Load ncbi (6.1.20041020) into ncbi-tools6/branches/upstream/current.

5 files changed, 174 insertions, 98 deletions

diff --git a/corelib/ncbienv.c b/corelib/ncbienv.c
index 04b178ab..9b20295b 100644
--- a/corelib/ncbienv.c
+++ b/corelib/ncbienv.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   7/7/91
 *
-* $Revision: 6.36 $
+* $Revision: 6.37 $
 *
 * File Description:
 *       portable environment functions, companions for ncbimain.c
@@ -37,6 +37,9 @@
 * Modifications:
 * --------------------------------------------------------------------------
 * $Log: ncbienv.c,v $
+* Revision 6.37  2004/08/06 20:56:27  kans
+* G/SetAppParam on PC no longer uses PrivateProfileString functions - instead it checks USERPROFILE, SYSTEMROOT, and then NCBI environment variables
+*
 * Revision 6.36  2004/02/11 18:40:00  kans
 * enhanced GetOpSysString to report specific version of MS Windows
 *
@@ -303,7 +306,6 @@ static void Nlm_TransientLogSetApp(const Nlm_Char* file, const Nlm_Char* section
 static void Nlm_FreeEnvData(Nlm_env_sectPtr esp);
 static void Nlm_FreeTransientData(void);
 
-#ifndef OS_MSWIN
 static FILE* Nlm_OpenConfigFile(const Nlm_Char* file, Nlm_Boolean writeMode, Nlm_Boolean create);
 static Nlm_Char* Nlm_TrimString(Nlm_Char* str);
 static Nlm_Boolean Nlm_ReadConfigFile(FILE* fp);
@@ -681,6 +683,7 @@ static Nlm_Boolean Nlm_GetHome(Nlm_Char* buf, Nlm_Int2 buflen)
 static FILE* Nlm_OpenConfigFile(const Nlm_Char* file, Nlm_Boolean writeMode, Nlm_Boolean create)
 
 {
+  Nlm_Char  ch;
   FILE      *fp;
   Nlm_Int2  i;
   Nlm_Int2  len;
@@ -703,7 +706,8 @@ static FILE* Nlm_OpenConfigFile(const Nlm_Char* file, Nlm_Boolean writeMode, Nlm
     /* if the name isn't all lowercase, make it so now */
     len = (Nlm_Int2) Nlm_StringLen (str);
     for (i = 0; i < len; i++) {
-      str [i] = TO_LOWER (str [i]);
+      ch = str [i];
+      str [i] = TO_LOWER (ch);
     }
     if (Nlm_GetHome (path, sizeof (path))) {
       Nlm_FileBuildPath(path, "Library", NULL);
@@ -745,7 +749,8 @@ static FILE* Nlm_OpenConfigFile(const Nlm_Char* file, Nlm_Boolean writeMode, Nlm
     }
     len = (Nlm_Int2) Nlm_StringLen (str);
     for (i = 0; i < len; i++) {
-      str [i] = TO_LOWER (str [i]);
+      ch = str [i];
+      str [i] = TO_LOWER (ch);
     }
     Nlm_StringNCpy_0(path, str, sizeof(path));
 
@@ -796,6 +801,109 @@ static FILE* Nlm_OpenConfigFile(const Nlm_Char* file, Nlm_Boolean writeMode, Nlm
 
