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Diffstat (limited to 'desktop')
-rw-r--r--desktop/biosrc.c6
-rw-r--r--desktop/cdrgn.c19
-rw-r--r--desktop/dlgutil1.c19
-rw-r--r--desktop/dlgutil2.c10
-rw-r--r--desktop/e2docsum.c26
-rw-r--r--desktop/gbfview.c89
-rw-r--r--desktop/salsa.c166
-rw-r--r--desktop/seqpanel.c357
-rw-r--r--desktop/vsm.c12
9 files changed, 494 insertions, 210 deletions
diff --git a/desktop/biosrc.c b/desktop/biosrc.c
index e745fdcd..9f6802e1 100644
--- a/desktop/biosrc.c
+++ b/desktop/biosrc.c
@@ -29,7 +29,7 @@
*
* Version Creation Date: 1/22/95
*
-* $Revision: 6.48 $
+* $Revision: 6.49 $
*
* File Description:
*
@@ -1907,11 +1907,11 @@ EnumFieldAssocPtr subsource_alists [] = {
};
Uint2 orgmod_widths [] = {
- 0, 15
+ 0, 25
};
Uint2 subsource_widths [] = {
- 0, 15
+ 0, 25
};
Uint2 orgmod_types [] = {
diff --git a/desktop/cdrgn.c b/desktop/cdrgn.c
index 587ced29..59282919 100644
--- a/desktop/cdrgn.c
+++ b/desktop/cdrgn.c
@@ -29,7 +29,7 @@
*
* Version Creation Date: 1/22/95
*
-* $Revision: 6.57 $
+* $Revision: 6.60 $
*
* File Description:
*
@@ -2272,9 +2272,9 @@ static DialoG CreateCdRgnDialog (GrouP h, CharPtr title, Int2 genCode,
x = HiddenGroup (cfp->protTextGrp, 2, 0, NULL);
SetGroupSpacing (x, 3, 5);
StaticPrompt (x, "Name", 0, dialogTextHeight, programFont, 'l');
- cfp->protNameText = DialogText (x, "", 15, NULL);
+ cfp->protNameText = DialogText (x, "", 25, NULL);
StaticPrompt (x, "Description", 0, dialogTextHeight, programFont, 'l');
- cfp->protDescText = DialogText (x, "", 15, NULL);
+ cfp->protDescText = DialogText (x, "", 25, NULL);
cfp->protPromptGrp = HiddenGroup (f, -1, 0, NULL);
StaticPrompt (cfp->protPromptGrp,
"Press Edit Protein Feature to change protein name",
@@ -2841,7 +2841,7 @@ extern ForM CreateCdRgnForm (Int2 left, Int2 top, CharPtr title,
StdFeatIntEdPartialCallback);
cfp->pages [LOCATION_PAGE] = s;
Hide (cfp->pages [LOCATION_PAGE]);
- cfp->locvisited = FALSE;
+ cfp->locvisited = TRUE;
AlignObjects (ALIGN_CENTER, (HANDLE) cfp->pages [CODING_REGION_PAGE],
(HANDLE) cfp->pages [COMMON_PAGE],
@@ -4210,11 +4210,11 @@ static DialoG CreateProtDialog (GrouP h, CharPtr title, ProtRefPtr prp, SeqFeatP
ppp->protGrp [0] = HiddenGroup (k, -1, 0, NULL);
g = HiddenGroup (ppp->protGrp [0], 0, 10, NULL);
StaticPrompt (g, "Protein Names", 0, 0, programFont, 'c');
- ppp->name = CreateVisibleStringDialog (g, 3, -1, 15);
+ ppp->name = CreateVisibleStringDialog (g, 3, -1, 25);
f = HiddenGroup (ppp->protGrp [0], 0, 4, NULL);
StaticPrompt (f, "Description", 0, dialogTextHeight, programFont, 'c');
- ppp->desc = DialogText (f, "", 20, NULL);
+ ppp->desc = DialogText (f, "", 25, NULL);
r = HiddenGroup (ppp->protGrp [0], 2, 0, NULL);
StaticPrompt (r, "Processing", 0, dialogTextHeight, programFont, 'l');
@@ -4242,7 +4242,7 @@ static DialoG CreateProtDialog (GrouP h, CharPtr title, ProtRefPtr prp, SeqFeatP
ppp->protGrp [2] = HiddenGroup (k, 0, 10, NULL);
StaticPrompt (ppp->protGrp [2], "Activity", 0, 0, programFont, 'c');
- ppp->activity = CreateVisibleStringDialog (ppp->protGrp [2], 3, -1, 15);
+ ppp->activity = CreateVisibleStringDialog (ppp->protGrp [2], 3, -1, 25);
Hide (ppp->protGrp [2]);
ppp->protGrp [3] = HiddenGroup (k, -1, 0, NULL);
@@ -5219,11 +5219,6 @@ static void PopulateAAPopup (PopuP AAitem)
sprintf (item, "%c %s", ch, str);
PopupItem (AAitem, item);
}
- i = '*';
- ch = GetSymbolForResidue (sctp, i);
- str = (CharPtr) GetNameForResidue (sctp, i);
- sprintf (item, "%c %s", ch, str);
- PopupItem (AAitem, item);
SetValue (AAitem, 1);
}
diff --git a/desktop/dlgutil1.c b/desktop/dlgutil1.c
index dbb332dd..86167dd2 100644
--- a/desktop/dlgutil1.c
+++ b/desktop/dlgutil1.c
@@ -29,7 +29,7 @@
*
* Version Creation Date: 1/22/95
*
-* $Revision: 6.43 $
+* $Revision: 6.44 $
*
* File Description:
*
@@ -50,6 +50,7 @@
#include <gbfeat.h>
#include <gbftdef.h>
#include <edutil.h>
+#include <explore.h>
#define NUMBER_OF_SUFFIXES 8
@@ -1008,9 +1009,12 @@ extern Boolean FeatFormReplaceWithoutUpdateProc (ForM f)
Char ch;
Char desc [128];
Int2 expev;
+ SeqMgrFeatContext fcontext;
FeatureFormPtr ffp;
+ SeqFeatPtr gene;
GeneGatherList ggl;
GeneRefPtr grp;
+ GeneRefPtr grpfeat;
GatherScope gs;
SeqLocPtr gslp;
Boolean hasNulls;
