[svn-upgrade] Integrating new upstream version, ncbi-tools6 (6.1.20070822)

16 files changed, 442 insertions, 124 deletions

diff --git a/corelib/drwnmfls.c b/corelib/drwnmfls.c
index fb69b829..144d7692 100644
--- a/corelib/drwnmfls.c
+++ b/corelib/drwnmfls.c
@@ -7,4 +7,4 @@
 #endif
 #if defined(OS_MAC)  ||  defined(OS_UNIX_DARWIN_OLD)
 #  include "MoreFilesX.c"
-#endif
\ No newline at end of file
+#endif
diff --git a/corelib/ncbiargs.c b/corelib/ncbiargs.c
index 68217b3f..ea2f24d2 100644
--- a/corelib/ncbiargs.c
+++ b/corelib/ncbiargs.c
@@ -35,6 +35,12 @@
 * Modifications:  
 * --------------------------------------------------------------------------
 * $Log: ncbiargs.c,v $
+* Revision 6.10  2006/10/19 14:57:03  lavr
+* Fix repetitive arg error message to show no argument value since it's empty
+*
+* Revision 6.9  2006/10/18 19:15:43  lavr
+* Allow repetitive (boolean) flags to increment arg's intvalue [spec.cased]
+*
 * Revision 6.8  2004/04/01 13:43:06  lavr
 * Spell "occurred", "occurrence", and "occurring"
 *
@@ -125,10 +131,10 @@ NLM_EXTERN Nlm_Boolean Nlm_GetArgs(const char* progname,
           Nlm_FreeArgs(i, ap);
           return FALSE;
         }
-      curarg->intvalue = 0;
+      curarg->intvalue   = 0;
       curarg->floatvalue = 0.0;
-      curarg->strvalue = NULL;
-      if (curarg->defaultvalue != NULL)
+      curarg->strvalue   = NULL;
+      if (curarg->defaultvalue)
         {
           resolved[i] = TRUE;
           switch (curarg->type)
@@ -139,24 +145,18 @@ NLM_EXTERN Nlm_Boolean Nlm_GetArgs(const char* progname,
               else
                 curarg->intvalue = 0;
               break;
-            case ARG_INT: {
-              long val;
-              sscanf(curarg->defaultvalue, "%ld", &val);
-              curarg->intvalue = val;
+            case ARG_INT:
+              curarg->intvalue = atol(curarg->defaultvalue);
               break;
-            }
-            case ARG_FLOAT: {
-              double val;
-              sscanf(curarg->defaultvalue, "%lf", &val);
-              curarg->floatvalue = val;
+            case ARG_FLOAT:
+              curarg->floatvalue = atof(curarg->defaultvalue);
               break;
-            }
             case ARG_STRING:
             case ARG_FILE_IN:
             case ARG_FILE_OUT:
             case ARG_DATA_IN:
             case ARG_DATA_OUT:
-              curarg->strvalue = StringSave (curarg->defaultvalue);
+              curarg->strvalue = StringSave(curarg->defaultvalue);
               break;
             }
         }
@@ -184,17 +184,21 @@ NLM_EXTERN Nlm_Boolean Nlm_GetArgs(const char* progname,
           if (curarg->optional)
             printf("  Optional");
           printf("\n");
-          if (curarg->defaultvalue != NULL)
+          if (curarg->defaultvalue)
             printf("    default = %s\n", curarg->defaultvalue);
-          if ((curarg->from != NULL) || (curarg->to != NULL))
+          if (curarg->from  ||  curarg->to)
             {
-              if ((curarg->type == ARG_DATA_IN) ||
-                  (curarg->type == ARG_DATA_OUT))
+              if (curarg->type == ARG_DATA_IN  ||
+                  curarg->type == ARG_DATA_OUT)
                 printf("    Data Type = %s\n", curarg->from);
-              else
-                printf("    range from %s to %s\n", 
-                       (curarg->from ? curarg->from: "<NULL>"),
-                       (curarg->to   ? curarg->to  : "<NULL>"));
+              else if (curarg->type == ARG_BOOLEAN  ||
+                       curarg->type == ARG_INT      ||
+                       curarg->type == ARG_FLOAT)
+                {
+                  printf("    range from %s to %s\n", 
+                         (curarg->from ? curarg->from: "?"),
+                         (curarg->to   ? curarg->to  : "?"));
+                }
             }
         }
 
@@ -260,7 +264,7 @@ NLM_EXTERN Nlm_Boolean Nlm_GetArgs(const char* progname,
           if (!ok  &&  curarg->type != ARG_BOOLEAN)
             {
               ErrPostEx(SEV_ERROR, 0, 0,
-                        "No argument given for %s", curarg->prompt);
+                        "No argument value given for %s", curarg->prompt);
               Nlm_MemFree( resolved );
               Nlm_FreeArgs(numargs, ap);
               return FALSE;
@@ -276,15 +280,38 @@ NLM_EXTERN Nlm_Boolean Nlm_GetArgs(const char* progname,
           else if (TO_UPPER(*arg) == 'F')
             curarg->intvalue = 0;
           else if (*arg == '\0')
-            curarg->intvalue = 1;
-          else {
-            ErrPostEx(SEV_ERROR, 0, 0,
-                      "%s [%s] must be one of {'T', 't', 'F', 'f'} or omitted",
-                      curarg->prompt, arg);
-            Nlm_MemFree( resolved );
-            Nlm_FreeArgs(numargs, ap);
-            return FALSE;
-          }
+            {
+              long idef, ifrom, ito;
+              if (curarg->from  &&  curarg->to  &&
+                  sscanf(curarg->defaultvalue, "%ld", &idef)  > 0  &&
+                  sscanf(curarg->from,         "%ld", &ifrom) > 0  &&
+                  sscanf(curarg->to,           "%ld", &ito)   > 0  &&
+                  idef == 0  &&  ifrom == 0  &&  ito > 1)
+                {
+                  if (curarg->intvalue >= ito)
+                    {
+                      ErrPostEx(SEV_ERROR, 0, 0,
+                                "%s allowed no more than %s times",
+                                curarg->prompt, curarg->to);
+                      Nlm_MemFree( resolved );
+                      Nlm_FreeArgs(numargs, ap);
+                      return FALSE;
+                    }
+                  else
+                    curarg->intvalue++;
+                }
+              else
+                curarg->intvalue = 1;
+            }
+          else
+            {
+              ErrPostEx(SEV_ERROR, 0, 0,
+                        "%s [%s] must be one of {'T', 't', 'F', 'f'}"
+                        " or omitted", curarg->prompt, arg);
+              Nlm_MemFree( resolved );
+              Nlm_FreeArgs(numargs, ap);
+              return FALSE;
+            }
           break;
 