 #endif /* OS_UNIX */
 
+#ifdef OS_MSWIN
+/*****************************************************************************
+*
+*   Nlm_OpenConfigFile (file, writeMode, create)
+*      returns a file pointer to the specified configuration file.
+*      1)  looks in the current directory for "file.ini", but will not
+*          create a new file in this directory.
+*      2)  then looks in the home directory for ".filerc".
+*      3)  then looks for an environment variable "NCBI" and takes its
+*          value as a complete path to a directory containing the
+*          configuration file "filerc" or ".filerc".
+*
+*      Steps (1) and (2) above are omitted if the NCBI_DONT_USE_LOCAL_CONFIG
+*      environment variable is set.  This can be used to allow specific
+*      production applications to avoid stray .ncbirc files which may have
+*      been erroneously generated.
+*
+*****************************************************************************/
+
+static FILE* Nlm_OpenConfigFile(const Nlm_Char* file, Nlm_Boolean writeMode, Nlm_Boolean create)
+
+{
+  Nlm_Char  ch;
+  FILE      *fp;
+  Nlm_Int2  i;
+  Nlm_Int2  len;
+  FILE      *newfp;
+  Nlm_Char  path [PATH_MAX+1];
+  Nlm_Char  str [FILENAME_MAX+1];
+  Nlm_CharPtr  tmp;
+
+  fp = NULL;
+  newfp = NULL;
+
+  if (file != NULL) {
+
+    /* normalize file name */
+    Nlm_StringNCpy_0(str, file, sizeof(str) - 4);
+    if ( ! Nlm_Qualified (str) ) {
+        /* if the user has already supplied a name with .xxx use that name
+         * otherwise add the .ini here */
+        Nlm_StringCat(str, ".INI");
+    }
+    /* if the name isn't all uppercase, make it so now */
+    len = (Nlm_Int2) Nlm_StringLen (str);
+    for (i = 0; i < len; i++) {
+      ch = str [i];
+      str [i] = TO_UPPER (ch);
+    }
+
+    /* first try user directory */
+
+    tmp = getenv ("USERPROFILE");
+    if (tmp != NULL && *tmp != '\0') {
+      StringNCpy_0 (path, tmp, sizeof (path));
+      Nlm_FileBuildPath(path, NULL, str);
+      fp = Nlm_FileOpen (path, "r");
+      if (fp == NULL && create) {
+        newfp = Nlm_FileOpen (path, "w");
+        Nlm_FileClose (newfp);
+        newfp = Nlm_FileOpen (path, "r");
+      }
+    }
+
+    /* next try c:\winnt for backward compatibility - read only */
+
+    if (fp == NULL) {
+      tmp = getenv ("SYSTEMROOT");
+      if (tmp != NULL && *tmp != '\0') {
+        StringNCpy_0 (path, tmp, sizeof (path));
+        Nlm_FileBuildPath(path, NULL, str);
+        fp = Nlm_FileOpen (path, "r");
+      }
+    }
+
+    /* last try environment variable path - read only */
+
+    if (fp == NULL) {
+      tmp = getenv ("NCBI");
+      if (tmp != NULL && *tmp != '\0') {
+        StringNCpy_0 (path, tmp, sizeof (path));
+        Nlm_FileBuildPath(path, NULL, str);
+        fp = Nlm_FileOpen (path, "r");
+      }
+    }
+
+    if (newfp != NULL) {
+      if (fp != NULL) {
+        Nlm_FileClose (newfp);
+        newfp = NULL;
+      } else {
+        fp = newfp;
+      }
+    }
+    if (writeMode && fp != NULL) {
+      Nlm_FileClose (fp);
+      fp = Nlm_FileOpen (path, "w");
+    }
+  }
+  return fp;
+}
+#endif /* OS_MSWIN */
+
 
 #if defined(OS_MAC) && !defined(OS_UNIX_DARWIN)
 /*****************************************************************************
@@ -832,6 +940,7 @@ Nlm_OpenConfigFile(const Nlm_Char* file,
                    Nlm_Boolean writeMode,
                    Nlm_Boolean create )
 {
+    Nlm_Char    ch;
     Nlm_Char    str [FILENAME_MAX+1];
     Nlm_Int2    len;
     long        gesResponse;
@@ -857,7 +966,8 @@ Nlm_OpenConfigFile(const Nlm_Char* file,
     /* if the name isn't all lowercase, make it so now */
     len = (Nlm_Int2) Nlm_StringLen (str);
     for (i = 0; i < len; i++) {
-      str [i] = TO_LOWER (str [i]);
+      ch = str [i];
+      str [i] = TO_LOWER (ch);
     }
     
     /* convert to pascal string for Mac toolbox */
@@ -956,6 +1066,7 @@ static Nlm_Boolean Nlm_GetHome(Nlm_Char* buf, Nlm_Int2 buflen)
 static FILE* Nlm_OpenConfigFile(const Nlm_Char* file, Nlm_Boolean writeMode, Nlm_Boolean create)
 