@@ -1029,6 +1033,7 @@ extern Boolean FeatFormReplaceWithoutUpdateProc (ForM f)
SeqEntryPtr sep;
SeqFeatPtr sfp;
SeqLocPtr slp;
+ CharPtr str;
Char symbol [128];
Int2 usexref;
Int2 val;
@@ -1152,7 +1157,17 @@ extern Boolean FeatFormReplaceWithoutUpdateProc (ForM f)
}
if (vnp != NULL) {
if (vnp->choice == 1) {
- grp = CreateNewGeneRef ((CharPtr) vnp->data.ptrvalue, NULL, NULL, FALSE);
+ str = (CharPtr) vnp->data.ptrvalue;
+ if (StringDoesHaveText (str)) {
+ grp = CreateNewGeneRef (str, NULL, NULL, FALSE);
+ gene = SeqMgrGetFeatureByLabel (bsp, str, SEQFEAT_GENE, 0, &fcontext);
+ if (gene != NULL && gene->data.choice == SEQFEAT_GENE) {
+ grpfeat = (GeneRefPtr) gene->data.value.ptrvalue;
+ if (grpfeat != NULL) {
+ grp->locus_tag = StringSaveNoNull (grpfeat->locus_tag);
+ }
+ }
+ }
} else if (vnp->choice == 3) {
grp = GeneRefNew ();
if (grp != NULL) {
diff --git a/desktop/dlgutil2.c b/desktop/dlgutil2.c
index a2a38bd8..30548432 100644
--- a/desktop/dlgutil2.c
+++ b/desktop/dlgutil2.c
@@ -29,7 +29,7 @@
*
* Version Creation Date: 1/22/95
*
-* $Revision: 6.48 $
+* $Revision: 6.49 $
*
* File Description:
*
@@ -1264,7 +1264,7 @@ static void ChangeCannedMessage (PopuP p)
SetStatus (ffp->exception, TRUE);
break;
case 5 :
- SetTitle (ffp->exceptText, "trans splicing");
+ SetTitle (ffp->exceptText, "trans-splicing");
SetStatus (ffp->exception, TRUE);
break;
case 6 :
@@ -1419,7 +1419,7 @@ extern GrouP CreateCommonFeatureGroupEx (GrouP h, FeatureFormPtr ffp,
PopupItem (canned, "RNA editing");
PopupItem (canned, "reasons given in citation");
PopupItem (canned, "ribosomal slippage");
- PopupItem (canned, "trans splicing");
+ PopupItem (canned, "trans-splicing");
PopupItem (canned, "artificial frameshift");
PopupItem (canned, "nonconsensus splice site");
PopupItem (canned, "rearrangement required");
@@ -1433,8 +1433,8 @@ extern GrouP CreateCommonFeatureGroupEx (GrouP h, FeatureFormPtr ffp,
} else if (StringICmp (sfp->except_text, "ribosomal slippage") == 0 ||
StringICmp (sfp->except_text, "ribosome slippage") == 0) {
SetValue (canned, 4);
- } else if (StringICmp (sfp->except_text, "trans splicing") == 0 ||
- StringICmp (sfp->except_text, "trans-splicing") == 0) {
+ } else if (StringICmp (sfp->except_text, "trans-splicing") == 0 ||
+ StringICmp (sfp->except_text, "trans splicing") == 0) {
SetValue (canned, 5);
} else if (StringICmp (sfp->except_text, "artificial frameshift") == 0) {
SetValue (canned, 6);
diff --git a/desktop/e2docsum.c b/desktop/e2docsum.c
index 2875ff75..659011df 100644
--- a/desktop/e2docsum.c
+++ b/desktop/e2docsum.c
@@ -29,7 +29,7 @@
*
* Version Creation Date: 10/30/01
*
-* $Revision: 6.48 $
+* $Revision: 6.49 $
*
* File Description:
*
@@ -1295,6 +1295,10 @@ static CharPtr Query_FetchFields (DoC d, Int2 item, Pointer ptr)
/* */
/*==================================================================*/
+static CharPtr file_is_too_long_mssg =
+"The record is too large to display in this format in the document summary window.\n\
+Please double click here to launch a separate viewer that can display this record.";
+
static CharPtr FileToString (CharPtr path)
{
@@ -1307,16 +1311,20 @@ static CharPtr FileToString (CharPtr path)
ptr = NULL;
len = FileLength (path);
if (len > 0 && len < MAXALLOC) {
- fp = FileOpen (path, "r");
- if (fp != NULL) {
- ptr = MemNew (sizeof (Char) * (size_t) (len + 4));
- if (ptr != NULL) {
- actual = FileRead (ptr, 1, (size_t) len, fp);
- if (actual > 0 && actual <= len) {
- ptr [actual] = '\0';
+ if (len > 65000) {
+ ptr = StringSave (file_is_too_long_mssg);
+ } else {
+ fp = FileOpen (path, "r");
+ if (fp != NULL) {
+ ptr = MemNew (sizeof (Char) * (size_t) (len + 4));
+ if (ptr != NULL) {
+ actual = FileRead (ptr, 1, (size_t) len, fp);
+ if (actual > 0 && actual <= len) {
+ ptr [actual] = '\0';
+ }
}
- }
FileClose (fp);
+ }
}
}
return ptr;
diff --git a/desktop/gbfview.c b/desktop/gbfview.c
index f6b8aaec..2671d9ce 100644
--- a/desktop/gbfview.c
+++ b/desktop/gbfview.c
@@ -29,7 +29,7 @@
*
* Version Creation Date: 2/5/97
*
-* $Revision: 6.73 $
+* $Revision: 6.75 $
*
* File Description:
*
@@ -896,37 +896,40 @@ static void LookForTpa (
static void PopulateFlatFile (BioseqViewPtr bvp, FmtType format, FlgType flags)
{