         case ARG_INT: {
@@ -293,21 +320,14 @@ NLM_EXTERN Nlm_Boolean Nlm_GetArgs(const char* progname,
           if (sscanf(arg, "%ld", &val) <= 0)
             range = FALSE;
           curarg->intvalue = val;
-          if (range  &&  curarg->from)
+          if (range && curarg->from && curarg->intvalue < atol(curarg->from))
             {
-              long ifrom;
-              sscanf(curarg->from, "%ld", &ifrom);
-              if (curarg->intvalue < ifrom)
                 range = FALSE;
             }
-          if (range  &&  curarg->to)
+          if (range && curarg->to && curarg->intvalue > atol(curarg->to))
             {
-              long ito;
-              sscanf(curarg->to, "%ld", &ito);
-              if (curarg->intvalue > ito)
                 range = FALSE;
             }
-
           if ( !range )
             {
               ErrPostEx(SEV_ERROR, 0, 0,
@@ -328,18 +348,12 @@ NLM_EXTERN Nlm_Boolean Nlm_GetArgs(const char* progname,
           if (sscanf(arg, "%lf", &val) <= 0)
             range = FALSE;
           curarg->floatvalue = val;
-          if (range  &&  curarg->from)
+          if (range && curarg->from && curarg->floatvalue < atof(curarg->from))
             {
-              double ffrom;
-              sscanf(curarg->from, "%lf", &ffrom);
-              if (curarg->floatvalue < ffrom)
                 range = FALSE;
             }
-          if (range  &&  curarg->to)
+          if (range && curarg->to && curarg->floatvalue > atof(curarg->to))
             {
-              double fto;
-              sscanf(curarg->to, "%lf", &fto);
-              if (curarg->floatvalue > fto)
                 range = FALSE;
             }
           if ( !range )
@@ -363,7 +377,7 @@ NLM_EXTERN Nlm_Boolean Nlm_GetArgs(const char* progname,
         case ARG_DATA_OUT:
           if ( curarg->strvalue )
             MemFree(curarg->strvalue);
-          curarg->strvalue = StringSave (arg);
+          curarg->strvalue = StringSave(arg);
           break;
         }    /*** end switch ****/
     }
diff --git a/corelib/ncbienv.c b/corelib/ncbienv.c
index 9529e122..1ae09269 100644
--- a/corelib/ncbienv.c
+++ b/corelib/ncbienv.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   7/7/91
 *
-* $Revision: 6.43 $
+* $Revision: 6.46 $
 *
 * File Description:
 *       portable environment functions, companions for ncbimain.c
@@ -37,6 +37,15 @@
 * Modifications:
 * --------------------------------------------------------------------------
 * $Log: ncbienv.c,v $
+* Revision 6.46  2007/05/04 13:43:59  kans
+* GetOpSysString now checks for Windows VISTA
+*
+* Revision 6.45  2007/04/06 21:47:56  kans
+* Nlm_GetOpSysString checks gestaltSystemVersion and returns actual Mac OS X version
+*
+* Revision 6.44  2007/04/03 00:39:41  kans
+* GetOpSysString does run-time check for Rosetta
+*
 * Revision 6.43  2005/12/02 13:40:00  rsmith
 * In ProgramPath on Mac use case-insensitive compare to check the file extension.
 *
@@ -2396,9 +2405,22 @@ NLM_EXTERN Nlm_Boolean Nlm_FreeArgs(Nlm_Int2 numargs, Nlm_ArgPtr ap)
   return TRUE;
 }
 
+#ifdef OS_UNIX_DARWIN
+#include <sys/sysctl.h>
+#endif
+
 NLM_EXTERN Nlm_CharPtr Nlm_GetOpSysString (void)
 
 {
+#ifdef OS_UNIX_DARWIN
+#ifdef PROC_PPC
+  Nlm_Boolean  isRosetta = FALSE;
+  size_t       len;
+  int          mib [2];
+  Nlm_Char     model [32];
+#endif
+  long         sysVer;
+#endif
   Nlm_CharPtr  str = "unknown";
 
 #if defined(OS_MAC) && !defined(OS_UNIX_DARWIN)
@@ -2422,10 +2444,71 @@ NLM_EXTERN Nlm_CharPtr Nlm_GetOpSysString (void)
 
