegister(datatype,dataptr);
+		AssignIDsInEntity (*entityID,0,NULL);
+		switch(datatype){
+			case OBJ_SEQENTRY:
+			case OBJ_SEQALIGN:
+			case OBJ_SEQANNOT:
+			case OBJ_BIOSEQ:
+			case OBJ_BIOSEQSET:
+				DDV_GetSeqAlign(dataptr,datatype,&vnp_ali);
+				break;
+			default:
+				break;
+		}
+		if (dodp){
+			dodp->choice=DDV_OPENTYPE_FILE;
+			dodp->vnp=head;
+		}
+	} else if (gi!=0){/*retrieve a Network Entry given a GI*/
+		if (fetchSepProc) {/*fetch the SeqEntry*/
+			sep=fetchSepProc(gi, 0);
+			if (!sep) {
+				nRet=DVV_MSG_O_E_READGI;
+				goto error;
+			}
+			*entityID=ObjMgrGetEntityIDForPointer((Pointer)sep);
+			AssignIDsInEntity (*entityID,0,NULL);
+			SeqEntryExplore(sep,(Pointer)&vnp_ali,DDV_SearchAli);
+			if (dodp){
+				dodp->choice=DDV_OPENTYPE_GI;
+				dodp->sep=sep;
+			}
+		} else {
+			nRet=DVV_MSG_O_E_NOFETCHFUNC;
+			goto error;
+		}
+	} else if (sep2!=NULL){/*analyse a SeqEntry*/
+		*entityID=ObjMgrGetEntityIDForPointer((Pointer)sep2);
+		AssignIDsInEntity (*entityID,0,NULL);
+		SeqEntryExplore(sep2,(Pointer)&vnp_ali,DDV_SearchAli);
+		if (dodp){
+			dodp->choice=DDV_OPENTYPE_SEP;
+			dodp->sep=sep2;
+		}
+	} else {
+		nRet=DVV_MSG_O_E_NOTHINGTODO;
+		goto error;
+	}
+	
+	/*register for ObjMgr*/
+	if (!vnp_ali) {
+		nRet=DVV_MSG_O_E_BADTYPE;
+		goto error;
+	}
+
+	
+	return(vnp_ali);
+
+error:
+	/*to add : Msg Handler with nRet*/
+	return(NULL);
+}
+
+/*******************************************************************************
+
+  Function : DDV_FOpenTextProc()
+  
+  Purpose : manage File name edit control of the FileOpen dialog box 
+  
+  Parameters : t; edit control
+  
+  Return value : none 
+
+*******************************************************************************/
+static void DDV_FOpenTextProc(TexT t)
+{
+Char 				szFName[PATH_MAX]={""};
+WindoW				hOpenDlg;
+DlgFileOpenDataPtr  dfodp;
+
+	hOpenDlg=(WindoW)ParentWindow(t);
+
+	if (!hOpenDlg) return;
+	
+	dfodp = (DlgFileOpenDataPtr) GetObjectExtra (hOpenDlg);
+
+	if (dfodp==NULL) return;
+	
+	GetTitle(t, szFName, sizeof(szFName)-1);
+
+	if (StringLen(szFName) == 0)
+		Disable(dfodp->Ok);
+	else Enable(dfodp->Ok);
+
+	return;
+}
+
+/*******************************************************************************
+
+  Function : DDV_FOpenBrowseProc()
+  
+  Purpose : manage browse button of the FileOpen dialog box 
+  
+  Parameters : g; button
+  
+  Return value : none 
+
+*******************************************************************************/
+static void DDV_FOpenBrowseProc(ButtoN g)
+{
+DlgFileOpenDataPtr  dfodp;
+WindoW				hOpenDlg;
+Char 				path[PATH_MAX]={""};
+
+	hOpenDlg=(WindoW)ParentWindow(g);
+
+	if (!hOpenDlg) return;
+
+	dfodp = (DlgFileOpenDataPtr) GetObjectExtra (hOpenDlg);
+
+	if (dfodp==NULL) return;
+	if (!dfodp->FNameEditCtrl) return;
+
+	if (GetInputFileName (path, sizeof(path), NULL, NULL)){ 
+		SetTitle(dfodp->FNameEditCtrl, path);
+		DDV_FOpenTextProc(dfodp->FNameEditCtrl);
+	}
+
+	return;   
+}
+
+/*******************************************************************************
+
+  Function : DDV_FOpenCancelProc()
+  
+  Purpose : manage cancel button of the FileOpen dialog box 
+  
+  Parameters : g; button
+  
+  Return value : none 
+
+*******************************************************************************/
+static void DDV_FOpenCancelProc(ButtoN g)
+{
+WindoW				hOpenDlg;
+DlgFileOpenDataPtr  dfodp;
+DdvMainWinPtr 		mWin_d;
+
+	hOpenDlg=(WindoW)ParentWindow(g);
+
+	if (!hOpenDlg) return;
+	dfodp = (DlgFileOpenDataPtr) GetObjectExtra (hOpenDlg);
+	
+	if (dfodp){
+		mWin_d = (DdvMainWinPtr) GetObjectExtra (dfodp->parent);
+		if (mWin_d) Enable(mWin_d->MainMenu.FileOpen);
+	}
+	
+	Remove(hOpenDlg);
+}
+
+/*******************************************************************************
+
+  Function : DDV_FOpenAcceptProc()
+  
+  Purpose : manage ok button of the FileOpen dialog box 
+  
+  Parameters : g; button
+  
+  Return value : none 
+
+*******************************************************************************/
+static void DDV_FOpenAcceptProc(ButtoN g)
+{
+WindoW				hOpenDlg;
+DlgFileOpenDataPtr  dfodp;
+DdvMainPtr          dmp;
+DdvMainWinPtr 		mWin_d;
+Char 				szFName[PATH_MAX]={""};
+Boolean				isBinary;
+FILE				*fp;
+ValNodePtr 			vnp_ali=NULL;
+Uint2 				nRet=DVV_MSG_M_OK,The_entityID;
+Int2				procval;
+
+	hOpenDlg=(WindoW)ParentWindow(g);
+
+	if (!hOpenDlg) return;
+	dfodp = (DlgFileOpenDataPtr) GetObjectExtra (hOpenDlg);
+	
+	if (dfodp){
+
+		mWin_d = (DdvMainWinPtr) GetObjectExtra (dfodp->parent);
+		if (mWin_d!=NULL){
+			/*try to connect Entrez; if failure, still ok : the user can
+			use DDV with a local file. Otherwise he/she will be in trouble ;-)*/
+			if (mWin_d->AutonomeViewer && mWin_d->NetStartProc){
+				mWin_d->NetStartProc(mWin_d->UseNetwork);
+			}
+
+			Enable(mWin_d->MainMenu.FileOpen);
+			/*file name*/
+			GetTitle(dfodp->FNameEditCtrl, szFName, sizeof(szFName));
+
+			/*file reading mode*/
+			if (GetValue(dfodp->ReadMode)==2) isBinary=TRUE;
+			else isBinary=FALSE;
+	
+			Remove(hOpenDlg);
+
+			/* open the i/o files in the correct mode */
+			if ((fp = FileOpen (szFName, isBinary?"rb":"r")) == NULL){
+				nRet=DVV_MSG_O_E_OPENFILEFAIL;
+				goto error;
+			}
+			/*restrieve a list of registered seqalign(s)*/
+			WatchCursor();
+			/*delete old data, if needed*/
+			dmp=(DdvMainPtr)GetObjectExtra(mWin_d->hWndDDV);
+			DDV_CleanupDDVPdata_g(dmp);
+			DDV_CloseData(mWin_d,FALSE);
+			
+			vnp_ali=DDV_GetAndCheckSeqAlign(fp,0,NULL,mWin_d->fetchSepProc,&(dmp->dod),
+				&The_entityID);
+			ArrowCursor();
+			if (vnp_ali && The_entityID!=0){
+				Uint2 entityID,itemID;
+				SeqAlignPtr sap;
+								
+				/*get the first SeqAlign in the list and load the viewer panel*/
+				dmp->vnp_ali=vnp_ali;
+				
+				if(mWin_d->Show_logo){
+					mWin_d->Show_logo=FALSE;
+				}
+				sap=(SeqAlignPtr)vnp_ali->data.ptrvalue;
+				entityID=sap->idx.entityID;
+				itemID=sap->idx.itemID;
+				SetAppProperty("ddvinterndata",(void *)dmp);
+				procval=GatherProcLaunch ((dmp->bEditor==TRUE? OMPROC_EDIT : OMPROC_VIEW), FALSE, 
+					entityID, itemID, OBJ_SEQALIGN, 0, 0, OBJ_SEQALIGN, 0);
+				if ((procval = OM_MSG_RET_ERROR))
+					mWin_d->Show_logo=TRUE;
+				RemoveAppProperty("ddvinterndata");
+			}
+			FileClose(fp);
+		}
+	}
+	
+error:	
+	return;
+}
+
+/*******************************************************************************
+
+  Function : DDV_OpenFile()
+  
+  Purpose : callback of the File|Open command 
+  
+  Parameters : i; command item
+  
+  Return value : none 
+
+*******************************************************************************/
+extern void DDV_OpenFile(IteM i)
+{
+DlgFileOpenDataPtr  dfodp;
+DdvMainWinPtr 		mWin_d;
+WindoW				hWinMain,hOpenDlg;
+GrouP				g,g4;
+ButtoN				b1;
+TexT				t1;    
+
+	hWinMain=(WindoW)ParentWindow(i);
+
+	if (!hWinMain) return;
+	
+	mWin_d = (DdvMainWinPtr) GetObjectExtra (hWinMain);
+
+	if (mWin_d==NULL) return;
+		
+	dfodp=(DlgFileOpenDataPtr)MemNew(sizeof(DlgFileOpenData));
+	if (!dfodp) return;
+	MemSet(dfodp,0,sizeof(DlgFileOpenData));
+
+    hOpenDlg = MovableModalWindow(-30, -20,  -10,  -10, 
+				"DDV - Open a local file",  NULL);
+    g = NormalGroup(hOpenDlg, 2, 1, "File name:",  systemFont, NULL);
+    SetGroupMargins(g, 10, 10);
+    SetGroupSpacing(g, 10, 20);  
+    t1 = DialogText(g,"",25, DDV_FOpenTextProc);
+    PushButton(g, " browse...", DDV_FOpenBrowseProc);
+   
+    g = HiddenGroup(hOpenDlg, 3, 1, NULL);
+    SetGroupMargins(g, 10, 10);
+    SetGroupSpacing(g, 30, 30);
+ 
+    g4 = NormalGroup(g, 2, 1, "File type", systemFont,  NULL);
+    SetGroupMargins(g4, 10, 10);
+    RadioButton(g4, "Ascii");
+    RadioButton(g4, "Binary");
+    SetValue(g4, 1);
+
+    b1 = DefaultButton(g, "OK",  DDV_FOpenAcceptProc);
+    PushButton(g, "Cancel",  DDV_FOpenCancelProc);
+   
+    Disable(b1);
+
+	dfodp->parent=hWinMain;	
+	dfodp->FNameEditCtrl=t1;
+	dfodp->Ok=b1;
+	dfodp->ReadMode=g4;
+
+	SetObjectExtra (hOpenDlg, (Pointer) dfodp, StdCleanupExtraProc);
+	
+    Select(hOpenDlg);
+    Show(hOpenDlg);
+
+	/*allow only one FOpen dlg at a time*/
+    /*UDV_set_PullMenus(&vmp->MainMenu,FALSE);*/
+}
+
+/*******************************************************************************
+
+  Function : DDV_NetOpen_cancelProc()
+  
+  Purpose : manage ok button of the Network open dialog box 
+  
+  Parameters : g; button
+  
+  Return value : none 
+
+*******************************************************************************/
+static void DDV_NetOpen_cancelProc(ButtoN g)
+{
+WindoW			hOpenDlg;
+DDVNetOpenPtr 	dnop;
+
+	hOpenDlg=(WindoW)ParentWindow(g);
+
+	if (!hOpenDlg) return;
+	
+	dnop = (DDVNetOpenPtr) GetObjectExtra (hOpenDlg);
+
+	if (dnop==NULL) return;
+
+	Remove(hOpenDlg);
+}
+
+/*******************************************************************************
+
+  Function : DDV_IsInt()
+  
+  Purpose : test if an entry access code is a GI number, i.e. an Int
+  
+  Parameters : t; edit control
+  
+  Return value : none 
+
+*******************************************************************************/
+static Boolean DDV_IsInt(CharPtr szAccess)
+{
+Int2 i=0;
+
+	while(szAccess[i]){
+		if (!IS_DIGIT(szAccess[i])){
+			Message (MSG_OK, "Not a GI number.");
+			return(FALSE);
+		}
+		i++;
+	}
+	return(TRUE);
+}
+
+/*******************************************************************************
+
+  Function : DDV_NetOpen_okProc()
+  
+  Purpose : manage ok button of the Network open dialog box 
+  
+  Parameters : g; button
+  
+  Return value : none 
+
+*******************************************************************************/
+static void DDV_NetOpen_okProc(ButtoN g)
+{
+WindoW			hOpenDlg;
+DDVNetOpenPtr 	dnop;
+Char 			szAccess[50]={""};
+Int2			AccessType,procval;
+Int4			uid=0;
+DdvMainWinPtr 	mWin_d;
+ValNodePtr      vnp_ali;
+MonitorPtr      mon;
+DdvMainPtr      dmp;
+Uint2           The_entityID;
+
+	hOpenDlg=(WindoW)ParentWindow(g);
+
+	if (!hOpenDlg) return;
+	
+	dnop = (DDVNetOpenPtr) GetObjectExtra (hOpenDlg);	
+
+	if (dnop==NULL) return;
+
+	mWin_d = (DdvMainWinPtr) GetObjectExtra (dnop->hWndMain);
+	if (mWin_d==NULL) return;
+
+	dmp=(DdvMainPtr)GetObjectExtra(mWin_d->hWndDDV);	
+	
+	Hide(hOpenDlg);
+	
+	/*retrieve a Gi*/
+	GetTitle(dnop->Entry, szAccess, sizeof(szAccess));
+
+	if (StringHasNoText (szAccess)) {
+		Message (MSG_OK, "Please enter a GI number");
+		Show (hOpenDlg);
+		Select (hOpenDlg);
+		Select (dnop->Entry);
+		return;
+	}
+
+	AccessType=GetValue(dnop->AccessType);
+	if (!StrToLong(szAccess,&uid)) 
+		uid=0;
+	/*Connect ID1 with a valid UID*/
+	if (uid==0){
+		ArrowCursor();
+		Message (MSG_OK, "Unable to find your record in the database.");
+		Show (hOpenDlg);
+		Select (hOpenDlg);
+		Select (dnop->Entry);
+		return;
+	}
+	else{
+		/*delete old data, if needed*/
+		DDV_CleanupDDVPdata_g(dmp);
+		DDV_CloseData(mWin_d,FALSE);
+		
+		WatchCursor();
+
+		mon = MonitorStrNewEx (szAppName, 30, FALSE);
+		MonitorStrValue (mon, "Retrieving your record...");
+		Update ();
+
+		vnp_ali=DDV_GetAndCheckSeqAlign(NULL,uid,NULL,mWin_d->fetchSepProc,
+			&(dmp->dod),&The_entityID);
+
+		ArrowCursor();
+
+		MonitorFree (mon);
+
+		if (vnp_ali && The_entityID!=0){
+			Uint2 entityID,itemID;
+			SeqAlignPtr sap;
+			
+			/*get the first SeqAlign in the list and load the viewer panel*/
+			dmp->vnp_ali=vnp_ali;
+
+			if(mWin_d->Show_logo){
+				/*Hide(mWin_d->Logo_Panel);*/
+				mWin_d->Show_logo=FALSE;
+			}
+			sap=(SeqAlignPtr)vnp_ali->data.ptrvalue;
+			entityID=sap->idx.entityID;
+			itemID=sap->idx.itemID;
+			SetAppProperty("ddvinterndata",(void *)dmp);
+			procval=GatherProcLaunch ((dmp->bEditor==TRUE? OMPROC_EDIT : OMPROC_VIEW), FALSE, 
+				entityID, itemID, OBJ_SEQALIGN, 0, 0, OBJ_SEQALIGN, 0);
+			if ((procval = OM_MSG_RET_ERROR))
+				mWin_d->Show_logo=TRUE;
+			RemoveAppProperty("ddvinterndata");
+		}
+	}
+
+	Remove(hOpenDlg);
+}
+
+/*******************************************************************************
+
+  Function : DDV_NetOpen_access()
+  
+  Purpose : manage Accession edit control of the Download dialog box 
+  
+  Parameters : t; edit control
+  
+  Return value : none 
+
+*******************************************************************************/
+static void DDV_NetOpen_access(TexT t)
+{
+Char 			szAccess[50]={""};
+WindoW			hOpenDlg;
+DDVNetOpenPtr 	dnop;
+
+	hOpenDlg=(WindoW)ParentWindow(t);
+
+	if (!hOpenDlg) return;
+	
+	dnop = (DDVNetOpenPtr) GetObjectExtra (hOpenDlg);
+
+	if (dnop==NULL) return;
+	
+	GetTitle(t, szAccess, sizeof(szAccess));
+
+	if (StringLen(szAccess) == 0)
+		Disable(dnop->ok);
+	else Enable(dnop->ok);
+
+	return;
+}
+
+/*******************************************************************************
+
+  Function : DDV_OpenNetwork()
+  
+  Purpose : callback of the File|Network command 
+  
+  Parameters : i; command item
+  
+  Return value : none 
+
+*******************************************************************************/
+extern void DDV_OpenNetwork(IteM i)
+{
+DdvMainWinPtr 		mWin_d;
+WindoW				hWinMain,hOpenDlg;
+GrouP				g,c;
+DDVNetOpenPtr       dnopp;
+
+	hWinMain=(WindoW)ParentWindow(i);
+
+	if (!hWinMain) return;
+	
+	mWin_d = (DdvMainWinPtr) GetObjectExtra (hWinMain);
+
+	if (mWin_d==NULL) return;
+		
+	dnopp=(DDVNetOpenPtr)MemNew(sizeof(DDVNetOpen));
+	if (!dnopp) return;
+
+	/*init the Network, if needed*/
+	if (mWin_d->AutonomeViewer && mWin_d->NetStartProc){
+		if (!mWin_d->NetStartProc(mWin_d->UseNetwork)) return;
+	}
+
+    hOpenDlg = MovableModalWindow(-30, -20,  -10,  -10, 
+				"DDV - Fetch a network entry",  NULL);
+	SetGroupSpacing (hOpenDlg, 10, 10);
+	
+	dnopp->hWndMain=hWinMain;
+	
+	/*accesion*/
+	g = NormalGroup (hOpenDlg, 3, 0, "Entry", systemFont,NULL);
+
+#ifdef WIN_MAC
+	dnopp->AccessType = PopupList (g, TRUE, NULL);
+#endif
+
+#ifndef WIN_MAC
+	dnopp->AccessType = PopupList (g, FALSE, NULL);
+#endif
+
+	PopupItem(dnopp->AccessType,"PopSet");
+	
+	SetValue (dnopp->AccessType, 1);
+
+	dnopp->Entry = DialogText (g, "", 10, DDV_NetOpen_access);
+
+	c = HiddenGroup (hOpenDlg, 4, 0, NULL);
+	SetGroupSpacing (c, 10, 2);
+	dnopp->ok=DefaultButton (c, "Retrieve", DDV_NetOpen_okProc);
+	Disable (dnopp->ok);
+	PushButton (c, "Cancel", DDV_NetOpen_cancelProc);
+	
+	SetObjectExtra (hOpenDlg, (Pointer) dnopp, StdCleanupExtraProc);
+
+	/*display*/
+	AlignObjects (ALIGN_CENTER, (HANDLE) g, (HANDLE) c, NULL);
+	RealizeWindow (hOpenDlg);
+	Show (hOpenDlg);
+	Select (hOpenDlg);
+	Update ();
+}
+
+NLM_EXTERN void DDV_SlaveQuit(WindoW hWinMain)
+{
+  DdvMainWinPtr  mWin_d;
+  DdvMainPtr     dmp;
+  WindoW				 hDialog;
+  GrouP          g1, g2;
+  Boolean        QuitElseWhere = FALSE;
+
+	mWin_d = (DdvMainWinPtr) GetObjectExtra((Handle)hWinMain);
+	if (mWin_d==NULL) return;
+
+  /* if there are unsaved edits, ask the user if they'd like to save */
+  dmp = (DdvMainPtr)GetObjectExtra(mWin_d->hWndDDV);
+  if (dmp->bEditor) {
+    if (dmp->dsp->SomethingToSave) {
+      QuitElseWhere = TRUE;
+      hDialog = MovableModalWindow(-30, -20,  -10,  -10, "DDE - Save Query",  NULL);
+      g1 = HiddenGroup(hDialog, 1, 1, NULL);
+      StaticPrompt(g1, "Save Changes?", 0, stdLineHeight, systemFont, 'c');
+      g2 = HiddenGroup(hDialog, 3, 1, NULL);
+      PushButton(g2, "Yes", DDV_Save);
+      PushButton(g2, "No",  DDV_NoSave);
+      PushButton(g2, "Cancel", DDV_Cancel);
+      SetObjectExtra (hDialog, (Pointer)hWinMain, NULL);
+      Select(hDialog);
+      Show(hDialog);
+    }
+  }
+  if (!QuitElseWhere) {
+    if (mWin_d->AutonomeViewer)
+      QuitProgram(); /*standalone DDV*/
+    else
+      Remove(hWinMain);/*slave viewer : just kill the main window*/
+  }
+}
+
+/*******************************************************************************
+
+  Function : DDV_StartMainWin_Slave()
+  
+  Purpose : start DDV main window as a slave module: init 'dmp' data structure,
+  			set 'DDV_MAIN_DATA' property, start a dlg (the parent window of DDV
+			panel).