- BioseqPtr bsp;
- CstType custom = 0;
- DoC doc;
- Boolean doLockFarComponents = FALSE;
- Uint2 entityID;
- FonT fnt;
- FILE *fp;
- Boolean hastpaaligns;
- Int2 into;
- Boolean isAEorCH;
- Boolean isGED;
- Boolean isNTorNW;
- Boolean isNC;
- Boolean isTPA;
- Int2 item;
- ErrSev level;
- Boolean lockFar = FALSE;
- Boolean lookupFar = FALSE;
- ModType mode = SEQUIN_MODE;
- SeqEntryPtr oldsep;
- Char path [PATH_MAX];
- BaR sb = NULL;
- SeqEntryPtr sep;
- Int4 startsAt;
- CharPtr str;
- StlType style = NORMAL_STYLE;
- SeqViewProcsPtr svpp;
- SeqEntryPtr topsep;
- TexT txt;
- SeqEntryPtr usethetop = NULL;
- Int2 val;
+ BioseqPtr bsp;
+ SeqMgrFeatContext context;
+ CstType custom = 0;
+ DoC doc;
+ Boolean doLockFarComponents = FALSE;
+ Uint2 entityID;
+ Int4 feats_with_product_count;
+ FonT fnt;
+ FILE *fp;
+ Boolean hastpaaligns;
+ Int2 into;
+ Boolean isAEorCH;
+ Boolean isGED;
+ Boolean isNTorNW;
+ Boolean isNC;
+ Boolean isTPA;
+ Int2 item;
+ ErrSev level;
+ Boolean lockFar = FALSE;
+ Boolean lookupFar = FALSE;
+ ModType mode = SEQUIN_MODE;
+ SeqEntryPtr oldsep;
+ Char path [PATH_MAX];
+ BaR sb = NULL;
+ SeqEntryPtr sep;
+ SeqFeatPtr sfp;
+ Int4 startsAt;
+ CharPtr str;
+ StlType style = NORMAL_STYLE;
+ SeqViewProcsPtr svpp;
+ SeqEntryPtr topsep;
+ TexT txt;
+ SeqEntryPtr usethetop = NULL;
+ Int2 val;
if (bvp == NULL) return;
if (bvp->hasTargetControl && bvp->ffModeCtrl != NULL) {
@@ -1033,6 +1036,14 @@ static void PopulateFlatFile (BioseqViewPtr bvp, FmtType format, FlgType flags)
doLockFarComponents = TRUE;
}
}
+
+ if (mode == ENTREZ_MODE) {
+ doLockFarComponents = FALSE;
+ lockFar = FALSE;
+ lookupFar = FALSE;
+ flags = flags ^ (SHOW_CONTIG_FEATURES | SHOW_CONTIG_SOURCES | SHOW_FAR_TRANSLATION);
+ }
+
if (doLockFarComponents) {
entityID = ObjMgrGetEntityIDForPointer (bsp);
sep = GetTopSeqEntryForEntityID (entityID);
@@ -1040,6 +1051,20 @@ static void PopulateFlatFile (BioseqViewPtr bvp, FmtType format, FlgType flags)
bvp->bsplist = LockFarComponentsEx (sep, TRUE, FALSE, FALSE, NULL);
}
if (lookupFar) {
+ feats_with_product_count = 0;
+ sfp = SeqMgrGetNextFeature (bsp, NULL, 0, 0, &context);
+ while (sfp != NULL) {
+ if (sfp->product != NULL) {
+ feats_with_product_count++;
+ }
+ sfp = SeqMgrGetNextFeature (bsp, sfp, 0, 0, &context);
+ }
+ if (feats_with_product_count > 500) {
+ /* too many to lookup with current caching implementation */
+ lookupFar = FALSE;
+ }
+ }
+ if (lookupFar) {
hastpaaligns = FALSE;
VisitDescriptorsInSep (sep, (Pointer) &hastpaaligns, LookForTpa);
LookupFarSeqIDs (sep, TRUE, TRUE, TRUE, FALSE, hastpaaligns);
diff --git a/desktop/salsa.c b/desktop/salsa.c
index 9540fed9..90a3fa7f 100644
--- a/desktop/salsa.c
+++ b/desktop/salsa.c
@@ -28,7 +28,7 @@
*
* Version Creation Date: 1/27/96
*
-* $Revision: 6.159 $
+* $Revision: 6.160 $
*
* File Description:
*
@@ -3418,6 +3418,7 @@ static Boolean SetupAlignDataSap (EditAlignDataPtr adp, SeqAlignPtr salp_origina
if (adp == NULL || salp_original == NULL)
return FALSE;
+
/*************************************/
/** check if all ->type are NOT 0
*** if all 0 -> all cached from CN3D viewer
@@ -3428,6 +3429,12 @@ static Boolean SetupAlignDataSap (EditAlignDataPtr adp, SeqAlignPtr salp_origina
if (newsalp== NULL)
return FALSE;
/**************************************/
+ if (salp_original->segtype == SAS_DISC)
+ {
+ salp_original = (SeqAlignPtr) salp_original->segs;
+ }
+
+
if ( salp_original->segtype == 1 )
{
adp->blocks = create_list_alignedsegs (salp_original);
@@ -4110,6 +4117,7 @@ static ForM CreateSeqAlignEditForm (Int2 left, Int2 top, CharPtr windowname, Seq
if (salp==NULL)
return NULL;
+
moltype = SeqAlignMolType(salp);
if (moltype == 0)
return NULL;
@@ -5164,6 +5172,85 @@ extern Int2 LIBCALLBACK AlgEditFunc (Pointer data)
return OM_MSG_RET_ERROR;
}
+/* opens window for editing alignment */
+static Int2
+FinishOpeningEditAlignmentWindow
+(SeqAlignPtr salp,
+ OMProcControlPtr ompcp)
+{
+ SelStruct ss;
+ Char str [64];
+ WindoW w;
+ SeqEditViewFormPtr wdp = NULL;
+ OMUserDataPtr omudp;
+ SeqAnnotPtr sap;
+
+ ss.entityID = ompcp->input_entityID;
+ ss.itemID = ompcp->input_itemID;
+ ss.itemtype = ompcp->input_itemtype;
+ ss.regiontype =0;
+ ss.region = NULL;
+