 #ifdef OS_UNIX_DARWIN
 #ifdef PROC_PPC
-  str = "MAC PPC on OS X";
+  mib [0] = CTL_HW;
+  mib [1] = HW_MODEL;
+  len = sizeof (model);
+  if (sysctl (mib, 2, &model, &len, NULL, 0) == 0) {
+    isRosetta = (Nlm_Boolean) (len == 9 && strcmp (model, "PowerMac") == 0);
+  }
+  if (isRosetta) {
+    str = "MAC Rosetta on OS X";
+    if ( Gestalt (gestaltSystemVersion, &sysVer) == noErr) {
+      if (sysVer >= 4192) {
+        str = "MAC Rosetta on OS 10.6";
+      } else if (sysVer >= 4176) {
+        str = "MAC Rosetta on OS 10.5";
+      } else if (sysVer >= 4160) {
+        str = "MAC Rosetta on OS 10.4";
+      } else if (sysVer >= 4144) {
+        str = "MAC Rosetta on OS 10.3";
+      } else if (sysVer >= 4128) {
+        str = "MAC Rosetta on OS 10.2";
+      } else if (sysVer >= 4112) {
+        str = "MAC Rosetta on OS 10.1";
+      } else {
+        str = "MAC Rosetta on OS X";
+      }
+    }
+  } else {
+    str = "MAC PPC on OS X";
+    if ( Gestalt (gestaltSystemVersion, &sysVer) == noErr) {
+      if (sysVer >= 4192) {
+        str = "MAC PPC on OS 10.6";
+      } else if (sysVer >= 4176) {
+        str = "MAC PPC on OS 10.5";
+      } else if (sysVer >= 4160) {
+        str = "MAC PPC on OS 10.4";
+      } else if (sysVer >= 4144) {
+        str = "MAC PPC on OS 10.3";
+      } else if (sysVer >= 4128) {
+        str = "MAC PPC on OS 10.2";
+      } else if (sysVer >= 4112) {
+        str = "MAC PPC on OS 10.1";
+      } else {
+        str = "MAC PPC on OS X";
+      }
+    }
+  }
 #else
 #ifdef PROC_I80X86
   str = "MAC 386 on OS X";
+  if ( Gestalt (gestaltSystemVersion, &sysVer) == noErr) {
+    if (sysVer >= 4192) {
+      str = "MAC 386 on OS 10.6";
+    } else if (sysVer >= 4176) {
+      str = "MAC 386 on OS 10.5";
+    } else if (sysVer >= 4160) {
+      str = "MAC 386 on OS 10.4";
+    } else if (sysVer >= 4144) {
+      str = "MAC 386 on OS 10.3";
+    } else if (sysVer >= 4128) {
+      str = "MAC 386 on OS 10.2";
+    } else if (sysVer >= 4112) {
+      str = "MAC 386 on OS 10.1";
+    } else {
+      str = "MAC 386 on OS X";
+    }
+  }
 #else
   str = "MAC UNIX on OS X";
 #endif
@@ -2461,7 +2544,9 @@ NLM_EXTERN Nlm_CharPtr Nlm_GetOpSysString (void)
   version = GetVersion ();
   lowbyte = (version & 0x0000FF);
   if ((version & 0x80000000) == 0) {
-    if (lowbyte == 5) {
+    if (lowbyte == 6) {
+      str = "MS WINDOWS VISTA";
+    } else if (lowbyte == 5) {
       str = "MS WINDOWS 2000/XP";
     } else if (lowbyte == 4) {
       str = "MS WINDOWS NT 4.0";
diff --git a/corelib/ncbierr.c b/corelib/ncbierr.c
index d6c29bba..302b56b4 100644
--- a/corelib/ncbierr.c
+++ b/corelib/ncbierr.c
@@ -23,9 +23,9 @@
 *
 * ===========================================================================
 *
-* $Id: ncbierr.c,v 6.23 2006/07/13 17:10:35 bollin Exp $
+* $Id: ncbierr.c,v 6.24 2006/11/09 17:46:58 kans Exp $
 *
-* $Revision: 6.23 $
+* $Revision: 6.24 $
 *
 * Authors:  Schuler, Sirotkin (UserErr stuff)
 *
@@ -71,6 +71,9 @@
 * 03-06-95 Schuler     Fixed problem with ErrMsgRoot_fopen
 *
 * $Log: ncbierr.c,v $
+* Revision 6.24  2006/11/09 17:46:58  kans
+* added cast to quiet CodeWarrior complaint
+*
 * Revision 6.23  2006/07/13 17:10:35  bollin
 * use Uint4 instead of Uint2 for itemID values
 *
@@ -536,7 +539,7 @@ NLM_EXTERN int LIBCALL Nlm_ErrPostStr (ErrSev sev, int lev1, int lev2, const cha
     }
 
   if ( s_HookOnly ) {
-      die_if_necessary(severity, info);
+      die_if_necessary((ErrSev)severity, info);
       ErrClear();
       return ANS_NONE;
   }
diff --git a/corelib/ncbifile.c b/corelib/ncbifile.c
index d24a77a3..54d8c15f 100644
--- a/corelib/ncbifile.c
+++ b/corelib/ncbifile.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   3/4/91
 *
-* $Revision: 6.39 $
+* $Revision: 6.40 $
 *
 * File Description: 
 *     portable file routines
@@ -43,6 +43,9 @@
 * 11-27-94 Ostell      moved includes to ncbiwin.h to avoid conflict MSC
 *
 * $Log: ncbifile.c,v $
+* Revision 6.40  2007/08/16 17:09:22  kans
+* moved DirExplore from sqnutils
+*
 * Revision 6.39  2006/07/13 17:10:36  bollin
 * use Uint4 instead of Uint2 for itemID values
 *
@@ -1271,6 +1274,89 @@ NLM_EXTERN ValNodePtr LIBCALL Nlm_DirCatalog (Nlm_CharPtr pathname)
 
 /*****************************************************************************
 *
+*   general file recursion functio
+*
+*****************************************************************************/
+
+NLM_EXTERN Nlm_Int4 Nlm_DirExplore (
+  Nlm_CharPtr directory,
+  Nlm_CharPtr filter,
+  Nlm_CharPtr suffix,
+  Nlm_Boolean recurse,
+  Nlm_DirExpProc proc,
+  Nlm_VoidPtr userdata
+)
+
+{
+  Nlm_Int4     count = 0;
+  Nlm_Char     file [FILENAME_MAX], path [PATH_MAX];
+  Nlm_CharPtr  ptr, str;
+  ValNodePtr   head, vnp;
+
+  if (proc == NULL) return 0;
+  if (Nlm_StringHasNoText (directory) || Nlm_StringHasNoText (suffix)) return 0;
+
+  /* get list of all files in source directory */
+
+  head = Nlm_DirCatalog (directory);
+
+  for (vnp = head; vnp != NULL; vnp = vnp->next) {
+    if (vnp->choice == 0) {
+      str = (Nlm_CharPtr) vnp->data.ptrvalue;
+      if (! Nlm_StringHasNoText (str)) {
+
+        /* check filename for indicated suffix */
+
+        ptr = Nlm_StringStr (str, suffix);
+        if (ptr != NULL) {
+
+          /* make sure detected suffix is really at end of filename */
+
+          if (Nlm_StringCmp (ptr, suffix) == 0) {
+            *ptr = '\0';
+          } else {
+            ptr = NULL;
+          }
+        }
+
+        if (Nlm_StringHasNoText (suffix) || ptr != NULL) {
+
+          Nlm_StringNCpy_0 (path, directory, sizeof (path));
+          sprintf (file, "%s%s", str, suffix);
+          Nlm_FileBuildPath (path, NULL, file);
+
+          /* check full path/file name for desired filter */
+
+          if (Nlm_StringHasNoText (filter) || Nlm_StringStr (path, filter) != NULL) {
+
+            /* process file that satisfies optional filter and suffix constraints */
+
+            proc (path, userdata);
+            count++;
+          }
+        }
+      }
+    } else if (vnp->choice == 1 && recurse) {
+
+      /* recurse into subdirectory */
+
+      Nlm_StringNCpy_0 (path, directory, sizeof (path));
+      str = (Nlm_CharPtr) vnp->data.ptrvalue;
+      Nlm_FileBuildPath (path, str, NULL);
+
+      count += Nlm_DirExplore (path, filter, suffix, recurse, proc, userdata);
+    }
+  }
+
+  /* clean up file list */
+
+  ValNodeFreeData (head);
+
+  return count;
+}
+
+/*****************************************************************************
+*
 *   TmpNam()
 *
 *****************************************************************************/
diff --git a/corelib/ncbifile.h b/corelib/ncbifile.h
index 853e3e64..a6f440ec 100644
--- a/corelib/ncbifile.h
+++ b/corelib/ncbifile.h
@@ -32,7 +32,7 @@
 *
 * Version Creation Date:   1/1/91
 *
-* $Revision: 6.6 $
+* $Revision: 6.7 $
 *
 * File Description:
 *   	prototypes for portable file routines
@@ -40,6 +40,9 @@
 * Modifications:
 * --------------------------------------------------------------------------
 * $Log: ncbifile.h,v $
+* Revision 6.7  2007/08/16 17:09:22  kans
+* moved DirExplore from sqnutils
+*
 * Revision 6.6  2004/05/07 15:57:14  kans
 * added FileCache functions for buffered read, graceful handing of Unix, Mac, and DOS line endings
 *
@@ -118,7 +121,18 @@ NLM_EXTERN void Nlm_FileCacheSeek (Nlm_FileCache PNTR fcp, Nlm_Int4 pos);
 NLM_EXTERN Nlm_Int4 Nlm_FileCacheTell (Nlm_FileCache PNTR fcp);
 NLM_EXTERN Nlm_Boolean Nlm_FileCacheFree (Nlm_FileCache PNTR fcp, Nlm_Boolean restoreFilePos);
 