+  
+  Parameters : vgp; sets defaults for non-autonomous viewers
+							 
+  Return value : handle to the DDV main window
+
+*******************************************************************************/
+extern WindoW DDV_StartMainWin_Slave(SAM_ViewGlobal *vgp,Boolean bEditor)
+{
+Int2	Margins;
+DdvMainWinPtr mWin_d;
+WindoW	w; 
+Boolean bRet;
+Char AppName[40];
+
+  /* use "DDE" for editor, "DDV" for viewer, for title */
+  if (bEditor) {StringCpy(AppName, szAppName2);}
+  else         {StringCpy(AppName, szAppName);}
+	
+	/*init data blocks*/
+	mWin_d=(DdvMainWinPtr)MemNew(sizeof(DdvMainWin));
+	if (!mWin_d) return(NULL);
+	
+	/*main window*/
+	Margins=15*stdCharWidth;
+    if(vgp == NULL)
+        w=DocumentWindow(Margins,Margins ,-10, -10,
+           AppName, 
+           DDV_SlaveQuit,
+           DDV_WinMainResize);
+    else
+        w=DocumentWindow(vgp->Rect.left,vgp->Rect.top ,-10, -10,
+            AppName, 
+            DDV_SlaveQuit,
+            DDV_WinMainResize);
+
+	if (!w) return(NULL);
+
+	SetObjectExtra (w, (Pointer) mWin_d, (FreeProc)DDV_WinMainCleanup);
+	mWin_d->hWndMain=w;
+	/*this is a slave editor/viewer*/
+	mWin_d->AutonomeViewer=FALSE;
+
+	/*build GUI*/
+	bRet=DDV_CreateViewerPanel(w,mWin_d, vgp, bEditor);
+
+	if (!bRet) return(NULL);
+
+	mWin_d->Show_logo=FALSE;
+
+	return(w);
+}
+
+
+static Boolean DDV_DigitsOnly(Char* str)
+{
+    while(*str) {
+        if (!isdigit(*str)) 
+            return FALSE;
+        str++;
+    }
+    return TRUE;
+}
+
+/*******************************************************************************
+
+  Function : DDV_ImportEnableProc
+  
+  Purpose : this function does the actual bioseq import.  note that it doesn't
+            require a vibrant dialog to operate, only that idp is filled out
+  
+  Return value : none 
+
+*******************************************************************************/
+
+static void DDV_ImportEnableProc(TexT t)
+{
+    Char str[32];
+    WindoW hImportDlg;
+    DDV_ImportDialog *idp;
+
+	hImportDlg= (WindoW)ParentWindow(t);
+	if(hImportDlg == NULL) return;	
+	idp = (DDV_ImportDialog *) GetObjectExtra(hImportDlg);
+	if(idp == NULL) return;
+
+    GetTitle(idp->DDV_tAccession, str, sizeof(str));
+    if (StringLen(str) == 0) {
+        Disable(idp->DDV_bImportAccept);
+    } else {
+        Enable(idp->DDV_bImportAccept);
+        if(DDV_DigitsOnly(str)) SetValue(idp->DDV_gAccType, 2);
+        else SetValue(idp->DDV_gAccType, 1);
+    }
+    return;
+}
+
+static SeqAlignPtr ddv_truncate_overlaps (SeqAlignPtr sap)
+{
+   AMAlignIndexPtr  amaip;
+   DenseDiagPtr     ddp;
+   DenseDiagPtr     ddp_head;
+   DenseDiagPtr     ddp_prev;
+   DenseSegPtr      dsp1;
+   DenseSegPtr      dsp2;
+   Int4             i;
+   SeqAlignPtr      salp;
+   Int4             start1;
+   Int4             start2;
+   Int4             stop1;
+   Int4             stop2;
+   Int4             tmp;
+
+   if (sap == NULL) return(NULL);
+   if (sap->saip == NULL) return(NULL);
+   if (sap->saip->indextype != INDEX_PARENT) return(NULL);
+
+   amaip = (AMAlignIndexPtr)(sap->saip);
+   for (i=0; i<amaip->numsaps-1; i++)
+   {
+      AlnMgrGetNthSeqRangeInSA(amaip->saps[i], 1, &start1, &stop1);
+      AlnMgrGetNthSeqRangeInSA(amaip->saps[i+1], 1, &start2, &stop2);
+      if (start2 <= stop1)
+      {
+         dsp1 = (DenseSegPtr)(amaip->saps[i]->segs);
+         dsp2 = (DenseSegPtr)(amaip->saps[i+1]->segs);
+         dsp1->lens[0] = dsp1->lens[0] - (stop1-start2)/2;
+         tmp = dsp1->starts[0]+dsp1->lens[0];
+         tmp = tmp - dsp2->starts[0];
+         dsp2->starts[1] = tmp + dsp2->starts[1];
+         dsp2->starts[0] = dsp1->starts[0]+dsp1->lens[0];
+         dsp2->lens[0] = stop2 - dsp2->starts[0] + 1;
+         SAIndexFree(amaip->saps[i]->saip);
+         SAIndexFree(amaip->saps[i+1]->saip);
+         amaip->saps[i]->saip = amaip->saps[i+1]->saip = NULL;
+         AlnMgrIndexSingleChildSeqAlign(amaip->saps[i]);
+         AlnMgrIndexSingleChildSeqAlign(amaip->saps[i+1]);
+      }
+      AlnMgrGetNthSeqRangeInSA(amaip->saps[i], 2, &start1, &stop1);
+      AlnMgrGetNthSeqRangeInSA(amaip->saps[i+1], 2, &start2, &stop2);
+      if (start2 <= stop1)
+      {
+         dsp1 = (DenseSegPtr)(amaip->saps[i]->segs);
+         dsp2 = (DenseSegPtr)(amaip->saps[i+1]->segs);
+         dsp1->lens[0] = dsp1->lens[0] - (stop1-start2)/2;
+         tmp = dsp1->starts[1]+dsp1->lens[0];
+         tmp = tmp - dsp2->starts[1];
+         dsp2->starts[0] = tmp + dsp2->starts[0];
+         dsp2->starts[1] = dsp1->starts[1]+dsp1->lens[0];
+         dsp2->lens[0] = stop2 - dsp2->starts[1] + 1;
+         SAIndexFree(amaip->saps[i]->saip);
+         SAIndexFree(amaip->saps[i+1]->saip);
+         amaip->saps[i]->saip = amaip->saps[i+1]->saip = NULL;
+         AlnMgrIndexSingleChildSeqAlign(amaip->saps[i]);
+         AlnMgrIndexSingleChildSeqAlign(amaip->saps[i+1]);
+      }
+   }
+   ddp_head = ddp_prev = NULL;
+   for (i=0; i<amaip->numsaps; i++)
+   {
+      ddp = DenseDiagNew();
+      AlnMgrGetNthSeqRangeInSA(amaip->saps[i], 1, &start1, &stop1);
+      AlnMgrGetNthSeqRangeInSA(amaip->saps[i], 2, &start2, &stop2);
+      dsp1 = (DenseSegPtr)(amaip->saps[i]->segs);
+      ddp->starts = (Int4Ptr)MemNew(2*sizeof(Int4));
+      ddp->dim = 2;
+      ddp->id = dsp1->ids;
+      dsp1->ids = NULL;
+      ddp->starts[0] = start1;
+      ddp->starts[1] = start2;
+      ddp->len = stop1 - start1 + 1;
+      if (ddp_head != NULL)
+      {
+         ddp_prev->next = ddp;
+         ddp_prev = ddp;
+      } else
+         ddp_head = ddp_prev = ddp;
+   }
+   salp = SeqAlignNew();
+   salp->dim = 2;
+   salp->segtype = SAS_DENDIAG;
+   salp->type = SAT_DIAGS;
+   salp->segs = (Pointer)(ddp_head);
+   SeqAlignFree(sap);
+   return salp;
+}
+
+NLM_EXTERN SeqAlignPtr DDV_ShredAln(SeqAlignPtr sap)
+{
+   AMAlignIndexPtr  amaip;
+   AlnMsgPtr        amp1;
+   AlnMsgPtr        amp2;
+   DenseDiagPtr     ddp;
+   DenseDiagPtr     ddp_head;
+   DenseDiagPtr     ddp_prev;
+   Int4             i;
+   Boolean          more1;
+   Boolean          more2;
+   SeqAlignPtr      salp;
+
+   if (sap == NULL || sap->saip == NULL || sap->saip->indextype != INDEX_PARENT)
+      return NULL;
+   amaip = (AMAlignIndexPtr)(sap->saip);
+   if (amaip->numrows > 2)
+      return NULL;
+   amp1 = AlnMsgNew();
+   amp2 = AlnMsgNew();
+   ddp_head = ddp_prev = NULL;
+   for (i=0; i<amaip->numsaps; i++)
+   {
+      amp1 = AlnMsgReNew(amp1);
+      amp2 = AlnMsgReNew(amp2);
+      amp1->from_m = amp2->from_m = 0;
+      amp1->to_m = amp2->to_m = -1;
+      amp1->row_num = 1;
+      amp2->row_num = 2;
+      while ((more1 = AlnMgrGetNextAlnBit(amaip->saps[i], amp1)) && (more2 = AlnMgrGetNextAlnBit(amaip->saps[i], amp2)))
+      {
+         if (amp1->gap == 0 && amp2->gap == 0)
+         {
+            ddp = DenseDiagNew();
+            ddp->dim = 2;
+            ddp->starts = (Int4Ptr)MemNew(2*sizeof(Int4));
+            ddp->strands = (Uint1Ptr)MemNew(2*sizeof(Uint1));
+            ddp->id = AlnMgrGetNthSeqIdPtr(sap, 1);
+            ddp->id->next = AlnMgrGetNthSeqIdPtr(sap, 2);
+            ddp->starts[0] = amp1->from_b;
+            ddp->starts[1] = amp2->from_b;
+            ddp->len = amp1->to_b - amp1->from_b + 1;
+            ddp->strands[0] = AlnMgrGetNthStrand(sap, 1);
+            ddp->strands[1] = AlnMgrGetNthStrand(sap, 2);
+            if (ddp_head != NULL)
+            {
+               ddp_prev->next = ddp;
+               ddp_prev = ddp;
+            } else 
+               ddp_head = ddp_prev = ddp;
+         }
+      }
+   }
+   salp = SeqAlignNew();
+   salp->type = SAT_DIAGS;
+   salp->segtype = SAS_DENDIAG;
+   salp->dim = 2;
+   salp->segs = (Pointer)(ddp_head);
+   SeqAlignFree(sap);
+   AlnMsgFree(amp1);
+   AlnMsgFree(amp2);
+   return salp;
+}
+
+/*******************************************************************************
+
+  Function : DDV_DoAlign
+  
+  Purpose : this function does the actual bioseq import.  note that it doesn't
+            require a vibrant dialog to operate, only that idp is filled out
+  
+  Return value : none 
+
+*******************************************************************************/
+
+NLM_EXTERN void DDV_DoAlign(DDV_ImportDialog *idp)
+{
+    Char str[32];
+    Bioseq *bsp1 = NULL, *bsp2 = NULL;
+    SeqId si;
+    SeqAlign *sap, *salp;
+    Int4 value, i;
+    ValNode *pvn;
+    ErrSev sev;
+    
+    if(idp->mode & DDVIMP2SE) {
+        value = GetValue(idp->DDV_lsip); /*one-base value*/
+        for(pvn = idp->pvnSips, i = 1; i != value && pvn != NULL;
+            i++, pvn = pvn->next) continue;
+        if(pvn != NULL)
+            bsp1 = BioseqLockById((SeqId *)pvn->data.ptrvalue);
+    } else bsp1 = BioseqLockById(idp->sip);
+    if (bsp1 == NULL) {
+        Message (MSG_ERROR, "Unable to load sequence");
+        goto out2;
+    }
+    
+    if(idp->mode & DDVIMPNET) {
+        si.choice = SEQID_GI;
+        GetTitle(idp->DDV_tAccession, str, sizeof(str));
+        if(GetValue(idp->DDV_gAccType) == 1 && idp->AccessionCB)
+            si.data.intvalue = idp->AccessionCB(str, ISA_aa(bsp1->mol));
+        else si.data.intvalue = atoi(str);
+        if (si.data.intvalue <= 0) {
+            Message (MSG_ERROR, "Unable to understand accession");
+            goto out2;
+        }
+        bsp2 = BioseqLockById(&si);
+    } else bsp2 = BioseqLockById((SeqId *)idp->sipslave->data.ptrvalue);
+    if(bsp2 == NULL) {
+        Message (MSG_ERROR, "Unable to load sequence");
+        BioseqUnlock(bsp1);
+        goto out2;
+    }
+    idp->bsp = bsp2;
+    
+    if(ISA_aa(bsp1->mol) != ISA_aa(bsp2->mol) ||
+        ISA_na(bsp1->mol) != ISA_na(bsp1->mol)) {
+        Message (MSG_ERROR, "Sequences to be aligned not of same type");
+        BioseqUnlock(bsp1);
+        BioseqUnlock(bsp2);
+        goto out2;
+    }
+
+    sev = ErrSetMessageLevel(SEV_FATAL);
+    
+/*    sap = ACT_GlobalAlignSimple(bsp1, bsp2, TRUE); */
+    if(ISA_aa(bsp1->mol))
+        sap = DDV_Blast2Seqs(bsp1, bsp2, idp->Gap, "blastp");
+    else 
+        sap = DDV_Blast2Seqs(bsp1, bsp2, idp->Gap, "blastn");
+
+    ErrSetMessageLevel(sev);
+    BioseqUnlock(bsp1);
+    BioseqUnlock(bsp2);
+    
+    if(sap == NULL) {
+        Message (MSG_OK, "Not able to align the sequence");
+        goto out2;
+    }
+    
+    SAM_ReplaceGI(sap);
+    AlnMgrIndexSeqAlign(sap);
+
+    if(idp->Gap) {
+        AlnMgrMakeMultipleByScore(sap);
+        AlnMgrDeleteHidden(sap, FALSE);
+        salp = DDV_ShredAln(sap);
+    } else {
+        AlnMgrMakeMultipleByScoreEx(sap, 10);
+        AlnMgrDeleteHidden(sap, FALSE);
+        salp = ddv_truncate_overlaps(sap);
+    }
+
+    if(idp->callback) idp->callback(idp, idp->sap, salp);
+    /*SeqAlignFree(sap);*/
+    
+out2:
+    MemFree(idp->userdata);
+    ValNodeFree(idp->pvnSips); /* don't free the data */
+    ValNodeFree(idp->sipslave);
+}
+
+/*******************************************************************************
+
+  Function : DDV_ImportAcceptProc
+  
+  Purpose : fired by clicking OK in the bioseq import dialog
+  
+  Return value : none 
+
+*******************************************************************************/
+
+static void DDV_ImportAcceptProc(ButtoN b)
+{
+    WindoW hImportDlg;
+    DDV_ImportDialog *idp;
+
+	hImportDlg= (WindoW)ParentWindow(b);
+	if(hImportDlg == NULL) goto out;	
+	idp = (DDV_ImportDialog *) GetObjectExtra(hImportDlg);
+	if(idp == NULL) goto out;
+
+    WatchCursor();
+    DDV_DoAlign(idp);
+    ArrowCursor();
+
+out:
+    Remove(hImportDlg);
+    return;
+}
+
+/*******************************************************************************
+
+  Function : DDV_ImportCB
+  
+  Purpose : callback for import bioseq dialog.  used to clean up after the
+            import
+  
+  Return value : none 
+
+*******************************************************************************/
+
+NLM_EXTERN void DDV_ImportCB(DDV_ImportDialog *idp, SeqAlign *salpdest,
+                             SeqAlign *salp)
+{
+    if (salpdest == NULL || salp == NULL) return;
+    SeqAlignSetFree(salp->next);
+    salp->next = NULL;
+    ViewMgr_Add(salpdest, salp);
+}
+
+/*******************************************************************************
+
+  Function : DDV_ImportCancelProc
+  
+  Purpose : cancel function for the import bioseq dialog
+  
+  Return value : none 
+
+*******************************************************************************/
+
+static void DDV_ImportCancelProc(ButtoN b)
+{
+    WindoW hImportDlg;
+    DDV_ImportDialog *idp;
+
+	hImportDlg= (WindoW)ParentWindow(b);
+	if(hImportDlg == NULL) return;	
+	idp = (DDV_ImportDialog *) GetObjectExtra(hImportDlg);
+	if(idp == NULL) return;
+    MemFree(idp->userdata);
+
+    Remove(idp->DDV_wImport);
+    return;
+}
+
+/*******************************************************************************
+
+  Function : DDV_ImportBioseqDlg
+  
+  Purpose : dialog to import a bioseq into a seqalign.  Note that it has
+            several modes listed in ddvopen.h
+  
+  Return value : none 
+
+*******************************************************************************/
+
+NLM_EXTERN void DDV_ImportBioseqDlg(DDV_ImportDialog *idp)
+{
+    GrouP g, hg;
+    ButtoN b;
+    DDVUpdateMSG  *dump;
+    ValNode *pvn;
+    Char szName[21]={""};
+
+    if(idp == NULL) return;
+    
+    /* check if we have the right data for each mode */
+    if(idp->mode == DDVIMPSE2SA 
+        && (idp->sip == NULL || idp->sap == NULL || idp->sipslave == NULL)) return;
+    else if (idp->mode == DDVIMPSE2SE 
+        && (idp->pvnSips == NULL || idp->sipslave == NULL)) return;
+    else if (idp->mode == DDVIMPNET2SA 
+        && (idp->sap == NULL || idp->sip == NULL)) return;
+    else if (idp->mode == DDVIMPNET2SE  
+        && idp->pvnSips == NULL) return;
+
+    idp->DDV_wImport = NULL;
+    idp->DDV_gAccType = NULL;
+    idp->DDV_bImportAccept = NULL;
+    idp->DDV_tAccession = NULL;
+    dump = MemNew(sizeof(DDVUpdateMSG));
+    if(dump == NULL) {
+        MemFree(idp);
+        return;
+    }
+    idp->userdata = dump;
+    dump->data = NULL;
+	dump->type=UPDATE_TYPE_EDIT_DELBSP;
+
+    idp->DDV_wImport = MovableModalWindow(-30, -20, -10, -10,
+        "Import sequence using BLAST", NULL);
+    Nlm_SetObjectExtra (idp->DDV_wImport, (Nlm_VoidPtr)idp, StdCleanupExtraProc);
+
+    if(idp->mode & DDVIMP2SE) {
+        hg = HiddenGroup(idp->DDV_wImport, 1, 4, NULL);
+        g = NormalGroup(hg, 1, 2, "Choose sequence to align to:", systemFont, NULL);
+        idp->DDV_lsip = SingleList(g,10,6,NULL);
+
+        for(pvn = idp->pvnSips; pvn != NULL; pvn = pvn->next) {
+            SeqIdWrite((SeqId *)pvn->data.ptrvalue,szName,
+                PRINTID_TEXTID_ACCESSION, 10);
+            ListItem(idp->DDV_lsip, szName);
+        }
+        SetValue(idp->DDV_lsip, 1);
+    } else hg = HiddenGroup(idp->DDV_wImport, 1, 3, NULL);
+
+    if(idp->mode & DDVIMPNET) {
+        g = NormalGroup(hg, 1, 2, " Enter sequence identifier:", systemFont, NULL);
+        idp->DDV_tAccession = DialogText(g, "", 10, (TxtActnProc) DDV_ImportEnableProc);
+        idp->DDV_gAccType =
+            NormalGroup(hg, 1, 2, " accession type", systemFont, NULL);
+        RadioButton(idp->DDV_gAccType, "Accession");
+        RadioButton(idp->DDV_gAccType, "gi");
+    }
+
+    g = HiddenGroup(hg, 2, 1, NULL);
+    SetGroupSpacing(g, 15, 15);
+    idp->DDV_bImportAccept =
+        DefaultButton(g, "OK", (BtnActnProc) DDV_ImportAcceptProc);
+    b = PushButton(g, "Cancel", (BtnActnProc) DDV_ImportCancelProc);
+
+    if(idp->mode & DDVIMPNET) {
+        SetValue(idp->DDV_gAccType, 1);
+        Disable(idp->DDV_bImportAccept);
+        Select(idp->DDV_tAccession);
+    }
+    Show(idp->DDV_wImport);
+    return;
+}
+
+/*******************************************************************************
+
+  Function : DDV_ImportBioseq
+  
+  Purpose : sets up dialog to import a bioseq into a seqalign
+  
+  Return value : none 
+
+*******************************************************************************/
+
+NLM_EXTERN void DDV_ImportBioseq(IteM i)
+{
+    DDV_ImportDialog *idp;
+    DdvMainPtr    dmp;  /*DDV panel data*/
+    DdvMainWinPtr mWin_d;
+    WindoW		  hWinMain;
+
+    idp = MemNew(sizeof(DDV_ImportDialog));
+    if(idp == NULL) return;
+
+	hWinMain=(WindoW)ParentWindow(i);
+	if (hWinMain==NULL) return;
+	mWin_d = (DdvMainWinPtr) GetObjectExtra (hWinMain);
+	if (mWin_d==NULL) return;
+
+    if (mWin_d->NetStartProc) mWin_d->NetStartProc(mWin_d->UseNetwork);
+
+	if (mWin_d->hWndDDV==NULL) return;
+	dmp = (DdvMainPtr) GetObjectExtra(mWin_d->hWndDDV);
+	if (dmp==NULL) return;
+
+    if(dmp->MSA_d.pgp_l.sap == NULL) return;
+
+    idp->sap = dmp->MSA_d.pgp_l.sap;
+    idp->sip = AlnMgrFindMaster(idp->sap);
+    if(idp->sip == NULL) {
+        Message (MSG_ERROR, "Alignment must have master sequence");
+        MemFree(idp);
+        return;
+    }
+
+    idp->callback = DDV_ImportCB;
+    idp->mode = DDVIMPNET2SA;
+
+    DDV_ImportBioseqDlg(idp);
+}
+
+
+NLM_EXTERN SeqAlign *DDV_Blast2Seqs(Bioseq *bsp1, Bioseq *bsp2, Boolean gapped,
+                         Char *progname)
+{
+    BLAST_OptionsBlkPtr options;
+    SeqAlign  *salp;
+    
+    if(bsp1 == NULL || bsp2 == NULL || progname == NULL) return NULL;
+    options = BLASTOptionNew(progname, gapped);
+    if(options == NULL) return NULL;
+/*    options->discontinuous = FALSE; */
+    salp = BlastTwoSequences(bsp1, bsp2, progname, options);
+    BLASTOptionDelete(options);
+    return salp;
+}
+
+
+/*******************************************************************************
+
+  Function : DDV_ImportSeqAlign(), DDV_ImportNucSeqAlign() and DDV_ImportProtSeqAlign()
+  
+  Purpose : import a sequence alignment of text type
+  
+  Return value : none 
+
+*******************************************************************************/
+static void DDV_ImportSeqAlign(Boolean is_prot,IteM i)
+{
+WindoW        hWinMain;
+DdvMainPtr    dmp;
+DdvMainWinPtr mWin_d;
+SeqEntryPtr   sep;
+ValNodePtr    vnp_ali;
+SeqAlignPtr   sap;
+Uint2 		  The_entityID,entityID,itemID;
+Int2		  procval;
+
+	hWinMain=(WindoW)ParentWindow(i);
+	
+	mWin_d = (DdvMainWinPtr) GetObjectExtra (hWinMain);
+
+	sep=ReadAnyAlignment(is_prot,NULL);
+
+	if (sep!=NULL && mWin_d!=NULL){
+		/*try to connect Entrez; if failure, still ok : the user can
+		use DDV with a local file. Otherwise he/she will be in trouble ;-)*/
+		if (mWin_d->AutonomeViewer && mWin_d->NetStartProc){
+			mWin_d->NetStartProc(mWin_d->UseNetwork);
+		}
+		/*delete old data, if needed*/
+		dmp=(DdvMainPtr)GetObjectExtra(mWin_d->hWndDDV);
+		DDV_CleanupDDVPdata_g(dmp);
+		DDV_CloseData(mWin_d,FALSE);
+
+		vnp_ali=DDV_GetAndCheckSeqAlign(NULL,0,sep,mWin_d->fetchSepProc,&(dmp->dod),
+			&The_entityID);
+		if (vnp_ali && The_entityID!=0){
+
+			/*get the first SeqAlign in the list and load the viewer panel*/
+			dmp->vnp_ali=vnp_ali;
+
+			if(mWin_d->Show_logo){
+				mWin_d->Show_logo=FALSE;
+			}
+			sap=(SeqAlignPtr)vnp_ali->data.ptrvalue;
+			entityID=sap->idx.entityID;
+			itemID=sap->idx.itemID;
+			SetAppProperty("ddvinterndata",(void *)dmp);
+			procval=GatherProcLaunch ((dmp->bEditor==TRUE? OMPROC_EDIT : OMPROC_VIEW), FALSE, entityID, itemID, 
+				OBJ_SEQALIGN, 0, 0, OBJ_SEQALIGN, 0);
+			if ((procval = OM_MSG_RET_ERROR))
+				mWin_d->Show_logo=TRUE;
+			RemoveAppProperty("ddvinterndata");
+		}
+	}
+	else{
+		ErrPostEx (SEV_ERROR, 0, 0, "We do not support this format yet");
+	}
+}
+
+extern void DDV_ImportNucSeqAlign(IteM i)
+{
+	DDV_ImportSeqAlign(FALSE,i);
+}
+
+extern void DDV_ImportProtSeqAlign(IteM i)
+{
+	DDV_ImportSeqAlign(TRUE,i);
+}
+
+static Int4 DDV_GetLastRow(DDV_HideDialog *hdp)
+{
+  int i, max=0;
+
+  for (i = 1; i <= hdp->numrows; i++) {
+    if (ViewMgr_TRow2VRow(hdp->salp, i) > 0) {
+      max = i;
+    }
+  }
+  return(max);
+}
+
+static void DDV_SetHideList(DDV_HideDialog *hdp)
+{
+    int i;
+    
+    for(i = 1; i <= hdp->numrows; i++) {
+        if(ViewMgr_TRow2VRow(hdp->salp, i) > 0) 
+            SetItemStatus(hdp->DDV_lsip, i, TRUE);
+        else SetItemStatus(hdp->DDV_lsip, i, FALSE);
+    }
+    SetItemStatus(hdp->DDV_lsip, hdp->amaip->master, TRUE);
+}
+
+static void DDV_HideList(Nlm_LisT l)
+/*******************************************************************************
+*  this function is called each time an item from the list is clicked.
+*  it sets the status for each row, making sure not to allow the
+*  master to be hidden, nor the number of rows to be less than 2.
+*******************************************************************************/
+{
+    WindoW hHideDlg;
+    DDV_HideDialog *hdp;
+    Int4 i, LastRow, count = 0;
+
+    hHideDlg = (WindoW)ParentWindow(l);
+    if(hHideDlg == NULL) return;	
+    hdp = (DDV_HideDialog *) GetObjectExtra(hHideDlg);
+    if(hdp == NULL) return;
+
+    /* get row count, and last displayed row */
+    for(i = 1; i <= hdp->numrows; i++) {
+      if (GetItemStatus(hdp->DDV_lsip, i)) {
+        count++;
+        LastRow = i;
+      }
+    }
+
+    /* don't let number of rows fall below 2 */
+    if (count < 2) {
+      if (hdp->LastValidRow == -1) {
+        SetItemStatus(hdp->DDV_lsip, DDV_GetLastRow(hdp), TRUE);
+      }
+      else {
+        SetItemStatus(hdp->DDV_lsip, hdp->LastValidRow, TRUE);
+      }
+    }
+    else {
+      /* each time a row is clicked, update the last saved row */
+      hdp->LastValidRow = LastRow;
+    }
+
+    /* don't let master be hidden */
+    if (!GetItemStatus(hdp->DDV_lsip, 1)) {
+      SetItemStatus(hdp->DDV_lsip, 1, TRUE);
+    }
+}
+
+
+static void DDV_HideAcceptProc(ButtoN b)
+{
+    WindoW hHideDlg;
+    DDV_HideDialog *hdp;
+    Int4  i;
+    Boolean  status;
+
+    hHideDlg = (WindoW)ParentWindow(b);
+    if(hHideDlg == NULL) return;	
+    hdp = (DDV_HideDialog *) GetObjectExtra(hHideDlg);
+    if(hdp == NULL) return;
+
+    for(i = 1; i <= hdp->numrows; i++) {
+      status = GetItemStatus(hdp->DDV_lsip, i);
+      ViewMgr_SetHidden(hdp->salp, !status, i);
+    }
+    ViewMgr_Update(hdp->salp);
+    DDV_SetHideList(hdp);
+
+    MemFree(hdp->userdata);
+    Remove(hdp->DDV_wHide);
+}
+
+
+/*******************************************************************************
+
+  Function : DDV_HideDlg
+  
+  Purpose : dialog to import a bioseq into a seqalign.  Note that it has
+            several modes listed in ddvopen.h
+  
+  Return value : none 
+
+*******************************************************************************/
+
+NLM_EXTERN void DDV_HideDlg(DDV_HideDialog *hdp)
+{
+    GrouP g, hg;
+    ButtoN b;
+    DDVUpdateMSG  *dump;
+    Char szName[181], szName2[161];
+    Int4 i;
+    SeqId *sip;
+    Bioseq *bsp;
+
+    if(hdp == NULL) return;
+    hdp->DDV_wHide = NULL;
+    
+    hdp->target = ViewMgr_GetBeginIndexed(hdp->salp);
+
+    if(hdp->target == NULL) return;
+    if( AlnMgrCheckAlignForParent(hdp->target) != AM_PARENT) return;
+    hdp->amaip = (AMAlignIndexPtr)(hdp->target->saip);
+    if (!hdp->amaip) return;
+    
+    dump = MemNew(sizeof(DDVUpdateMSG));
+    if(dump == NULL) {
+        MemFree(hdp);
+        return;
+    }
+    hdp->userdata = dump;
+    dump->data = NULL;
+    dump->type=UPDATE_TYPE_EDIT_DELBSP;
+
+    hdp->DDV_wHide = MovableModalWindow(-30, -20, -10, -10,
+        "Hide/Show Sequences", NULL);
+    /* need to do something more than std cleanup.  also for blast dialog */
+    Nlm_SetObjectExtra (hdp->DDV_wHide, (void *)hdp, StdCleanupExtraProc);
+    
+    hg = HiddenGroup(hdp->DDV_wHide, 1, 2, NULL);
+    g = NormalGroup(hg, 1, 2, "Choose sequences to show:", systemFont, NULL);
+    hdp->DDV_lsip = MultiList(g,40, 6, DDV_HideList);
+
+    hdp->numrows = AlnMgrGetNumRows(hdp->target);
+
+    for(i = 1; i <= hdp->numrows; i++) {
+        sip = AlnMgrGetNthSeqIdPtr(hdp->target, i);
+        if(sip == NULL) continue;
+        bsp=BioseqLockById(sip);
+        if(bsp == NULL) continue;
+        sip = SeqIdFindBestAccession(bsp->id);
+        SeqIdWrite(sip, szName, PRINTID_TEXTID_ACCESSION, 10);
+        CreateDefLine(NULL,bsp,szName2,157,0,NULL,NULL);
+        BioseqUnlock(bsp);
+        StrNCat(szName, " - ", 180);
+        StrNCat(szName, szName2, 180);
+        ListItem(hdp->DDV_lsip, szName);
+    }   
+    DDV_SetHideList(hdp);
+
+    g = HiddenGroup(hg, 2, 1, NULL);
+    SetGroupSpacing(g, 15, 15);
+    b = DefaultButton(g, "OK", (BtnActnProc) DDV_HideAcceptProc);
+
+    Show(hdp->DDV_wHide);
+
+    /* set scroll to upper left */
+    SetOffset(hdp->DDV_lsip, 0, 0);
+
+    return;
+}
+
+NLM_EXTERN void DDV_HideDlgItem(IteM i)
+{
+    DDV_HideDialog *hdp;
+    DdvMainPtr    dmp;  /*DDV panel data*/
+    DdvMainWinPtr mWin_d;
+    WindoW		  hWinMain;
+
+    hdp = MemNew(sizeof(DDV_HideDialog));
+    if(hdp == NULL) return;
+
+    /* init LastValidRow to something illegal */
+    hdp->LastValidRow = -1;
+
+    hWinMain=(WindoW)ParentWindow(i);
+    if (hWinMain==NULL) return;
+    mWin_d = (DdvMainWinPtr) GetObjectExtra (hWinMain);
+    if (mWin_d==NULL) return;
+
+    if (mWin_d->hWndDDV==NULL) return;
+    dmp = (DdvMainPtr) GetObjectExtra(mWin_d->hWndDDV);
+    if (dmp==NULL) return;
+
+    if(dmp->MSA_d.pgp_l.sap == NULL) return;
+
+    hdp->salp = dmp->MSA_d.pgp_l.sap;
+
+    DDV_HideDlg(hdp);
+}
+
+
+/*******************************************************************************
+
+  Function : DDV_GetCharBufferForEditor()
+  
+  Purpose : get a char buffer from a row of a SeqAlign, given display coords
+
+  Return value : an allocated char buffer ready for use by the editor. Null if
+  failure
+
+*******************************************************************************/
+NLM_EXTERN void DDV_GetCharBufferForEditor(ParaGPtr pgp,CharPtr szEditSeq)
+{
+BioseqPtr  bsp;
+Int4       bspLength;
+Boolean    IsAA;
+
+	/*get sequence size and type*/
+	bsp=BioseqLockById(pgp->sip);
+	if (!bsp) return;
+	bspLength=BioseqGetLen(bsp);
+	IsAA=ISA_aa(bsp->mol);
+	BioseqUnlock(bsp);
+
+	/*get the sequence*/
+	DDV_GetSequenceFromParaG(pgp,&szEditSeq,bspLength,IsAA,NULL,NULL,NULL);
+	
+}
+
+/*******************************************************************************
+
+  Function : DDV_GetMtdpListForEditor()
+  
+  Purpose : get the descriptor for a row of a SeqAlign, given display coords
+
+  Note : in plain english, this function creates the pTxtList ValNode for
+     a ParaG designed to be used in the editor.
+	 
+  Return value : a valnode ready for use by the editor. Null if
+  failure. 
+
+*******************************************************************************/
+NLM_EXTERN ValNodePtr DDV_GetMtdpListForEditor(ValNodePtr row,Int4 from_disp,
+		Int4 to_disp)
+{
+MsaTxtDispPtr mtdp,new_mtdp,prev_mtdp;
+ValNodePtr vnp,vnp2,vnp3,vnpTxt;
+ParaGPtr   pgp;
+Int4       cumulMtdp,beginCopy,endCopy,mtdp_size,mtdp_from_disp,
+           mtdp_to_disp,mtdp_from,mtdp_to;
+Boolean    bPop;
+
+
+	
+	prev_mtdp=NULL;
+	vnpTxt=NULL;
+	for (vnp=row;vnp!=NULL;vnp=vnp->next){
+		pgp=(ParaGPtr)vnp->data.ptrvalue;
+		/*not yet in the first ParaG ?*/
+		if (pgp->StopLetter<from_disp) {
+			continue;
+		}
+		/*get the mtdp nodes*/
+		cumulMtdp=0;
+		for(vnp2=pgp->ptxtList;vnp2!=NULL;vnp2=vnp2->next){
+			mtdp=(MsaTxtDispPtr)vnp2->data.ptrvalue;
+			mtdp_size=mtdp->to-mtdp->from+1;
+			/*convert mtdp coordinates (can Bioseq coord, gap coord, etc.)
+			to display coordinates*/
+			mtdp_from_disp=pgp->StartLetter+cumulMtdp;
+			mtdp_to_disp=mtdp_from_disp+mtdp_size-1;
+			if (mtdp_to_disp<from_disp) {
+				cumulMtdp+=mtdp_size;
+				continue;
+			}
+			beginCopy=_max_(from_disp,mtdp_from_disp);
+			endCopy=_min_(mtdp_to_disp,to_disp);
+
+			/*convert display coordinates back to mtdp coordinates*/
+			mtdp_from=mtdp->from+(beginCopy-mtdp_from_disp);
+			mtdp_to=mtdp->from+(endCopy-mtdp_from_disp);
+
+			/*in order to merge nodes of same type, i keep track of
+			the previous populated mtdp node. Same style==yes, then
+			just extend to the right the previous node*/
+			if (prev_mtdp){
+				if (prev_mtdp->TextStyle==mtdp->TextStyle){
+					prev_mtdp->to=mtdp_to;
+					bPop=TRUE;
+				}
+				else{
+					bPop=FALSE;
+				}
+			}
+			else{
+				bPop=FALSE;
+			}
+			if (!bPop){
+				new_mtdp=(MsaTxtDispPtr)MemNew(sizeof(MsaTxtDisp));
+				if (!new_mtdp) goto erreur;
+				MemCopy(new_mtdp,mtdp,sizeof(MsaTxtDisp));
+				new_mtdp->from=mtdp_from;
+				new_mtdp->to=mtdp_to;
+				if (!vnpTxt){
+					vnp3=ValNodeAddPointer(&vnpTxt,0,(Pointer)new_mtdp);
+				}
+				else{
+					vnp3=ValNodeAddPointer(&vnp3,0,(Pointer)new_mtdp);
+				}
+				prev_mtdp=new_mtdp;
+			}
+			if (mtdp_to_disp>=to_disp) break;
+			cumulMtdp+=mtdp_size;
+		}
+		/*done ?*/
+		if (pgp->StopLetter>=to_disp) break;
+	}
+	return(vnpTxt);
+
+erreur:
+	if (vnpTxt){
+		DDV_DeleteTxtList(&vnpTxt);
+	}
+	return(NULL);
+}
+
+/*******************************************************************************
+
+  Function : DDV_CreateDataForEditor()
+  
+  Purpose : create a MsaParaGPopListPtr intended to be used by the editor
+
+  Return value : an allocated data block ready for use by the editor. Null if
+  failure
+
+*******************************************************************************/
+NLM_EXTERN MsaParaGPopListPtr DDV_CreateDataForEditor(MsaParaGPopListPtr mpplp, 
+	Int4 from_disp,Int4 to_disp)
+{
+MsaParaGPopListPtr new_mpplp;
+
+ParaGPtr           pgp,old_pgp;
+Int4               i,iNewAliSize,diff;
+
+	if (from_disp<0 || from_disp>=mpplp->LengthAli || from_disp>to_disp ||
+		to_disp<0 || to_disp>=mpplp->LengthAli){
+		return(NULL);
+	}
+	
+	diff=to_disp-from_disp;
+	iNewAliSize = diff+50;
+
+	if (iNewAliSize<1 || iNewAliSize>LIMIT_EDITOR_SIZE)
+		return(NULL);
+
+	new_mpplp=(MsaParaGPopListPtr)MemNew(sizeof(MsaParaGPopList));
+	if (!new_mpplp) return(NULL);
+	
+	/*table of ParaG list (each cell of that table corresponds to one row
+	of the seqalign to display*/
+	new_mpplp->TableHead=(ValNodePtr *)MemNew(mpplp->nBsp*sizeof(ValNodePtr));
+	if (!new_mpplp->TableHead) {
+		MemFree(new_mpplp);
+		return(NULL);
+	}
+	/*allocate the new ParaG list; for the editor there is a single ParaG for
+	each row (for the viewer there are usually n ParaGs for each row. For the
+	editor, the ParaG size = to_disp-from_disp+50 (whereas in the viewer a
+	ParaG size = ParaG_Size (usually 70; see pgppop.h)*/
+	for (i=0;i<mpplp->nBsp;i++){
+		/*allocations*/
+		pgp=(ParaGPtr)MemNew(sizeof(ParaG));
+		if (!pgp) goto erreur;
+		pgp->szEditSeq=(CharPtr)MemNew(iNewAliSize*sizeof(Char));
+		if (pgp->szEditSeq==NULL) goto erreur;
+		/*get the ParaG line descriptor */
+		pgp->ptxtList=DDV_GetMtdpListForEditor(mpplp->TableHead[i],from_disp,
+				to_disp);
+		if (!pgp->ptxtList) goto erreur;
+		/*get the char buffer*/
+                old_pgp=(ParaGPtr)mpplp->TableHead[i]->data.ptrvalue;
+                pgp->sip = old_pgp->sip;
+		DDV_GetCharBufferForEditor(pgp,pgp->szEditSeq);
+		if (*(pgp->szEditSeq)=='\0') goto erreur;
+		/*copy/init values*/
+		pgp->StartLetter = 0;
+		pgp->StopLetter = diff;
+		pgp->NumOrder = i;
+		pgp->StartLine = i;
+		pgp->nLines = 1;
+		pgp->ScaleStyle=SCALE_POS_NONE;
+		/*store pgp*/
+                new_mpplp->TableHead[i]=(ValNodePtr)MemNew(sizeof(ValNode));
+                if (!new_mpplp->TableHead[i]) goto erreur;
+		new_mpplp->TableHead[i]->data.ptrvalue=(Pointer)pgp;
+	}
+
+	/*seqali size and type*/
+	new_mpplp->LengthAli=diff+1;
+	new_mpplp->nBsp=mpplp->nBsp;
+	new_mpplp->sap=mpplp->sap;
+	new_mpplp->DisplayType=mpplp->DisplayType;
+	
+	/*entities table*/
+	new_mpplp->entitiesTbl=(Uint4Ptr)MemNew(new_mpplp->nBsp*sizeof(Uint4));
+	if (new_mpplp->entitiesTbl==NULL) goto erreur;
+	MemCopy(new_mpplp->entitiesTbl,mpplp->entitiesTbl,
+		new_mpplp->nBsp*sizeof(Uint4));
+	/*ruler descriptor*/
+	new_mpplp->RulerDescr=DDV_GetRulerForEditor(mpplp->RulerDescr,from_disp,
+			to_disp);
+	if (new_mpplp->RulerDescr==NULL) goto erreur;
+	return(new_mpplp);	
+	
+erreur : /*serious problem*/	
+	if (new_mpplp->entitiesTbl) 
+		MemFree(new_mpplp->entitiesTbl);
+	if (new_mpplp->RulerDescr)
+		ValNodeFreeData(new_mpplp->RulerDescr);
+	DDV_DeleteDisplayList(new_mpplp);
+	MemFree(new_mpplp);
+	return(NULL);
+}
+
+
diff --git a/ddv/ddvopen.h b/ddv/ddvopen.h
new file mode 100644
index 00000000..9f4900b8
--- /dev/null
+++ b/ddv/ddvopen.h
@@ -0,0 +1,336 @@
+/*  $Id: ddvopen.h,v 1.23 2000/07/17 17:46:48 hurwitz Exp $
+* ===========================================================================
+*
+*                            PUBLIC DOMAIN NOTICE
+*            National Center for Biotechnology Information (NCBI)
+*
+*  This software/database is a "United States Government Work" under the
+*  terms of the United States Copyright Act.  It was written as part of
+*  the author's official duties as a United States Government employee and
+*  thus cannot be copyrighted.  This software/database is freely available
+*  to the public for use. The National Library of Medicine and the U.S.