+ SeqIdWrite (SeqAlignId(salp, 0), str, PRINTID_REPORT, 64);
+ w = (WindoW) CreateSeqAlignEditForm (-40, -90, str, salp, &ss);
+ if (w != NULL)
+ {
+ wdp = (SeqEditViewFormPtr) GetObjectExtra (w);
+ if (wdp != NULL)
+ {
+ wdp->input_entityID = ompcp->input_entityID;
+ wdp->input_itemID = ompcp->input_itemID;
+ wdp->input_itemtype = ompcp->input_itemtype;
+ wdp->this_itemtype = OBJ_SEQALIGN;
+ wdp->this_subtype = 0;
+ wdp->procid = ompcp->proc->procid;
+ wdp->proctype = ompcp->proc->proctype;
+ wdp->userkey = OMGetNextUserKey ();
+ omudp = ObjMgrAddUserData (ompcp->input_entityID, ompcp->proc->procid, OMPROC_EDIT, wdp->userkey);
+ if (omudp != NULL)
+ {
+ omudp->userdata.ptrvalue = (Pointer) wdp;
+ omudp->messagefunc = BioseqEditMsgFunc;
+ }
+ checkEntityIDForMsg (wdp);
+ }
+ Show (w);
+ Update ();
+ CaptureSlateFocus ((SlatE) wdp->pnl);
+ Select (w);
+
+ if (salp->segtype == 1) {
+ SeqAlignPtr tmp, newsalp;
+ Boolean ok;
+ EditAlignDataPtr adp;
+
+ adp = GetAlignDataPanel(wdp->pnl);
+ for ( tmp=salp; tmp!=NULL; tmp=tmp->next)
+ {
+ if (tmp->type<1)
+ {
+ sap=adp->sap_original;
+ if (sap)
+ {
+ newsalp = (SeqAlignPtr)sap->data;
+ ok = SeqAlignIDCache (newsalp, SeqAlignId (tmp, 1));
+ if (ok)
+ {
+/*
+ if (adp->sap1_original)
+ SeqAlignIDCache ((SeqAlignPtr)adp->sap1_original->data, SeqIdFindBest (bsp->id, 0));
+*/
+ repopulate_panel (w, adp, newsalp);
+ }
+ }
+ }
+ }
+ }
+ return OM_MSG_RET_DONE;
+ }
+ return OM_MSG_RET_ERROR;
+}
+
/************************************************
***
*** AnnotAlgEditFunc : to launch SEQANNOT editor
@@ -5171,14 +5258,10 @@ extern Int2 LIBCALLBACK AlgEditFunc (Pointer data)
************************************************/
extern Int2 LIBCALLBACK AnnotAlgEditFunc (Pointer data)
{
- WindoW w;
SeqAnnotPtr sap;
SeqAlignPtr salp = NULL;
- SeqEditViewFormPtr wdp = NULL;
OMProcControlPtr ompcp;
- OMUserDataPtr omudp;
- Char str [64];
- SelStruct ss;
+ Int2 rval = OM_MSG_RET_ERROR;
ompcp = (OMProcControlPtr) data;
if (ompcp == NULL || ompcp->proc == NULL) {
@@ -5217,70 +5300,19 @@ extern Int2 LIBCALLBACK AnnotAlgEditFunc (Pointer data)
if (salp == NULL)
return OM_MSG_RET_ERROR;
- ss.entityID = ompcp->input_entityID;
- ss.itemID = ompcp->input_itemID;
- ss.itemtype = ompcp->input_itemtype;
- ss.regiontype =0;
- ss.region = NULL;
-
- SeqIdWrite (SeqAlignId(salp, 0), str, PRINTID_REPORT, 64);
- w = (WindoW) CreateSeqAlignEditForm (-40, -90, str, salp, &ss);
- if (w != NULL)
- {
- wdp = (SeqEditViewFormPtr) GetObjectExtra (w);
- if (wdp != NULL)
- {
- wdp->input_entityID = ompcp->input_entityID;
- wdp->input_itemID = ompcp->input_itemID;
- wdp->input_itemtype = ompcp->input_itemtype;
- wdp->this_itemtype = OBJ_SEQALIGN;
- wdp->this_subtype = 0;
- wdp->procid = ompcp->proc->procid;
- wdp->proctype = ompcp->proc->proctype;
- wdp->userkey = OMGetNextUserKey ();
- omudp = ObjMgrAddUserData (ompcp->input_entityID, ompcp->proc->procid, OMPROC_EDIT, wdp->userkey);
- if (omudp != NULL)
- {
- omudp->userdata.ptrvalue = (Pointer) wdp;
- omudp->messagefunc = BioseqEditMsgFunc;
- }
- checkEntityIDForMsg (wdp);
- }
- Show (w);
- Update ();
- CaptureSlateFocus ((SlatE) wdp->pnl);
- Select (w);
-
-if (salp->segtype == 1) {
-SeqAlignPtr tmp, newsalp;
-Boolean ok;
-EditAlignDataPtr adp;
-
- adp = GetAlignDataPanel(wdp->pnl);
- for ( tmp=salp; tmp!=NULL; tmp=tmp->next)
+ if (salp->dim == 2)
{
- if (tmp->type<1)
- {
- sap=adp->sap_original;
- if (sap)
- {
- newsalp = (SeqAlignPtr)sap->data;
- ok = SeqAlignIDCache (newsalp, SeqAlignId (tmp, 1));
- if (ok)
- {
-/*
- if (adp->sap1_original)
- SeqAlignIDCache ((SeqAlignPtr)adp->sap1_original->data, SeqIdFindBest (bsp->id, 0));
-*/
- repopulate_panel (w, adp, newsalp);
- }
- }
- }
+ rval = FinishOpeningEditAlignmentWindow (salp, ompcp);
}
-}
- return OM_MSG_RET_DONE;
+ else
+ {
+ while (salp != NULL)
+ {
+ rval = FinishOpeningEditAlignmentWindow (salp, ompcp);
+ salp = salp->next;
+ }
}
- return OM_MSG_RET_ERROR;
+ return rval;
}
extern Int2 LIBCALLBACK AlgViewFunc (Pointer data)
diff --git a/desktop/seqpanel.c b/desktop/seqpanel.c
index 0d7797b2..3727bd00 100644
--- a/desktop/seqpanel.c
+++ b/desktop/seqpanel.c
@@ -1,4 +1,4 @@
-/* $Id: seqpanel.c,v 6.34 2004/04/13 16:52:26 bollin Exp $