+/* general file recursion function - directory must not be empty, proc callback function must not be NULL */
+
+typedef void (*Nlm_DirExpProc) (Nlm_CharPtr filename, Nlm_VoidPtr userdata);
 
+NLM_EXTERN Nlm_Int4 Nlm_DirExplore (
+  Nlm_CharPtr directory,
+  Nlm_CharPtr filter,
+  Nlm_CharPtr suffix,
+  Nlm_Boolean recurse,
+  Nlm_DirExpProc proc,
+  Nlm_VoidPtr userdata
+);
 
 #define FileOpen Nlm_FileOpen
 #define FileClose Nlm_FileClose
@@ -149,6 +163,9 @@ NLM_EXTERN Nlm_Boolean Nlm_FileCacheFree (Nlm_FileCache PNTR fcp, Nlm_Boolean re
 #define FileCacheTell Nlm_FileCacheTell
 #define FileCacheFree Nlm_FileCacheFree
 
+#define DirExpProc Nlm_DirExpProc
+#define DirExplore Nlm_DirExplore
+
 #define EjectCd(sVolume, deviceName, rawDeviceName, mountPoint, mountCmd)  FALSE
 #define MountCd(sVolume, deviceName, mountPoint, mountCmd)                 FALSE
 
diff --git a/corelib/ncbilcl.dwn b/corelib/ncbilcl.dwn
index cf0bfadd..b8f0aa0b 100644
--- a/corelib/ncbilcl.dwn
+++ b/corelib/ncbilcl.dwn
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   8/1/94
 *
-* $Revision: 6.7 $
+* $Revision: 6.9 $
 *
 * File Description:
 *		system dependent header
@@ -41,6 +41,12 @@
 * -------  ----------    ---------------------------------------------------
 *
 * $Log: ncbilcl.dwn,v $
+* Revision 6.9  2007/04/06 21:10:32  kans
+* also check for 64-bit processor conditional symbols
+*
+* Revision 6.8  2007/04/02 16:06:12  kans
+* use __ppc__ and __i386__ to set proper PROC_ platform flags
+*
 * Revision 6.7  2005/11/16 16:22:32  kans
 * support for PowerPC and Intel chips in PROC_ and _ENDIAN flags
 *
@@ -87,10 +93,10 @@
 #define OS_UNIX_DARWIN
 
 /* Mac may be PowerPC or Intel chip */
-#ifdef PER_ARCH_CFLAGS_ppc
+#if defined(__ppc__) || defined(__ppc64__)
 #define PROC_PPC
 #endif
-#ifdef PER_ARCH_CFLAGS_i386
+#if defined(__i386__) || defined(__x86_64__)
 #define PROC_I80X86
 #define PROC_I80_386
 #endif
diff --git a/corelib/ncbimisc.c b/corelib/ncbimisc.c
index 96e2ab64..88fc7a93 100644
--- a/corelib/ncbimisc.c
+++ b/corelib/ncbimisc.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   10/23/91
 *
-* $Revision: 6.30 $
+* $Revision: 6.32 $
 *
 * File Description: 
 *   	miscellaneous functions
@@ -43,6 +43,12 @@
 * 02-16-94 Epstein     Retired Gestalt functions and definitions
 *
 * $Log: ncbimisc.c,v $
+* Revision 6.32  2006/11/09 17:47:16  kans
+* added ValNodeMergeStrs
+*
+* Revision 6.31  2006/10/17 14:16:48  lavr
+* ValNodeCopyStr() to take "const char*"
+*
 * Revision 6.30  2005/11/16 16:36:11  kans
 * support for PowerPC and Intel chips for Macintosh
 *
@@ -619,7 +625,7 @@ NLM_EXTERN ValNodePtr LIBCALL ValNodeAddStr (ValNodePtr PNTR head, Nlm_Int2 choi
 *      if str == NULL, does not add a ValNode
 *
 *****************************************************************************/
-NLM_EXTERN ValNodePtr LIBCALL ValNodeCopyStr (ValNodePtr PNTR head, Nlm_Int2 choice, Nlm_CharPtr str)
+NLM_EXTERN ValNodePtr LIBCALL ValNodeCopyStr (ValNodePtr PNTR head, Nlm_Int2 choice, const char* str)
 {
 	ValNodePtr newnode;
 
@@ -934,6 +940,41 @@ NLM_EXTERN ValNodePtr LIBCALL ValNodeSort (ValNodePtr list, int (LIBCALLBACK *co
 