 {
+  Nlm_Char  ch;
   FILE      *fp;
   Nlm_Int2  i;
   Nlm_Int2  len;
@@ -974,7 +1085,8 @@ static FILE* Nlm_OpenConfigFile(const Nlm_Char* file, Nlm_Boolean writeMode, Nlm
     }
     len = (Nlm_Int2) Nlm_StringLen (str);
     for (i = 0; i < len; i++) {
-      str [i] = TO_LOWER (str [i]);
+      ch = str [i];
+      str [i] = TO_LOWER (ch);
     }
     Nlm_StringNCpy_0(path, str, sizeof(path));
 
@@ -1407,89 +1519,6 @@ static void Nlm_PutComment(const Nlm_Char* s, FILE* fp)
     fputs(s, fp);
 }
 
-#else /* ndef OS_MSWIN */
-
-static void        Nlm_FlushAppParam_ST(void) {}
-static Nlm_Boolean Nlm_CacheAppParam_ST(Nlm_Boolean value)  { return TRUE; }
-
-/*****************************************************************************
-*
-* The "guts" of:
-*   Nlm_GetAppParam (file, section, type, buf, buflen)
-*      finds parameters from configuration files
-*      if configuration file is found, trys to read the parameter from it.
-*
-*****************************************************************************/
-static Nlm_Int2 Nlm_WorkGetAppParam(const Nlm_Char* file, const Nlm_Char* section, const Nlm_Char* type, const Nlm_Char* dflt, Nlm_Char* buf, Nlm_Int2 buflen, Nlm_Boolean searchTransient)
-{
-  static char _empty_string[] = "";
-  Nlm_Char path[PATH_MAX + 1];
-
-  if (buf == NULL  ||  buflen <= 0)
-    return 0;
-
-  *buf = '\0';
-  if (searchTransient  &&
-      Nlm_TransientLookup(file, section, type, dflt, buf, buflen))
-    {
-      return (Nlm_Int2)Nlm_StringLen(buf);
-    }
-
-  if ( dflt )
-    Nlm_StringNCpy_0(buf, dflt, buflen);
-
-  if (file != NULL && *file != '\0' && section != NULL && *section != '\0')
-    {
-      Nlm_StringNCpy_0(path, file, sizeof(path) - 4);
-      if ( !Nlm_Qualified( path ) )
-        Nlm_StringCat(path, ".INI");
-      if (dflt == NULL)
-        dflt = _empty_string;  /* can't use NULL, must be empty string */
-      return (Nlm_Int2)GetPrivateProfileString(section,
-                                               type, dflt, buf, buflen, path);
-    }
-  else
-    return (Nlm_Int2)Nlm_StringLen( buf );
-}
-
-/*****************************************************************************
-*
-*   Nlm_SetAppParam (file, section, type, value)
-*      finds paths for types of data and fills in path in buf
-*      if configuration file is found, trys to write the parameter to it.
-*
-*****************************************************************************/
-
-static Nlm_Boolean Nlm_SetAppParam_ST(const Nlm_Char* file, const Nlm_Char* section, const Nlm_Char* type, const Nlm_Char* value)
-{
-  Nlm_Char     path [PATH_MAX+1];
-  Nlm_Boolean  rsult;
-
-  rsult = FALSE;
-  if (file != NULL && *file != '\0' && section != NULL && *section != '\0') {
-    Nlm_StringNCpy_0(path, file, sizeof(path) - 4);
-    if ( ! Nlm_Qualified (path) ) {
-      Nlm_StringCat (path, ".INI");
-    }
-    Nlm_TransientLogSetApp (file, section, type, value);
-    if (WritePrivateProfileString (section, type, value, path)) {
-      rsult = TRUE;
-    }
-  }
-  return rsult;
-}
-
-/*****************************************************************************
-*   Nlm_FreeConfigStruct ()
-*      frees parameter structure in memory
-*****************************************************************************/
-static void Nlm_FreeConfigStruct_ST(void)
-{
-  Nlm_FreeTransientData ();
-}
-
-#endif /* else !OS_MSWIN */
-
 