+/* $Id: seqpanel.c,v 6.35 2004/05/20 20:10:20 bollin Exp $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
@@ -42,7 +42,7 @@
enum ESeqNum { eNumNone=1, eNumSide=2, eNumTop=3 };
enum ELineType { eTypeTopSeqNumbers, eTypeTopScaleMarks, eTypeSequence,
- eTypeAlignSequence, eTypeFeature };
+ eTypeAlignSequence, eTypeFeature, eTypeAlignDivider };
enum EDrawGrid { eDrawGridOn=1, eDrawGridOff=2 };
enum EShowFeatures { eShowFeaturesOn=1, eShowFeaturesOff=2, eShowFeaturesAll=3 };
@@ -214,22 +214,57 @@ static SeqPanLinePtr PNTR CreateSeqPanelLines(Int2 lineLength, BioseqViewPtr bvp
Int4 lCount = 0, i, j;
Int4 pCount; /* Total number of paragraphs */
Int4 alnRows = -1;
- Int4 alnValidRows = 0;
+ Int4Ptr alnValidRows = NULL;
Int4 featRows = 1;
+ SeqAlignPtr tmp_salp;
+ Int4Ptr lines_per_alignment = NULL;
+ Int4 num_alignments;
+ Int4 aln_idx;
+ SeqParaGPtr PNTR ref_offset;
if (bvp->seqAlignMode) {
- fLines = GetValue(bvp->newNumControl) == eNumTop ? 2 : 0;
alnRows = AlnMgr2GetNumRows(bvp->salp); /* size of the alignment */
- if (bvp->viewWholeEntity || GetValue(bvp->newFeatControl) == eShowFeaturesAll) featRows = alnRows; /* show features for all rows */
- pCount = floor((AlnMgr2GetAlnLength(bvp->salp, FALSE)-1) / lineLength) + 1; /* alignment length */
- for (j = 1; j != alnRows + 1; j++) { /* AlnMgr counts from 1, not 0 */
- SeqIdPtr tmp_sip = AlnMgr2GetNthSeqIdPtr(bvp->salp, j);
- BioseqPtr tmp_bsp = BioseqLockById(tmp_sip);
- if (tmp_bsp != NULL) {
- alnValidRows++; /* count avaliable alignments */
- BioseqUnlock (tmp_bsp);
+ fLines = GetValue(bvp->newNumControl) == eNumTop ? 2 : 0;
+ pCount = 0;
+ num_alignments = 0;
+ for (tmp_salp = bvp->salp; tmp_salp != NULL; tmp_salp = tmp_salp->next)
+ {
+ num_alignments ++;
+ }
+ lines_per_alignment = (Int4Ptr) MemNew (sizeof (Int4) * num_alignments);
+ if (lines_per_alignment == NULL) return;
+ alnValidRows = (Int4Ptr) MemNew (sizeof (Int4) * num_alignments);
+ if (alnValidRows == NULL)
+ {
+ MemFree (lines_per_alignment);
+ return;
+ }
+ for (i=0; i < num_alignments; i++)
+ {
+ lines_per_alignment [i] = 0;
+ alnValidRows [i] = 0;
+ }
+ for (tmp_salp = bvp->salp, aln_idx = 0; tmp_salp != NULL; tmp_salp = tmp_salp->next, aln_idx++)
+ {
+ lines_per_alignment [aln_idx] = floor((AlnMgr2GetAlnLength(tmp_salp, FALSE)-1) / lineLength) + 1; /* alignment length */
+ pCount += lines_per_alignment [aln_idx];
+ if (bvp->viewWholeEntity || GetValue(bvp->newFeatControl) == eShowFeaturesAll)
+ {
+ if (featRows == 1)
+ featRows = alnRows;
+ else
+ featRows += alnRows;
+ } /* show features for all rows */
+
+ for (j = 1; j != alnRows + 1; j++) { /* AlnMgr counts from 1, not 0 */
+ SeqIdPtr tmp_sip = AlnMgr2GetNthSeqIdPtr(tmp_salp, j);
+ BioseqPtr tmp_bsp = BioseqLockById(tmp_sip);
+ if (tmp_bsp != NULL) {
+ alnValidRows [aln_idx]++; /* count avaliable alignments */
+ BioseqUnlock (tmp_bsp);
+ }
+ SeqIdFree (tmp_sip);
}
- SeqIdFree (tmp_sip);
}
} else {
fLines = GetValue(bvp->newNumControl) == eNumTop ? 3 : 1;
@@ -241,68 +276,112 @@ static SeqPanLinePtr PNTR CreateSeqPanelLines(Int2 lineLength, BioseqViewPtr bvp
ref[i] = (SeqParaGPtr) MemNew(sizeof(SeqParaG));
ref[i]->pFeatList = (ValNodePtr*) MemNew( (size_t)(sizeof(ValNodePtr)*featRows) );
}
+ ref_offset = ref;
if (GetValue(bvp->newFeatControl) != eShowFeaturesOff) {
if (bvp->seqAlignMode) { /* in alignment mode */
- for (i = 1; i != alnRows + 1; i++) {
- SeqIdPtr sip_tmp = AlnMgr2GetNthSeqIdPtr(bvp->salp, i);
- BioseqPtr bsp_tmp = BioseqLockById(sip_tmp);
-
- if (bsp_tmp != NULL) {
- if (bvp->viewWholeEntity || GetValue(bvp->newFeatControl) == eShowFeaturesAll) {
- FillFeatureInfo(bvp, bsp_tmp, lineLength, pCount, i, i - 1, ref); /* show features for each seq in alignment */
- } else if (i == bvp->TargetRow) {
- FillFeatureInfo(bvp, bsp_tmp, lineLength, pCount, i, 0, ref); /* show features for target seq in alignment */
- }
- BioseqUnlock (bsp_tmp);
- } /* bsp_tmp != NULL */
- SeqIdFree (sip_tmp);
- } /* for */
+ for (tmp_salp = bvp->salp, aln_idx = 0; tmp_salp != NULL; tmp_salp = tmp_salp->next, aln_idx ++)
+ {
+ for (i = 1; i != alnRows + 1; i++) {
+ SeqIdPtr sip_tmp = AlnMgr2GetNthSeqIdPtr(tmp_salp, i);
+ BioseqPtr bsp_tmp = BioseqLockById(sip_tmp);
+
+ if (bsp_tmp != NULL) {