 /*****************************************************************************
 *
+*   ValNodeMergeStrs(list)
+*   	Merges chain of val node strings into a single character array
+*
+*****************************************************************************/
+NLM_EXTERN Nlm_CharPtr LIBCALL ValNodeMergeStrs (ValNodePtr list)
+
+{
+  size_t       len;
+  Nlm_CharPtr  ptr;
+  Nlm_CharPtr  str;
+  Nlm_CharPtr  tmp;
+  ValNodePtr   vnp;
+
+
+  if (list == NULL) return NULL;
+
+  for (vnp = list, len = 0; vnp != NULL; vnp = vnp->next) {
+    str = (Nlm_CharPtr) vnp->data.ptrvalue;
+    len += Nlm_StringLen (str);
+  }
+  if (len == 0) return NULL;
+
+  ptr = Nlm_MemNew (sizeof (Nlm_Char) * (len + 2));
+  if (ptr == NULL) return NULL;
+
+  for (vnp = list, tmp = ptr; vnp != NULL; vnp = vnp->next) {
+    str = (Nlm_CharPtr) vnp->data.ptrvalue;
+    tmp = Nlm_StringMove (tmp, str);
+  }
+
+  return ptr;
+}
+
+/*****************************************************************************
+*
 *   Start Of Node List Functions
 *
 *****************************************************************************/
diff --git a/corelib/ncbimisc.h b/corelib/ncbimisc.h
index 97db6edb..8a4ae690 100644
--- a/corelib/ncbimisc.h
+++ b/corelib/ncbimisc.h
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   10/23/91
 *
-* $Revision: 6.14 $
+* $Revision: 6.16 $
 *
 * File Description:
 *   	prototypes of miscellaneous functions
@@ -43,6 +43,12 @@
 * 06-15-93 Schuler     Added macros for Gestalt functins.
 *
 * $Log: ncbimisc.h,v $
+* Revision 6.16  2006/11/09 17:47:16  kans
+* added ValNodeMergeStrs
+*
+* Revision 6.15  2006/10/17 14:16:48  lavr
+* ValNodeCopyStr() to take "const char*"
+*
 * Revision 6.14  2002/12/17 16:45:09  kans
 * CtoPstr and PtoCstr if OS_MAC or OS_UNIX_DARWIN
 *
@@ -269,25 +275,29 @@ typedef struct valnode {
 *   	Copied from SortValNode in jzcoll, renamed, for more general access
 *   	Makes array from ValNode list, calls HeapSort, reconnects ValNode list
 *
+*   ValNodeMergeStrs(list)
+*   	Merges chain of val node strings into a single character array
+*
 *****************************************************************************/
-NLM_EXTERN ValNodePtr LIBCALL ValNodeNew PROTO((ValNodePtr vnp));
-NLM_EXTERN Nlm_Int4   LIBCALL ValNodeLen PROTO((ValNodePtr vnp));
-NLM_EXTERN ValNodePtr LIBCALL ValNodeAdd PROTO((ValNodePtr PNTR head));
-NLM_EXTERN ValNodePtr LIBCALL ValNodeLink PROTO((ValNodePtr PNTR head, ValNodePtr newnode));
-NLM_EXTERN ValNodePtr LIBCALL ValNodeAddStr PROTO((ValNodePtr PNTR head, Nlm_Int2 choice, Nlm_CharPtr str));
-NLM_EXTERN ValNodePtr LIBCALL ValNodeCopyStr PROTO((ValNodePtr PNTR head, Nlm_Int2 choice, Nlm_CharPtr str));
-NLM_EXTERN ValNodePtr LIBCALL ValNodeAddInt PROTO((ValNodePtr PNTR head, Nlm_Int2 choice, Nlm_Int4 value));
-NLM_EXTERN ValNodePtr LIBCALL ValNodeAddBigInt (ValNodePtr PNTR head, Nlm_Int2 choice, Nlm_Int8 value);
-NLM_EXTERN ValNodePtr LIBCALL ValNodeAddBoolean PROTO((ValNodePtr PNTR head, Nlm_Int2 choice, Nlm_Boolean value));
-NLM_EXTERN ValNodePtr LIBCALL ValNodeAddFloat PROTO((ValNodePtr PNTR head, Nlm_Int2 choice, Nlm_FloatHi value));
-NLM_EXTERN ValNodePtr LIBCALL ValNodeAddPointer PROTO((ValNodePtr PNTR head, Nlm_Int2 choice, Nlm_VoidPtr value));
-NLM_EXTERN ValNodePtr LIBCALL ValNodeAddFunction PROTO((ValNodePtr PNTR head, Nlm_Int2 choice, Nlm_FnPtr value));
-NLM_EXTERN ValNodePtr LIBCALL ValNodeFree PROTO((ValNodePtr vnp));
-NLM_EXTERN ValNodePtr LIBCALL ValNodeFreeData PROTO((ValNodePtr vnp));
-NLM_EXTERN ValNodePtr LIBCALL ValNodeExtract PROTO((ValNodePtr PNTR headptr, Nlm_Int2 choice));
-NLM_EXTERN ValNodePtr LIBCALL ValNodeExtractList PROTO((ValNodePtr PNTR headptr, Nlm_Int2 choice));
-NLM_EXTERN ValNodePtr LIBCALL ValNodeFindNext PROTO((ValNodePtr head, ValNodePtr curr, Nlm_Int2 choice));
-NLM_EXTERN ValNodePtr LIBCALL ValNodeSort PROTO((ValNodePtr list, int (LIBCALLBACK *compar) (VoidPtr, VoidPtr)));
+NLM_EXTERN ValNodePtr  LIBCALL ValNodeNew PROTO((ValNodePtr vnp));
+NLM_EXTERN Nlm_Int4    LIBCALL ValNodeLen PROTO((ValNodePtr vnp));
+NLM_EXTERN ValNodePtr  LIBCALL ValNodeAdd PROTO((ValNodePtr PNTR head));
+NLM_EXTERN ValNodePtr  LIBCALL ValNodeLink PROTO((ValNodePtr PNTR head, ValNodePtr newnode));
+NLM_EXTERN ValNodePtr  LIBCALL ValNodeAddStr PROTO((ValNodePtr PNTR head, Nlm_Int2 choice, Nlm_CharPtr str));
+NLM_EXTERN ValNodePtr  LIBCALL ValNodeCopyStr PROTO((ValNodePtr PNTR head, Nlm_Int2 choice, const char* str));
+NLM_EXTERN ValNodePtr  LIBCALL ValNodeAddInt PROTO((ValNodePtr PNTR head, Nlm_Int2 choice, Nlm_Int4 value));
+NLM_EXTERN ValNodePtr  LIBCALL ValNodeAddBigInt (ValNodePtr PNTR head, Nlm_Int2 choice, Nlm_Int8 value);
+NLM_EXTERN ValNodePtr  LIBCALL ValNodeAddBoolean PROTO((ValNodePtr PNTR head, Nlm_Int2 choice, Nlm_Boolean value));
+NLM_EXTERN ValNodePtr  LIBCALL ValNodeAddFloat PROTO((ValNodePtr PNTR head, Nlm_Int2 choice, Nlm_FloatHi value));
+NLM_EXTERN ValNodePtr  LIBCALL ValNodeAddPointer PROTO((ValNodePtr PNTR head, Nlm_Int2 choice, Nlm_VoidPtr value));
+NLM_EXTERN ValNodePtr  LIBCALL ValNodeAddFunction PROTO((ValNodePtr PNTR head, Nlm_Int2 choice, Nlm_FnPtr value));
+NLM_EXTERN ValNodePtr  LIBCALL ValNodeFree PROTO((ValNodePtr vnp));
+NLM_EXTERN ValNodePtr  LIBCALL ValNodeFreeData PROTO((ValNodePtr vnp));
+NLM_EXTERN ValNodePtr  LIBCALL ValNodeExtract PROTO((ValNodePtr PNTR headptr, Nlm_Int2 choice));
+NLM_EXTERN ValNodePtr  LIBCALL ValNodeExtractList PROTO((ValNodePtr PNTR headptr, Nlm_Int2 choice));
+NLM_EXTERN ValNodePtr  LIBCALL ValNodeFindNext PROTO((ValNodePtr head, ValNodePtr curr, Nlm_Int2 choice));
+NLM_EXTERN ValNodePtr  LIBCALL ValNodeSort PROTO((ValNodePtr list, int (LIBCALLBACK *compar) (VoidPtr, VoidPtr)));
+NLM_EXTERN Nlm_CharPtr LIBCALL ValNodeMergeStrs PROTO((ValNodePtr list));
 