 /*****************************************************************************
 *   Nlm_Qualified ()
diff --git a/corelib/ncbifile.c b/corelib/ncbifile.c
index 1b881b88..f0c05cfa 100644
--- a/corelib/ncbifile.c
+++ b/corelib/ncbifile.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   3/4/91
 *
-* $Revision: 6.35 $
+* $Revision: 6.37 $
 *
 * File Description: 
 *     portable file routines
@@ -43,6 +43,12 @@
 * 11-27-94 Ostell      moved includes to ncbiwin.h to avoid conflict MSC
 *
 * $Log: ncbifile.c,v $
+* Revision 6.37  2004/07/21 18:08:30  kans
+* FileCacheSetup calls _setmode (_fileno (fp), _O_BINARY) if OS_MSWIN
+*
+* Revision 6.36  2004/07/20 19:37:30  kans
+* FileCacheSeek always initializes fields, calls fseek to keep file pointer in sync
+*
 * Revision 6.35  2004/05/07 15:57:14  kans
 * added FileCache functions for buffered read, graceful handing of Unix, Mac, and DOS line endings
 *
@@ -1369,6 +1375,11 @@ NLM_EXTERN Nlm_CharPtr LIBCALL Nlm_TmpNam (Nlm_CharPtr s)
 
 /* attach file pointer (text read mode expected) to cache object (usually on stack) */
 
+#ifdef OS_MSWIN
+#include <fcntl.h>
+#include <io.h>
+#endif
+
 NLM_EXTERN Nlm_Boolean Nlm_FileCacheSetup (
   Nlm_FileCache PNTR fcp,
   FILE *fp
@@ -1377,6 +1388,10 @@ NLM_EXTERN Nlm_Boolean Nlm_FileCacheSetup (
 {
   if (fp == NULL || fcp == NULL) return FALSE;
 
+#ifdef OS_MSWIN
+  _setmode (_fileno (fp), _O_BINARY);
+#endif
+
   MemSet ((Nlm_VoidPtr) fcp, 0, sizeof (Nlm_FileCache));
 
   fcp->fp = fp;
@@ -1427,7 +1442,7 @@ static Nlm_Char Nlm_FileCacheGetChar (
     Nlm_FileCacheReadBlock (fcp);
   }
 
-  /* get next Nlm_Character in buffer */
+  /* get next character in buffer */
 
   if (fcp->ctr < fcp->total) {
     ch = fcp->buf [(int) fcp->ctr];
@@ -1444,7 +1459,7 @@ static Nlm_Char Nlm_FileCacheGetChar (
 
       nxt = fcp->buf [(int) fcp->ctr];
 
-      /* advance past second Nlm_Character in cr/lf pair */
+      /* advance past second character in cr/lf pair */
 
       if (ch == '\n' && nxt == '\r') {
         (fcp->ctr)++;
@@ -1547,10 +1562,12 @@ NLM_EXTERN void Nlm_FileCacheSeek (
 {
   if (fcp == NULL || fcp->fp == NULL) return;
 
+  /*
   if (fcp->offset <= pos && fcp->offset + (Nlm_Int4) fcp->total >= pos) {
     fcp->ctr = (Nlm_Int2) (pos - fcp->offset);
     return;
   }
+  */
 
   fcp->ctr = 0;
   fcp->total = 0;
diff --git a/corelib/ncbilcl.fbd b/corelib/ncbilcl.fbd
index 53431e44..96b0d077 100644
--- a/corelib/ncbilcl.fbd
+++ b/corelib/ncbilcl.fbd
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   8/1/94
 *
-* $Revision: 1.2 $
+* $Revision: 1.3 $
 *
 * File Description:
 *		system dependent header
@@ -41,6 +41,9 @@
 * -------  ----------    ---------------------------------------------------
 *
 * $Log: ncbilcl.fbd,v $
+* Revision 1.3  2004/08/12 12:06:45  beloslyu
+* fix for FreeBSD 5.2.1
+*
 * Revision 1.2  2002/11/22 20:05:04  lavr
 * Configure HAVE_STRDUP and HAVE_STRCASECMP
 *
@@ -66,7 +69,7 @@
 /*      Desired or available feature list                               */
 /*----------------------------------------------------------------------*/
 #define SYSV_IPC_AVAIL	/* System V Interprocess Communication available */
-#define _POSIX_C_SOURCE 199309L
+/* #define _POSIX_C_SOURCE 199309L */
 #define HAVE_STRCASECMP 1
 #define HAVE_STRDUP 1
 