+ /* TODO: Need to calculate better values for passing to FillFeatureInfo */
+ if (bvp->viewWholeEntity || GetValue(bvp->newFeatControl) == eShowFeaturesAll) {
+ FillFeatureInfo(bvp, bsp_tmp, lineLength, lines_per_alignment [aln_idx], i, i - 1, ref_offset); /* show features for each seq in alignment */
+ } else if (i == bvp->TargetRow) {
+ FillFeatureInfo(bvp, bsp_tmp, lineLength, lines_per_alignment [aln_idx], i, 0, ref_offset); /* show features for target seq in alignment */
+ }
+ BioseqUnlock (bsp_tmp);
+ } /* bsp_tmp != NULL */
+ SeqIdFree (sip_tmp);
+ } /* for */
+ ref_offset += lines_per_alignment [aln_idx];
+ }
} else {
FillFeatureInfo(bvp, bsp, lineLength, pCount, 0, 0, ref);
}
} /* done with features */
-
bvp->TotalLines = 0; /* go through all pararaphs and count total */
- for (i = 0; i < pCount; i++) {
- Int4 sub_total = 0;
- for (j = 0; j < featRows; j++) sub_total += ValNodeLen(ref[i]->pFeatList[j]);
- bvp->TotalLines += fLines + sub_total + (alnRows == -1 ? 0 : alnValidRows); /* reserve space for alignment */
+ if (bvp->seqAlignMode)
+ {
+ for (tmp_salp = bvp->salp, aln_idx = 0; tmp_salp != NULL; tmp_salp = tmp_salp->next, aln_idx ++)
+ {
+ for (i = 0; i < lines_per_alignment [aln_idx]; i++) {
+ Int4 sub_total = 0;
+ for (j = 0; j < featRows; j++) sub_total += ValNodeLen(ref[i]->pFeatList[j]);
+ bvp->TotalLines += fLines + sub_total + (alnRows == -1 ? 0 : alnValidRows[aln_idx]); /* reserve space for alignment */
+ }
+ /* add one more for divider */
+ if (tmp_salp->next != NULL) bvp->TotalLines ++;
+ }
+
+ }
+ else
+ {
+ for (i = 0; i < pCount; i++) {
+ Int4 sub_total = 0;
+ for (j = 0; j < featRows; j++) sub_total += ValNodeLen(ref[i]->pFeatList[j]);
+ bvp->TotalLines += fLines + sub_total;
+ }
}
+
splp = (SeqPanLinePtr*) MemNew( (size_t)(sizeof(SeqPanLinePtr)*bvp->TotalLines) );
- for (i = 0; i < pCount; i++) {
- if (fLines > 1) { /* Numbers on top */
- splp[lCount++] = MakeSeqPanLine(eTypeTopSeqNumbers, i);
- splp[lCount++] = MakeSeqPanLine(eTypeTopScaleMarks, i);
- }
+ if (bvp->seqAlignMode)
+ {
+ ref_offset = ref;
+ for (tmp_salp = bvp->salp, aln_idx = 0; tmp_salp != NULL; tmp_salp = tmp_salp->next, aln_idx ++)
+ {
+ for (i = 0; i < lines_per_alignment [aln_idx]; i++)
+ {
+ if (fLines > 1) { /* Numbers on top */
+ splp[lCount++] = MakeSeqPanLine(eTypeTopSeqNumbers, i);
+ splp[lCount++] = MakeSeqPanLine(eTypeTopScaleMarks, i);
+ }
- if (bvp->seqAlignMode) {
- for (j = 1; j != alnRows + 1; j++) { /* AlnMgr counts from 1, not 0 */
- SeqIdPtr tmp_sip = AlnMgr2GetNthSeqIdPtr(bvp->salp, j);
- BioseqPtr tmp_bsp = BioseqLockById(tmp_sip);
+ for (j = 1; j != alnRows + 1; j++) { /* AlnMgr counts from 1, not 0 */
+ SeqIdPtr tmp_sip = AlnMgr2GetNthSeqIdPtr(tmp_salp, j);
+ BioseqPtr tmp_bsp = BioseqLockById(tmp_sip);
- if (tmp_bsp != NULL) {
- SeqPanLinePtr plp = MakeSeqPanLine(eTypeAlignSequence, i); /* Add align sequence line*/
- plp->row = j; /* Index position in the alignment (row) */
- splp[lCount++] = plp;
- BioseqUnlock (tmp_bsp);
+ if (tmp_bsp != NULL) {
+ SeqPanLinePtr plp = MakeSeqPanLine(eTypeAlignSequence, i); /* Add align sequence line*/
+ plp->row = j; /* Index position in the alignment (row) */
+ splp[lCount++] = plp;
+ BioseqUnlock (tmp_bsp);
- if (bvp->viewWholeEntity || GetValue(bvp->newFeatControl) == eShowFeaturesAll) {
- MakeFeatureLine(&lCount, i, j, j - 1, ref, splp); /* Add feature line */
- } else if (j == bvp->TargetRow) {
- MakeFeatureLine(&lCount, i, j, 0, ref, splp);
+ if (bvp->viewWholeEntity || GetValue(bvp->newFeatControl) == eShowFeaturesAll) {
+ MakeFeatureLine(&lCount, i, j, j - 1, ref_offset, splp); /* Add feature line */
+ } else if (j == bvp->TargetRow) {
+ MakeFeatureLine(&lCount, i, j, 0, ref_offset, splp);
+ }
}
- }
- SeqIdFree(tmp_sip);
+ SeqIdFree(tmp_sip);
+ }
+ }
+ /* add divider line between alignments */
+ if (tmp_salp->next != NULL)
+ {
+ splp[lCount++] = MakeSeqPanLine (eTypeAlignDivider, i);
+ }
+ ref_offset += lines_per_alignment [aln_idx];
+ }
+
+ }
+ else
+ {
+ for (i = 0; i < pCount; i++) {
+ if (fLines > 1) { /* Numbers on top */
+ splp[lCount++] = MakeSeqPanLine(eTypeTopSeqNumbers, i);
+ splp[lCount++] = MakeSeqPanLine(eTypeTopScaleMarks, i);
}