+*  Government do not place any restriction on its use or reproduction.
+*  We would, however, appreciate having the NCBI and the author cited in
+*  any work or product based on this material
+*
+*  Although all reasonable efforts have been taken to ensure the accuracy
+*  and reliability of the software and data, the NLM and the U.S.
+*  Government do not and cannot warrant the performance or results that
+*  may be obtained by using this software or data. The NLM and the U.S.
+*  Government disclaim all warranties, express or implied, including
+*  warranties of performance, merchantability or fitness for any particular
+*  purpose.
+*
+* ===========================================================================
+*
+* File Name:  ddvopen.h
+*
+* Author:  Patrick Durand
+*
+* Version Creation Date:   06/19/99
+*
+* $Revision: 1.23 $
+*
+* File Description: 
+*
+* Modifications:
+* --------------------------------------------------------------------------
+* $Log: ddvopen.h,v $
+* Revision 1.23  2000/07/17 17:46:48  hurwitz
+* made it so show/hide dialog only updates view when ok is clicked
+*
+* Revision 1.22  2000/07/08 20:43:58  vakatov
+* Get all "#include" out of the 'extern "C" { }' scope;  other cleanup...
+*
+* Revision 1.21  2000/06/16 14:57:03  lewisg
+* move entrez calls out of desktop
+*
+* Revision 1.20  2000/05/15 23:39:34  lewisg
+* shred cblast, add menu items for gapped/ungapped, fix pdbheaders
+*
+* Revision 1.19  2000/05/15 22:00:36  hurwitz
+* put save-edits query into DDV_SlaveQuit where it belongs
+*
+* Revision 1.18  2000/05/11 16:28:44  wheelan
+* made DDV_ShredAln NLM_EXTERN
+*
+* Revision 1.17  2000/04/17 13:30:42  durand
+* removed g_hParent and unused functions DDV_LaunchAlignViewer and DDV_LaunchAlignEditor
+*
+* Revision 1.16  2000/04/08 00:37:32  lewisg
+* multiple seqentries, NEWSEQ message, etc.
+*
+* Revision 1.15  2000/03/27 22:15:08  lewisg
+* add show/hide row dialog
+*
+* Revision 1.14  2000/03/24 20:34:58  lewisg
+* add blast from file, bug fixes, get rid of redundant code, etc.
+*
+* Revision 1.13  2000/01/26 13:38:54  durand
+* update the GUI for the editor. Add functions to create the data to be used by the editor
+*
+* Revision 1.12  2000/01/12 21:52:17  durand
+* add import function; update menus when DDV is loaded from Cn3D
+*
+* Revision 1.11  1999/12/30 21:08:45  lewisg
+* bioseq import dialog
+*
+* Revision 1.10  1999/12/29 22:55:03  lewisg
+* get rid of seqalign id
+*
+* Revision 1.9  1999/12/20 20:20:41  lewisg
+* allow cn3d to do color and ddv to do case when both are running
+*
+* Revision 1.8  1999/12/03 23:17:23  lewisg
+* Patrick's new global update msg, argument passing when launching ddv, experimental editing
+*
+* Revision 1.7  1999/11/29 15:26:26  durand
+* designed a new GUI to fix problems under MacOS, Linux and SGI
+*
+* Revision 1.6  1999/11/03 21:29:47  durand
+* add CTRL and SHFT keys for mouse selection. redesign the loader functions of DDV to properly register the message callbacks
+*
+* Revision 1.5  1999/10/29 19:04:21  durand
+* move DDVUpdateMSG in objmgr.h
+*
+* Revision 1.4  1999/10/29 14:15:39  durand
+* add simple mouse selection functions
+*
+* Revision 1.3  1999/10/20 13:17:18  durand
+* add display for disc. SeqAlign tails
+*
+* Revision 1.2  1999/10/16 15:02:25  durand
+* fixes due to toolkit build failed
+*
+* Revision 1.1  1999/09/30 14:10:28  durand
+* add ddv to toolkit
+*
+* Revision 1.8  1999/09/28 17:29:41  durand
+* add include of udviewer.h
+*
+* Revision 1.7  1999/09/16 13:07:53  durand
+* add File|Close and File|Open|Network commands
+*
+* Revision 1.6  1999/09/09 21:55:06  durand
+* instantiate the Fle|Close command of DDV
+*
+* Revision 1.5  1999/07/29 12:43:07  durand
+* update DDV_GetAndCheckSeqAlign
+*
+* Revision 1.4  1999/07/01 15:28:29  durand
+* validate function loaders of DDV
+*
+* Revision 1.2  1999/06/28 22:07:21  durand
+* add loader functions and clean the code with Lint and Purify
+*
+* Revision 1.1  1999/06/19 17:21:07  durand
+* add Vibrant DDV code
+*
+*
+*
+* ==========================================================================
+*/
+
+#ifndef _DDVOPEN_
+#define _DDVOPEN_
+
+#include <ncbi.h>
+#include <udviewer.h>
+#include <samutil.h>
+#include <accentr.h>
+#include <pgppop.h>
+#include <alignmgr.h>
+
+#undef NLM_EXTERN
+#ifdef NLM_IMPORT
+#define NLM_EXTERN NLM_IMPORT
+#else
+#define NLM_EXTERN extern
+#endif
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+
+/******************************************************************************
+
+	ERROR / Information messages from DDV_OPEN module 
+
+******************************************************************************/
+#define DVV_MSG_O_I_NOMAINDATA   2000
+#define DVV_MSG_O_E_READFILE     2001
+#define DVV_MSG_O_E_READGI       2002
+#define DVV_MSG_O_E_NOFETCHFUNC  2003
+#define DVV_MSG_O_E_BADTYPE      2004
+#define DVV_MSG_O_E_NOTHINGTODO  2005
+#define DVV_MSG_O_E_OPENFILEFAIL 2006
+
+/******************************************************************************
+
+	other defines
+
+******************************************************************************/
+	/*use only by the standalone version of DDV */
+#define REG_DDV_AUTO_EDIT ObjMgrProcLoad(OMPROC_EDIT, \
+		"DDV", "MSA_Editor", OBJ_SEQALIGN, 0, OBJ_SEQALIGN, 0, \
+		NULL, DDV_ObjRegMasterEditDDV, 0)	
+#define REG_DDV_AUTO_VIEW ObjMgrProcLoad(OMPROC_VIEW, \
+		"DDV", "MSA_Viewer", OBJ_SEQALIGN, 0, OBJ_SEQALIGN, 0, \
+		NULL, DDV_ObjRegMasterViewDDV, 0)	
+
+	/*slave 1 : the editor in a separate window*/
+#define REG_DDV_SLA_EDIT ObjMgrProcLoad(OMPROC_EDIT, \
+		"DDV", "MSA_Editor", OBJ_SEQALIGN, 0, OBJ_SEQALIGN, 0, \
+		NULL, DDV_ObjRegSlaveEditDDV, 0)	
+
+	/*slave 2 : the viewer in a separate window*/
+#define REG_DDV_SLA_VIEW ObjMgrProcLoad(OMPROC_VIEW, \
+		"DDV", "MSA_Viewer", OBJ_SEQALIGN, 0, OBJ_SEQALIGN, 0, \
+		NULL, DDV_ObjRegSlaveViewDDV, 0)	
+
+/*the following are used to delete data when closing DDV*/
+#define DDV_OPENTYPE_NOTRESP ((Uint1)1)/*if DDV is not responsible to delete
+                                         data when closing*/
+#define DDV_OPENTYPE_FILE    ((Uint1)2)/*if ReadAsnFastaOrFlatFile was used*/
+#define DDV_OPENTYPE_SEP     ((Uint1)3)/*if get a SEP*/
+#define DDV_OPENTYPE_GI      ((Uint1)4)/*if fetch GI from DB was used*/
+
+/******************************************************************************
+
+	Data structures
+
+******************************************************************************/
+typedef struct dlgfileopendata {/*use to manage the FileOpen dialog box*/
+	WindoW 		parent;			/*main window of the application*/
+	TexT		FNameEditCtrl;	/*handle of the file text control*/
+	ButtoN		Ok;				/*handle of the Ok button*/
+	GrouP		ReadMode;		/*handle of the file type control*/
+} DlgFileOpenData, PNTR DlgFileOpenDataPtr;
+
+typedef struct ddvopendata {
+	Uint1           choice;
+	SeqEntryPtr     sep;
+	ValNodePtr      vnp;
+	} DdvOpenData, PNTR DdvOpenDataPtr;
+
+typedef struct ddvupdatelayoutdata{
+	/*color display ?*/
+	Boolean bUseColors;
+	/*styles for a disc. seqalign*/
+	Boolean ShowLeftTail;
+	Boolean ShowRightTail;
+	Uint1   DispDiscStyle;
+	Uint1   SpacerSize;
+    Uint1   DiscJustification;
+	/*style for sequences*/
+	Int4    nSeq;	/*number of rows (sequences) to update*/
+	Int4Ptr SeqList; /*list of row number; one-based array*/
+	Uint1   RulerStyle;
+	/*DDV panel handle*/
+	PaneL   ddv_panel;
+	}DDVUpdateLayoutData, PNTR DDVUpdateLayoutDataPtr;
+
+struct _DDV_ImportDialog;
+typedef void (*DDV_ImportProcCB)(struct _DDV_ImportDialog *idp, SeqAlign *salpdest,
+                                 SeqAlign *salp);
+
+typedef Int4 (*DDV_AccessionCB)(CharPtr string, Boolean IsAmino);
+
+/* for the BLAST import dialog */
+typedef struct _DDV_ImportDialog {
+    WindoW DDV_wImport; /*the import dialog*/
+    GrouP DDV_gAccType; /*the type of accession*/
+    ButtoN DDV_bImportAccept; /*accept button*/
+    TexT DDV_tAccession; /* the accession */
+    LisT DDV_lsip;  /* list box of sips */
+    SeqId *sip;  /* the master sequence */
+    SeqAlign *sap; /* the seqalign to add to */
+    SeqId *sipslave;  /* the slave sequence if it exists */
+    void *userdata; /* for the update message */
+    DDV_ImportProcCB callback;  /* called after alignment created */
+    ValNode *pvnSips;  /* list of sips to blast against */
+    Int4 mode; /* see below */
+    SeqEntry *sep;  /* used to pass new seqentry to call back */
+    Bioseq *bsp; /* the bioseq being added */
+    Boolean Gap; /* should the alignment used gapped blast? */
+    DDV_AccessionCB AccessionCB; /* converts accession to gi */
+} DDV_ImportDialog;
+
+/* import to sequence to seqalign */
+#define DDVIMPSE2SA 0x0
+/* import sequence to sequence */
+#define DDVIMPSE2SE 0x1
+#define DDVIMP2SE 0x1
+/* import net sequence to seqalign */
+#define DDVIMPNET2SA 0x2
+#define DDVIMPNET 0x2
+/* import net sequence to sequence */
+#define DDVIMPNET2SE 0x3
+
+struct _DDV_HideDialog;
+typedef void (*DDV_HideProcCB)(struct _DDV_HideDialog *hdp);
+
+typedef struct _DDV_HideDialog {
+    WindoW DDV_wHide; /*the show/hide dialog*/
+    LisT DDV_lsip;  /* multilist box of sips */
+    SeqAlign *salp; /* the seqalign that is shown/hid */
+    SeqAlign *target; /* the original seqalign */
+    AMAlignIndexPtr amaip; /* target index */
+    void *userdata; /* for the update message */
+    DDV_HideProcCB callback;  /* called on every show/hide */
+    Int4 numrows;  /* true number of rows in target seqalign */
+    Int4 LastValidRow; /* must be 2 valid rows in list, this and master */
+} DDV_HideDialog;
+
+/******************************************************************************
+
+	Extern functions
+
+******************************************************************************/
+extern Int2 LIBCALLBACK DDV_ObjRegMasterEditDDV (Pointer data);
+extern Int2 LIBCALLBACK DDV_ObjRegMasterViewDDV (Pointer data);
+extern Int2 LIBCALLBACK DDV_ObjRegSlaveEditDDV (Pointer data);
+extern Int2 LIBCALLBACK DDV_ObjRegSlaveViewDDV (Pointer data);
+extern void DDV_OpenFile(IteM i);
+extern void DDV_OpenNetwork(IteM i);
+extern ValNodePtr DDV_GetAndCheckSeqAlign(FILE *fp,Int4 gi,SeqEntryPtr sep2,
+	UdvFetchSeqEntryProc fetchSepProc,DdvOpenDataPtr dodp,Uint2Ptr entityID);
+extern WindoW DDV_StartMainWin_Slave(SAM_ViewGlobal *vgp,Boolean bEditor);
+
+extern ValNodePtr DDV_GetSelectedRegions(SelStructPtr om_slp, Uint2 bsp_eID,
+	Uint2 bsp_iID);
+extern Boolean DDV_IsLetterSelected(ValNodePtr vnp_bsp, Int4 bsp_pos);
+
+NLM_EXTERN void DDV_ImportBioseqDlg(DDV_ImportDialog *idp);
+NLM_EXTERN void DDV_ImportBioseq(IteM i);
+NLM_EXTERN SeqAlignPtr DDV_ShredAln(SeqAlignPtr sap);
+NLM_EXTERN void DDV_DoAlign(DDV_ImportDialog *idp);
+NLM_EXTERN void DDV_ImportCB(DDV_ImportDialog *idp, SeqAlign *salpdest,
+                             SeqAlign *salp);
+NLM_EXTERN SeqAlign *DDV_Blast2Seqs(Bioseq *bsp1, Bioseq *bsp2, Boolean gapped,
+                         Char *progname);
+extern void DDV_ImportNucSeqAlign(IteM i);
+extern void DDV_ImportProtSeqAlign(IteM i);
+NLM_EXTERN void DDV_HideDlgItem(IteM i);
+NLM_EXTERN void DDV_HideDlg(DDV_HideDialog *hdp);
+NLM_EXTERN void DDV_GetCharBufferForEditor(ParaGPtr pgp,CharPtr szEditSeq);
+NLM_EXTERN ValNodePtr DDV_GetMtdpListForEditor(ValNodePtr row,Int4 from_disp,
+		Int4 to_disp);
+NLM_EXTERN MsaParaGPopListPtr DDV_CreateDataForEditor(MsaParaGPopListPtr mpplp, 
+	Int4 from_disp,Int4 to_disp);
+NLM_EXTERN void DDV_SlaveQuit(WindoW w);
+
+
+#ifdef __cplusplus
+}
+#endif
+
+#undef NLM_EXTERN
+#ifdef NLM_EXPORT
+#define NLM_EXTERN NLM_EXPORT
+#else
+#define NLM_EXTERN
+#endif
+
+#endif /* ndef _DDVOPEN_ */
diff --git a/ddv/ddvpanel.c b/ddv/ddvpanel.c
new file mode 100644
index 00000000..0b73b966
--- /dev/null
+++ b/ddv/ddvpanel.c
@@ -0,0 +1,3674 @@
+/*  $Id: ddvpanel.c,v 1.107 2000/08/30 14:31:28 hurwitz Exp $
+* ===========================================================================
+*
+*                            PUBLIC DOMAIN NOTICE
+*            National Center for Biotechnology Information (NCBI)
+*
+*  This software/database is a "United States Government Work" under the
+*  terms of the United States Copyright Act.  It was written as part of
+*  the author's official duties as a United States Government employee and
+*  thus cannot be copyrighted.  This software/database is freely available
+*  to the public for use. The National Library of Medicine and the U.S.
+*  Government do not place any restriction on its use or reproduction.
+*  We would, however, appreciate having the NCBI and the author cited in
+*  any work or product based on this material
+*
+*  Although all reasonable efforts have been taken to ensure the accuracy
+*  and reliability of the software and data, the NLM and the U.S.
+*  Government do not and cannot warrant the performance or results that
+*  may be obtained by using this software or data. The NLM and the U.S.
+*  Government disclaim all warranties, express or implied, including
+*  warranties of performance, merchantability or fitness for any particular
+*  purpose.
+*
+* ===========================================================================
+*
+* File Name:  ddvpanel.c
+*
+* Author:  Patrick Durand
+*
+* Version Creation Date:   06/19/99
+*
+* $Revision: 1.107 $
+*
+* File Description: window management module of DeuxD-Viewer (DDV)
+*
+* Modifications:
+* --------------------------------------------------------------------------
+* $Log: ddvpanel.c,v $
+* Revision 1.107  2000/08/30 14:31:28  hurwitz
+* quick fix so build does not crash
+*
+* Revision 1.106  2000/07/25 20:30:23  hurwitz
+* bug fixes: panel update when file is closed, double-click launches UDV from DDE, seqName agrees in status line and left col
+*
+* Revision 1.105  2000/07/24 22:00:09  hurwitz
+* fixed bug that 1/2 characters were displayed sometimes
+*
+* Revision 1.104  2000/07/20 22:25:57  hurwitz
+* bug fix.  mouse-mode query working again
+*
+* Revision 1.103  2000/07/19 19:04:02  hurwitz
+* fixed bug that was causing overwrite of numbering over tick marks in DDE
+*
+* Revision 1.102  2000/07/17 13:32:33  lewisg
+* move DDV_args out of the library
+*
+* Revision 1.101  2000/07/17 12:38:53  kans
+* DDV_myargs is extern in header, instantiated in ddvpanel.c, since it is accessed from that library file
+*
+* Revision 1.100  2000/07/14 22:24:56  lewisg
+* fix scroll, click, visual c++ build bugs.  add command line arg parse to ddv
+*
+* Revision 1.99  2000/07/12 22:22:41  hurwitz
+* added delete block to DDV
+*
+* Revision 1.98  2000/07/10 14:38:08  lewisg
+* move seqalign and sequentry data from window to panels
+*
+* Revision 1.97  2000/07/07 22:31:14  lewisg
+* interface tweaks
+*
+* Revision 1.96  2000/07/05 19:23:13  lewisg
+* add two panes to ddv, update msvc project files
+*
+* Revision 1.95  2000/07/05 18:42:16  hurwitz
+* added split block function to DDV
+*
+* Revision 1.94  2000/06/30 22:31:51  hurwitz
+* added merge block function for DDV
+*
+* Revision 1.93  2000/06/29 23:15:13  hurwitz
+* leave single space between aligned blocks with no unaligned sequence between them, no auto-merge of adjacent aligned blocks
+*
+* Revision 1.92  2000/06/27 20:46:38  hurwitz
+* fixed bugs with select rectangle, added select row option
+*
+* Revision 1.91  2000/06/22 20:56:51  hurwitz
+* assorted bug fixes
+*
+* Revision 1.90  2000/06/20 19:35:11  hurwitz
+* use indexed seqAlign when necessary, make multiple when redrawing
+*
+* Revision 1.89  2000/06/15 20:26:05  hurwitz
+* added left/right/center justify for DDE
+*
+* Revision 1.88  2000/06/15 17:33:18  hurwitz
+* used view seqAlignPtr to get original (bug fix), and started working on left/right/center justify for DDE
+*
+* Revision 1.87  2000/06/15 16:01:07  hurwitz
+* rewrote section that calls ViewMgr_Attach when SeqAlign is not editable but IBMable
+*
+* Revision 1.86  2000/06/12 23:02:40  hurwitz
+* enable launch of DDE from Cn3D, swith from DDV_ComputeRuler to DDE_ReMakeRuler, get rid of styles option for DDE
+*
+* Revision 1.85  2000/06/08 20:04:39  hurwitz
+* made warning about converting to true multiple alignment into a Message window, and other small fixes
+*
+* Revision 1.84  2000/06/02 19:57:03  hurwitz
+* added a query dialog when converting from pairwise multiple to true multiple, bug fix of double freeing of a seqAlignPtr
+*
+* Revision 1.83  2000/05/31 23:07:26  hurwitz
+* made NoGaps a runtime parameter, fixed bug with vertical scroll of show/hide list, save edits query is not performed if nothing to save
+*
+* Revision 1.82  2000/05/25 21:40:43  hurwitz
+* rows hidden in DDV are hidden in DDE, can save edits when rows are hidden in DDE
+*
+* Revision 1.81  2000/05/24 21:43:00  hurwitz
+* getting hide/show rows to work with DDV and DDE together
+*
+* Revision 1.80  2000/05/23 22:00:15  hurwitz
+* working on launch of DDE from DDV
+*
+* Revision 1.79  2000/05/19 13:48:31  hurwitz
+* made a version of DDE that doesn't allow aligned gaps, changed wording for adding new rows
+*
+* Revision 1.78  2000/05/16 19:43:01  hurwitz
+* grey out create block, delete block, undo, and redo as needed
+*
+* Revision 1.77  2000/05/15 23:39:34  lewisg
+* shred cblast, add menu items for gapped/ungapped, fix pdbheaders
+*
+* Revision 1.76  2000/05/15 22:00:36  hurwitz
+* put save-edits query into DDV_SlaveQuit where it belongs
+*
+* Revision 1.75  2000/05/12 21:18:13  hurwitz
+* added window asking if user wants to save unsaved edits for dde
+*
+* Revision 1.74  2000/05/10 21:54:54  hurwitz
+* free memory when DDE is closed
+*
+* Revision 1.73  2000/05/10 16:17:00  hurwitz
+* can show tails for just 1 aligned block
+*
+* Revision 1.72  2000/05/09 17:56:49  hurwitz
+* bug fix of vertical scrolling problem
+*
+* Revision 1.71  2000/05/08 22:48:33  hurwitz
+* on launch of DDE, merge nodes that are same MsaTxtDisp alignment and gap
+*
+* Revision 1.70  2000/05/05 20:24:13  hurwitz
+* some bug fixes, also redraw proper block in DDE after a save operation that causes a merge of 2 blocks
+*
+* Revision 1.69  2000/05/04 22:43:38  hurwitz
+* don't launch DDE on top of DDV, change some wording, redraw DDE after save to AlnMgr
+*
+* Revision 1.68  2000/04/28 14:43:37  hurwitz
+* send message to DDV after edits in DDE are accepted by AlnMgr
+*
+* Revision 1.67  2000/04/27 22:24:36  lewisg
+* misc bugs
+*
+* Revision 1.66  2000/04/27 20:05:54  kans
+* added stub functions for Sequin
+*
+* Revision 1.65  2000/04/27 19:57:59  hurwitz
+* scroll to aligned block on launch of DDE
+*
+* Revision 1.64  2000/04/27 15:38:02  hurwitz
+* changed wording on menu
+*
+* Revision 1.63  2000/04/27 13:33:42  durand
+* SpacerSize min value fixed to 1; update view when SpacerSize is changed
+*
+* Revision 1.62  2000/04/26 21:54:27  hurwitz
+* added save function to tell AlnMgr about edits made in DDE
+*
+* Revision 1.61  2000/04/21 23:00:50  hurwitz
+* can launch DDE from DDV
+*
+* Revision 1.60  2000/04/18 19:50:26  lewisg
+* add deselect menu item
+*
+* Revision 1.59  2000/04/17 21:46:56  lewisg
+* do not do double index on viewmgr update, rename menus
+*
+* Revision 1.58  2000/04/10 21:41:26  lewisg
+* move alignment menus into ddv, udv from cn3d
+*
+* Revision 1.57  2000/04/10 20:58:42  hurwitz
+* added GUI controls for DeleteBlock in DDE
+*
+* Revision 1.56  2000/04/07 16:21:08  hurwitz
+* made delete block faster, added delete block to edit menu
+*
+* Revision 1.55  2000/03/31 19:33:50  durand
+* added DDV_ShowHideUnAlignGap for import seq. debugging purpose
+*
+* Revision 1.54  2000/03/27 22:15:08  lewisg
+* add show/hide row dialog
+*
+* Revision 1.53  2000/03/25 00:22:09  hurwitz
+* put DDE_StackPtr in DDV_Main, add to stack inside DDE api's, added insert char, delete char, home and end keyboard control
+*
+* Revision 1.52  2000/03/23 00:00:00  hurwitz
+* DDE api's are called with stack now
+*
+* Revision 1.51  2000/03/21 14:29:49  durand
+* fixed a problem with menus setup
+*
+* Revision 1.49  2000/03/20 22:22:48  hurwitz
+* added more checks to verify subroutine, 1 bug fix
+*
+* Revision 1.48  2000/03/17 16:15:30  durand
+* added ASN.1 SeqAlign and SeqAnoot export
+*
+* Revision 1.47  2000/03/16 20:53:48  thiessen
+* removed C++ style comment
+*
+* Revision 1.46  2000/03/16 15:51:32  hurwitz
+* added function to create an aligned block
+*
+* Revision 1.45  2000/03/16 14:11:59  durand
+* set corretly mouse mode menu
+*
+* Revision 1.44  2000/03/14 22:08:21  hurwitz
+* undo and redo working properly, restore-original function added
+*
+* Revision 1.43  2000/03/10 23:01:43  hurwitz
+* added undo and redo functions, first pass
+*
+* Revision 1.42  2000/03/09 22:28:40  hurwitz
+* added shift block and delete block, a bug fix too
+*
+* Revision 1.41  2000/03/08 22:02:07  hurwitz
+* added verify function, debugging, handle align_start != 0
+*
+* Revision 1.40  2000/03/06 22:45:58  hurwitz
+* can shift right boundary of an aligned block left and right, DDVRuler updates added
+*
+* Revision 1.39  2000/03/02 15:43:11  durand
+* use MovableModalWindow for dialog boxes
+*
+* Revision 1.38  2000/03/01 22:49:41  lewisg
+* import bioseq, neatlyindex, get rid of dead code
+*
+* Revision 1.37  2000/02/29 21:13:06  hurwitz
+* added low level functions for shifting left and right the left alignment boundary
+*
+* Revision 1.36  2000/02/28 16:28:39  hurwitz
+* added functions for deleting an aligned gap
+*
+* Revision 1.35  2000/02/24 23:37:00  hurwitz
+* added ability to insert gaps
+*
+* Revision 1.34  2000/02/18 16:06:22  hurwitz
+* for editing multiple sequence alignments: shift row right now working
+*
+* Revision 1.33  2000/02/14 20:58:57  hurwitz
+* added functions for editing multiple sequence alignments: hide/show row, move row, shift row left
+*
+* Revision 1.32  2000/02/08 14:10:42  durand
+* made extern the functions DDV_UpdateHScrollVal and
+*
+* Revision 1.31  2000/02/07 14:03:35  durand
+* replace BioseqUnlockById by BioseqUnlock
+*
+* Revision 1.30  2000/02/05 01:32:22  lewisg
+* add viewmgr, move place freeing is done in ddv, modify visual c++ projects
+*
+* Revision 1.29  2000/02/04 16:05:41  durand
+* add click action to select a row
+*
+* Revision 1.28  2000/01/26 13:38:55  durand
+* update the GUI for the editor. Add functions to create the data to be used by the editor
+*
+* Revision 1.27  2000/01/18 22:49:16  lewisg
+* send OM_MSG_FLUSH to ddv/udv, tweak CPK coloration, misc bugs
+*
+* Revision 1.26  2000/01/12 21:52:17  durand
+* add import function; update menus when DDV is loaded from Cn3D
+*
+* Revision 1.25  2000/01/12 15:49:42  durand
+* add About dlg box and fix a bug in selection
+*
+* Revision 1.24  2000/01/11 15:05:23  durand
+* remove network stuff
+*
+* Revision 1.23  2000/01/10 15:09:45  durand
+* Use Entrez instead of ID1
+*
+* Revision 1.22  1999/12/23 19:22:07  durand
+* modify default options for DDV when loaded from Cn3D
+*
+* Revision 1.21  1999/12/21 15:27:24  durand
+* avoid to quit Cn3D when closing DDV
+*
+* Revision 1.20  1999/12/20 20:20:41  lewisg
+* allow cn3d to do color and ddv to do case when both are running
+*
+* Revision 1.19  1999/12/07 21:40:14  durand
+* add mouse modes menu and caret facility for the editor
+*
+* Revision 1.18  1999/12/06 16:19:19  durand
+* add GoTo facility to DDV
+*
+* Revision 1.17  1999/12/03 23:17:23  lewisg
+* Patrick's new global update msg, argument passing when launching ddv, experimental editing
+*
+* Revision 1.16  1999/11/30 18:19:48  durand
+* fix a problem with function declaration DDV_CloseData
+*
+* Revision 1.15  1999/11/30 17:28:59  durand
+* fix a problem of redeclaration of the function DDV_CloseData
+*
+* Revision 1.14  1999/11/30 14:17:31  durand
+* fix a bug occuring when deleting a SeqAlign
+*
+* Revision 1.13  1999/11/29 15:26:26  durand
+* designed a new GUI to fix problems under MacOS, Linux and SGI
+*
+* Revision 1.12  1999/11/17 22:43:59  durand
+* speed up the selection manager for large SeqAlign
+*
+* Revision 1.11  1999/11/04 22:11:37  durand
+* add the Desktop to DDV. Add a better set of cleanup functions when closing DDV. Before creating color tables, try to get them from the SeqAlign
+*
+* Revision 1.10  1999/11/03 21:29:48  durand
+* add CTRL and SHFT keys for mouse selection. redesign the loader functions of DDV to properly register the message callbacks
+*
+* Revision 1.9  1999/10/29 19:04:59  durand
+* move DDVUpdateMSG in objmgr.h
+*
+* Revision 1.8  1999/10/29 14:15:38  durand
+* add simple mouse selection functions
+*
+* Revision 1.7  1999/10/22 20:12:47  durand
+* add Export command (text, HTML and Phylip formats)
+*
+* Revision 1.6  1999/10/20 15:01:16  durand
+* bug fixed when closing Display Styles DlgBox
+*
+* Revision 1.5  1999/10/20 13:17:19  durand
+* add display for disc. SeqAlign tails
+*
+* Revision 1.4  1999/10/16 15:02:25  durand
+* fixes due to toolkit build failed
+*
+* Revision 1.3  1999/10/15 21:57:36  durand
+* add a UI for display options
+*
+* Revision 1.2  1999/10/02 15:11:20  durand
+* update the code to reuse more functions from UDV
+*
+* Revision 1.1  1999/09/30 14:10:29  durand
+* add ddv to toolkit
+*
+* Revision 1.9  1999/09/21 14:19:08  durand
+* add mouse click management layout
+*
+* Revision 1.8  1999/09/16 13:07:53  durand