 /*** old prototypes ******
 NLM_EXTERN ValNodePtr LIBCALL ValNodeLink PROTO((ValNodePtr vnp, ValNodePtr newnode));
diff --git a/corelib/ncbimsg.c b/corelib/ncbimsg.c
index d18ce7ee..a3a5ab47 100644
--- a/corelib/ncbimsg.c
+++ b/corelib/ncbimsg.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   2/13/91
 *
-* $Revision: 6.10 $
+* $Revision: 6.12 $
 *
 * File Description:
 *   	user alert and error messages
@@ -54,6 +54,12 @@
 *                      input will be read properly.
 *
 * $Log: ncbimsg.c,v $
+* Revision 6.12  2006/12/07 14:13:56  lavr
+* #include <stdio.h> just in case for *_FILENO macros
+*
+* Revision 6.11  2006/12/07 14:13:02  lavr
+* Add checks for whether the message device is a terminal (UNIX)
+*
 * Revision 6.10  2002/06/17 15:07:01  ivanov
 * Added fix for BeOS platform in GetOneChar
 *
@@ -151,6 +157,10 @@ static char *_filename = __FILE__;
 
 #include "corepriv.h"
 #include <tsprintf.h>
+#if defined(OS_UNIX)
+#  include <stdio.h>
+#  include <unistd.h>
+#endif
 
 #ifdef __cplusplus
 extern "C" {
@@ -407,7 +417,10 @@ MsgAnswer PASCAL _DefMessageHook (MsgKey key, ErrSev sev,
     fprintf(stderr,"[%s] %s\n",
             caption ? caption : "NULL_Caption",
             message ? message : "NULL_Message");
-	
+
+#if defined(OS_UNIX)
+  if (isatty(STDIN_FILENO))
+#endif
     if (key>KEY_NONE && key<KEY_other)
       {
         int ch;
@@ -558,7 +571,10 @@ void LIBCALLBACK _DefBeepHook (void)
 #endif
 
 #elif defined(OS_UNIX) || defined(OS_VMS)
-  putc(7, stderr);
+#  if defined(OS_UNIX)
+  if (isatty(STDERR_FILENO))
+#  endif
+    putc(7, stderr);
 #endif
 }
 
diff --git a/corelib/ncbistr.c b/corelib/ncbistr.c
index 247d575a..cc6f6ebf 100644
--- a/corelib/ncbistr.c
+++ b/corelib/ncbistr.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   3/4/91
 *
-* $Revision: 6.14 $
+* $Revision: 6.16 $
 *
 * File Description: 
 *   	portable string routines
@@ -37,6 +37,12 @@
 * Modifications:  
 * --------------------------------------------------------------------------
 * $Log: ncbistr.c,v $
+* Revision 6.16  2006/10/17 02:02:31  lavr
+* Fix a typo
+*
+* Revision 6.15  2006/10/16 21:06:27  lavr
+* String{HasNo|DoesHave}Text() to accept const pointer
+*
 * Revision 6.14  2006/09/12 16:22:55  ludwigf
 * CHANGED: Internal logic on LabelCopy() to no longer touch memory outside
 *  the buffer it is given to operate on.
@@ -505,29 +511,20 @@ NLM_EXTERN Nlm_CharPtr LIBCALL  Nlm_StrMove (char FAR *to, const char FAR *from)
 	return to;
 }
 
-NLM_EXTERN Nlm_Boolean LIBCALL Nlm_StringHasNoText (Nlm_CharPtr str)
-
+NLM_EXTERN Nlm_Boolean LIBCALL Nlm_StringHasNoText (const char FAR *str)
 {
-  Nlm_Uchar  ch;	/* to use 8bit characters in multibyte languages */
-
-  if (str != NULL) {
-    ch = *str;
-    while (ch != '\0') {
-      if (ch > ' ') {
+  if (str) {
+    while (*str) {
+      if ((unsigned char)(*str++) > ' ')
         return FALSE;
-      }
-      str++;
-      ch = *str;
     }
   }
   return TRUE;
 }
 
-NLM_EXTERN Nlm_Boolean LIBCALL Nlm_StringDoesHaveText (Nlm_CharPtr str)
-
+NLM_EXTERN Nlm_Boolean LIBCALL Nlm_StringDoesHaveText (const char FAR *str)
 {
-  if (Nlm_StringHasNoText (str)) return FALSE;
-  return TRUE;
+  return ! Nlm_StringHasNoText (str);
 }
 
 NLM_EXTERN Nlm_CharPtr LIBCALL Nlm_TrimSpacesAroundString (Nlm_CharPtr str)
diff --git a/corelib/ncbistr.h b/corelib/ncbistr.h
index 481addbc..de276cf8 100644
--- a/corelib/ncbistr.h
+++ b/corelib/ncbistr.h
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   1/1/91
 *
-* $Revision: 6.8 $
+* $Revision: 6.9 $
 *
 * File Description:
 *   	prototypes for portable string routines
@@ -37,6 +37,9 @@
 * Modifications:
 * --------------------------------------------------------------------------
 * $Log: ncbistr.h,v $
+* Revision 6.9  2006/10/16 21:06:27  lavr
+* String{HasNo|DoesHave}Text() to accept const pointer
+*
 * Revision 6.8  2003/09/15 16:21:32  kans
 * moved StringDoesHaveText from sqnutils3.c
 *
@@ -174,8 +177,8 @@ NLM_EXTERN Nlm_Int2 LIBCALL Nlm_MeshStringICmp PROTO((const char FAR *str1, cons
 NLM_EXTERN Nlm_CharPtr LIBCALL Nlm_StringSearch PROTO((const char FAR *str, const char FAR *sub));
 NLM_EXTERN Nlm_CharPtr LIBCALL Nlm_StringISearch PROTO((const char FAR *str, const char FAR *sub));
 