- } else { /* Add usual sequence and features if not in alignment mode */
splp[lCount++] = MakeSeqPanLine(eTypeSequence, i); /* Add sequence line */
- MakeFeatureLine(&lCount, i, 0, 0, ref, splp); /* Add feature line */
- } /* bvp->seqAlignMode */
- } /* for */
+ MakeFeatureLine(&lCount, i, 0, 0, ref, splp); /* Add feature line */
+ }
+ }/* bvp->seqAlignMode */
for (i = 0; i < pCount; i++) {
for (j = 0; j < featRows; j++) ValNodeFree (ref[i]->pFeatList[j]);
@@ -310,6 +389,8 @@ static SeqPanLinePtr PNTR CreateSeqPanelLines(Int2 lineLength, BioseqViewPtr bvp
MemFree (ref[i]);
}
MemFree (ref);
+ MemFree (lines_per_alignment);
+ MemFree (alnValidRows);
return splp;
}
@@ -488,30 +569,111 @@ static void PopulateSeqView (BioseqViewPtr bvp)
PopulateSeqAlnView(bvp);
}
-
static void PopulateAlnView (BioseqViewPtr bvp)
{
SeqIdPtr sip = bvp->bsp->id;
+ SeqIdPtr tmpsip;
+ SeqLocPtr slp;
+ SeqEntryPtr sep;
+ SeqAlignPtr tmp_salp, next_salp;
+
bvp->seqAlignMode = TRUE;
bvp->SeqStartPosX = 150;
+
+ /* if we're switching between segments we might need to load a
+ * different alignment */
+ if (bvp->salp != NULL)
+ {
+ if ((bvp->bsp->repr != Seq_repr_seg && bvp->salp->next != NULL)
+ || (bvp->TargetRow = AlnMgr2GetFirstNForSip (bvp->salp, sip)) == -1)
+ {
+ bvp->salp = SeqAlignFree (bvp->salp);
+ }
+ else
+ {
+ PopulateSeqAlnView(bvp);
+ return;
+ }
+ }
+
if (bvp->salp == NULL && bvp->seqAlignMode) { /* Try to find an alignment */
- bvp->salp = SeqAlignListDup((SeqAlignPtr) FindSeqAlignInSeqEntry(bvp->bsp->seqentry, OBJ_SEQALIGN));
+ /* need conglomerate view if we're looking at a segmented sequence */
+ if (bvp->bsp->repr == Seq_repr_seg)
+ {
+ slp = (SeqLocPtr) bvp->bsp->seq_ext;
+ while (slp != NULL && bvp->salp == NULL)
+ {
+ tmpsip = SeqLocId (slp);
+ sep = SeqEntryFind (tmpsip);
+ bvp->salp = SeqAlignListDup((SeqAlignPtr) FindSeqAlignInSeqEntry(sep, OBJ_SEQALIGN));
+ slp = slp->next;
+ }
+ }
+ else
+ {
+ bvp->salp = SeqAlignListDup((SeqAlignPtr) FindSeqAlignInSeqEntry(bvp->bsp->seqentry, OBJ_SEQALIGN));
+ }
+
if (bvp->salp == NULL) { /* No alignment found or bug in AlignMgr (which is more likely). Switch to sequence mode */
PopulateSeqView(bvp);
return;
}
- if (bvp->salp->segtype == SAS_DENSEG && bvp->salp->next == NULL) {
- AlnMgr2IndexSingleChildSeqAlign(bvp->salp);
- } else {
- AlnMgr2IndexSeqAlign(bvp->salp);
+
+ if (bvp->bsp->repr == Seq_repr_seg)
+ {
+ /* if segmented set, index each segment individually */
+ tmp_salp = bvp->salp;
+ while (tmp_salp != NULL)
+ {
+ next_salp = tmp_salp->next;
+ tmp_salp->next = NULL;
+ if (tmp_salp->segtype == SAS_DENSEG) {
+ AlnMgr2IndexSingleChildSeqAlign(tmp_salp);
+ } else {
+ AlnMgr2IndexSeqAlign(tmp_salp);
+ }
+ tmp_salp->next = next_salp;
+ tmp_salp = next_salp;
+ }
+ }
+ else
+ {
+ /* do not incorporate other segments in segmented alignment */
+ if (!is_dim2seqalign (bvp->salp) && bvp->salp->next != NULL)
+ {
+ bvp->salp->next = SeqAlignFree (bvp->salp->next);
+ }
+
+ if (bvp->salp->segtype == SAS_DENSEG && bvp->salp->next == NULL) {
+ AlnMgr2IndexSingleChildSeqAlign(bvp->salp);
+ } else {
+ AlnMgr2IndexSeqAlign(bvp->salp);
+ }
}
}
bvp->TargetRow = ROW_UNDEFINED;
- while (sip && bvp->TargetRow == ROW_UNDEFINED) {
- bvp->TargetRow = AlnMgr2GetFirstNForSip(bvp->salp, sip);
- sip = sip->next;
+ if (bvp->bsp->repr == Seq_repr_seg)
+ {
+ slp = (SeqLocPtr) bvp->bsp->seq_ext;
+ while (slp != NULL && bvp->TargetRow == ROW_UNDEFINED)
+ {
+ tmpsip = SeqLocId (slp);
+ while (tmpsip && bvp->TargetRow == ROW_UNDEFINED)
+ {
+ bvp->TargetRow = AlnMgr2GetFirstNForSip(bvp->salp, tmpsip);
+ tmpsip = tmpsip->next;
+ }
+ slp = slp->next;
+ }
}
-
+ else
+ {
+ while (sip && bvp->TargetRow == ROW_UNDEFINED) {
+ bvp->TargetRow = AlnMgr2GetFirstNForSip(bvp->salp, sip);
+ sip = sip->next;
+ }
+ }
+
PopulateSeqAlnView(bvp);
}
@@ -557,6 +719,17 @@ static void DrawTopSeqNums(Int2 x, Int2 y, Int4 line, BioseqViewPtr bvp)
}
}
+static void DrawAlignmentDivider (Int2 x, Int2 y, BioseqViewPtr bvp)
+{
+ Int2 block, ctr=0;
+ char buf[20];
+
+ Magenta ();
+ for (block = 0; block != bvp->BlocksAtLine && ctr >= 0; block++) {
+ sprintf(buf, "~~~~~~~~~~");
+ PaintStringEx (buf, x+SEQ_X_OFFSET+bvp->SeqStartPosX+(block+1)*SEQ_GROUP_SIZE*bvp->CharWidth+block*bvp->CharWidth - bvp->CharWidth*StrLen(buf), y);