+* add File|Close and File|Open|Network commands
+*
+* Revision 1.7  1999/09/09 21:55:06  durand
+* instantiate the Fle|Close command of DDV
+*
+* Revision 1.6  1999/07/20 14:58:02  durand
+* use the Color Manager to display colored MSA
+*
+* Revision 1.5  1999/07/01 15:28:29  durand
+* validate function loaders of DDV
+*
+* Revision 1.2  1999/06/28 22:07:19  durand
+* add loader functions and clean the code with Lint and Purify
+*
+* Revision 1.1  1999/06/19 17:21:06  durand
+* add Vibrant DDV code
+*
+*
+*
+* ==========================================================================
+*/
+
+#include <ncbi.h>
+#include <vibrant.h>
+#include <udviewer.h>
+#include <ddvpanel.h>
+#include <ddvopen.h>
+#include <ddvmain.h>
+#include <ddvgraph.h>
+#include <ddvclick.h>
+#include <ddvcreate.h>
+#include <alignmgr.h>
+#include <objmgr.h>
+#include <pgppop.h>
+#include <vsm.h>
+#include <salfiles.h>
+#include <viewmgr.h>
+
+Char szAppName[]="DDV";
+Char szAppName2[]="DDE";
+
+/*local text*/
+static Char szAbout[]="DeuxD-Viewer : A sequence alignment viewer for GenBank\n\
+Version 1.0\n\nInformation Engineering Branch\n\
+NCBI - NLM - NIH, Bldg 38A\n\
+8600 Rockville Pike\n\
+Bethesda, MD 20894 - USA\n\n\
+info@ncbi.nlm.nih.gov";
+
+#ifdef DEBUG_DDV
+static void DDV_ShowHideUnAlignGap(IteM i);
+#endif
+static void DDV_ExportTexte(IteM i);
+static void UDV_GotoBtnProc(ButtoN g);
+static void DDV_DeleteRow(IteM i);
+static void DDV_MoveRowLeft(IteM i);
+static void DDV_MoveRowRight(IteM i);
+static void DDV_MoveLeftBoundaryLeft(IteM i);
+static void DDV_MoveLeftBoundaryRight(IteM i);
+static void DDV_MoveRightBoundaryLeft(IteM i);
+static void DDV_MoveRightBoundaryRight(IteM i);
+static void DDV_DeleteBlock(IteM i);
+static void DDV_CreateBlock(IteM i);
+static void DDV_Prev(IteM i);
+static void DDV_Next(IteM i);
+static void DDV_Orig(IteM i);
+static void DDV_DoEditFunction(IteM i, Int4 WhichOne);
+static void DDV_LaunchEditor(IteM i);
+static void DDV_MergeBlocks(IteM i);
+static void DDV_SplitBlock(IteM i);
+static void DDV_DeleteBlock2(IteM i);
+static void DDV_CallSaveEdits(IteM i);
+
+/*******************************************************************************
+
+  Function : DDV_AboutProc()
+  
+  Purpose : about dialog box
+  
+  Parameters : -
+  
+  Return value : none 
+
+*******************************************************************************/
+static void  DDV_AboutProc(IteM i)
+{
+  MsgAlert(KEY_OK, SEV_INFO, "About DeuxD-Viewer",szAbout);
+}
+
+/*******************************************************************************
+
+  Function : DDV_EnableGotoTBItems()
+  
+  Purpose : enable/disable the controls for "GoTo col,row" toolbar 
+  
+  Return value : none 
+
+*******************************************************************************/
+typedef void (*MyEnaDisable) (Handle a);
+extern void DDV_EnableGotoTBItems(WindoW hParent,Boolean bEnable)
+{
+DdvMainWinPtr      dmwp;
+MyEnaDisable       my_func;
+
+	dmwp=(DdvMainWinPtr)GetObjectExtra(hParent);
+	if (!dmwp) return;
+	
+	if (bEnable)	
+		my_func=Enable;
+	else
+		my_func=Disable;
+	
+	my_func(dmwp->gotoBtn);
+	my_func(dmwp->gotoValCol);
+	my_func(dmwp->gotoValRow);
+}
+
+
+/*******************************************************************************
+
+  Function : DDV_WhatSize()
+  
+  Purpose : compute nTotLines and nTotCol depending on the display type 
+  
+  Parameters : -
+  
+  Return value : -
+
+*******************************************************************************/
+extern void DDV_WhatSize(DdvMainPtr dmp)
+{
+Int4 i;
+ParaGPtr pgp;
+	
+	if (dmp==NULL) return;
+	
+	dmp->GrData.udv_panel.nTotLines=0;
+	
+	if (dmp->MSA_d.pgp_l.DisplayType==0) return;
+	if(dmp->MSA_d.pgp_l.DisplayType==DDV_DISP_HORZ){
+		for(i=0;i<dmp->MSA_d.pgp_l.nBsp;i++){
+			if (dmp->MSA_d.pgp_l.TableHead[i]->data.ptrvalue){
+				pgp=(ParaGPtr)(dmp->MSA_d.pgp_l.TableHead[i]->data.ptrvalue);
+				dmp->GrData.udv_panel.nTotLines+=pgp->nLines;
+			}
+		}	
+		dmp->GrData.udv_panel.nTotCol=dmp->MSA_d.pgp_l.LengthAli;
+	}
+	else{/*full vertical display*/
+		/*not yet implemented*/
+		return;/*add to avoid a 'lint' warning*/
+	}
+}
+
+/*******************************************************************************
+
+  Function : DDV_CalcVHScrollPgUD()
+  
+  Purpose : compute PageUp & Down (V & H Scrolls) 
+  
+  Parameters : cxyClient; either width of height of DDV panel
+			LineHeight; either width of a col. or height of one data line
+  
+  Return value : PageUpDn
+
+*******************************************************************************/
+static Int4 DDV_CalcVHScrollPgUD(Int2 cxy_Client,Int2 LineColSize)
+{
+	return((Int4)(cxy_Client/LineColSize));
+}
+
+/*******************************************************************************
+
+  Function : DDV_UpdateVScrollVal()
+  
+  Purpose : update the DDV VScroll bar 
+  
+  Parameters : p; handel of the DDV panel
+  				bInit; TRUE only when the DDV is created 
+  				CurPos ; new position
+  
+  Return value : none 
+
+*******************************************************************************/
+extern void DDV_UpdateVScrollVal(PaneL p,Boolean bInit,Int4 CurPos)
+{
+BaR vsb;
+DdvMainPtr 	dmp;
+	
+	dmp = (DdvMainPtr) GetObjectExtra((Handle)p);
+	/*GetAppProperty("DDV_MAIN_DATA");*/
+	if (dmp==NULL) return;
+
+	/*current scroll status*/
+	vsb = GetSlateVScrollBar ((SlatE) p);
+	
+	if (bInit) CurPos=0;
+	
+	/*given curpos (lineNumber) retrieve letter number*/
+	
+	/*compute new values*/
+	dmp->GrData.udv_vscrl.ScrollPage=
+		DDV_CalcVHScrollPgUD((Int2)(dmp->GrData.udv_panel.cyClient-
+			3*dmp->GrData.udv_panel.cyScale/2-5),
+			dmp->GrData.udv_font.LineHeight);
+	
+	if (dmp->GrData.udv_panel.nTotLines>dmp->GrData.udv_vscrl.ScrollPage){
+		dmp->GrData.udv_vscrl.ScrollMax=dmp->GrData.udv_panel.nTotLines-
+							dmp->GrData.udv_vscrl.ScrollPage+3/**/;
+	}
+	else{
+		dmp->GrData.udv_vscrl.ScrollMax=0;
+		dmp->GrData.udv_vscrl.ScrollPos=0;
+		dmp->GrData.udv_vscrl.ScrollPage=0;
+	}
+	
+	if (CurPos<0) CurPos=0;
+
+	if (CurPos>=dmp->GrData.udv_vscrl.ScrollMax)
+		dmp->GrData.udv_vscrl.ScrollPos=dmp->GrData.udv_vscrl.ScrollMax;
+	else dmp->GrData.udv_vscrl.ScrollPos=CurPos;
+				
+	/*update scroll*/
+	CorrectBarMax(vsb,dmp->GrData.udv_vscrl.ScrollMax);
+	CorrectBarValue(vsb,dmp->GrData.udv_vscrl.ScrollPos);
+	CorrectBarPage(vsb,dmp->GrData.udv_vscrl.ScrollPage,
+			dmp->GrData.udv_vscrl.ScrollPage);
+	
+}
+
+/*******************************************************************************
+
+  Function : DDV_UpdateHScrollVal()
+  
+  Purpose : update the DDV HScroll bar 
+  
+  Parameters : p; handel of the DDV panel
+  				bInit; TRUE only when the DDV is created 
+  				CurPos ; new position
+  
+  Return value : none 
+
+*******************************************************************************/
+extern void DDV_UpdateHScrollVal(PaneL p,Boolean bInit,Int4 CurPos)
+{
+BaR hsb;
+DdvMainPtr 	dmp;
+	
+	dmp = (DdvMainPtr) GetObjectExtra((Handle)p);
+	if (dmp==NULL) return;
+
+	/*current scroll status*/
+	hsb = GetSlateHScrollBar ((SlatE) p);
+	if (!hsb) return;/*not always present*/
+	
+	if (bInit) CurPos=0;
+	
+	/*given curpos (lineNumber) retrieve letter number*/
+	
+	/*compute new values*/
+	dmp->GrData.udv_hscrl.ScrollPage=
+		DDV_CalcVHScrollPgUD((Int2)(dmp->GrData.udv_panel.cxClient-
+			dmp->GrData.udv_panel.cxName),
+			dmp->GrData.udv_font.ColWidth);
+	
+	if (dmp->GrData.udv_panel.nTotCol>dmp->GrData.udv_hscrl.ScrollPage){
+		dmp->GrData.udv_hscrl.ScrollMax=dmp->GrData.udv_panel.nTotCol-
+							dmp->GrData.udv_hscrl.ScrollPage+5/**/;
+	}
+	else{
+		dmp->GrData.udv_hscrl.ScrollMax=0;
+		dmp->GrData.udv_hscrl.ScrollPos=0;
+		dmp->GrData.udv_hscrl.ScrollPage=0;
+	}
+	
+	if (CurPos<0) CurPos=0;
+
+	if (CurPos>=dmp->GrData.udv_hscrl.ScrollMax)
+		dmp->GrData.udv_hscrl.ScrollPos=dmp->GrData.udv_hscrl.ScrollMax;
+	else dmp->GrData.udv_hscrl.ScrollPos=CurPos;
+				
+	/*update scroll*/
+	CorrectBarMax(hsb,dmp->GrData.udv_hscrl.ScrollMax);
+	CorrectBarValue(hsb,dmp->GrData.udv_hscrl.ScrollPos);
+	CorrectBarPage(hsb,dmp->GrData.udv_hscrl.ScrollPage,
+			dmp->GrData.udv_hscrl.ScrollPage);
+	
+}
+
+
+/*****************************************************************************
+
+  Function : DDV_VHScrl()
+  
+  Purpose : DD Viewer Horizontal/Vertical Scroll Bar function 
+  
+  Parameters : p; viewer
+  			vdp; viewer data structure
+			newval; new value of the thumb
+			oldval; old value of the thumb
+			IsVscroll; TRUE means Vertical scrollbar
+			
+  Note : this function can be used to scroll the panel for any reasons.
+  
+  Return value : none 
+
+*****************************************************************************/
+extern void DDV_VHScrl(PaneL p,UnDViewerGraphDataPtr gdp, Int4 newval, Int4 oldval,
+	Boolean IsVscroll)
+{
+  RecT 	      rcP;
+  WindoW 	    temport;
+  Int4 	      n,limit;
+  Int2	      dx,dy;
+  DdvMainPtr  dmp;
+
+	if (!gdp || !p) return;
+
+  dmp = (DdvMainPtr) GetObjectExtra(p);
+	if (dmp==NULL) return;
+
+	/*compute scroll offset*/
+	if (oldval>newval)n=oldval-newval;
+	else n=newval-oldval;
+	
+	temport=SavePort(ParentWindow((WindoW)p));
+	Select(p);
+	ObjectRect(p,&rcP);
+	InsetRect(&rcP,4,4);
+	/*drawing region:*/
+  DDV_AdjustDrawingRect(&rcP, &(gdp->udv_font), dmp);
+
+	if (IsVscroll){/*Vertical scroll*/
+		gdp->udv_vscrl.ScrollPos=newval;
+		limit=(Int4)gdp->udv_vscrl.ScrollPage;
+		dx=0;
+		dy=(Int2)((oldval-newval)*gdp->udv_font.LineHeight);
+		rcP.top+=3*gdp->udv_panel.cyScale/2;
+	}
+	else{/*horizontal scroll*/
+		gdp->udv_hscrl.ScrollPos=newval;
+		limit=(Int4)gdp->udv_hscrl.ScrollPage;
+		dx=(Int2)((oldval-newval)*gdp->udv_font.ColWidth);
+		dy=0;
+		rcP.left+=(gdp->udv_panel.cxName+gdp->udv_scale.cxLeftScale);
+	}
+	
+	ClipRect(&rcP);
+
+	if (n<limit){/*Line UP/Down or Column left/right*/
+		ScrollRect (&rcP, dx, dy);
+	}
+	else{/*Page Up/Down or Page left/right*/
+		InvalRect(&rcP);
+	}
+	ResetClip();
+	RestorePort(temport);
+	Update ();
+}
+
+/*****************************************************************************
+
+  Function : DDV_VScrlProc()
+  
+  Purpose : DD Viewer Vertical Scroll Bar Callback 
+  
+  Parameters : see vibrant library
+  
+  Return value : none 
+
+*****************************************************************************/
+extern void DDV_VScrlProc (BaR sb, SlatE s, Int4 newval, Int4 oldval)
+{
+
+DdvMainPtr 	dmp;
+
+	/*get the application data*/
+	dmp = (DdvMainPtr) GetObjectExtra((Handle)s);
+	if (dmp==NULL) return;
+
+	DDV_VHScrl((PaneL)s,&(dmp->GrData),newval,oldval,TRUE);
+}
+
+/*****************************************************************************
+
+  Function : DDV_HScrlProc()
+  
+  Purpose : DD Viewer Horizontal Scroll Bar Callback 
+  
+  Parameters : see vibrant library
+  
+  Return value : none 
+
+*****************************************************************************/
+extern void DDV_HScrlProc (BaR sb, SlatE s, Int4 newval, Int4 oldval)
+{
+
+DdvMainPtr 	dmp;
+
+	/*get the application data*/
+	dmp = (DdvMainPtr) GetObjectExtra((Handle)s);
+	if (dmp==NULL) return;
+
+	DDV_VHScrl((PaneL)s,&(dmp->GrData),newval,oldval,FALSE);
+}
+
+/*****************************************************************************
+
+Function: DDV_InitPanelData()
+
+Purpose: Init numerical values for DDViewer. Called one times at the
+		start of the soft.
+
+Return value: none (results are in sdp)
+
+*****************************************************************************/
+extern void  DDV_InitPanelData(UDVPanelDataPtr pdp)
+{
+	pdp->cxClient=0;
+	pdp->cyClient=0;
+	pdp->nTotLines=0;
+	pdp->nTotCol=0;
+	pdp->nCharByLine=DDV_DEFAULT_PARAG_SIZE;
+	pdp->nBlockByLine=0;
+	pdp->ShowFeatures=FALSE;
+	pdp->ShowScale=TRUE;
+	pdp->ShowByBlock=FALSE;
+}
+
+/*****************************************************************************
+
+  Function : DDV_SetupWin()
+  
+  Purpose : resize DD viewer panel
+  
+  Parameters :  w; handle of the DD viewer window
+  				bInit; is the window new?
+  
+*****************************************************************************/
+extern void DDV_SetupWin (WindoW w,Boolean bInit)
+{
+RecT rWin, rButton;
+RecT rStatus1, rStatus2, rPanel1, rPanel2;
+Int2 height,diff,gap,width;
+DdvMainWinPtr dmwp;
+
+	dmwp=(DdvMainWinPtr)GetObjectExtra(w);
+	
+	ObjectRect(w,&rWin);
+	width= rWin.right-rWin.left;
+
+	GetPosition(dmwp->StatusGroup,&rStatus1);
+	diff=rStatus1.bottom-rStatus1.top;
+	gap= 4;
+
+    ObjectRect(dmwp->gotoBtn, &rButton);
+	height= rWin.bottom - rWin.top - rButton.bottom - gap;
+    
+    if(GetStatus(dmwp->MainMenu.ShowLowerPanel)) {
+        Show(dmwp->LowerInfoPanel);
+        Show(dmwp->StatusGroupLower);
+        Show(dmwp->hLowerPanel);
+
+        rPanel1.right = width;
+        rPanel1.left = 0;
+        rPanel1.top = rButton.bottom + gap;
+        rPanel1.bottom = rPanel1.top + 2*height/3 - diff;
+        
+        rStatus1.right = rPanel1.right;
+        rStatus1.left = rPanel1.left;
+        rStatus1.top = rPanel1.bottom;
+        rStatus1.bottom = rStatus1.top + diff;
+        
+        rPanel2.right = rPanel1.right;
+        rPanel2.left = rPanel1.left;
+        rPanel2.top = rStatus1.bottom;
+        rPanel2.bottom = rPanel2.top + height/3 - diff;
+        
+        rStatus2.right = rPanel1.right;
+        rStatus2.left = rPanel1.left;
+        rStatus2.top = rPanel2.bottom;
+        rStatus2.bottom = rStatus2.top + diff;
+        
+        
+        SetPosition (dmwp->StatusGroup, &rStatus1);
+        SetPosition (dmwp->UpperInfoPanel, &rStatus1);
+        SetPosition (dmwp->StatusGroupLower, &rStatus2);
+        SetPosition (dmwp->LowerInfoPanel, &rStatus2);
+        SetPosition (dmwp->hUpperPanel, &rPanel1);
+        SetPosition (dmwp->hLowerPanel, &rPanel2);
+    } else {
+        Hide(dmwp->LowerInfoPanel);
+        Hide(dmwp->StatusGroupLower);
+        Hide(dmwp->hLowerPanel);
+
+        /* set focus */
+        dmwp->hWndDDV = dmwp->hUpperPanel;
+        DDV_SetMenuFocus(w);
+        dmwp->InfoPanel = dmwp->UpperInfoPanel;
+        SetTitle(dmwp->InfoPanel,"Ready !");
+        SetTitle(dmwp->LowerInfoPanel,"");
+        
+        rPanel1.right = width;
+        rPanel1.left = 0;
+        rPanel1.top = rButton.bottom + gap;
+        rPanel1.bottom = rPanel1.top + height - diff;
+        
+        rStatus1.right = rPanel1.right;
+        rStatus1.left = rPanel1.left;
+        rStatus1.top = rPanel1.bottom;
+        rStatus1.bottom = rStatus1.top + diff;
+        
+        SetPosition (dmwp->StatusGroup, &rStatus1);
+        SetPosition (dmwp->UpperInfoPanel, &rStatus1);
+        SetPosition (dmwp->hUpperPanel, &rPanel1);
+    }
+    AdjustPrnt (dmwp->hUpperPanel, &rPanel1, FALSE);
+
+/*	Update();*/
+}
+
+/*****************************************************************************
+
+  Function : DDV_ResizeDDV
+  
+  Purpose : update DDV panel (size and scrolls) 
+  
+  Parameters : p; DDV panel
+  			   bInit; TRUE only when DDV panel is created
+	
+  Return value : none 
+
+*****************************************************************************/
+extern void DDV_Resize_DDV (PaneL p, Boolean bInit)
+{
+DdvMainPtr 	dmp;
+RecT		rcP;
+Int4        vCurPos,hCurPos;
+BaR	        vsb,hsb;
+WindoW      temport;
+
+	if (!p) return;
+	dmp = (DdvMainPtr) GetObjectExtra((Handle)p);
+	if (dmp==NULL) return;
+
+    GetPosition(p, &rcP);
+	/*panels of DDV; */
+
+	UDV_ComputePanelSize(rcP,&(dmp->GrData.udv_panel.cxClient),
+		&(dmp->GrData.udv_panel.cyClient));
+
+	temport=SavePort(ParentWindow(p));
+	Select(p);
+
+	/*current scroll status*/
+	vsb = GetSlateVScrollBar ((SlatE) p);
+	vCurPos=GetBarValue(vsb);
+	hsb = GetSlateHScrollBar ((SlatE) p);
+	hCurPos=GetBarValue(hsb);
+			
+	/*update scrolls*/
+	DDV_UpdateVScrollVal(p,bInit,vCurPos);
+	DDV_UpdateHScrollVal(p,bInit,hCurPos);
+
+	InvalRect(&rcP);
+	RestorePort(temport);
+}
+
+/*****************************************************************************
+
+  Function : DDV_WinMainResize()
+  
+  Purpose : Main Window Resize function 
+  
+  Parameters : w; handle of the parent window
+  
+  Return value : none 
+
+*****************************************************************************/
+extern void DDV_WinMainResize (WindoW w)
+{		
+    DdvMainWinPtr  mWin_d;
+    
+    mWin_d = (DdvMainWinPtr) GetObjectExtra(w);
+    if(mWin_d == NULL) return;
+    
+    DDV_SetupWin (w,FALSE);
+    DDV_Resize_DDV (mWin_d->hUpperPanel, FALSE);
+    DDV_Resize_DDV (mWin_d->hLowerPanel, FALSE);
+	Update();
+}
+
+/*****************************************************************************
+
+Function: DDV_CleanupDDVPdata() & DDV_FreeDDVPdata()
+
+Purpose: delete the data attached to the DDV panel 
+
+Return value: none
+
+*****************************************************************************/
+static void DDV_FreeDDVPdata(DdvMSADataPtr dmdp,Uint2 userkey,Uint2 procid,
+	Uint2 proctype)
+{
+ParaGPtr  pgp;
+BioseqPtr bsp;
+Int4      i;
+Uint2     bsp_eID;
+
+	if (!dmdp) return;
+	/*before deleting the list of ParaG, I need to delete the user object
+	containing the Msg Func*/
+	if (userkey>0 && procid>0 && proctype>0) {
+		for(i=0;i<dmdp->pgp_l.nBsp;i++){
+			pgp=(ParaGPtr)(dmdp->pgp_l.TableHead[i]->data.ptrvalue);
+			bsp=BioseqLockById(pgp->sip);
+			if (bsp != NULL){
+				bsp_eID=ObjMgrGetEntityIDForPointer((Pointer)bsp);
+				BioseqUnlock(bsp);
+				if (bsp_eID>0 && bsp_eID!=dmdp->entityID){
+					ObjMgrFreeUserData(bsp_eID,procid,proctype,userkey);
+				}
+			}
+		}
+	}
+	
+	if (dmdp->pgp_l.TableHead) {
+		DDV_DeleteDisplayList(&dmdp->pgp_l);
+		dmdp->pgp_l.TableHead=NULL;
+	}
+	if (dmdp->pgp_l.DisplayVert) {
+		UDV_FreeListParaG(&dmdp->pgp_l.DisplayVert);
+		dmdp->pgp_l.DisplayVert=NULL;
+	}
+	if (dmdp->pgp_l.sabp) {
+		CleanupBlocks(dmdp->pgp_l.sabp);
+		dmdp->pgp_l.sabp=NULL;
+	}
+	if (dmdp->pgp_l.bspp) {
+		dmdp->pgp_l.bspp=DDV_BspInfoDeleteList(dmdp->pgp_l.bspp);
+		dmdp->pgp_l.bspp=NULL;
+	}
+	if (dmdp->pgp_l.RulerDescr) {
+		ValNodeFreeData(dmdp->pgp_l.RulerDescr);
+		dmdp->pgp_l.RulerDescr=NULL;
+	}
+	if (dmdp->pgp_l.entitiesTbl) {
+		MemFree(dmdp->pgp_l.entitiesTbl);
+		dmdp->pgp_l.entitiesTbl=NULL;
+	}
+
+  /* no rows, no cols */
+  dmdp->pgp_l.LengthAli = 0;
+  dmdp->pgp_l.nBsp = 0;
+	
+    if(dmdp->entityID != 0)
+	    ObjMgrFreeUserData(dmdp->entityID,procid,proctype,userkey);
+	dmdp->entityID=0;
+	dmdp->itemID=0;
+}
+
+extern void DDV_CleanupDDVPdata_g (DdvMainPtr dmp)
+{
+ValNodePtr      vnp;
+
+	/*SeqAlign Idx & ParaG List*/
+	DDV_FreeDDVPdata(&(dmp->MSA_d),dmp->userkey,dmp->procid,dmp->proctype);
+	/*graphical data*/
+	DDV_InitDefSAPdispStyles(&(dmp->ddo));
+  ClearUDV_mouse_select(&(dmp->ms));
+	dmp->ms.Action_type=MS_ACTION_FEAT_NOTHING;
+	dmp->procid=0;
+	dmp->proctype=0;
+	dmp->userkey=0;
+
+    switch(dmp->dod.choice){
+    case DDV_OPENTYPE_NOTRESP:
+        break;
+    case DDV_OPENTYPE_FILE:
+        vnp=dmp->dod.vnp;
+        while(vnp){
+            ObjMgrFree(vnp->choice, (Pointer)vnp->data.ptrvalue);
+            vnp=vnp->next;
+        }
+        ValNodeFree(dmp->dod.vnp);
+        break;
+    case DDV_OPENTYPE_SEP:
+    case DDV_OPENTYPE_GI:
+        if (dmp->dod.sep) SeqEntryFree(dmp->dod.sep);
+        break;
+    }
+    memset(&(dmp->dod),0,sizeof(DdvOpenData));
+
+	/*delete list of SeqAligns*/
+	if (dmp->vnp_ali){
+		dmp->vnp_ali=ValNodeFree(dmp->vnp_ali);
+	}
+
+	memset(&dmp->GrData.udv_vscrl,0,sizeof(UDVScrollData));
+	memset(&dmp->GrData.udv_hscrl,0,sizeof(UDVScrollData));
+	dmp->GrData.udv_panel.nTotLines=0;
+	dmp->GrData.udv_panel.nTotCol=0;
+
+	/*colors; deleted only by the autonomous DDV*/
+/*	if (bRemoveBioseq && dmp->Globals.colorp){ 
+		DDV_DeleteColorGlobal(dmp->Globals.colorp);*/
+		dmp->Globals.colorp=NULL;
+/*	}*/
+
+}
+
+/*WindoW callback*/
+static void DDV_CleanupDDVPdata (GraphiC g, VoidPtr data)
+{
+DdvMainPtr dmp;
+
+	if (data){
+		dmp=(DdvMainPtr)data;
+    if (dmp->bEditor) {
+      DDE_FreeStack(dmp->dsp);
+    }
+		DDV_CleanupDDVPdata_g (dmp);
+	}
+}
+
+
+static PaneL DDV_PanelInit(GrouP g, WindoW w,DdvMainWinPtr dmwp,
+                           SAM_ViewGlobal *vgp, Boolean bEditor,
+                           Nlm_PnlClckProc ClickProc, Int4 Width)
+{
+    PaneL  p;
+    DdvMainPtr dmp;
+    Int2 Margins;
+
+    Margins=20*stdCharWidth;
+
+    	/*init data blocks*/
+	dmp=(DdvMainPtr)MemNew(sizeof(DdvMain));
+	if (!dmp) return(FALSE);
+
+	/*init default SeqAlign display options for standalon DDV and for
+	DDV started from Cn3D*/
+	if (dmwp->AutonomeViewer)
+		dmp->MasterViewer=SAMVIEWDDV;
+    if(vgp == NULL) {
+		DDV_InitDefSAPdispStyles(&(dmp->ddo));
+	}
+    else if(vgp->MasterViewer == SAMVIEWCN3D) {
+		DDV_InitCn3DSAPdispStyles(&(dmp->ddo));
+		dmp->MouseMode=DDV_MOUSEMODE_SELECT;
+	}
+
+	dmp->ms.Action_type=MS_ACTION_FEAT_NOTHING;
+
+    if(vgp == NULL)
+        p = AutonomousPanel4 (g, 
+            (Int2)2*((screenRect.right-screenRect.left)-Margins)/3, 
+            (Int2)2*((screenRect.bottom-screenRect.top)-Margins)/Width, 
+            DDV_DrawViewer,DDV_VScrlProc,DDV_HScrlProc,
+            sizeof(DdvMainPtr),NULL,NULL);
+    else
+        p = AutonomousPanel4 (g, 
+            (Int2)vgp->Rect.right - vgp->Rect.left, 
+            (Int2)vgp->Rect.bottom - vgp->Rect.top, 
+            DDV_DrawViewer,DDV_VScrlProc,DDV_HScrlProc,
+            sizeof(DdvMainPtr),NULL,NULL);
+
+    if(!p) return NULL;
+
+    Nlm_SetSlateBorder ((SlatE) p, FALSE);
+	SetPanelClick(p,ClickProc,
+		DDV_DragProc,DDV_HoldProc,DDV_ReleaseProc);
+	SetSlateChar ((SlatE) p, DDV_KeyboardProc);
+
+	SetObjectExtra (p, (Pointer) dmp, (FreeProc)DDV_CleanupDDVPdata);
+
+	dmp->hWndDDV=p;
+	dmp->hParent=w;
+	dmp->bEditor=bEditor;
+	if (!dmp->bEditor){
+		dmp->deri.curEditRow=(Int4)-1;
+		dmp->deri.curMasterRow=(Int4)0;
+	}
+	UDV_InitFont(&(dmp->GrData.udv_font));
+	SelectFont(dmp->GrData.udv_font.hFnt);
+	UDV_FontDim(&(dmp->GrData.udv_font.cxChar),&(dmp->GrData.udv_font.cyChar));
+
+	/*init the graphical elements of DDV*/
+	DDV_InitGraphGlobal(dmp);
+    return p;
+}
+
+/*****************************************************************************
+
+Function: DDV_CreateViewerPanel()
+
+Purpose: create the Viewer main panel
+
+Return value: none
+
+*****************************************************************************/
+extern Boolean DDV_CreateViewerPanel(WindoW w,DdvMainWinPtr dmwp,
+                                     SAM_ViewGlobal *vgp, Boolean bEditor)
+{
+PaneL  p, p2;
+GrouP  g,g2,StatusGroup,StatusGroupLower;
+ButtoN gotoBtn;
+TexT   gotoRowTxt,gotoColTxt;
+PrompT info, infoLower;
+FonT   hFnt;
+Int2   cxChar,cyChar;
+
+
+#ifdef WIN_MAC
+		hFnt = ParseFont ("Monaco, 9");
+#endif
+
+#ifdef WIN_MSWIN
+		hFnt = ParseFont ("Courier, 7");
+#endif
+
+#ifdef WIN_MOTIF
+		hFnt = ParseFont ("fixed, 12");
+#endif
+
+	SelectFont (hFnt);
+	cxChar=MaxCharWidth();
+	cyChar=LineHeight();
+	g = HiddenGroup (w, 5, 0, NULL);                  
+	gotoBtn = PushButton (g, "Go to:",UDV_GotoBtnProc);
+	StaticPrompt (g, "row:", 0, 3*cyChar/2, hFnt, 'l');
+	gotoRowTxt = DialogText (g, "0", (Int2)4, NULL);
+	StaticPrompt (g, "col:", 0, 3*cyChar/2, hFnt, 'l');
+	gotoColTxt = DialogText (g, "0", (Int2)4, NULL);
+	
+	g = HiddenGroup (w, 1, 2, NULL);
+    g2 = HiddenGroup(g,1,1,NULL);
+    DDV_SetupMenus(w,dmwp->UseNetwork,bEditor, vgp);
+    p=DDV_PanelInit(g2, w, dmwp, vgp, bEditor, DDV_ClickProcUpper, 4);
+    if(!p) return FALSE;
+    dmwp->hUpperPanel = p; /*handle of the upper DDV panel (the multiple)*/
+	dmwp->hWndDDV=p; /* default focus */
+
+	StatusGroup = HiddenGroup (g, 1, 1, NULL);
+	info = StaticPrompt (StatusGroup, "Ready !", 0, 3*cyChar/2, hFnt, 'l');
+
+    g2 = HiddenGroup (g, 1, 1, NULL);
+    p2=DDV_PanelInit(g2, w, dmwp, vgp, bEditor, DDV_ClickProcLower, 6);
+    if(!p) return FALSE;
+    dmwp->hLowerPanel = p2; /*handle of the DDV panel (the pairwise) */
+
+	StatusGroupLower = HiddenGroup (g, 1, 0, NULL);
+    infoLower = StaticPrompt (StatusGroupLower, "", 0, 3*cyChar/2, hFnt, 'l');
+    
+    AlignObjects(ALIGN_RIGHT, (HANDLE) p,(HANDLE) StatusGroup,(HANDLE) p2,
+        (HANDLE) StatusGroupLower, NULL);
+
+	if (gotoBtn==NULL || gotoRowTxt==NULL || 
+		gotoColTxt==NULL || info==NULL || infoLower == NULL) 
+		return(FALSE);
+
+	SetWindowTimer (w, DDV_TimerProc);
+
+	dmwp->gotoBtn=gotoBtn;
+	dmwp->gotoValRow=gotoRowTxt;
+	dmwp->gotoValCol=gotoColTxt;
+	dmwp->StatusGroup=StatusGroup;
+    dmwp->StatusGroupLower=StatusGroupLower;
+	dmwp->InfoPanel=info;
+    dmwp->UpperInfoPanel = info;
+    dmwp->LowerInfoPanel = infoLower;
+
+    DDV_SetMenuFocus(w);
+	Disable(dmwp->gotoBtn);
+	Disable(dmwp->gotoValRow);
+	Disable(dmwp->gotoValCol);
+	/*init graph objects: call UDV functions ...*/
+    
+
+	return(TRUE);
+}
+
+/*******************************************************************************
+
+  Function : DDV_WinMainProgQuit()
+  
+  Purpose : end of prog 
+  
+  Parameters : w; main window handle
+  
+  Return value : none 
+
+*******************************************************************************/
+extern void DDV_WinMainProgQuit(WindoW w)
+{
+	QuitProgram();
+}
+
+/*******************************************************************************
+
+  Function : QuitProc()
+  
+  Purpose : bye-bye procedure ! 