-NLM_EXTERN Nlm_Boolean LIBCALL Nlm_StringHasNoText PROTO((Nlm_CharPtr str));
-NLM_EXTERN Nlm_Boolean LIBCALL Nlm_StringDoesHaveText PROTO((Nlm_CharPtr str));
+NLM_EXTERN Nlm_Boolean LIBCALL Nlm_StringHasNoText PROTO((const char FAR *str));
+NLM_EXTERN Nlm_Boolean LIBCALL Nlm_StringDoesHaveText PROTO((const char FAR *str));
 NLM_EXTERN Nlm_CharPtr LIBCALL Nlm_TrimSpacesAroundString PROTO((Nlm_CharPtr str));
 
 /* Printing 8-byte integer into platform-independent array of 8 bytes
diff --git a/corelib/ncbitime.c b/corelib/ncbitime.c
index 32260c14..9c6ac630 100644
--- a/corelib/ncbitime.c
+++ b/corelib/ncbitime.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:  1/1/90
 *
-* $Revision: 6.2 $
+* $Revision: 6.3 $
 *
 * File Description:
 *   misc portable routines for
@@ -38,6 +38,9 @@
 * Modifications:
 * --------------------------------------------------------------------------
 * $Log: ncbitime.c,v $
+* Revision 6.3  2006/10/19 16:58:26  lavr
+* Cache clock rate instead of requesting it each time on OS_UNIX
+*
 * Revision 6.2  2001/01/19 20:26:12  kans
 * support for OS_UNIX_DARWIN (contributed by William Van Etten)
 *
@@ -189,6 +192,7 @@ struct _StopWatch {
 #elif defined(OS_UNIX)
     clock_t	start;
     clock_t	stop;
+    clock_t	rate;
 #else
     int         dummy;
 #endif
@@ -198,7 +202,12 @@ typedef struct _StopWatch Nlm_StopWatch;
 NLM_EXTERN Nlm_StopWatchPtr Nlm_StopWatchNew(void)
 {
 #if defined(WIN32) || defined(OS_UNIX)
-    return (Nlm_StopWatchPtr) Nlm_MemNew(sizeof(Nlm_StopWatch));
+    Nlm_StopWatchPtr pSW = (Nlm_StopWatchPtr)Nlm_MemNew(sizeof(Nlm_StopWatch));
+#  if defined(OS_UNIX)
+    if (pSW != NULL)
+      pSW->rate = sysconf(_SC_CLK_TCK);
+#  endif
+    return pSW;
 #else
     ErrPostEx(SEV_WARNING, 0, 0,
 	"StopWatch is not implemented for this platform");
@@ -274,7 +283,7 @@ NLM_EXTERN Nlm_FloatHi Nlm_GetElapsedTime(Nlm_StopWatchPtr pSW)
     return res = (Nlm_FloatHi)ft.dwHighDateTime/5000000L*0x80000000L +
 	(Nlm_FloatHi)ft.dwLowDateTime/10000000L;
 #elif defined(OS_UNIX)
-    res = ((Nlm_FloatHi)pSW->stop - pSW->start) / sysconf(_SC_CLK_TCK);
+    res = ((Nlm_FloatHi)pSW->stop - pSW->start) / pSW->rate;
 #else
     ErrPostEx(SEV_WARNING, 0, 0,
 	"StopWatch is not implemented for this platform");
@@ -292,6 +301,7 @@ struct _CPUTime {
 	FILETIME	usrtime;
 #elif defined(OS_UNIX)
     struct tms	times;
+    clock_t    rate;
 #else
     int         dummy;
 #endif
@@ -315,6 +325,7 @@ NLM_EXTERN Nlm_CPUTimePtr Nlm_CPUTimeMeasure(void)
                     );
 #elif defined(OS_UNIX)
     times(&pTime->times);
+    pTime->rate = sysconf(_SC_CLK_TCK);
 #else
     ErrPostEx(SEV_WARNING, 0, 0,
               "CPU time measuring is not implemented for this platform");
@@ -345,7 +356,7 @@ NLM_EXTERN Nlm_FloatHi Nlm_CPUTimeGetSys(Nlm_CPUTimePtr pTime)
   return (Nlm_FloatHi)pTime->systime.dwHighDateTime * 0x80000000L/5000000L
 		+ (Nlm_FloatHi)pTime->systime.dwLowDateTime / 10000000L;
 #elif defined(OS_UNIX)
-  return (Nlm_FloatHi)pTime->times.tms_stime / sysconf(_SC_CLK_TCK);
+  return (Nlm_FloatHi)pTime->times.tms_stime / pTime->rate;
 #else
   ErrPostEx(SEV_WARNING, 0, 0,
             "CPU time measuring is not implemented for this platform");
@@ -359,7 +370,7 @@ NLM_EXTERN Nlm_FloatHi Nlm_CPUTimeGetUser(Nlm_CPUTimePtr pTime)
   return (Nlm_FloatHi)pTime->usrtime.dwHighDateTime * 0x80000000L/5000000L
     + (Nlm_FloatHi)pTime->usrtime.dwLowDateTime / 10000000L;
 #elif defined(OS_UNIX)
-  return (Nlm_FloatHi)pTime->times.tms_utime / sysconf(_SC_CLK_TCK);
+  return (Nlm_FloatHi)pTime->times.tms_utime / pTime->rate;
 #else
   ErrPostEx(SEV_WARNING, 0, 0,
             "CPU time measuring is not implemented for this platform");
diff --git a/corelib/ncbiwin.h b/corelib/ncbiwin.h
index ded5abbf..81eb9e70 100644
--- a/corelib/ncbiwin.h
+++ b/corelib/ncbiwin.h
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   1/1/91
 *
-* $Revision: 6.11 $
+* $Revision: 6.12 $
 *
 * File Description:
 *               underlying window toolbox import
@@ -37,6 +37,9 @@
 * Modifications:
 * --------------------------------------------------------------------------
 * $Log: ncbiwin.h,v $
+* Revision 6.12  2006/11/24 20:05:36  kans
+* include Carbon/Carbon.h if not MWERKS - attempting to simplify Xcode search paths
+*
 * Revision 6.11  2006/09/14 19:51:37  ivanov
 * Added defines for missed *LongPtr on MSVC6
 *
@@ -132,6 +135,10 @@
 #undef FloatHiPtr
 