+ }
+}
static void DrawSeqSideLineNumbers(Int2 x, Int2 y, Int4 line, BioseqViewPtr bvp)
{
@@ -718,6 +891,7 @@ AlignmentIntervalToString
MemSet(alnbuf, '-', alnbuf_len); /* assume all gaps and fill the sequence later */
MemSet(seqbuf, 0, alnbuf_len);
+ if (target_row < 0) return;
if (stop > aln_len) {
MemSet (alnbuf + aln_len - start, 0, stop - aln_len);
@@ -847,20 +1021,28 @@ AlignmentIntervalToString
}
}
-static void DrawAlignment(Int2 x, Int2 y, Int4 line, Int4 row, Uint1Ptr buf, Uint1Ptr seqbuf, Uint1Ptr alnbuf, BioseqViewPtr bvp)
+static void DrawAlignment
+(Int2 x, Int2 y, Int4 line, Int4 row, Uint1Ptr buf, Uint1Ptr seqbuf,
+ Uint1Ptr alnbuf, BioseqViewPtr bvp, Int4 aln_idx)
{
- Int2 block;
- Char alnlabel[13];
- SeqIdPtr sip = AlnMgr2GetNthSeqIdPtr(bvp->salp, row);
- BioseqPtr bsp = BioseqLockById(sip);
- Int4 start = line * bvp->CharsAtLine;
- Int4 stop = start + bvp->BlocksAtLine * SEQ_GROUP_SIZE;
- Int4 alnbuf_len;
- SeqIdPtr best_id;
+ Int2 block;
+ Char alnlabel[13];
+ SeqIdPtr sip = AlnMgr2GetNthSeqIdPtr(bvp->salp, row);
+ BioseqPtr bsp = BioseqLockById(sip);
+ Int4 start = line * bvp->CharsAtLine;
+ Int4 stop = start + bvp->BlocksAtLine * SEQ_GROUP_SIZE;
+ Int4 alnbuf_len;
+ SeqIdPtr best_id;
+ SeqAlignPtr tmp_salp;
+ Int4 i;
+
+ for (i=0, tmp_salp = bvp->salp; i < aln_idx && tmp_salp != NULL; i++, tmp_salp = tmp_salp->next)
+ {
+ }
+ if (tmp_salp == NULL) return;
- AlignmentIntervalToString (bvp->salp, row, start, stop, bvp->TargetRow,
+ AlignmentIntervalToString (tmp_salp, row, start, stop, bvp->TargetRow,
bvp->viewWholeEntity, seqbuf, alnbuf, &alnbuf_len);
-
/* finally draw everything */
best_id = SeqIdFindBestAccession (bsp->id);
@@ -1148,6 +1330,8 @@ static void onDrawSeqPanel (PaneL p)
RecT r;
Int4 line;
Int2 x, y;
+ Int4 aln_idx;
+ Int4 start;
bvp = GetBioseqViewPtr (p);
bsp = bvp->bsp;
@@ -1165,7 +1349,18 @@ static void onDrawSeqPanel (PaneL p)
y = r.top + bvp->CharHeight + SEQ_Y_OFFSET;
SelectFont ((FonT)(bvp->displayFont));
- for (line = GetBarValue(sb); line < bvp->TotalLines && y <= r.bottom-2*SEQ_Y_OFFSET; line++) {
+ aln_idx = 0;
+ start = GetBarValue (sb);
+ for (line = 0; line < start && line < bvp->TotalLines; line++)
+ {
+ splp = bvp->SeqPanLines[line];
+ if (splp->lineType == eTypeAlignDivider)
+ {
+ aln_idx++;
+ }
+ }
+
+ for (line = start; line < bvp->TotalLines && y <= r.bottom-2*SEQ_Y_OFFSET; line++) {
if (IsInRange(y, updateRect.top,updateRect.bottom) ||
IsInRange(y+bvp->LineHeight,updateRect.top,updateRect.bottom))
{
@@ -1187,9 +1382,13 @@ static void onDrawSeqPanel (PaneL p)
break;
case eTypeAlignSequence:
DrawAlignSideLineNumbers(x, y, splp->bioSeqLine, splp->row, bvp);
- DrawAlignment(x, y, splp->bioSeqLine, splp->row, buf, seqbuf, alnbuf, bvp); /* Draw the alignment */
+ DrawAlignment(x, y, splp->bioSeqLine, splp->row, buf, seqbuf, alnbuf, bvp, aln_idx); /* Draw the alignment */
if (bvp->DrawGrid) DrawLtGrid(x, y+bvp->LineSpace/2, r.right, y+bvp->LineSpace/2);
break;
+ case eTypeAlignDivider:
+ DrawAlignmentDivider (x, y, bvp);
+ aln_idx++;
+ break;
case eTypeFeature:
if (bvp->DrawGrid) DrawLtGrid(x, y+bvp->LineSpace/2, r.right, y+bvp->LineSpace/2);
DrawFeature(x, y, splp->bioSeqLine, splp->row, splp->idx, splp->protProduct, bsp, bvp); /* Draw Features */
diff --git a/desktop/vsm.c b/desktop/vsm.c
index 01adaf06..a30aa559 100644
--- a/desktop/vsm.c
+++ b/desktop/vsm.c
@@ -29,7 +29,7 @@
*
* Version Creation Date: 11-29-94
*
-* $Revision: 6.15 $
+* $Revision: 6.16 $
*
* File Description:
*
@@ -1062,12 +1062,22 @@ static void VSMDragAndDrop(VSMWinPtr vsmwp, Uint2 entityID, Uint2 itemID, Uint2
ompc.input_itemtype = vsmwp->itemtype1;
ompc.do_not_reload_from_cache = TRUE;
+
if (! DetachDataForProc(&ompc, FALSE))
{
ErrShow();
return;
}
+ if (ompc.input_choicetype)
+ {
+ WarnIfAlignment (ompc.input_choicetype, ompc.input_choice, ompc.input_entityID);
+ }
+ else
+ {
+ WarnIfAlignment (ompc.input_itemtype, ompc.input_data, ompc.input_entityID);
+ }
+
if (! ompc.whole_entity) /* just a part gone, so need an update */
ObjMgrSendMsg(OM_MSG_DEL, ompc.input_entityID, ompc.input_itemID, ompc.input_itemtype);
generated by cgit v1.2.3 (git 2.25.1) at 2024-07-05 17:36:51 +0000