+  
+  Parameters : i; menu item which has called this function
+  
+  Return value : none 
+
+*******************************************************************************/
+static void QuitProc(IteM i)
+{
+WindoW  hWinMain;
+
+  hWinMain=(WindoW)ParentWindow(i);
+  if (!hWinMain) return;
+  DDV_SlaveQuit(hWinMain);
+}
+
+NLM_EXTERN void DDV_Save(ButtoN g) {
+/*----------------------------------------------------------------------------
+*  save edits, quit pop-up, quit DDE
+*---------------------------------------------------------------------------*/
+  WindoW         hDialog;
+  WindoW         hWinMain;
+  DdvMainWinPtr  mWin_d;
+  DdvMainPtr     dmp;
+
+  /* quit pop-up */
+	hDialog = (WindoW)ParentWindow(g);
+	if (!hDialog) return;
+	Remove(hDialog);
+
+  /* save the edits */
+  hWinMain = (WindoW) GetObjectExtra(hDialog);
+  mWin_d = (DdvMainWinPtr) GetObjectExtra(hWinMain);
+	dmp = (DdvMainPtr) GetObjectExtra(mWin_d->hWndDDV);
+  DDV_SaveEdits(dmp, TRUE);
+
+  /* quit DDE */
+  if (mWin_d->AutonomeViewer)
+    QuitProgram(); /*standalone DDV*/
+  else
+    Remove(hWinMain);/*slave viewer : just kill the main window*/
+}
+
+
+NLM_EXTERN void DDV_NoSave(ButtoN g) {
+/*----------------------------------------------------------------------------
+*  quit pop-up, quit DDE
+*---------------------------------------------------------------------------*/
+  WindoW         hDialog;
+  WindoW         hWinMain;
+  DdvMainWinPtr  mWin_d;
+
+  /* quit the pop-up */
+	hDialog = (WindoW)ParentWindow(g);
+	if (!hDialog) return;
+	Remove(hDialog);
+
+  /* quit DDE */
+  hWinMain = (WindoW) GetObjectExtra(hDialog);
+  mWin_d = (DdvMainWinPtr) GetObjectExtra(hWinMain);
+  if (mWin_d->AutonomeViewer)
+    QuitProgram(); /*standalone DDV*/
+  else
+    Remove(hWinMain);/*slave viewer : just kill the main window*/
+}
+
+
+NLM_EXTERN void DDV_Cancel(ButtoN g) {
+/*----------------------------------------------------------------------------
+*  quit pop-up
+*---------------------------------------------------------------------------*/
+  WindoW  hDialog;
+
+  /* quit the pop-up */
+	hDialog = (WindoW)ParentWindow(g);
+	if (!hDialog) return;
+	Remove(hDialog);
+}
+
+
+/*******************************************************************************
+
+  Function : DDV_CloseData()
+  
+  Purpose : bye-bye data, i.e. use that function to delete all the data
+            loaded within DDV.
+  
+  Parameters : mWin_d; main data block
+  
+  Return value : none 
+
+*******************************************************************************/
+extern void DDV_CloseData(DdvMainWinPtr mWin_d,Boolean bFinalExit)
+{
+
+	WatchCursor();
+	/*dmp=(DdvMainPtr)GetObjectExtra(mWin_d->hWndDDV);*/
+	
+	/*DDV_CleanupDDVPdata_g(dmp);*/
+	if (!bFinalExit)
+		DDV_SetupWin (mWin_d->hWndMain,TRUE);
+	ArrowCursor();
+}
+
+
+NLM_EXTERN void DDV_FileCloseIt(WindoW hWinMain) {
+/*----------------------------------------------------------------------------
+*  part of DDV_FileClose
+*---------------------------------------------------------------------------*/
+  DdvMainPtr    dmp;
+  DdvMainWinPtr mWin_d;
+  RecT          rc;
+
+	mWin_d = (DdvMainWinPtr) GetObjectExtra((Handle)hWinMain);
+	if (mWin_d==NULL) return;
+
+	/* delete data */
+	dmp=(DdvMainPtr)GetObjectExtra(mWin_d->hWndDDV);
+	DDV_CleanupDDVPdata_g(dmp);
+	DDV_CloseData(mWin_d,FALSE);
+	DDV_EnableGotoTBItems(hWinMain,FALSE);
+
+	/* blank the panel that's closed */
+	mWin_d->Show_logo=FALSE;
+  ObjectRect(mWin_d->hUpperPanel, &rc);
+  InvalRect(&rc);
+  ObjectRect(mWin_d->hLowerPanel, &rc);
+  InvalRect(&rc);
+
+  Update();
+}
+
+
+/*******************************************************************************
+
+  Function : DDV_FileClose()
+  
+  Purpose : close a SeqAlign 
+  
+  Parameters : i; menu item which has called this function
+  
+  Return value : none 
+
+*******************************************************************************/
+static void DDV_FileClose(IteM i)
+{
+  WindoW  hWinMain;
+
+	hWinMain=(WindoW)ParentWindow(i);
+	if (!hWinMain) return;
+
+  DDV_FileCloseIt(hWinMain);
+  return;
+}
+
+
+#ifdef DEBUG_DDV
+static Uint1 DDV_GetCurrentUAGAPStyle(MsaParaGPopListPtr mpplp)
+{
+Int4          j;
+ValNodePtr    vnp,vnp2;
+ParaGPtr      pgp;
+MsaTxtDispPtr mtdp;
+
+	if (mpplp->TableHead){
+		for(j=0;j<mpplp->nBsp;j++){
+			vnp=mpplp->TableHead[j];
+			while(vnp){
+				pgp=(ParaGPtr)vnp->data.ptrvalue;
+				if (pgp){
+					vnp2=pgp->ptxtList;
+					while(vnp2){
+						mtdp=(MsaTxtDispPtr)vnp2->data.ptrvalue;
+						if (mtdp->IsUnAligned && mtdp->IsGap){
+							return(mtdp->TextStyle);
+						}
+						vnp2=vnp2->next;
+					}
+				}
+				vnp=vnp->next;
+			}
+		}
+	}
+	return(0);
+}
+
+static void DDV_SetCurrentUAGAPStyle(MsaParaGPopListPtr mpplp,Uint1 UATextStyle)
+{
+Int4          j;
+ValNodePtr    vnp,vnp2;
+ParaGPtr      pgp;
+MsaTxtDispPtr mtdp;
+
+	if (mpplp->TableHead){
+		for(j=0;j<mpplp->nBsp;j++){
+			vnp=mpplp->TableHead[j];
+			while(vnp){
+				pgp=(ParaGPtr)vnp->data.ptrvalue;
+				if (pgp){
+					vnp2=pgp->ptxtList;
+					while(vnp2){
+						mtdp=(MsaTxtDispPtr)vnp2->data.ptrvalue;
+						if (mtdp->IsUnAligned && mtdp->IsGap){
+							mtdp->TextStyle=UATextStyle;
+						}
+						vnp2=vnp2->next;
+					}
+				}
+				vnp=vnp->next;
+			}
+		}
+	}
+}
+
+
+/*******************************************************************************
+
+  Function : DDV_ShowHideUnAlignGap()
+  
+  Purpose : use or not the ~ char to display an unalign gap
+  
+  Return value : none 
+
+*******************************************************************************/
+static void DDV_ShowHideUnAlignGap(IteM i)
+{
+static Boolean bFirst=TRUE;
+static Uint1 UA_TextStyle;
+DdvMainWinPtr mWin_d;
+DdvMainPtr 	  dmp;
+WindoW		  hWinMain,hDispDlg;
+
+	/*get some data*/
+	hWinMain=(WindoW)ParentWindow(i);
+	if (hWinMain==NULL) return;
+	mWin_d = (DdvMainWinPtr) GetObjectExtra (hWinMain);
+	if (mWin_d==NULL) return;
+	if (mWin_d->hWndDDV==NULL) return;
+	dmp = (DdvMainPtr) GetObjectExtra(mWin_d->hWndDDV);
+	if (dmp==NULL) return;
+
+	if (bFirst){
+		UA_TextStyle=DDV_GetCurrentUAGAPStyle(&(dmp->MSA_d.pgp_l));
+		bFirst=FALSE;
+	}
+	
+	if (UA_TextStyle==MSA_TXT_STYLE_UAGAP)
+		UA_TextStyle=MSA_TXT_STYLE_GAP;
+	else
+		UA_TextStyle=MSA_TXT_STYLE_UAGAP;
+		
+	DDV_SetCurrentUAGAPStyle(&(dmp->MSA_d.pgp_l),UA_TextStyle);
+}
+#endif
+
+/*******************************************************************************
+
+  Function : DDV_DispStyles_OkProc()
+  
+  Purpose : manage ok button of the  Display Styles dialog box 
+  
+  Parameters : g; button
+  
+  Return value : none 
+
+*******************************************************************************/
+static void DDV_DispStyles_OkProc(ButtoN g)
+{
+WindoW              hDispDlg;
+DdvMainWinPtr       mWin_d;
+DdvDispStylesMSGPtr dsmp;
+DdvMainPtr          dmp;
+DDVUpdateLayoutDataPtr dumdp;
+DDVUpdateMSGPtr     dump;
+Char                szBuf[15]={""};
+Int2                value;
+Char                title[10]={""};
+Int4                j;
+
+	hDispDlg=(WindoW)ParentWindow(g);
+	Hide(hDispDlg);
+	if (!hDispDlg) return;
+	
+	dsmp = (DdvDispStylesMSGPtr) GetObjectExtra (hDispDlg);
+
+	if (dsmp==NULL) return;
+	
+	mWin_d = (DdvMainWinPtr) GetObjectExtra (dsmp->hWinMain);
+	dmp = (DdvMainPtr) GetObjectExtra(mWin_d->hWndDDV);
+
+	dumdp=(DDVUpdateLayoutDataPtr)MemNew(sizeof(DDVUpdateLayoutData));
+	if (!dumdp){
+		MemFree(dsmp);
+		Remove(hDispDlg);
+		/*todo : add user message to inform for error*/
+		return;
+	}
+
+	dump=(DDVUpdateMSGPtr)MemNew(sizeof(DDVUpdateMSG));
+	if (!dump){
+		MemFree(dsmp);
+		MemFree(dumdp);
+		Remove(hDispDlg);
+		/*todo : add user message to inform for error*/
+		return;
+	}
+
+	/*check box for color display*/
+	dumdp->bUseColors=GetStatus((Handle)dsmp->chk2);
+	/*show left tail check box*/
+	dumdp->ShowLeftTail=GetStatus((Handle)dsmp->chk3);
+	/*show right tail check box*/
+	dumdp->ShowRightTail=GetStatus((Handle)dsmp->chk4);
+	
+	if (Enabled((Handle)dsmp->g1)){
+		/*size of the spacer*/
+		GetTitle(dsmp->edit1, title, 9);
+		value=(Int2)atoi(title);
+		if (value<1)
+			dumdp->SpacerSize=1;
+		else if (value>20){
+			dumdp->SpacerSize=20;
+		}
+		else dumdp->SpacerSize=(Uint1)value;
+		/*get the values back from the user*/
+		value=GetValue((Handle)dsmp->g2);
+		if (value==1){/*use spacer ?*/
+			dumdp->DispDiscStyle=MSA_TXT_STYLE_1;
+		}
+		else{/*use justification*/
+			dumdp->DispDiscStyle=MSA_TXT_STYLE_2;
+			value=GetValue((Handle)dsmp->g5);
+			switch(value){
+				case 1:
+					dumdp->DiscJustification=DISP_JUST_LEFT;
+					break;
+				case 2:
+					dumdp->DiscJustification=DISP_JUST_RIGHT;
+					break;
+				case 3:
+					dumdp->DiscJustification=DISP_JUST_CENTER;
+					break;
+				case 4:
+					dumdp->DiscJustification=DISP_JUST_SPLIT;
+					break;
+			}
+		}
+	}
+	
+	/*sequence list... something selected?*/
+	/*set the ruler styles*/
+	for(j=0;j<dmp->MSA_d.pgp_l.nBsp;j++){
+		if (GetItemStatus (dsmp->BspNames, (Int2)(j+1))){/*selected ?*/
+			if(!dumdp->SeqList){
+				dumdp->SeqList=(Int4Ptr)MemNew(sizeof(Int4));
+				if (!dumdp->SeqList) break;
+				dumdp->SeqList[0]=j+1;
+				dumdp->nSeq++;
+			}
+			else{
+				dumdp->SeqList=(Int4Ptr)MemExtend(dumdp->SeqList,
+						(dumdp->nSeq+1)*sizeof(Int4),dumdp->nSeq*sizeof(Int4));
+				if (dumdp->SeqList==NULL){
+					dumdp->nSeq=0;
+					break;
+				}
+				dumdp->SeqList[dumdp->nSeq]=j+1;
+				dumdp->nSeq++;
+			}
+		}
+	}
+	if (dumdp->nSeq>0){
+		value=GetValue((Handle)dsmp->g12);
+		switch(value){
+			case 1:
+				dumdp->RulerStyle=SCALE_POS_TOP;
+				break;
+			case 2:
+				dumdp->RulerStyle=SCALE_POS_NONE;
+				break;
+		}			
+	}
+	
+	dumdp->ddv_panel=mWin_d->hWndDDV;
+
+	/*send a OM_MSG_UPDATE message*/
+	dump->type=UPDATE_TYPE_LAYOUT;
+	dump->data=(Pointer)dumdp;
+	ObjMgrSendProcMsg(OM_MSG_UPDATE, dmp->MSA_d.entityID,dmp->MSA_d.itemID,
+			OBJ_SEQALIGN,0,0,(Pointer)dump);
+	
+	/*close the dlg box*/
+	Remove(hDispDlg);
+}
+
+/*******************************************************************************
+
+  Function : DDV_DispStyles_cancelProc()
+  
+  Purpose : manage cancel button of the Display Styles dialog box 
+  
+  Parameters : g; button
+  
+  Return value : none 
+
+*******************************************************************************/
+static void DDV_DispStyles_cancelProc(ButtoN g)
+{
+WindoW			    hDispDlg;
+DdvDispStylesMSGPtr dsmp;
+
+	hDispDlg=(WindoW)ParentWindow(g);
+
+	if (!hDispDlg) return;
+
+	dsmp = (DdvDispStylesMSGPtr) GetObjectExtra (hDispDlg);
+
+	if (dsmp==NULL) return;
+
+	Remove(hDispDlg);
+}
+
+
+/*******************************************************************************
+
+  Function : DDV_DispStyles_SelAllProc()
+  
+  Purpose : manage SelAll BSP button of the Display Styles dialog box 
+  
+  Parameters : g; button
+  
+  Return value : none 
+
+*******************************************************************************/
+static void DDV_DispStyles_SelAllProc(ButtoN g)
+{
+WindoW			hDispDlg;
+DdvMainWinPtr       mWin_d;
+DdvDispStylesMSGPtr dsmp;
+DdvMainPtr          dmp;
+Int4                j;
+	
+	hDispDlg=(WindoW)ParentWindow(g);
+	if (!hDispDlg) return;
+	dsmp = (DdvDispStylesMSGPtr) GetObjectExtra (hDispDlg);
+	if (dsmp==NULL) return;
+	mWin_d = (DdvMainWinPtr) GetObjectExtra (dsmp->hWinMain);
+	dmp = (DdvMainPtr) GetObjectExtra(mWin_d->hWndDDV);
+	
+	for(j=0;j<dmp->MSA_d.pgp_l.nBsp;j++){
+		SetItemStatus (dsmp->BspNames, (Int2)(j+1), TRUE);	
+	}
+}
+
+/*******************************************************************************
+
+  Function : DDV_DispStyles_SelNoneProc()
+  
+  Purpose : manage Sel None BSP button of the Display Styles dialog box 
+  
+  Parameters : g; button
+  
+  Return value : none 
+
+*******************************************************************************/
+static void DDV_DispStyles_SelNoneProc(ButtoN g)
+{
+WindoW			hDispDlg;
+DdvMainWinPtr       mWin_d;
+DdvDispStylesMSGPtr dsmp;
+DdvMainPtr          dmp;
+Int4                j;
+	
+	hDispDlg=(WindoW)ParentWindow(g);
+	if (!hDispDlg) return;
+	dsmp = (DdvDispStylesMSGPtr) GetObjectExtra (hDispDlg);
+	if (dsmp==NULL) return;
+	mWin_d = (DdvMainWinPtr) GetObjectExtra (dsmp->hWinMain);
+	dmp = (DdvMainPtr) GetObjectExtra(mWin_d->hWndDDV);
+	
+	for(j=0;j<dmp->MSA_d.pgp_l.nBsp;j++){
+		SetItemStatus (dsmp->BspNames, (Int2)(j+1), FALSE);	
+	}
+}
+
+
+/*******************************************************************************
+
+  Function : DDV_DispStyles_DiscSetCtrlVal()
+  
+  Purpose : set the values for the ctrl in the group "disc. align options" 
+  
+  Return value : none 
+
+*******************************************************************************/
+static void DDV_DispStyles_DiscSetCtrlVal(DdvDispStylesMSGPtr dsmp,
+	DDV_Disp_OptPtr ddop)
+{
+Char szBuf[15]={""};
+
+
+	Enable(dsmp->g1);
+
+	if (ddop->DispDiscStyle==MSA_TXT_STYLE_1)
+		SetValue(dsmp->g2,1);
+	else
+		SetValue(dsmp->g2,2);
+
+	sprintf(szBuf,"%i",ddop->SpacerSize);
+	SetTitle(dsmp->edit1,szBuf);/*spacer size*/
+
+	if (ddop->DiscJustification>0)
+		SetValue(dsmp->g5,(Int2)(ddop->DiscJustification-DISP_JUST_LEFT+1));
+	else
+		SetValue(dsmp->g5,1);
+}
+
+/*******************************************************************************
+
+  Function : DDV_DeselectItem()
+  
+  Purpose : Deselects everything 
+  
+  Return value : none 
+
+*******************************************************************************/
+static void  DDV_DeselectItem(IteM i)
+{
+    DdvMainWinPtr mWin_d;
+    DdvMainPtr 	  dmp;
+    WindoW		  hWinMain;
+
+	hWinMain=(WindoW)ParentWindow(i);
+	if (hWinMain==NULL) return;
+	mWin_d = (DdvMainWinPtr) GetObjectExtra (hWinMain);
+	if (mWin_d==NULL) return;
+	if (mWin_d->hWndDDV==NULL) return;
+	dmp = (DdvMainPtr) GetObjectExtra(mWin_d->hWndDDV);
+	if (dmp==NULL) return;
+
+    ObjMgrDeSelectAll();
+    ObjMgrSendProcMsg(OM_MSG_UPDATE, dmp->MSA_d.entityID,dmp->MSA_d.itemID,
+        OBJ_SEQALIGN,0,0,NULL);
+    ObjMgrSendMsg(OM_MSG_MOUSEUP, dmp->MSA_d.entityID, dmp->MSA_d.itemID,
+        OBJ_SEQALIGN);
+}
+
+/*******************************************************************************
+
+  Function : DDV_DisplayStyles()
+  
+  Purpose : create the Display Styles dialog box 
+  
+  Return value : none 
+
+*******************************************************************************/
+static void DDV_DisplayStyles(IteM i)
+{
+DdvMainWinPtr mWin_d;
+DdvMainPtr 	  dmp;
+WindoW		  hWinMain,hDispDlg;
+GrouP         g0,g1,g2,g3,g4,g5,g6,g7,g8,g9,g10,g11,g12,g13;
+LisT          BspNames;
+ButtoN        chk2,chk3,chk4;
+TexT          edit1;
+DdvDispStylesMSGPtr  dsmp;
+SeqIdPtr      sip;
+Char          szAccess[21];
+Char          szBuf[10];
+Int4          j;
+ValNodePtr    vnp;
+ParaGPtr      pgp;
+
+	/*get some data*/
+	hWinMain=(WindoW)ParentWindow(i);
+	if (hWinMain==NULL) return;
+	mWin_d = (DdvMainWinPtr) GetObjectExtra (hWinMain);
+	if (mWin_d==NULL) return;
+	if (mWin_d->hWndDDV==NULL) return;
+	dmp = (DdvMainPtr) GetObjectExtra(mWin_d->hWndDDV);
+	if (dmp==NULL) return;
+
+	/*init MsgStruct; to be used when user clicks on [OK]*/
+	dsmp=(DdvDispStylesMSGPtr)MemNew(sizeof(DdvDispStylesMSG));	
+	if (!dsmp) return;
+	
+	/*DlgBox window*/
+	hDispDlg=MovableModalWindow(-30, -20,  -10,  -10, 
+				"DDV - display options",  NULL);
+	if (!hDispDlg){
+		MemFree(dsmp);
+		return;
+	}
+
+	SetObjectExtra (hDispDlg, (Pointer) dsmp, StdCleanupExtraProc);
+/*
+    the dlg controls
+
+    g6                 main group for all the dlg; put all the controls there
+     |->chk2           check for color display 
+     |
+     |->g0             main group for "Disc. SeqAlign display options"
+     |   |->g1 
+     |   |   |->g2     radio group 1 (spacer/seq.)