 #ifdef WIN_MAC
+#ifndef __MWERKS__
+#include <Carbon/Carbon.h>
+#endif
+#ifdef __MWERKS__
 #include <Controls.h>
 #if UNIVERSAL_INTERFACES_VERSION > 0x0320
 #include <ControlDefinitions.h>  /* pjc added 11/20/99 */
@@ -161,14 +168,17 @@
 #include <Sound.h>
 #include <Folders.h>
 #endif
+#endif
 
 	                   /* used in ncbifile.c *****/
 #ifdef OS_MAC
+#ifdef __MWERKS__
 #include <Errors.h>
 #include <Gestalt.h>
 #include <MacMemory.h>
 #include <Processes.h>
 #endif
+#endif
 
 #ifdef OS_UNIX_SUN
 #include <sys/file.h>
diff --git a/corelib/ncbiwww.h b/corelib/ncbiwww.h
index cd074056..89ab01b4 100644
--- a/corelib/ncbiwww.h
+++ b/corelib/ncbiwww.h
@@ -1,4 +1,4 @@
-/* $Id: ncbiwww.h,v 6.7 2002/02/07 14:48:22 ivanov Exp $
+/* $Id: ncbiwww.h,v 6.8 2007/06/20 22:05:40 vakatov Exp $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -29,7 +29,7 @@
 *
 * Version Creation Date: 11/03/1996
 *
-* $Revision: 6.7 $
+* $Revision: 6.8 $
 *
 * File Description:
 *   This file contains main definitions to read and process HTTP
@@ -37,6 +37,11 @@
 *   Currently it works for all ncbi supported platforms.
 *
 * $Log: ncbiwww.h,v $
+* Revision 6.8  2007/06/20 22:05:40  vakatov
+* MAX_WWW_ENTRIES -- increased from 4096 to 32768.
+* It is just a quick-fix to let this code live a little longer, requested
+* by Karl and Vasuki.
+*
 * Revision 6.7  2002/02/07 14:48:22  ivanov
 * Added WWWGetEntriesEx(), WWWGetEntriesFormDataEx(), WWWReadFileInMemoryEx(),
 * WWWGetValueSizeByIndex() -- support binary files in the multipart form-data.
@@ -113,7 +118,7 @@
 /* DEFINES */
 /****************************************************************************/
 
-#define MAX_WWW_ENTRIES  4096 /* maximum number of html tags in input */
+#define MAX_WWW_ENTRIES  32768 /* maximum number of html tags in input */
 #define WWW_MAX_NAME_LEN 512  /* Limit for Name in HTML tag */
 
 #define MISC_BROWSER     0    /* Any Browser Netscape Ver. 1 included */
diff --git a/corelib/tsprintf.c b/corelib/tsprintf.c
index 43dfaedc..35f92d13 100644
--- a/corelib/tsprintf.c
+++ b/corelib/tsprintf.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   07/10/96
 *
-* $Revision: 6.10 $
+* $Revision: 6.12 $
 *
 * File Description:
 *   	Memory- and MT-safe "sprintf()"
@@ -38,6 +38,12 @@
 * --------------------------------------------------------------------------
 *
 * $Log: tsprintf.c,v $
+* Revision 6.12  2007/08/02 17:59:11  kans
+* do_div needed to take Int8 n argument
+*
+* Revision 6.11  2007/08/02 16:14:31  ucko
+* Support "ll"-prefixed arguments (assumed to be [U]Int8).
+*
 * Revision 6.10  2003/12/12 23:28:25  dondosha
 * Correction for Opteron, at suggestion from Nicolas Joly
 *
@@ -144,7 +150,7 @@ static int skip_atoi(const char **s)
 #define LARGE	64		/* use 'ABCDEF' instead of 'abcdef' */
 
 
-static int do_div(long *n, int base)
+static int do_div(Nlm_Int8 *n, int base)
   {
     int res = ((unsigned long) *n) % (unsigned) base;
     *n =      ((unsigned long) *n) / (unsigned) base;
@@ -194,7 +200,8 @@ static int fp_count(double fp, char type, int size, int precision, int flags)
 }
 
 
-static int number_count(long num, int base, int size, int precision, int type)
+static int number_count(Nlm_Int8 num, int base, int size, int precision,
+                        int type)
 {
   int counter = 0;
   int i       = 0;
@@ -266,13 +273,13 @@ static size_t vsprintf_count_args(const Char PNTR fmt, va_list args,
   size_t counter = 0;
 
   const Char PNTR start_fmt = fmt;
-  unsigned long num;
+  Nlm_Uint8 num;
   int base;
   int flags;         /* flags to number() */
   int field_width;   /* width of output field */
   int precision;     /* min. # of digits for integers; max
 			number of chars for from string */
-  int qualifier;     /* 'h', 'l', or 'L' for integer fields */
+  int qualifier;     /* 'h', 'l', 'L', or 'q' ("ll") for integer fields */
 
   *cut_fmt = 0;
 
@@ -333,6 +340,10 @@ static size_t vsprintf_count_args(const Char PNTR fmt, va_list args,
       if (*fmt == 'h' || *fmt == 'l' || *fmt == 'L') {
         qualifier = *fmt;
         ++fmt;
+        if (qualifier == 'l' && *fmt == 'l') {
+          qualifier = 'q';
+          ++fmt;
+        }
       }
 
       /* default base */
@@ -386,6 +397,9 @@ static size_t vsprintf_count_args(const Char PNTR fmt, va_list args,
         if (qualifier == 'l') {
           long * ip = va_arg(args, long *);
           *ip = (long)counter;
+        } else if (qualifier == 'q') {
+          Nlm_Uint8 * ip = va_arg(args, Nlm_Uint8 *);
+          *ip = (Nlm_Uint8)counter;
         } else {
           int * ip = va_arg(args, int *);
           *ip = (int)counter;
@@ -430,13 +444,13 @@ static size_t vsprintf_count_args(const Char PNTR fmt, va_list args,
       }
 
       if (qualifier == 'l')
-        num = va_arg(args, unsigned long);
-      else if (qualifier == 'h')
         if (flags & SIGNED)
-          num = va_arg(args, int);  /* sic! -- not a "short"! */
+          num = va_arg(args, long);
         else
-          num = va_arg(args, unsigned int);
-      else if (flags & SIGNED)
+          num = va_arg(args, unsigned long);
+      else if (qualifier == 'q')
+        num = va_arg(args, Nlm_Uint8);
+      else if (flags & SIGNED) /* plain or 'h' -- short promotes to int */
         num = va_arg(args, int);
       else
         num = va_arg(args, unsigned int);