+     |   |   |->g3
+     |   |       |->g4 TexT ctrl, spacer size
+     |   |       |->g5 radio group 2 (justification)
+     |   |->g13        check btns for tails
+     |        
+     |->g8             main group for "Bioseq ruler"
+     |   |->g9
+     |       |->BspNames BSP names listbox
+     |       |->g10     the controls (radio & buttons)
+     |            |->g11
+     |            |->g12
+     |->g7            (ok/cancel buttons)
+*/
+	/*top-level group*/
+	g6=HiddenGroup(hDispDlg, -1, 0,NULL);
+	
+	chk2=CheckBox(g6,"Use a color display",NULL);
+
+	/*Disc. SeqAlign display options group - start*/
+	g0=NormalGroup(g6, -1, 0, "Disc. SeqAlign display options",NULL, NULL);
+	g1=HiddenGroup(g0, 2, 0,NULL);
+	g2=HiddenGroup(g1,0,2,NULL);
+	RadioButton(g2,"spacer");
+	RadioButton(g2,"sequence");
+	g3=HiddenGroup(g1,0,2,NULL);
+	g4=HiddenGroup(g3,2,0,NULL);
+	edit1=DialogText(g4,NULL,6,NULL);
+	g5=HiddenGroup(g3,0,4,NULL);
+	RadioButton(g5,"Left");
+	RadioButton(g5,"Right");
+	RadioButton(g5,"Center");
+	RadioButton(g5,"Split");
+	g13=HiddenGroup(g0,0,2,NULL);
+	chk3=CheckBox(g13,"Show left tail",NULL);
+	chk4=CheckBox(g13,"Show right tail",NULL);
+	/*Disc. SeqAlign display options group - end*/
+
+	/*Bioseq list - start*/
+	g8=NormalGroup(g6, -1, 0, "Bioseq ruler",NULL, NULL);
+	g9=HiddenGroup(g8,0,2,NULL);
+	BspNames=MultiList(g9,6,6,NULL);
+	if (dmp->MSA_d.pgp_l.TableHead){
+		for(j=0;j<dmp->MSA_d.pgp_l.nBsp;j++){
+			vnp=dmp->MSA_d.pgp_l.TableHead[j];
+			pgp=(ParaGPtr)vnp->data.ptrvalue;
+			if (pgp->sip){
+				sip = SeqIdFindBest(pgp->sip, SEQID_GENBANK);
+				if (!sip)
+					sip = SeqIdFindBest(pgp->sip, 0);
+				SeqIdWrite(sip, szAccess,PRINTID_TEXTID_ACCESSION, 20);   
+				ListItem(BspNames,szAccess);
+			}
+		}
+	}
+	g10=HiddenGroup(g9,2,0,NULL);
+	g11=NormalGroup(g10, 2, 0, "Auto select",NULL, NULL);
+	PushButton (g11, "All", DDV_DispStyles_SelAllProc);
+	PushButton (g11, "None", DDV_DispStyles_SelNoneProc);
+	g12=NormalGroup(g10, 3, 0, "Ruler Style",NULL, NULL);
+	RadioButton(g12,"Top");
+	RadioButton(g12,"None");
+	SetValue(g12,2);
+	/*Bioseq list - end*/
+
+	/*ok - cancel group - start*/
+	g7=HiddenGroup(g6, 2, 0,NULL);
+	PushButton (g7, "Ok", DDV_DispStyles_OkProc);
+	PushButton (g7, "Cancel", DDV_DispStyles_cancelProc);
+	/*ok - cancel group - end*/
+	
+	/*copy data*/
+	dsmp->hWinMain=hWinMain;
+	dsmp->chk2=chk2;
+	dsmp->chk3=chk3;
+	dsmp->chk4=chk4;
+	dsmp->g1=g1;
+	dsmp->g2=g2;
+	dsmp->g5=g5;
+	dsmp->g12=g12;
+	dsmp->edit1=edit1;
+	dsmp->BspNames=BspNames;
+
+	/*build the dlgbox*/
+	RealizeWindow(hDispDlg);
+	Show(hDispDlg);
+
+	/*color display check box*/
+	SetStatus(chk2,dmp->ddo.bUseColors);
+	/*show left tail check box*/
+	SetStatus(chk3,dmp->ddo.ShowLeftTail);
+	/*show right tail check box*/
+	SetStatus(chk4,dmp->ddo.ShowRightTail);
+	/*spacer size*/
+	sprintf(szBuf,"%i",dmp->ddo.SpacerSize);
+	SetTitle(dsmp->edit1, szBuf);
+
+	/*depending on the SAP type, init some controls*/
+  DDV_DispStyles_DiscSetCtrlVal(dsmp,&(dmp->ddo));
+/*  
+	if (AlnMgrIsSAPDiscAli(dmp->MSA_d.pgp_l.sap)){
+		DDV_DispStyles_DiscSetCtrlVal(dsmp,&(dmp->ddo));
+	}
+	else{
+		Disable(g1);
+	}
+*/
+}
+
+
+static void SelectJustify(ChoicE i) {
+/*----------------------------------------------------------------------------
+*  handle the Justify left/right/center selection
+*---------------------------------------------------------------------------*/
+  DdvMainWinPtr  mWin_d;
+  DdvMainPtr     dmp;
+  WindoW         hWinMain;
+  Int2           Value;
+
+	hWinMain=(WindoW)ParentWindow(i);
+	if (!hWinMain) return;
+	mWin_d = (DdvMainWinPtr) GetObjectExtra(hWinMain);
+	if (mWin_d==NULL) return;
+	dmp=(DdvMainPtr)GetObjectExtra(mWin_d->hWndDDV);
+	if (dmp==NULL) return;
+	if (!dmp->MSA_d.pgp_l.TableHead) return;
+
+  Value = GetValue(i);
+  switch(Value) {
+    case 1:
+      DDE_LeftJustify(dmp->dsp, TRUE);
+      break;
+    case 2:
+      DDE_RightJustify(dmp->dsp, TRUE);
+      break;
+    case 3:
+      DDE_CenterJustify(dmp->dsp, TRUE);
+      break;
+    default:
+      break;
+  }
+
+  /* shut off the selection */
+  SetValue(mWin_d->MainMenu.Justify, 0);
+
+  DDV_ReDraw(dmp);
+  return;
+}
+
+
+/*******************************************************************************
+
+  Function : SelectMouseMode()
+  
+  Purpose : modification of the mouse mode
+  
+  Parameters :  i; menu item
+  
+  Return value : none 
+
+*******************************************************************************/
+static void SelectMouseMode(ChoicE i)
+{
+Int2 			value;
+DdvMainWinPtr 	mWin_d;/*program data*/
+DdvMainPtr      dmp;
+WindoW			hWinMain;
+Int4            from_col,to_col,from_row,to_row,bsp_pos;
+Char            szAccess[21];
+
+
+	hWinMain=(WindoW)ParentWindow(i);
+	if (!hWinMain) return;
+	mWin_d = (DdvMainWinPtr) GetObjectExtra (hWinMain);
+	if (mWin_d==NULL) return;
+	dmp=(DdvMainPtr)GetObjectExtra(mWin_d->hWndDDV);
+	if (dmp==NULL) return;
+	if (!dmp->MSA_d.pgp_l.TableHead) return;
+	
+	/*get the disp coord range*/
+	DDV_GetCurrentDispRange(dmp->hWndDDV,&(dmp->GrData),
+			dmp->MSA_d.pgp_l.LengthAli,&from_col,&to_col,
+			&from_row,&to_row);
+	/*switch to one-bsed value because dmp->dci values 
+	  are one-based values*/
+	from_row++;
+	to_row++;
+	
+	value=GetValue(i);
+	switch(value){
+		case 1:/*query mode*/
+      dmp->MouseMode=DDV_MOUSEMODE_QUERY;
+      goto Continue;
+		case 2:/*select mode*/
+      dmp->MouseMode=DDV_MOUSEMODE_SELECT;
+      goto Continue;
+    case 3:
+      dmp->MouseMode=DDV_MOUSEMODE_SELECT_ONE_ROW;
+
+Continue:
+      dmp->dci.old_row=dmp->dci.new_row;
+			dmp->dci.old_col=dmp->dci.new_col;
+			dmp->dci.new_row=(Int4)-1;
+			dmp->dci.new_col=(Int4)-1;
+			/*hide the caret from old coordinates*/
+			if (dmp->dci.old_col>=from_col && dmp->dci.old_col<=to_col &&
+				dmp->dci.old_row>=from_row && dmp->dci.old_row<=to_row){
+				DDV_InvalRegion(dmp->hWndDDV,&(dmp->GrData),
+					_max_(0,dmp->dci.old_col-1),dmp->dci.old_col+1,
+					dmp->dci.old_row,FALSE);
+			}
+			SetTitle(mWin_d->InfoPanel,"Ready !");
+			break;
+		case 4:/*edit mode*/
+			dmp->MouseMode=DDV_MOUSEMODE_EDIT;
+			dmp->dci.new_row=dmp->dci.old_row;
+			dmp->dci.new_col=dmp->dci.old_col;
+			/*show the caret from new coordinates*/
+			if (dmp->dci.new_col>=from_col && dmp->dci.new_col<=to_col &&
+				dmp->dci.new_row>=from_row && dmp->dci.new_row<=to_row){
+				DDV_InvalRegion(dmp->hWndDDV,&(dmp->GrData),
+					_max_(0,dmp->dci.new_col-1),dmp->dci.new_col+1,
+					dmp->dci.new_row,FALSE);
+			}
+			DDV_GetSeqNameGivenRow(dmp->MSA_d.pgp_l.TableHead, 
+				dmp->dci.new_row,szAccess);
+			bsp_pos=DDV_GetBspCoordGivenPgpList(
+				dmp->MSA_d.pgp_l.TableHead[dmp->dci.new_row-1],
+				dmp->dci.new_col);
+			if (bsp_pos!=(Int4)-1){
+				DDV_DispPositionInStatus(mWin_d->InfoPanel, 
+					bsp_pos+1,dmp->dci.new_row,szAccess);
+						/*+1 : switch to one-based value*/
+			}
+			break;
+	}
+}
+
+static void DDV_ShowLowerPanel(IteM i)
+{
+    DdvMainWinPtr 	mWin_d;/*program data*/
+
+    mWin_d = (DdvMainWinPtr) GetObjectExtra((Handle)i);
+    if(!mWin_d) return;
+    DDV_SetupWin (mWin_d->hWndMain,FALSE);
+}
+
+/*******************************************************************************
+
+  Function : DDV_SetMenuFocus()
+  
+  Purpose : Set menu item values depending on which panel has focus 
+  
+  Parameters : 	w; handle of the dialog box
+				
+  Return value : none 
+
+*******************************************************************************/
+
+NLM_EXTERN void DDV_SetMenuFocus(WindoW w)
+{
+DdvMainWinPtr 	mWin_d;/*program data*/
+DdvMainPtr      dmp;
+
+	mWin_d = (DdvMainWinPtr) GetObjectExtra((Handle)w);
+
+	if (!mWin_d) return;
+    dmp = (DdvMainPtr) GetObjectExtra(mWin_d->hWndDDV);
+
+    switch(dmp->MouseMode){
+		case DDV_MOUSEMODE_QUERY:
+			SetValue(mWin_d->MainMenu.MouseMode,1);
+			break;
+		case DDV_MOUSEMODE_SELECT:
+            SetValue(mWin_d->MainMenu.MouseMode,2);
+            break;
+        case DDV_MOUSEMODE_SELECT_ONE_ROW:
+            SetValue(mWin_d->MainMenu.MouseMode,3);
+            break;
+        case DDV_MOUSEMODE_EDIT:
+            SetValue(mWin_d->MainMenu.MouseMode,4);
+            break;
+    }
+
+}
+
+/*******************************************************************************
+
+  Function : DDV_SetupMenus()
+  
+  Purpose : create the menu of DD-Viewer 
+  
+  Parameters : 	w; handle of the dialog box
+  				isID1Ok;TRUE if ID1 is enabled
+  				bEditor; true = show editor's commands
+				
+  Return value : none 
+
+*******************************************************************************/
+extern void  DDV_SetupMenus(WindoW w,Boolean isID1Ok,Boolean bEditor,
+                            SAM_ViewGlobal *vgp)
+{
+MenU			m,s,s2;/*temp variable*/
+DdvMainWinPtr 	mWin_d;/*program data*/
+Boolean* pNoGaps;
+Boolean  NoGaps;
+
+	mWin_d = (DdvMainWinPtr) GetObjectExtra((Handle)w);
+
+	if (!mWin_d) return;
+
+	/*File menu*/
+	m=PulldownMenu(w,"File");
+	mWin_d->MainMenu.File=m;
+
+	if (mWin_d->AutonomeViewer){/*available only for the Auntonomous viewer*/
+		s=SubMenu(m,"Open from ");
+		mWin_d->MainMenu.FileOpen=CommandItem(s,"a local file...",
+				DDV_OpenFile);
+		mWin_d->MainMenu.EntrezOpen=CommandItem(s,"the network...",
+				DDV_OpenNetwork);
+		if (isID1Ok==FALSE) Disable(mWin_d->MainMenu.EntrezOpen);
+
+		mWin_d->MainMenu.FileClose=CommandItem(m,"Close",DDV_FileClose);
+		SeparatorItem(m);
+		mWin_d->MainMenu.FileExport=CommandItem(m,"Export...",DDV_ExportTexte);
+		s=SubMenu(m,"Import ");
+		mWin_d->MainMenu.ImportSeq=CommandItem(s,"a single sequence",DDV_ImportBioseq);
+		mWin_d->MainMenu.ImportNucSeqAlign=CommandItem(s,"a nuc. sequence alignment",DDV_ImportNucSeqAlign);
+		mWin_d->MainMenu.ImportProtSeqAlign=CommandItem(s,"a prot. sequence alignment",DDV_ImportProtSeqAlign);
+		SeparatorItem(m);
+		VSMAddToMenu(m, VSM_DESKTOP);
+		SeparatorItem(m);
+	}
+	else{
+        mWin_d->MainMenu.FileExport=CommandItem(m,"Export...",DDV_ExportTexte);
+        /* for editor allow save of edits */
+        if (bEditor) {
+            mWin_d->MainMenu.SaveEdits=CommandItem(m,"Save",DDV_CallSaveEdits);
+        }
+        SeparatorItem(m);
+    }
+	mWin_d->MainMenu.QuitViewer=CommandItem(m,"Quit/Q",QuitProc);
+
+	/*Edit Menu*/	
+	if (bEditor){
+		m=PulldownMenu(w,"Edit");
+		mWin_d->MainMenu.Edit=m;
+/*
+		mWin_d->MainMenu.DeleteRow=CommandItem(m,"Delete row", DDV_DeleteRow);
+		mWin_d->MainMenu.MoveRowLeft=CommandItem(m,"Move row to the left", DDV_MoveRowLeft);
+		mWin_d->MainMenu.MoveRowRight=CommandItem(m,"Move row to the right", DDV_MoveRowRight);
+    mWin_d->MainMenu.LeftBoundaryLeft=CommandItem(m,"Move left boundary left", DDV_MoveLeftBoundaryLeft);
+    mWin_d->MainMenu.LeftBoundaryRight=CommandItem(m,"Move left boundary right", DDV_MoveLeftBoundaryRight);
+    mWin_d->MainMenu.RightBoundaryLeft=CommandItem(m,"Move right boundary left", DDV_MoveRightBoundaryLeft);
+    mWin_d->MainMenu.RightBoundaryRight=CommandItem(m,"Move right boundary right", DDV_MoveRightBoundaryRight);
+*/
+    mWin_d->MainMenu.CreateBlock=CommandItem(m,"Create block...", DDV_CreateBlock);
+    mWin_d->MainMenu.DeleteBlock=CommandItem(m,"Delete block", DDV_DeleteBlock);
+    mWin_d->MainMenu.Prev=CommandItem(m,"Undo  (Ctrl + z)", DDV_Prev);
+    mWin_d->MainMenu.Next=CommandItem(m,"Redo  (Ctrl + y)", DDV_Next);
+    mWin_d->MainMenu.Orig=CommandItem(m,"Restore original", DDV_Orig);
+    /* to start, can't undo or redo anything */
+    Disable(mWin_d->MainMenu.Prev);
+    Disable(mWin_d->MainMenu.Next);
+	}
+
+	if (mWin_d->AutonomeViewer){
+        mWin_d->MainMenu.Align = PulldownMenu(w, "Alignment/A");
+        mWin_d->MainMenu.Hide=CommandItem(mWin_d->MainMenu.Align,
+            "Hide or Show Rows...",DDV_HideDlgItem);
+    }
+	
+    /* Align menu */
+    if(vgp != NULL) {
+        if(vgp->MasterViewer == SAMVIEWCN3D) {
+            mWin_d->MainMenu.Align = PulldownMenu(w, "Alignment/A");
+            mWin_d->MainMenu.Hide=CommandItem(mWin_d->MainMenu.Align,
+                "Hide or Show Rows...",DDV_HideDlgItem);
+            mWin_d->MainMenu.Deselect=CommandItem(mWin_d->MainMenu.Align,
+                "Deselect All",DDV_DeselectItem);           
+            SeparatorItem(mWin_d->MainMenu.Align);
+            mWin_d->MainMenu.AddRow = SubMenu(mWin_d->MainMenu.Align, "Add New Row");
+            mWin_d->MainMenu.FromFile = SubMenu(mWin_d->MainMenu.AddRow, "From FASTA file");
+                CommandItem(mWin_d->MainMenu.FromFile,
+                    "By gapped BLAST...", (Nlm_ItmActnProc)vgp->BlastFileGap);
+                CommandItem(mWin_d->MainMenu.FromFile,
+                    "By ungapped BLAST...", (Nlm_ItmActnProc)vgp->BlastFile);
+            if (vgp->NetStartProc) {
+                mWin_d->MainMenu.FromNet = SubMenu(mWin_d->MainMenu.AddRow, "Download from Entrez");
+                CommandItem(mWin_d->MainMenu.FromNet,
+                    "By gapped BLAST...", (Nlm_ItmActnProc)vgp->BlastNetGap);
+                CommandItem(mWin_d->MainMenu.FromNet,
+                    "By ungapped BLAST...", (Nlm_ItmActnProc)vgp->BlastNet);
+            } 
+        }
+    }
+
+	/*Options menu*/
+	m=PulldownMenu(w,"Options");
+	mWin_d->MainMenu.Options=m;
+  if (!bEditor) {
+    mWin_d->MainMenu.DispStyles=CommandItem(m,"Styles",DDV_DisplayStyles);
+  }
+
+#ifdef DEBUG_DDV
+	CommandItem(m,"Switch UA Gap",DDV_ShowHideUnAlignGap);
+#endif
+	s=SubMenu(m,"Mouse modes");
+	mWin_d->MainMenu.MouseMode=ChoiceGroup(s,SelectMouseMode);
+	ChoiceItem(mWin_d->MainMenu.MouseMode,"Query");
+	ChoiceItem(mWin_d->MainMenu.MouseMode,"Select rectangle");
+	ChoiceItem(mWin_d->MainMenu.MouseMode,"Select one row");
+  /* only allow "Edit" option for DDE, when not running in NoGaps mode */
+  pNoGaps = (Boolean*) GetAppProperty("dde_nogaps");
+  if (pNoGaps == NULL) NoGaps = TRUE;
+  else NoGaps = *pNoGaps;
+  if (!NoGaps) {
+    if (bEditor)
+      ChoiceItem(mWin_d->MainMenu.MouseMode,"Edit");
+  }
+
+  if (bEditor) {
+    s2=SubMenu(m,"Justify");
+    mWin_d->MainMenu.Justify=ChoiceGroup(s2,SelectJustify);
+    ChoiceItem(mWin_d->MainMenu.Justify,"Left");
+    ChoiceItem(mWin_d->MainMenu.Justify,"Right");
+    ChoiceItem(mWin_d->MainMenu.Justify,"Center");
+  } 
+
+  /* only launch the editor from the viewer */
+  if (!bEditor && mWin_d->EditAllowed) {
+    mWin_d->MainMenu.ShowLowerPanel = StatusItem(m,
+         "Show Lower Panel/L", DDV_ShowLowerPanel);
+    SetObjectExtra (mWin_d->MainMenu.ShowLowerPanel, (Pointer)mWin_d, NULL);
+    mWin_d->MainMenu.LaunchEditor=CommandItem(m,"Launch editor...",DDV_LaunchEditor);
+    mWin_d->MainMenu.MergeBlocks=CommandItem(m,"Merge 2 blocks...",DDV_MergeBlocks);
+    mWin_d->MainMenu.SplitBlock=CommandItem(m,"Split block in 2...",DDV_SplitBlock);
+    mWin_d->MainMenu.DeleteDDVBlock=CommandItem(m, "Delete block...",DDV_DeleteBlock2);
+  }
+
+	if (mWin_d->AutonomeViewer && mWin_d->NetCfgMenuProc){
+		mWin_d->MainMenu.ConfigNet=CommandItem(m,"Network...",
+				mWin_d->NetCfgMenuProc);
+	}
+	/*Help menu*/
+	m=PulldownMenu(w,"Help");
+	CommandItem(m,"About...",DDV_AboutProc);
+}
+
+/*******************************************************************************
+
+  Function : DDV_WinMainCleanup()
+  
+  Purpose : free memory before leaving viewer
+  
+  Parameters : mWin_d ; main window data
+  
+  Return value : none 
+
+*******************************************************************************/
+extern void DDV_WinMainCleanup(GraphiC g, VoidPtr data)
+{
+DdvMainWinPtr mWin_d;
+
+	if (!data) return;
+	mWin_d=(DdvMainWinPtr)data;
+
+	/*main window data - Logo*/
+/*	if (mWin_d->f1) DeleteFont(mWin_d->f1);
+	if (mWin_d->f2) DeleteFont(mWin_d->f2);
+	if (mWin_d->f3) DeleteFont(mWin_d->f3);
+*/
+	/*delete Align data*/
+	DDV_CloseData(mWin_d,TRUE);
+
+	MemFree(mWin_d);
+}
+
+/*******************************************************************************
+  
+  Purpose : init the graphical data structure of DDV. Use only when you start DDV. 
+
+  Function : DDV_InitGraphGlobal()
+  
+  Parameters : dmp; main DDV data block
+  
+  Return value : -
+
+*******************************************************************************/
+extern void DDV_InitGraphGlobal(DdvMainPtr dmp)
+{
+Int2 decal=0;
+
+	dmp->GrData.udv_font.LineHeight=
+		UDV_ComputeLineHeight(dmp->GrData.udv_font.cyChar);
+	dmp->GrData.udv_font.ColWidth=
+		DDV_ComputeColWidth(dmp->GrData.udv_font.cxChar);
+	UDV_Init_ScaleData(&(dmp->GrData));
+	UDV_Build_Other_Colors(&(dmp->GrData));
+	/*... then adjust values for DDV*/
+	dmp->GrData.udv_scale.ScalePosition=(Int2)SCALE_POS_TOP;
+	dmp->GrData.udv_panel.ShowFeatures=FALSE;
+	dmp->GrData.udv_panel.ShowByBlock=FALSE;
+	dmp->GrData.udv_scale.cxLeftScale=dmp->GrData.udv_font.cxChar*2;
+	dmp->GrData.udv_panel.cxName=PANEL_NAME_WIDTH*dmp->GrData.udv_font.cxChar;
+	if (dmp->GrData.udv_scale.ShowMajorTick) decal++;
+	if (dmp->GrData.udv_scale.ScalePosition==SCALE_POS_TOP) decal++;
+	dmp->GrData.udv_panel.cyScale=decal*dmp->GrData.udv_font.LineHeight;
+	dmp->MSA_d.pgp_l.DisplayType=DDV_DISP_HORZ;
+}	
+
+/*******************************************************************************
+
+  Function : DDV_SetRulerAttribInPGP()
+  
+  Purpose : modify the BSP ruler attribute for a row in the MSA
+  
+  Return value : -
+
+*******************************************************************************/
+extern void DDV_SetRulerAttribInPGP(ValNodePtr ParaG_Head, Uint1 RulerStyle)
+{
+ValNodePtr vnp;
+ParaGPtr   pgp;
+
+	vnp=ParaG_Head;
+	while(vnp){
+		pgp=(ParaGPtr)vnp->data.ptrvalue;
+		if (pgp){
+			pgp->ScaleStyle=RulerStyle;
+			switch (RulerStyle){
+				case SCALE_POS_NONE:
+					pgp->nLines=1;
+					break;
+				case SCALE_POS_TOP:
+					pgp->nLines=2;
+					break;
+				default:
+					pgp->nLines=1;
+					break;
+			}
+		}
+		vnp=vnp->next;
+	}
+}
+
+/*******************************************************************************
+
+  Function : DDV_SetRulerAttribInPGP()
+  
+  Purpose : modify the BSP ruler attribute for a row in the MSA
+  
+  Return value : -
+
+*******************************************************************************/
+extern void DDV_SortPGPLineNum(ValNodePtr PNTR Head, Int4 nBsp)
+{
+ValNodePtr vnp;
+ParaGPtr   pgp;
+Int4       n=0,j;
+
+	for(j=0;j<nBsp;j++){
+		vnp=Head[j];
+		while(vnp){
+			pgp=(ParaGPtr)vnp->data.ptrvalue;
+			pgp->StartLine=n;
+			vnp=vnp->next;
+		}
+		n+=pgp->nLines;
+	}	
+}
+
+/*******************************************************************************
+
+  Function : DDV_ExportSeqAlign()
+  
+  Purpose : export a SeqAlign
+  
+  Return value : none 
+
+*******************************************************************************/
+static void DDV_ExportSeqAlign(SeqAlignPtr sap,CharPtr szFName)
+{
+SeqAlignPtr  sap_to_save=NULL;
+AsnIoPtr     aip;
+AsnTypePtr   atp;
+AsnModulePtr amp;
+
+	sap_to_save=AlnMgrGetSubAlign(sap, NULL, 0, -1);
+	if (sap_to_save==NULL) goto error;
+
+	amp = AsnAllModPtr ();
+	atp = AsnTypeFind (amp,"Seq-align");
+
+	if ((aip = AsnIoOpen (szFName, "w")) == NULL) goto error;
+	SeqAlignAsnWrite( sap, aip, atp );
+	AsnIoReset(aip);
+	return;
+error:
+	if (sap_to_save) SeqAlignFree(sap_to_save);
+	Message(MSG_OK, "Sorry, ASN.1 SeqAlign cannot be exported.");
+	return;	
+}
+
+/*******************************************************************************
+
+  Function : DDV_ExportSeqAlign()
+  
+  Purpose : export a SeqAlign
+  
+  Return value : none 
+
+*******************************************************************************/
+static void DDV_ExportSeqAnnot(SeqAlignPtr sap,CharPtr szFName)
+{
+SeqAlignPtr  sap_to_save=NULL;
+
+	sap_to_save=AlnMgrGetSubAlign(sap, NULL, 0, -1);
+	if (sap_to_save==NULL){
+		Message(MSG_OK, "Sorry, ASN.1 SeqAlign cannot be exported.");
+		return;
+	}
+	/*Salsa export function*/
+	seqalign_write (sap_to_save, szFName);
+	if (sap_to_save) SeqAlignFree(sap_to_save);
+}
+
+/*******************************************************************************
+
+  Function : DDVExportTexteChooseFormat()
+  
+  Purpose : manage popup list of SeqAlign Format (export) 
+  
+  Return value : none 
+
+*******************************************************************************/
+static void DDVExportTexteChooseFormat (PopuP pop)
+{
+DdvExportTexteMSGPtr  detmp;
+WindoW				  hExportDlg;
+Int2                  value;
+
+	hExportDlg=(WindoW)ParentWindow(pop);
+
+	if (!hExportDlg) return;
+	
+	detmp = (DdvExportTexteMSGPtr) GetObjectExtra (hExportDlg);
+
+	if (detmp==NULL) return;
+	
+	value=GetValue(pop);
+	
+	if(value>2){
+		Disable(detmp->chk2);
+		Disable(detmp->chk3);
+		Disable(detmp->chk4);
+		Disable(detmp->chk5);
+		Disable(detmp->chk6);
+	}
+	else{
+		Enable(detmp->chk2);
+		Enable(detmp->chk3);
+		Enable(detmp->chk4);
+		Enable(detmp->chk5);
+		Enable(detmp->chk6);
+	}
+	return;
+}
+
+/*******************************************************************************
+
+  Function : DDVExportTexteOkProc()
+  
+  Purpose : manage ok button of the Export dialog box 
+    
+  Return value : none 
+
+*******************************************************************************/
+static void DDVExportTexteOkProc(ButtoN g)
+{
+DdvExportTexteMSGPtr  detmp;
+DdvMainWinPtr         mWin_d;
+DdvMainPtr            dmp;
+DDVOptionsBlock       dob;
+WindoW				  hExportDlg;
+Uint4                 disp_options=0;
+FILE                  *hFile;
+Int2                  value;
+Boolean               bRulerNum,bRulerTick,bShowBlock,bShowStrand,bShowBSPcoord,
+                      bPrintGap;
+Char 				  szFName[PATH_MAX]={""};
+
+	hExportDlg=(WindoW)ParentWindow(g);
+
+	if (!hExportDlg) return;
+	
+	detmp = (DdvExportTexteMSGPtr) GetObjectExtra (hExportDlg);
+
+	if (detmp==NULL) {
+		Remove(hExportDlg);
+		return;
+	}
+	
+	mWin_d = (DdvMainWinPtr) GetObjectExtra (detmp->hWinMain);
+	dmp = (DdvMainPtr) GetObjectExtra(mWin_d->hWndDDV);
+	
+	/*get the user's choices*/
+	value=GetValue(detmp->pop);
+	
+	bRulerNum=bRulerTick=bShowBlock=bShowStrand=bShowBSPcoord=FALSE;
+	disp_options = VIEW_FULLSEQ;
+	
+	if(value<3){/*text and HTML only*/
+		bRulerNum=GetStatus(detmp->chk2);
+		if (bRulerNum){
+			bRulerTick=GetStatus(detmp->chk3);
+		}
+		else{
+			bRulerTick=FALSE;
+		}
+		bShowBlock=GetStatus(detmp->chk4);
+		bShowStrand=GetStatus(detmp->chk5);
+		bShowBSPcoord=GetStatus(detmp->chk6);
+		if (bRulerNum) disp_options |= RULER_TOP;
+		if (bRulerTick) disp_options|=RULER_TICK;
+		if (bShowBlock) disp_options|=DISPE_SHOWBLOCK;
+		if (bShowStrand) disp_options|=DISP_STRAND;
+		if (bShowBSPcoord) disp_options|=DISP_BSP_COORD;
+	}
+
+	GetTitle(detmp->edit1, szFName, PATH_MAX-1);
+
+	switch(value){
+		case 1:/*text*/
+			disp_options|=DISP_FULL_TXT;
+			break;
+		case 2:/*html*/
+			disp_options|=DISP_FULL_HTML;
+			break;
+		case 3:/*philou*/
+			disp_options|=DISP_PHYLIP_TXT;
+			break;
+		case 4:/*fasta + gaps*/
+			bPrintGap=TRUE;
+			break;			
+		case 5:/*fasta without gaps*/
+			bPrintGap=FALSE;
+			break;			
+		case 6:/*seqalign*/
+			DDV_ExportSeqAlign(dmp->MSA_d.pgp_l.sap,szFName);
+			Remove(hExportDlg);
+			return;
+		case 7:/*seqannot*/
+			DDV_ExportSeqAnnot(dmp->MSA_d.pgp_l.sap,szFName);
+			Remove(hExportDlg);
+			return;
+	}
+
+	MemFill(&dob,0,sizeof(DDVOptionsBlock));
+	dob.LineSize=ParaG_Size;
+	hFile=fopen(szFName,"w");
+	if (!hFile){
+		Message(MSG_OK, "File creation failed !");
+	}
+	else{/*a last... save the SeqAlign*/
+		switch(value){
+			case 1:
+			case 2:
+			case 3:/*text,html,philou only*/
+				DDV_DumpSAPInAFile(&(dmp->MSA_d.pgp_l),&dob, hFile,disp_options,
+					dmp->Globals.colorp);
+				break;
+			case 4:
+			case 5:/*Fasta*/
+				DDV_DumpSAPInFastaFile(&(dmp->MSA_d.pgp_l),&dob, hFile,bPrintGap);
+				break;
+		}
+		fclose(hFile);
+	}
+	Remove(hExportDlg);
+}
+
+/*******************************************************************************
+
+  Function : DDVExportTextecancelProc()
+  
+  Purpose : manage cancel button of the Export dialog box 
+    
+  Return value : none 
+
+*******************************************************************************/
+static void DDVExportTextecancelProc(ButtoN g)
+{
+WindoW				hExportDlg;
+DdvExportTexteMSGPtr  detmp;
+
+	hExportDlg=(WindoW)ParentWindow(g);
+
+	if (!hExportDlg) return;
+	
+	detmp = (DdvExportTexteMSGPtr) GetObjectExtra (hExportDlg);
+
+	if (detmp==NULL) {
+		Remove(hExportDlg);
+		return;
+	}
+
+	Remove(hExportDlg);
+}
+
+/*******************************************************************************
+
+  Function : DDVExportTexteShowNumber()
+  
+  Purpose : manage ShoWNumber checkbox of the Export dialog box 
+    
+  Return value : none 
+
+*******************************************************************************/
+static void DDVExportTexteShowNumber(ButtoN g)
+{
+WindoW				hExportDlg;
+DdvExportTexteMSGPtr  detmp;
+
+	hExportDlg=(WindoW)ParentWindow(g);
+
+	if (!hExportDlg) return;
+	
+	detmp = (DdvExportTexteMSGPtr) GetObjectExtra (hExportDlg);
+
+	if (detmp==NULL) return;
+	
+	if (GetStatus(detmp->chk2)==FALSE){
+		Disable(detmp->chk3);
+	}
+	else{
+		Enable(detmp->chk3);
+	}
+
+	return;	
+}
+
+/*******************************************************************************
+
+  Function : DDVExportTexteFNameProc()
+  
+  Purpose : manage File name edit control of the Export dialog box 
+  
+  Parameters : t; edit control
+  
+  Return value : none 
+
+*******************************************************************************/
+static void DDVExportTexteFNameProc(TexT t)
+{
+Char 				szFName[PATH_MAX]={""};
+WindoW				hExportDlg;
+DdvExportTexteMSGPtr  detmp;
+
+	hExportDlg=(WindoW)ParentWindow(t);
+
+	if (!hExportDlg) return;
+	
+	detmp = (DdvExportTexteMSGPtr) GetObjectExtra (hExportDlg);
+
+	if (detmp==NULL) return;
+	
+	GetTitle(t, szFName, PATH_MAX-1);
+
+	if (StringLen(szFName) == 0)
+		Disable(detmp->ok);
+	else Enable(detmp->ok);
+
+	return;
+}
+
+/*******************************************************************************
+
+  Function : DDVExportTexteBrowseFile()
+  
+  Purpose : manage browse button of the Export dialog box 
+  
+  Parameters : g; button
+  
+  Return value : none 
+
+*******************************************************************************/
+static void DDVExportTexteBrowseFile(ButtoN g)
+{
+WindoW				hExportDlg;
+DdvExportTexteMSGPtr  detmp;
+Char 				path[PATH_MAX]={""};
+
+	hExportDlg=(WindoW)ParentWindow(g);
+
+	if (!hExportDlg) return;
+
+	detmp = (DdvExportTexteMSGPtr) GetObjectExtra (hExportDlg);
+
+	if (detmp==NULL) return;
+	if (!detmp->edit1) return;
+
+	if (GetOutputFileName (path, PATH_MAX-1, NULL)){ 
+		SetTitle(detmp->edit1, path);
+		DDVExportTexteFNameProc(detmp->edit1);
+	}
+
+	return;   
+}
+
+/*******************************************************************************
+
+  Function : DDV_ExportTexte()
+  
+  Purpose : create the Export dialog box 
+  
+  Return value : none 
+
+*******************************************************************************/
+static void DDV_ExportTexte(IteM i)
+{
+DdvExportTexteMSGPtr  detmp;
+DdvMainWinPtr mWin_d;
+DdvMainPtr 	  dmp;
+WindoW		  hWinMain,hExportDlg;
+GrouP         g0,g1,g4,g7,g8,g10;
+ButtoN        chk2,chk3,chk4,chk5,chk6,browse,ok;
+TexT          edit1;
+PopuP pop;
+PrompT txt;
+
+	/*get some data*/
+	hWinMain=(WindoW)ParentWindow(i);
+	if (hWinMain==NULL) return;
+	mWin_d = (DdvMainWinPtr) GetObjectExtra (hWinMain);
+	if (mWin_d==NULL) return;
+	if (mWin_d->hWndDDV==NULL) return;
+	dmp = (DdvMainPtr) GetObjectExtra(mWin_d->hWndDDV);
+	if (dmp==NULL) return;
+
+	/*init MsgStruct; to be used when user clicks on [OK]*/
+	detmp=(DdvExportTexteMSGPtr)MemNew(sizeof(DdvExportTexteMSG));	
+	if (!detmp) return;
+	
+	/*DlgBox window*/
+	hExportDlg=MovableModalWindow(-30, -20,  -10,  -10, 
+				"DDV - export a SeqAlign",  NULL);
+
+	if (!hExportDlg){
+		MemFree(detmp);
+		return;
+	}
+
+	SetObjectExtra (hExportDlg, (Pointer) detmp, StdCleanupExtraProc);
+
+	/*top-level groups*/
+	g0=HiddenGroup(hExportDlg, -1, 0,NULL);
+		
+	g1=NormalGroup(g0,2,0,"SeqAlign Ruler",NULL,NULL);
+/*	g2=HiddenGroup(g1,2,0);*/
+	chk2=CheckBox(g1,"Show number",DDVExportTexteShowNumber);
+	chk3=CheckBox(g1,"Show ticks",NULL);
+	
+	g4=NormalGroup(g0,0,4,"SeqAlign format",NULL,NULL);
+	chk4=CheckBox(g4,"Use block of 10 letters",NULL);
+	chk5=CheckBox(g4,"Display strand orientation",NULL);
+	chk6=CheckBox(g4,"Display BioSeq coordinates",NULL);
+	g7=HiddenGroup(g4,2,0,NULL);
+	txt=StaticPrompt(g7,"Format :",0,0,systemFont,'l');
+#ifdef WIN_MAC
+	pop=PopupList(g7,TRUE,DDVExportTexteChooseFormat);
+#endif
+
+#ifndef WIN_MAC
+	pop=PopupList(g7,FALSE,DDVExportTexteChooseFormat);
+#endif
+	AlignObjects(ALIGN_MIDDLE,(HANDLE) txt, (HANDLE) pop, NULL);
+	PopupItem(pop,"Text");
+	PopupItem(pop,"HTML");
+	PopupItem(pop,"Phylip");
+	PopupItem(pop,"Fasta with gaps");
+	PopupItem(pop,"Fasta without gaps");
+	PopupItem(pop,"ASN.1 SeqAlign");
+	PopupItem(pop,"ASN.1 SeqAnnot");
+
+	g8=NormalGroup(g0,3,0,"File name",NULL,NULL);
+	edit1=DialogText(g8,"",20,DDVExportTexteFNameProc);
+	browse=PushButton (g8, "Browse...", DDVExportTexteBrowseFile);
+
+	/*ok - cancel group - start*/
+	g10=HiddenGroup(g0, 2, 0,NULL);
+	ok=PushButton (g10, "Ok", DDVExportTexteOkProc);
+	PushButton (g10, "Cancel", DDVExportTextecancelProc);
+	/*build the dlgbox*/
+	RealizeWindow(hExportDlg);
+	Show(hExportDlg);
+	/*copy data*/
+	detmp->hWinMain=hWinMain;
+	detmp->chk2=chk2;
+	detmp->chk3=chk3;
+	detmp->chk4=chk4;
+	detmp->chk5=chk5;
+	detmp->chk6=chk6;
+	detmp->pop=pop;
+	detmp->edit1=edit1;
+	detmp->ok=ok;
+	/*color display check box*/
+	SetStatus(chk2,TRUE);
+	SetStatus(chk3,TRUE);
+	SetStatus(chk4,TRUE);
+	SetStatus(chk5,TRUE);
+	SetStatus(chk6,TRUE);
+	SetValue(pop,1);
+	Disable(detmp->ok);
+}
+
+/*******************************************************************************
+
+  Function : UDV_GotoBtnProc()
+  
+  Purpose : create the Export dialog box 
+  
+  Return value : none 
+
+*******************************************************************************/
+static void UDV_GotoBtnProc(ButtoN g)
+{
+DdvMainWinPtr      dmwp;
+DdvMainPtr         dmp;
+MsaParaGPopList    mppl;
+WindoW             hParent;
+Char               szCol[20],szRow[20],szInfo[255];
+Int4               col,row,from_col,to_col,from_row,to_row,old_pos;
+Boolean            bHorzScroll,bVertScroll;
+BaR                hsb,vsb;
+
+	/*get main data block*/
+	hParent=(WindoW)ParentWindow(g);
+	if (!hParent) return;
+	dmwp=(DdvMainWinPtr)GetObjectExtra(hParent);
+	if (!dmwp) return;
+	dmp=(DdvMainPtr)GetObjectExtra(dmwp->hWndDDV);
+	if (!dmp) return;	
+	
+	/*get user values*/
+	GetTitle(dmwp->gotoValCol,szCol,19);
+	GetTitle(dmwp->gotoValRow,szRow,19);
+	col=atoi(szCol);
+	row=atoi(szRow);
+	
+	/*check their validity*/
+	mppl=dmp->MSA_d.pgp_l;
+	if (row<1 || row>mppl.nBsp){
+		sprintf(szInfo,"Please enter a 'row' value in\nthe range [1..%i]",
+				mppl.nBsp);
+		Message(MSG_OK,szInfo);
+		Select(dmwp->gotoValRow);
+		return;
+	}
+	if (col<1 || col>mppl.LengthAli){
+		sprintf(szInfo,"Please enter a 'column' value in\nthe range [1..%i]",
+				mppl.LengthAli);
+		Message(MSG_OK,szInfo);
+		Select(dmwp->gotoValCol);
+		return;
+	}
+	
+	/*do I need to scroll the panel content*/
+	DDV_GetCurrentDispRange(dmwp->hWndDDV,&dmp->GrData,mppl.LengthAli,
+		&from_col,&to_col,&from_row,&to_row);
+	if (col>=from_col && col<=to_col)
+		bHorzScroll=FALSE;
+	else
+		bHorzScroll=TRUE;
+	if (row>=from_row && row<=to_row)
+		bVertScroll=FALSE;
+	else
+		bVertScroll=TRUE;
+
+	dmp->dtd.col=col;
+	dmp->dtd.row=row;
+	if (bHorzScroll){
+		hsb = GetSlateHScrollBar ((SlatE) dmp->hWndDDV);
+		col--;/*switch to zero-based values*/
+		old_pos=GetBarValue(hsb);
+		SetValue(hsb,old_pos+(col-old_pos)-5);
+	}
+	if (bVertScroll){
+		vsb = GetSlateVScrollBar ((SlatE) dmp->hWndDDV);
+		row--;/*switch to zero-based values*/
+		old_pos=GetBarValue(vsb);
+		SetValue(vsb,old_pos+(row-old_pos));
+	}
+	dmp->dtd.action=DDV_INVAL_REGION;
+	dmp->dtd.status=DDV_SET_TIMER;
+}
+
+/*******************************************************************************
+
+  Function : DDV_TimerProc()
+  
+  Purpose : timer callback of DDV 
+  
+  Return value : none 
+
+*******************************************************************************/
+extern void DDV_TimerProc (WindoW w)
+{
+DdvMainWinPtr dmwp;
+DdvMainPtr    dmp;
+Int4          col,row;
+
+	/*get main data block*/
+	dmwp=(DdvMainWinPtr)GetObjectExtra(w);
+	if (!dmwp) return;
+	dmp=(DdvMainPtr)GetObjectExtra(dmwp->hWndDDV);
+	if (!dmp) return;	
+	if (dmp->dtd.status==DDV_SET_TIMER){
+		dmp->dtd.delay=0;
+		if (dmp->dtd.action==DDV_INVAL_REGION){
+			DDV_InvalRegion(dmp->hWndDDV,&(dmp->GrData),
+				_max_(0,dmp->dtd.col-1),dmp->dtd.col+1,
+				dmp->dtd.row,FALSE);
+		}
+		dmp->dtd.status=DDV_TEST_TIMER;
+	}
+	if (dmp->dtd.status==DDV_TEST_TIMER){
+		if (dmp->dtd.delay>10){
+			if (dmp->dtd.action==DDV_INVAL_REGION){
+				col=dmp->dtd.col;
+				row=dmp->dtd.row;
+				dmp->dtd.col=0;
+				dmp->dtd.row=0;
+				DDV_InvalRegion(dmp->hWndDDV,&(dmp->GrData),
+					_max_(0,col-1),col+1,row,FALSE);
+				dmp->dtd.action=DDV_NOTHING;
+			}
+		}
+	}
+	dmp->dtd.delay++;
+}
+
+/*******************************************************************************
+
+  Function : DDV_DeleteRow()
+  
+  Purpose : UI to delete a row 
+  
+  Return value : none 
+
+*******************************************************************************/
+static void DDV_DeleteRow(IteM i)
+{
+DdvMainWinPtr       mWin_d;
+DdvMainPtr 	        dmp;
+WindoW		          hWinMain,temport;
+DDE_StackPtr        ddesp;
+RecT 	              rcP;
+static Int4         PassCount = 0;
+BaR                 hsb;
+
+	/*get some data*/
+	hWinMain=(WindoW)ParentWindow(i);
+	if (hWinMain==NULL) return;
+	mWin_d = (DdvMainWinPtr) GetObjectExtra (hWinMain);
+	if (mWin_d==NULL) return;
+	if (mWin_d->hWndDDV==NULL) return;
+	dmp = (DdvMainPtr) GetObjectExtra(mWin_d->hWndDDV);
+	if (dmp==NULL) return;
+
+  ddesp = dmp->dsp;
+  
+  if (PassCount == 0) {
+    DDE_ShiftBlock(ddesp, 0, 5, TRUE);
+  }
+
+  if (PassCount == 1) {
+    DDE_ShiftBlock(ddesp, 0, -5, TRUE);
+    PassCount = 4;
+  }
+  
+  if (PassCount == 5) {
+    DDE_InsertGap(ddesp, 7, 1649, TRUE);
+    DDE_InsertGap(ddesp, 7, 1649, TRUE);
+    DDE_InsertGap(ddesp, 7, 9, TRUE);
+    DDE_InsertGap(ddesp, 7, 9, TRUE);
+    DDE_InsertGap(ddesp, 7, 9, TRUE);
+    DDE_InsertGap(ddesp, 7, 11, TRUE);
+    DDE_InsertGap(ddesp, 7, 3, TRUE);
+    DDE_InsertGap(ddesp, 7, 1, TRUE);
+    DDE_InsertGap(ddesp, 7, 0, TRUE);
+    DDE_InsertGap(ddesp, 7, 0, TRUE);
+    DDE_InsertGap(ddesp, 7, 27, TRUE);
+    DDE_InsertGap(ddesp, 7, 23, TRUE);
+    DDE_InsertGap(ddesp, 7, 22, TRUE);
+    DDE_InsertGap(ddesp, 7, 1645, TRUE);
+    DDE_InsertGap(ddesp, 7, 1655, TRUE);
+    DDE_InsertGap(ddesp, 7, 1649, TRUE);
+    DDE_InsertGap(ddesp, 7, 1649, TRUE);
+    DDE_InsertGap(ddesp, 7, 1650, TRUE);
+    DDE_InsertGap(ddesp, 7, 1648, TRUE);
+    DDE_InsertGap(ddesp, 7, 1648, TRUE);
+    PassCount = 6;
+  }
+
+  if (PassCount == 7) {
+    DDE_RemoveGap(ddesp, 7, 1649, TRUE);
+    DDE_RemoveGap(ddesp, 7, 1645, TRUE);
+    DDE_RemoveGap(ddesp, 7, 15, TRUE);
+    DDE_RemoveGap(ddesp, 7, 15, TRUE);
+    DDE_RemoveGap(ddesp, 7, 1, TRUE);
+    DDE_RemoveGap(ddesp, 7, 1, TRUE);
+    DDE_RemoveGap(ddesp, 7, 25, TRUE);
+    DDE_RemoveGap(ddesp, 7, 20, TRUE);
+    DDE_RemoveGap(ddesp, 7, 18, TRUE);
+    DDE_RemoveGap(ddesp, 7, 12, TRUE);
+    DDE_RemoveGap(ddesp, 7, 11, TRUE);
+    DDE_RemoveGap(ddesp, 7, 4, TRUE);
+    DDE_RemoveGap(ddesp, 7, 0, TRUE);
+    DDE_RemoveGap(ddesp, 7, 0, TRUE);
+    DDE_InsertGap(ddesp, 7, 0, TRUE);
+    DDE_RemoveGap(ddesp, 7, 1636, TRUE);
+    DDE_InsertGap(ddesp, 7, 1645, TRUE);
+    DDE_InsertGap(ddesp, 7, 1647, TRUE);
+    DDE_RemoveGap(ddesp, 7, 1645, TRUE);
+    DDE_RemoveGap(ddesp, 7, 1646, TRUE);
+    DDE_InsertGap(ddesp, 7, 1645, TRUE);
+    DDE_InsertGap(ddesp, 7, 1647, TRUE);
+    DDE_RemoveGap(ddesp, 7, 1647, TRUE);
+    DDE_RemoveGap(ddesp, 7, 1645, TRUE);
+    DDE_RemoveGap(ddesp, 7, 0, TRUE);
+    DDE_InsertGap(ddesp, 7, 0, TRUE);
+    DDE_InsertGap(ddesp, 7, 0, TRUE);
+    DDE_InsertGap(ddesp, 7, 1, TRUE);
+    DDE_InsertGap(ddesp, 7, 3, TRUE);
+    DDE_InsertGap(ddesp, 7, 5, TRUE);
+    DDE_RemoveGap(ddesp, 7, 1, TRUE);
+    DDE_RemoveGap(ddesp, 7, 2, TRUE);
+    DDE_RemoveGap(ddesp, 7, 0, TRUE);
+    DDE_RemoveGap(ddesp, 7, 0, TRUE);
+    DDE_RemoveGap(ddesp, 7, 1, TRUE);
+    DDE_InsertGap(ddesp, 7, 1649, TRUE);
+    DDE_InsertGap(ddesp, 7, 1648, TRUE);
+    DDE_InsertGap(ddesp, 7, 1647, TRUE);
+    DDE_InsertGap(ddesp, 7, 1647, TRUE);
+    DDE_RemoveGap(ddesp, 7, 1647, TRUE);
+    DDE_InsertGap(ddesp, 7, 0, TRUE);
+    DDE_RemoveGap(ddesp, 7, 1648, TRUE);
+    DDE_InsertGap(ddesp, 7, 1649, TRUE);
+    DDE_RemoveGap(ddesp, 7, 1649, TRUE);
+    PassCount = 14;
+  }
+
+  if (PassCount == 15) {
+    DDE_HideRow(ddesp, 3, TRUE);
+    DDE_HideRow(ddesp, 3, TRUE);
+    DDE_HideRow(ddesp, 4, TRUE);
+    DDE_HideRow(ddesp, 0, TRUE);
+    DDE_HideRow(ddesp, 7, TRUE);
+  }
+
+  if (PassCount ==  16) {
+    DDE_ShowRow(ddesp, 2, TRUE);
+    DDE_ShowRow(ddesp, 3, TRUE);
+    DDE_ShowRow(ddesp, 0, TRUE);
+    DDE_ShowRow(ddesp, 4, TRUE);
+    DDE_ShowRow(ddesp, 7, TRUE);
+  }
+
+  if (PassCount == 17) {
+    DDE_MoveRow(ddesp, 5, 2, TRUE);
+  }
+
+  if (PassCount == 18) {
+    DDE_HideRow(ddesp, 3, TRUE);
+    DDE_HideRow(ddesp, 4, TRUE);
+    DDE_HideRow(ddesp, 0, TRUE);
+    DDE_HideRow(ddesp, 7, TRUE);
+    DDE_HideRow(ddesp, 2, TRUE);
+    DDE_HideRow(ddesp, 1, TRUE);
+    DDE_HideRow(ddesp, 6, TRUE);
+    DDE_HideRow(ddesp, 5, TRUE);
+    DDE_HideRow(ddesp, 4, TRUE);
+    PassCount = 19;
+  }
+
+  if (PassCount == 20) {
+    DDE_ShowRow(ddesp, 7, TRUE);
+    DDE_ShowRow(ddesp, 0, TRUE);
+    DDE_ShowRow(ddesp, 4, TRUE);
+    DDE_ShowRow(ddesp, 3, TRUE);
+    DDE_ShowRow(ddesp, 1, TRUE);
+    DDE_ShowRow(ddesp, 5, TRUE);
+    DDE_ShowRow(ddesp, 6, TRUE);
+    DDE_ShowRow(ddesp, 2, TRUE);
+    PassCount = 27;
+  }
+
+  if (PassCount == 28) {
+    DDE_MoveRow(ddesp, 3, 3, TRUE);
+    DDE_MoveRow(ddesp, 2, 5, TRUE);
+    DDE_MoveRow(ddesp, 0, 6, TRUE);
+    DDE_MoveRow(ddesp, 7, 1, TRUE);
+    DDE_MoveRow(ddesp, 7, 0, TRUE);
+    DDE_MoveRow(ddesp, 0, 7, TRUE);
+    PassCount = 33;
+  }
+
+  if (PassCount == 34) {
+    DDE_HideRow(ddesp, 6, TRUE);
+    DDE_HideRow(ddesp, 1, TRUE);
+    DDE_HideRow(ddesp, 0, TRUE);
+    DDE_HideRow(ddesp, 7, TRUE);
+    PassCount = 37;
+  }
+
+  if (PassCount == 38) {
+    DDE_MoveRow(ddesp, 3, 1, TRUE);
+    DDE_MoveRow(ddesp, 0, 2, TRUE);
+    DDE_MoveRow(ddesp, 0, 3, TRUE);
+    DDE_MoveRow(ddesp, 3, 0, TRUE);
+    PassCount = 41;
+  }
+
+  if (PassCount == 42) {
+    DDE_ShowRow(ddesp, 1, TRUE);
+    DDE_ShowRow(ddesp, 7, TRUE);
+    DDE_ShowRow(ddesp, 6, TRUE);
+    DDE_ShowRow(ddesp, 0, TRUE);
+    PassCount = 45;
+  }
+
+  if (PassCount == 46) {
+    DDE_HideNewRow(ddesp, 5, TRUE);
+    DDE_HideNewRow(ddesp, 2, TRUE);
+    DDE_HideNewRow(ddesp, 4, TRUE);
+    DDE_HideNewRow(ddesp, 3, TRUE);
+    PassCount = 49;
+  }
+
+  if (PassCount == 50) {
+    DDE_ShowNewRow(ddesp, 2, TRUE);
+    DDE_ShowNewRow(ddesp, 3, TRUE);
+    DDE_ShowNewRow(ddesp, 5, TRUE);
+    DDE_ShowNewRow(ddesp, 4, TRUE);
+    PassCount = 53;
+  }
+
+  if (PassCount == 54) {
+    DDE_HideRow(ddesp, 4, TRUE);
+    DDE_HideRow(ddesp, 7, TRUE);
+    DDE_HideRow(ddesp, 0, TRUE);
+    DDE_RestoreRowOrder(ddesp, TRUE);
+    DDE_ShowRow(ddesp, 7, TRUE);
+    DDE_ShowRow(ddesp, 0, TRUE);
+    DDE_ShowRow(ddesp, 4, TRUE);
+  }
+
+  if (PassCount == 55) {
+    DDE_ShiftRightBoundary(ddesp, 0, -1640, TRUE);
+    DDE_DeleteBlock(ddesp, 0, TRUE);
+    PassCount = 64;
+  }
+
+  if (PassCount == 65) {
+    DDE_CreateBlock(ddesp, 20, 30, TRUE);
+    DDE_CreateBlock(ddesp, 15, 35, TRUE);
+    DDE_CreateBlock(ddesp, 25, 40, TRUE);
+    DDE_CreateBlock(ddesp, 15, 40, TRUE);
+  }
+
+  MemCopy(&(dmp->MSA_d.pgp_l), ddesp->pEdit->pPopList, sizeof(MsaParaGPopList));
+
+  DDV_InitColour_When_Start(dmp->MSA_d.pgp_l.sap,
+    &(dmp->MSA_d.pgp_l),&(dmp->Globals.colorp), FALSE);
+
+  /* recalculate window size */
+  DDV_WhatSize(dmp);
+  /* adjust horizontal scroll bar */
+  hsb = GetSlateHScrollBar((SlatE) dmp->hWndDDV);
+  DDV_UpdateHScrollVal(dmp->hWndDDV, FALSE, GetBarValue(hsb));
+
+  PassCount++;
+
+  temport=SavePort(mWin_d->hWndDDV);
+  Select(mWin_d->hWndDDV);
+  ObjectRect(mWin_d->hWndDDV, &rcP);
+  InvalRect(&rcP);
+  Update();
+  RestorePort(temport);
+ 	return;
+}
+
+static void DDV_MoveRowLeft(IteM i)
+{
+  DDV_DoEditFunction(i, MOVE_ROW_LEFT);
+  return;
+}
+
+static void DDV_MoveRowRight(IteM i)
+{
+  DDV_DoEditFunction(i, MOVE_ROW_RIGHT);
+  return;
+}
+
+static void DDV_MoveLeftBoundaryLeft(IteM i)
+{
+  DDV_DoEditFunction(i, MOVE_LEFT_BOUNDARY_LEFT);
+  return;
+}
+
+static void DDV_MoveLeftBoundaryRight(IteM i)
+{
+  DDV_DoEditFunction(i, MOVE_LEFT_BOUNDARY_RIGHT);
+  return;
+}
+
+static void DDV_MoveRightBoundaryLeft(IteM i)
+{
+  DDV_DoEditFunction(i, MOVE_RIGHT_BOUNDARY_LEFT);
+  return;
+}
+
+static void DDV_MoveRightBoundaryRight(IteM i)
+{
+  DDV_DoEditFunction(i, MOVE_RIGHT_BOUNDARY_RIGHT);
+  return;
+}
+
+static void DDV_DeleteBlock(IteM i)
+{
+  DDV_DoEditFunction(i, DDE_DELETE_BLOCK);
+  return;
+}
+
+static void DDV_CreateBlock(IteM i)
+{
+  DDV_DoEditFunction(i, DDE_CREATE_BLOCK);
+  return;
+}
+
+static void DDV_Prev(IteM i)
+{
+  DDV_DoEditFunction(i, DDE_PREV);
+  return;
+}
+
+static void DDV_Next(IteM i)
+{
+  DDV_DoEditFunction(i, DDE_NEXT);
+  return;
+}
+
+static void DDV_Orig(IteM i)
+{
+  DDV_DoEditFunction(i, DDE_ORIG);
+  return;
+}
+
+static void DDV_LaunchEditor(IteM i)
+{
+  DDV_DoEditFunction(i, DDE_LAUNCH_EDITOR);
+  return;
+}
+
+static void DDV_MergeBlocks(IteM i)
+{
+  DDV_DoEditFunction(i, DDE_MERGE_BLOCKS);
+  return;
+}
+
+static void DDV_SplitBlock(IteM i)
+{
+  DDV_DoEditFunction(i, DDE_SPLIT_BLOCK);
+  return;
+}
+
+static void DDV_DeleteBlock2(IteM i)
+{
+  DDV_DoEditFunction(i, DDV_DELETE_BLOCK);
+  return;
+}
+
+
+static void DDV_CallSaveEdits(IteM i) {
+/*----------------------------------------------------------------------------
+*  get DDVMainPtr and call DDV_SaveEdits
+*---------------------------------------------------------------------------*/
+  WindoW		     hWinMain;
+  DdvMainWinPtr  mWin_d;
+  DdvMainPtr 	   dmp;
+
+	hWinMain=(WindoW)ParentWindow(i);
+	if (hWinMain==NULL) return;
+	mWin_d = (DdvMainWinPtr) GetObjectExtra (hWinMain);
+	if (mWin_d==NULL) return;
+	if (mWin_d->hWndDDV==NULL) return;
+	dmp = (DdvMainPtr) GetObjectExtra(mWin_d->hWndDDV);
+	if (dmp==NULL) return;
+
+  DDV_SaveEdits(dmp, TRUE);
+}
+
+
+static void write_annot(SeqAlignPtr align)
+{
+        SeqAnnotPtr annot;
+        AsnIoPtr aip;
+
+        annot = SeqAnnotNew();
+        annot->type = 2;
+        annot->data = align;
+
+        aip = AsnIoOpen("temp2.sat", "w");
+        SeqAnnotAsnWrite(annot, aip, NULL);
+        AsnIoClose(aip);
+
+        annot->data = NULL;
+        SeqAnnotFree(annot);
+}         
+
+
+NLM_EXTERN void DDV_SaveEdits(DdvMainPtr dmp, Boolean UpdateDDV) {
+/*----------------------------------------------------------------------------
+*  create a DenseSeg for the block that has been created or edited.
+*  pass this info to the AlnMgr and tell it to add or replace the block.
+*---------------------------------------------------------------------------*/
+  Int4*          pStarts;
+  Int4*          pLens;
+  Uint1*         pStrands;
+  Int4           ii, jj, NumSegs, NumRows, NumBlocksAtLastSave, NumBlocksNow;
+  DenseSegPtr    dsp;
+  SeqAlignPtr    sap, indexed_sap;
+  SeqId          head;
+  SeqIdPtr       sip_prev, sip;
+  DDVUpdateMSG   dum;
+  MsaParaGPopListPtr  mpplp;
+  Boolean        ReDraw;
+  BaR            hsb;
+  Int4           HPos, Col, i;
+
+  /* note:       dsp is DenseSegPtr */
+  /*        dmp->dsp is DDE_StackPtr */
+
+  NumRows = dmp->dsp->pEdit->TotalNumRows;
+  NumSegs = DDE_GetNumSegmentsInBlock(dmp->dsp->pEdit, 0);
+  sap = ViewMgr_GetBegin(dmp->MSA_d.pgp_l.viewed_sap);
+  indexed_sap = ViewMgr_GetBeginIndexed(dmp->MSA_d.pgp_l.viewed_sap);
+
+  /* if there's a block that gets added or replaced, create a DenseSeg */
+  if (NumSegs > 0) {
+    /* create the empty dense seg, do NOT free it in this routine */
+    dsp = DenseSegNew();
+    dsp->dim = dmp->dsp->pEdit->TotalNumRows;
+    dsp->numseg = NumSegs;
+    /* create the starts, lens, and strands arrays */
+    pStarts =  MemNew(NumRows * NumSegs * sizeof(Int4));
+    pLens =    MemNew(NumSegs * sizeof(Int4));
+    pStrands = MemNew(NumRows * NumSegs * sizeof(Uint1));
+    DDE_CreateArraysForDenseSeg(dmp->dsp->pEdit, 0, pStarts, pLens); /* fill starts and lens */
+    for (ii=0; ii<NumSegs; ii++) {
+      for (jj=0; jj<NumRows; jj++) {
+        pStrands[ii*NumRows + jj] = AlnMgrGetNthStrand(sap, jj+1); /* fill strands */
+      }
+    }
+    dsp->starts = pStarts;
+    dsp->lens = pLens;
+    dsp->strands = pStrands;
+    /* create the linked-list of SeqIdPtr's */
+    sip_prev = &head;
+    for (ii=0; ii<NumRows; ii++) {
+      sip = AlnMgrGetNthSeqIdPtr(indexed_sap, ii+1);
+      sip_prev->next = sip;
+      sip_prev = sip_prev->next;
+    }
+    dsp->ids = head.next;
+  }
+
+  if (NumSegs > 0) {NumBlocksNow = 1;}
+  else             {NumBlocksNow = 0;}
+
+  NumBlocksAtLastSave = dmp->dsp->NumBlocks;
+
+  ReDraw = FALSE;
+  if ((NumBlocksAtLastSave==1) && (NumBlocksNow==0)) {
+    /* delete block */
+    AlnMgrReplaceBlock(indexed_sap, NULL, dmp->dsp->LaunchBlock+1);
+  }
+  if ((NumBlocksAtLastSave==1) && (NumBlocksNow==1)) {
+    /* replace block */
+    AlnMgrReplaceBlock(indexed_sap, dsp, dmp->dsp->LaunchBlock+1);
+    ReDraw = TRUE;
+  }
+  if ((NumBlocksAtLastSave==0) && (NumBlocksNow==1)) {
+    /* add block */
+    AlnMgrAddBlock(indexed_sap, dsp);
+    dmp->dsp->IsUnAligned = FALSE;
+    ReDraw = TRUE;
+  }
+
+  SeqAlignListFree(sap);
+  sap = AlnMgrGetSubAlign(indexed_sap, NULL, 0, -1);
+
+  ViewMgr_SetBegin(dmp->MSA_d.pgp_l.viewed_sap, sap, FALSE, FALSE);
+  /* indicate there are no edits to save when quitting DDE */
+  dmp->dsp->SomethingToSave = FALSE;
+
+  dmp->dsp->NumBlocks = NumBlocksNow;
+
+  /* redraw the display when 2 aligned blocks are merged */
+  /* if merging with preceeding block, launch block is decremented */
+  /* (there's no need to redraw when the first block is left aligned */
+  /* or when the last block is right aligned.  however, since I have */
+  /* no way of knowing how many blocks there are, a right aligned last */
+  /* block always causes a redraw) */
+
+  /* update:  we decided not to do auto merge.  so, I'm setting */
+  /* ReDraw to FALSE here.  no redraw. no modifying block index. */
+  /* if we go back to auto-merge, just get rid of this one line. */
+  ReDraw = FALSE;
+
+  if (ReDraw) {
+    if (DDE_FirstColumnIsAligned(dmp->dsp->pEdit)) {
+      if (dmp->dsp->LaunchBlock == 0) {
+        ReDraw = FALSE;
+      }
+      else {
+        dmp->dsp->LaunchBlock--;
+      }
+    }
+    else if (!DDE_LastColumnIsAligned(dmp->dsp->pEdit)) {
+      ReDraw = FALSE;
+    }
+  }
+
+  if (ReDraw) {
+    mpplp = DDE_CreateDisplay(indexed_sap, dmp->dsp->LaunchBlock,
+                              dmp->dsp->IsUnAligned, &dmp->dsp->NumBlocks);
+    mpplp->viewed_sap = dmp->dsp->pEdit->pPopList->viewed_sap;
+    dmp->dsp->pEdit = DDE_New(mpplp, dmp->dsp->pEdit->TotalNumRows);
+    DDE_MergeNodesLists(dmp->dsp->pEdit);
+    /* hide the rows in DDE that are hidden in DDV */
+    NumRows = dmp->dsp->pEdit->TotalNumRows;
+    for (i=0; i<NumRows; i++) {
+      if (ViewMgr_TRow2VRow(dmp->MSA_d.pgp_l.viewed_sap, i+1) == -1) {
+        DDE_HideRow(dmp->dsp, i, FALSE);
+      }
+    }
+    DDE_Add(dmp->dsp);
+    dmp->dsp->SomethingToSave = FALSE;
+    /* position block at 5th col */
+    hsb = GetSlateHScrollBar((SlatE) dmp->hWndDDV);
+    HPos = GetBarValue(hsb);
+    Col = DDE_GetAlignStart(dmp->dsp->pEdit, 0);
+    DDV_ReDrawAtCol(dmp, HPos+Col-5, TRUE);
+  }
+
+  /* tell DDV to rebuild its display */
+  if (UpdateDDV) {
+	  dum.type = UPDATE_TYPE_VIEWMGR;
+	  dum.data = NULL;
+    ViewMgr_Update(dmp->MSA_d.pgp_l.viewed_sap);
+	  ObjMgrSendProcMsg(OM_MSG_UPDATE, dmp->MSA_d.entityID, dmp->MSA_d.itemID,
+      OBJ_SEQALIGN, 0, 0, (Pointer)&dum);
+  }
+
+  return;
+}
+
+/*******************************************************************************
+
+  Function : DDV_DoEditFunction(Item i, Int4 WhichOne)
+  
+  Purpose : UI to do one of the edit functions
+  
+  Return value : none 
+
+*******************************************************************************/
+static void DDV_DoEditFunction(IteM i, Int4 WhichOne)
+{
+DdvMainWinPtr       mWin_d;
+DdvMainPtr 	        dmp;
+WindoW		          hWinMain;
+DDE_StackPtr        ddesp;
+
+	/*get some data*/
+	hWinMain=(WindoW)ParentWindow(i);
+	if (hWinMain==NULL) return;
+	mWin_d = (DdvMainWinPtr) GetObjectExtra (hWinMain);
+	if (mWin_d==NULL) return;
+	if (mWin_d->hWndDDV==NULL) return;
+	dmp = (DdvMainPtr) GetObjectExtra(mWin_d->hWndDDV);
+	if (dmp==NULL) return;
+
+  ddesp = dmp->dsp;
+  
+  switch (WhichOne) {
+    case MOVE_ROW_LEFT:
+      DDE_ShiftRow(ddesp, 4, -1, TRUE, TRUE);
+      DDV_ReDraw(dmp);
+      break;
+    case MOVE_ROW_RIGHT:
+      DDE_ShiftRow(ddesp, 4,  1, TRUE, TRUE);
+      DDV_ReDraw(dmp);
+      break;
+    case MOVE_LEFT_BOUNDARY_LEFT:
+      DDE_ShiftLeftBoundary(ddesp, 0, -1, TRUE);
+      DDV_ReDraw(dmp);
+      break;
+    case MOVE_LEFT_BOUNDARY_RIGHT:
+      DDE_ShiftLeftBoundary(ddesp, 0,  1, TRUE);
+      DDV_ReDraw(dmp);
+      break;
+    case MOVE_RIGHT_BOUNDARY_LEFT:  
+      DDE_ShiftRightBoundary(ddesp, 0, -1, TRUE);
+      DDV_ReDraw(dmp);
+      break;
+    case MOVE_RIGHT_BOUNDARY_RIGHT:
+      DDE_ShiftRightBoundary(ddesp, 0,  1, TRUE);
+      DDV_ReDraw(dmp);
+      break;
+    case DDE_DELETE_BLOCK:
+      if (DDE_DeleteBlock(ddesp, 0, TRUE)) {
+        DDV_ReDraw(dmp);
+      }
+      break;
+    case DDE_CREATE_BLOCK:
+      /* switch to the mode that allows block creation */
+      dmp->SavedMouseMode = dmp->MouseMode;
+      dmp->MouseMode = DDV_MOUSEMODE_CREATEBLOCK;
+      CrossCursor();
+      break;
+    case DDE_PREV:
+      if (DDE_Prev(ddesp)) {
+        DDV_ReDraw(dmp);
+      }
+      break;
+    case DDE_NEXT:
+      if (DDE_Next(ddesp)){
+        DDV_ReDraw(dmp);
+      }
+      break;
+    case DDE_ORIG:
+      DDE_GetOriginal(ddesp, TRUE);
+      DDV_ReDraw(dmp);
+      break;
+    case DDE_LAUNCH_EDITOR:
+      dmp->SavedMouseMode = dmp->MouseMode;
+      dmp->MouseMode = DDV_MOUSEMODE_LAUNCHEDITOR;
+      CrossCursor();
+      break;
+    case DDE_MERGE_BLOCKS:
+      dmp->SavedMouseMode = dmp->MouseMode;
+      dmp->MouseMode = DDV_MOUSEMODE_MERGEBLOCKS1;
+      CrossCursor();
+      break;
+    case DDE_SPLIT_BLOCK:
+      dmp->SavedMouseMode = dmp->MouseMode;
+      dmp->MouseMode = DDV_MOUSEMODE_SPLITBLOCK;
+      CrossCursor();
+      break;
+    case DDV_DELETE_BLOCK:
+      dmp->SavedMouseMode = dmp->MouseMode;
+      dmp->MouseMode = DDV_MOUSEMODE_DELETEBLOCK;
+      CrossCursor();
+      break;
+  }
+  if (dmp->bEditor) {
+    DDV_GreyOut(mWin_d, DDE_AtStartOfStack(dmp->dsp), DDE_AtEndOfStack(dmp->dsp));
+  }
+ 	return;
+}
+
+
+NLM_EXTERN void DDVResetProc (PaneL p)
+
+{
+}
+
+static void PopulateDDV (BioseqViewPtr bvp)
+
+{
+}
+
+static void ShowDDV (BioseqViewPtr bvp, Boolean show)
+
+{
+}
+
+static void SelectDDV (BioseqViewPtr bvp, Uint2 selentityID, Uint2 selitemID,
+                       Uint2 selitemtype, SeqLocPtr region,
+                       Boolean select, Boolean scrollto)
+
+{
+}
+
+static void ResizeDDV (BioseqViewPtr bvp)
+
+{
+}
+
+BioseqPageData ddvPageData = {
+  "Multiple", TRUE, TRUE, TRUE, FALSE, -1,
+  PopulateDDV, ShowDDV, SelectDDV,
+  NULL, NULL,
+  NULL, NULL, ResizeDDV, NULL
+};
+
diff --git a/ddv/ddvpanel.h b/ddv/ddvpanel.h
new file mode 100644
index 00000000..cd3edb40
--- /dev/null
+++ b/ddv/ddvpanel.h
@@ -0,0 +1,278 @@
+/*  $Id: ddvpanel.h,v 1.30 2000/07/12 22:22:42 hurwitz Exp $
+* ===========================================================================
+*
+*                            PUBLIC DOMAIN NOTICE
+*            National Center for Biotechnology Information (NCBI)
+*
+*  This software/database is a "United States Government Work" under the
+*  terms of the United States Copyright Act.  It was written as part of
+*  the author's official duties as a United States Government employee and
+*  thus cannot be copyrighted.  This software/database is freely available
+*  to the public for use. The National Library of Medicine and the U.S.
+*  Government do not place any restriction on its use or reproduction.
+*  We would, however, appreciate having the NCBI and the author cited in
+*  any work or product based on this material
+*
+*  Although all reasonable efforts have been taken to ensure the accuracy
+*  and reliability of the software and data, the NLM and the U.S.
+*  Government do not and cannot warrant the performance or results that
+*  may be obtained by using this software or data. The NLM and the U.S.
+*  Government disclaim all warranties, express or implied, including
+*  warranties of performance, merchantability or fitness for any particular
+*  purpose.
+*
+* ===========================================================================
+*
+* File Name:  ddvpanel.h
+*
+* Author:  Patrick Durand
+*
+* Version Creation Date:   06/19/99
+*
+* $Revision: 1.30 $
+*
+* File Description: 
+*
+* Modifications:
+* --------------------------------------------------------------------------
+* $Log: ddvpanel.h,v $
+* Revision 1.30  2000/07/12 22:22:42  hurwitz
+* added delete block to DDV
+*
+* Revision 1.29  2000/07/08 20:43:58  vakatov
+* Get all "#include" out of the 'extern "C" { }' scope;  other cleanup...
+*
+* Revision 1.28  2000/07/05 19:23:14  lewisg
+* add two panes to ddv, update msvc project files
+*
+* Revision 1.27  2000/06/30 22:31:51  hurwitz
+* added merge block function for DDV
+*
+* Revision 1.26  2000/06/02 19:57:04  hurwitz
+* added a query dialog when converting from pairwise multiple to true multiple, bug fix of double freeing of a seqAlignPtr
+*
+* Revision 1.25  2000/05/15 22:00:36  hurwitz
+* put save-edits query into DDV_SlaveQuit where it belongs
+*
+* Revision 1.24  2000/04/29 21:49:24  kans
+* removed bad characters on Mac
+*
+* Revision 1.23  2000/04/27 20:05:55  kans
+* added stub functions for Sequin
+*
+* Revision 1.22  2000/04/27 19:57:59  hurwitz
+* scroll to aligned block on launch of DDE
+*
+* Revision 1.21  2000/04/21 23:00:50  hurwitz
+* can launch DDE from DDV
+*
+* Revision 1.20  2000/04/10 21:41:26  lewisg
+* move alignment menus into ddv, udv from cn3d
+*
+* Revision 1.19  2000/04/10 20:58:42  hurwitz
+* added GUI controls for DeleteBlock in DDE
+*
+* Revision 1.18  2000/04/07 16:21:08  hurwitz
+* made delete block faster, added delete block to edit menu
+*
+* Revision 1.17  2000/03/21 14:21:47  durand
+* fixed a problem with menus setup
+*
+* Revision 1.16  2000/03/14 22:08:21  hurwitz
+* undo and redo working properly, restore-original function added
+*
+* Revision 1.15  2000/03/10 23:01:43  hurwitz
+* added undo and redo functions, first pass
+*
+* Revision 1.14  2000/03/06 22:45:58  hurwitz
+* can shift right boundary of an aligned block left and right, DDVRuler updates added
+*
+* Revision 1.13  2000/02/08 14:10:43  durand
+* made extern the functions DDV_UpdateHScrollVal and
+*
+* Revision 1.12  2000/02/04 16:05:41  durand
+* add click action to select a row
+*
+* Revision 1.11  2000/01/26 13:38:55  durand
+* update the GUI for the editor. Add functions to create the data to be used by the editor
+*
+* Revision 1.10  2000/01/10 15:09:45  durand
+* Use Entrez instead of ID1
+*
+* Revision 1.9  1999/12/07 21:40:14  durand
+* add mouse modes menu and caret facility for the editor
+*
+* Revision 1.8  1999/12/06 16:19:20  durand
+* add GoTo facility to DDV
+*
+* Revision 1.7  1999/12/03 23:17:23  lewisg
+* Patrick's new global update msg, argument passing when launching ddv, experimental editing
+*
+* Revision 1.6  1999/11/30 17:29:00  durand
+* fix a problem of redeclaration of the function DDV_CloseData
+*
+* Revision 1.5  1999/11/29 15:26:26  durand
+* designed a new GUI to fix problems under MacOS, Linux and SGI
+*
+* Revision 1.4  1999/10/22 20:12:47  durand
+* add Export command (text, HTML and Phylip formats)
+*
+* Revision 1.3  1999/10/20 13:17:19  durand
+* add display for disc. SeqAlign tails
+*
+* Revision 1.2  1999/10/15 21:57:37  durand
+* add a UI for display options
+*
+* Revision 1.1  1999/09/30 14:10:29  durand
+* add ddv to toolkit
+*
+* Revision 1.5  1999/09/09 21:55:07  durand
+* instantiate the Fle|Close command of DDV
+*
+* Revision 1.4  1999/07/01 14:08:08  durand
+* the loader functions of DDV or now in ddvopen.c
+*
+* Revision 1.2  1999/06/28 22:07:22  durand
+* add loader functions and clean the code with Lint and Purify
+*
+* Revision 1.1  1999/06/19 17:21:08  durand
+* add Vibrant DDV code
+*
+*
+*
+* ==========================================================================
+*/
+
+#ifndef _DDVPANEL_
+#define _DDVPANEL_
+
+#include <udviewer.h>
+#include <ddvmain.h>
+
+#undef NLM_EXTERN
+#ifdef NLM_IMPORT
+#define NLM_EXTERN NLM_IMPORT
+#else
+#define NLM_EXTERN extern
+#endif
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/******************************************************************************
+
+	Data structures
+
+******************************************************************************/
+typedef struct ddvdispstylesmsg {/*used by the Display Styles Dlg box*/
+	WindoW hWinMain; /*DDV main window handle*/
+	ButtoN  chk2;/*use color display chk box*/
+	ButtoN  chk3;/*show left tail chk box*/
+	ButtoN  chk4;/*show right tail chk box*/
+	GrouP  g1;   /*main group for Highlight unaligned regions"*/
+	GrouP  g2;   /*"Spacer" group for Highlight unaligned regions"*/
+	GrouP  g5;   /*"seq. justification" group for Highlight unaligned regions"*/
+	GrouP  g12;  /*BSP ruler style group*/
+	TexT   edit1; /*size TexT */
+	LisT   BspNames;/*list of BSP names*/
+	} DdvDispStylesMSG, PNTR DdvDispStylesMSGPtr;
+
+typedef struct ddvexporttextemsg {/*used by the Display Styles Dlg box*/
+	WindoW hWinMain; /*DDV main window handle*/
+	ButtoN  chk2;/*show number*/
+	ButtoN  chk3;/*show ticks*/
+	ButtoN  chk4;/*Use block of 10 letters*/
+	ButtoN  chk5;/*Display strand orientation*/
+	ButtoN  chk6;/*Display BioSeq coordinates*/
+	ButtoN  ok;
+	PopuP   pop; /*list of available formats*/
+	TexT    edit1; /*filename */
+	} DdvExportTexteMSG, PNTR DdvExportTexteMSGPtr;
+
+
+/******************************************************************************
+
+	Defines
+
+******************************************************************************/
+
+#define DDV_DEFAULT_PARAG_SIZE 70
+
+#define MOVE_ROW_LEFT              0
+#define MOVE_ROW_RIGHT             1
+#define MOVE_LEFT_BOUNDARY_LEFT    2
+#define MOVE_LEFT_BOUNDARY_RIGHT   3
+#define MOVE_RIGHT_BOUNDARY_LEFT   4
+#define MOVE_RIGHT_BOUNDARY_RIGHT  5
+#define DDE_PREV                   6
+#define DDE_NEXT                   7
+#define DDE_ORIG                   8
+#define DDE_DELETE_BLOCK           9  /* for DDE */
+#define DDE_CREATE_BLOCK          10
+#define DDE_LAUNCH_EDITOR         11
+#define DDE_MERGE_BLOCKS          12
+#define DDE_SPLIT_BLOCK           13
+#define DDV_DELETE_BLOCK          14  /* for DDV */
+
+
+/******************************************************************************
+
+	Global varaibles
+
+******************************************************************************/
+extern Char szAppName[];
+extern Char szAppName2[];
+
+
+/******************************************************************************
+
+	Exported functions
+
+******************************************************************************/
+extern void DDV_EnableGotoTBItems(WindoW hParent,Boolean bEnable);
+extern void DDV_WhatSize(DdvMainPtr dmp);
+extern void DDV_InitPanelData(UDVPanelDataPtr pdp);
+extern void DDV_SetupWin (WindoW w,Boolean bInit);
+extern void DDV_Resize_DDV (PaneL p, Boolean bInit);
+extern void DDV_WinMainResize (WindoW w);
+extern void DDV_UpdateVScrollVal(PaneL p,Boolean bInit,Int4 CurPos);
+extern void DDV_UpdateHScrollVal(PaneL p,Boolean bInit,Int4 CurPos);
+extern void DDV_VHScrl(PaneL p,UnDViewerGraphDataPtr gdp, Int4 newval, Int4 oldval,
+	Boolean IsVscroll);
+extern void DDV_VScrlProc (BaR sb, SlatE s, Int4 newval, Int4 oldval);
+extern void DDV_HScrlProc (BaR sb, SlatE s, Int4 newval, Int4 oldval);
+extern Boolean DDV_CreateViewerPanel(WindoW w,DdvMainWinPtr dmwp,
+	SAM_ViewGlobal *vgp,Boolean bEditor);
+NLM_EXTERN void DDV_SetMenuFocus(WindoW w);
+extern void DDV_SetupMenus(WindoW w,Boolean isID1Ok,Boolean bEditor,
+                           SAM_ViewGlobal *vgp);
+extern void DDV_WinMainResize (WindoW w);
+extern void DDV_WinMainCleanup (GraphiC g, VoidPtr data);
+extern void DDV_WinMainProgQuit(WindoW w);
+extern void DDV_InitGraphGlobal(DdvMainPtr dmp);
+extern void DDV_CloseData(DdvMainWinPtr mWin_d,Boolean bFinalExit);
+extern void DDV_SetRulerAttribInPGP(ValNodePtr ParaG_Head, Uint1 RulerStyle);
+extern void DDV_SortPGPLineNum(ValNodePtr PNTR Head, Int4 nBsp);
+extern void DDV_CleanupDDVPdata_g (DdvMainPtr dmp);
+extern void DDV_TimerProc (WindoW w);
+NLM_EXTERN void DDVResetProc (PaneL p);
+
+NLM_EXTERN void DDV_Save(ButtoN g);
+NLM_EXTERN void DDV_NoSave(ButtoN g);
+NLM_EXTERN void DDV_Cancel(ButtoN g);
+NLM_EXTERN void DDV_FileCloseIt(WindoW hWinMain);
+NLM_EXTERN void DDV_SaveEdits(DdvMainPtr dmp, Boolean UpdateDDV);
+
+#ifdef __cplusplus
+}
+#endif
+
+#undef NLM_EXTERN
+#ifdef NLM_EXPORT
+#define NLM_EXTERN NLM_EXPORT
+#else
+#define NLM_EXTERN
+#endif
+
+#endif /* ndef _DDVPANEL_ */
diff --git a/ddv/udv.dsp b/ddv/udv.dsp
new file mode 100644
index 00000000..708f87d7
--- /dev/null
+++ b/ddv/udv.dsp
@@ -0,0 +1,117 @@
+# Microsoft Developer Studio Project File - Name="udv" - Package Owner=<4>
+# Microsoft Developer Studio Generated Build File, Format Version 6.00
+# ** DO NOT EDIT **
+
+# TARGTYPE "Win32 (x86) Application" 0x0101
+
+CFG=udv - Win32 Release
+!MESSAGE This is not a valid makefile. To build this project using NMAKE,
+!MESSAGE use the Export Makefile command and run
+!MESSAGE 
+!MESSAGE NMAKE /f "udv.mak".
+!MESSAGE 
+!MESSAGE You can specify a configuration when running NMAKE
+!MESSAGE by defining the macro CFG on the command line. For example:
+!MESSAGE 
+!MESSAGE NMAKE /f "udv.mak" CFG="udv - Win32 Release"
+!MESSAGE 
+!MESSAGE Possible choices for configuration are:
+!MESSAGE 
+!MESSAGE "udv - Win32 Debug" (based on "Win32 (x86) Application")
+!MESSAGE "udv - Win32 Release" (based on "Win32 (x86) Application")
+!MESSAGE 
+
+# Begin Project
+# PROP AllowPerConfigDependencies 0
+# PROP Scc_ProjName ""
+# PROP Scc_LocalPath ""
+CPP=cl.exe
+MTL=midl.exe
+RSC=rc.exe
+
+!IF  "$(CFG)" == "udv - Win32 Debug"
+
+# PROP BASE Use_MFC 0
+# PROP BASE Use_Debug_Libraries 1
+# PROP BASE Output_Dir "udv___Win32_Debug"
+# PROP BASE Intermediate_Dir "udv___Win32_Debug"
+# PROP BASE Target_Dir ""
+# PROP Use_MFC 0
+# PROP Use_Debug_Libraries 1
+# PROP Output_Dir "udv___Win32_Debug"
+# PROP Intermediate_Dir "udv___Win32_Debug"
+# PROP Ignore_Export_Lib 0
+# PROP Target_Dir ""
+# ADD BASE CPP /nologo /W3 /Gm /GX /ZI /Od /D "WIN32" /D "_DEBUG" /D "_WINDOWS" /D "_MBCS" /YX /FD /GZ /c
+# ADD CPP /nologo /W3 /Gm /GX /ZI /Od /I ".." /I "..\ddv" /I "..\cn3d" /I "..\access" /I "..\asnstat" /I "..\connect\lbapi" /I "..\connect" /I "..\asnlib" /I "..\vibrant" /I "..\biostruc" /I "..\object" /I "..\api" /I "..\cdromlib" /I "..\desktop" /I "..\tools" /I "..\corelib" /I "..\network\taxon1\common" /I "..\network\vibnet" /I "..\network\entrez\client" /I "..\network\nsclilib" /I "..\network\medarch\client" /I "..\network\id1arch" /I "..\network\taxon1\taxon2" /I "..\network\blast3\client" /D "WIN32" /D "_DEBUG" /D "_WINDOWS" /D "_MBCS" /YX /FD /GZ /c
+# SUBTRACT CPP /Fr
+# ADD BASE MTL /nologo /D "_DEBUG" /mktyplib203 /win32
+# ADD MTL /nologo /D "_DEBUG" /mktyplib203 /win32
+# ADD BASE RSC /l 0x409 /d "_DEBUG"
+# ADD RSC /l 0x409 /d "_DEBUG"
+BSC32=bscmake.exe
+# ADD BASE BSC32 /nologo
+# ADD BSC32 /nologo
+LINK32=link.exe
+# ADD BASE LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib /nologo /subsystem:windows /debug /machine:I386 /pdbtype:sept
+# ADD LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib wsock32.lib vibnet.lib ncbidesk.lib ddvlib.lib ncbitool.lib ncbinacc.lib netcli.lib vibrant.lib ncbicdr.lib ncbiobj.lib ncbi.lib opengl32.lib glu32.lib glaux.lib /nologo /subsystem:windows /debug /machine:I386 /pdbtype:sept /libpath:"..\cdromlib\debug" /libpath:"..\cdromlib\ncbicdr___Win32_Debug" /libpath:"..\corelib\debug" /libpath:"..\vibrant\debug" /libpath:"..\object\debug" /libpath:"..\biostruc\debug" /libpath:"..\desktop\debug" /libpath:"..\tools\debug" /libpath:"..\network\entrez\client\debug" /libpath:"..\network\vibnet\debug" /libpath:"..\network\nsclilib\debug" /libpath:"..\network\taxon1\taxon2\debug" /libpath:"..\network\id1arch\debug" /libpath:"..\network\medarch\client\debug" /libpath:"..\network\blast3\client\debug" /libpath:"ddvlib___Win32_Debug"
+# SUBTRACT LINK32 /pdb:none
+
+!ELSEIF  "$(CFG)" == "udv - Win32 Release"
+
+# PROP BASE Use_MFC 0
+# PROP BASE Use_Debug_Libraries 1
+# PROP BASE Output_Dir "udv___Win32_Release"
+# PROP BASE Intermediate_Dir "udv___Win32_Release"
+# PROP BASE Ignore_Export_Lib 0
+# PROP BASE Target_Dir ""
+# PROP Use_MFC 0
+# PROP Use_Debug_Libraries 1
+# PROP Output_Dir "udv___Win32_Release"
+# PROP Intermediate_Dir "udv___Win32_Release"
+# PROP Ignore_Export_Lib 0
+# PROP Target_Dir ""
+# ADD BASE CPP /nologo /W3 /Gm /GX /ZI /Od /I ".." /I "..\ddv" /I "..\cn3d" /I "..\access" /I "..\asnstat" /I "..\connect\lbapi" /I "..\connect" /I "..\asnlib" /I "..\vibrant" /I "..\biostruc" /I "..\object" /I "..\api" /I "..\cdromlib" /I "..\desktop" /I "..\tools" /I "..\corelib" /I "..\network\taxon1\common" /I "..\network\vibnet" /I "..\network\entrez\client" /I "..\network\nsclilib" /I "..\network\medarch\client" /I "..\network\id1arch" /I "..\network\taxon1\taxon2" /I "..\network\blast3\client" /D "WIN32" /D "_DEBUG" /D "_WINDOWS" /D "_MBCS" /YX /FD /GZ /c
+# SUBTRACT BASE CPP /Fr
+# ADD CPP /nologo /W3 /Gm /GX /Zi /I ".." /I "..\ddv" /I "..\cn3d" /I "..\access" /I "..\asnstat" /I "..\connect\lbapi" /I "..\connect" /I "..\asnlib" /I "..\vibrant" /I "..\biostruc" /I "..\object" /I "..\api" /I "..\cdromlib" /I "..\desktop" /I "..\tools" /I "..\corelib" /I "..\network\taxon1\common" /I "..\network\vibnet" /I "..\network\entrez\client" /I "..\network\nsclilib" /I "..\network\medarch\client" /I "..\network\id1arch" /I "..\network\taxon1\taxon2" /I "..\network\blast3\client" /D "_WINDOWS" /D "WIN32" /D "_MBCS" /YX /FD /c
+# ADD BASE MTL /nologo /D "_DEBUG" /mktyplib203 /win32
+# ADD MTL /nologo /mktyplib203 /win32
+# ADD BASE RSC /l 0x409 /d "_DEBUG"
+# ADD RSC /l 0x409
+BSC32=bscmake.exe
+# ADD BASE BSC32 /nologo
+# ADD BSC32 /nologo
+LINK32=link.exe
+# ADD BASE LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib wsock32.lib vibnet.lib ncbidesk.lib ddvlib.lib ncbitool.lib ncbinacc.lib netcli.lib vibrant.lib ncbicdr.lib ncbiobj.lib ncbi.lib opengl32.lib glu32.lib glaux.lib /nologo /subsystem:windows /debug /machine:I386 /pdbtype:sept /libpath:"..\cdromlib\debug" /libpath:"..\cdromlib\ncbicdr___Win32_Debug" /libpath:"..\corelib\debug" /libpath:"..\vibrant\debug" /libpath:"..\object\debug" /libpath:"..\biostruc\debug" /libpath:"..\desktop\debug" /libpath:"..\tools\debug" /libpath:"..\network\entrez\client\debug" /libpath:"..\network\vibnet\debug" /libpath:"..\network\nsclilib\debug" /libpath:"..\network\taxon1\taxon2\debug" /libpath:"..\network\taxon1\common\debug" /libpath:"..\network\id1arch\debug" /libpath:"..\network\medarch\client\debug" /libpath:"..\network\blast3\client\debug" /libpath:"ddvlib___Win32_Debug"
+# SUBTRACT BASE LINK32 /pdb:none
+# ADD LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib wsock32.lib vibnet.lib ncbidesk.lib ddvlib.lib ncbitool.lib ncbinacc.lib netcli.lib vibrant.lib ncbicdr.lib ncbiobj.lib ncbi.lib opengl32.lib glu32.lib glaux.lib /nologo /subsystem:windows /debug /machine:I386 /pdbtype:sept /libpath:"..\cdromlib\ncbicdr___Win32_Release" /libpath:"..\cdromlib\ncbinacc___Win32_Release" /libpath:"..\corelib\ncbi___Win32_Release" /libpath:"..\vibrant\vibrant___Win32_Release" /libpath:"..\object\object___Win32_Release" /libpath:"..\biostruc\mmdb___Win32_Release" /libpath:"..\desktop\desktop___Win32_Release" /libpath:"..\tools\tools___Win32_Release" /libpath:"..\network\entrez\client\netentr___Win32_Release" /libpath:"..\network\vibnet\vibnet___Win32_Release" /libpath:"..\network\nsclilib\netcli___Win32_Release" /libpath:"..\network\taxon1\taxon2\ncbitxc2___Win32_Release" /libpath:"..\network\id1arch\ncbiid1___Win32_Release" /libpath:"..\network\medarch\client\medarch___Win32_Release" /libpath:"..\network\blast3\client\netblast___Win32_Release" /libpath:"..\cn3d\ncbicn3d___Win32_Release" /libpath:"..\ddv\ddvlib___Win32_Release"
+# SUBTRACT LINK32 /pdb:none
+
+!ENDIF 
+
+# Begin Target
+
+# Name "udv - Win32 Debug"
+# Name "udv - Win32 Release"
+# Begin Group "Source Files"
+
+# PROP Default_Filter "cpp;c;cxx;rc;def;r;odl;idl;hpj;bat"
+# Begin Source File
+
+SOURCE=..\link\mswin\udv.rc
+# End Source File
+# Begin Source File
+
+SOURCE=..\demo\udvmain.c
+# End Source File
+# End Group
+# Begin Group "Header Files"
+
+# PROP Default_Filter "h;hpp;hxx;hm;inl"
+# End Group
+# Begin Group "Resource Files"
+
+# PROP Default_Filter "ico;cur;bmp;dlg;rc2;rct;bin;rgs;gif;jpg;jpeg;jpe"
+# End Group
+# End Target
+# End Project