@@ -77,6 +80,7 @@
 #include <limits.h>
 #include <sys/stat.h>
 #include <sys/param.h>
+#include <sys/select.h>
 #include <stddef.h>
 #include <stdio.h>
 #include <ctype.h>
diff --git a/corelib/ncbimem.c b/corelib/ncbimem.c
index fbfbcf82..589871bb 100644
--- a/corelib/ncbimem.c
+++ b/corelib/ncbimem.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   6/4/91
 *
-* $Revision: 6.25 $
+* $Revision: 6.26 $
 *
 * File Description:
 *   	portable memory handlers for Mac, PC, Unix
@@ -37,6 +37,9 @@
 * Modifications:
 * --------------------------------------------------------------------------
 * $Log: ncbimem.c,v $
+* Revision 6.26  2004/09/01 21:21:54  kans
+* if Windows but not DLL, handle functions now implemented with direct pointer
+*
 * Revision 6.25  2003/08/11 19:43:27  rsmith
 * Memory Handle functions apply to Mac OS Darwin (OSX) not just to OS_MAC (OS9)
 *
@@ -549,7 +552,11 @@ NLM_EXTERN Nlm_Handle LIBCALL  Nlm_HandGet (size_t size, Nlm_Boolean clear_out)
 #endif
 
 #ifdef OS_MSWIN
+#ifdef _DLL
     hnd = (Nlm_Handle) GlobalAlloc (GMEM_MOVEABLE, size);
+#else
+    hnd = (Nlm_Handle) malloc (size);
+#endif
 #endif
 
 #ifdef MSC_VIRT
@@ -620,7 +627,11 @@ NLM_EXTERN Nlm_Handle LIBCALL  Nlm_HandMore (Nlm_Handle hnd, size_t size)
 #endif
 
 #ifdef OS_MSWIN
-    hnd2 = (Nlm_Handle) GlobalReAlloc ((HANDLE)hnd, size, GHND);
+#ifdef _DLL
+    hnd2 = (Nlm_Handle) GlobalReAlloc ((HANDLE) hnd, size, GHND);
+#else
+    hnd2 = (Nlm_Handle) realloc (hnd, size);
+#endif
 #endif
 
 #ifdef MSC_VIRT
@@ -653,7 +664,11 @@ NLM_EXTERN Nlm_Handle LIBCALL  Nlm_HandFree (Nlm_Handle hnd)
 #endif
 
 #ifdef OS_MSWIN
+#ifdef _DLL
         GlobalFree ((HANDLE) hnd);
+#else
+        free (hnd);
+#endif
 #endif
 
 #ifdef MSC_VIRT
@@ -691,7 +706,11 @@ NLM_EXTERN Nlm_VoidPtr LIBCALL  Nlm_HandLock (Nlm_Handle hnd)
 #endif
 
 #ifdef OS_MSWIN
+#ifdef _DLL
     ptr = GlobalLock ((HANDLE) hnd);
+#else
+    ptr = hnd;
+#endif
 #endif
 
 #ifdef MSC_VIRT
@@ -721,7 +740,11 @@ NLM_EXTERN Nlm_VoidPtr LIBCALL  Nlm_HandUnlock (Nlm_Handle hnd)
 #endif
 
 #ifdef OS_MSWIN
+#ifdef _DLL
         GlobalUnlock ((HANDLE) hnd);
+#else
+        /* nothing */
+#endif
 #endif
 
 #ifdef MSC_VIRT
diff --git a/corelib/ncbiopt.h b/corelib/ncbiopt.h
index 8693e881..d3f38828 100644
--- a/corelib/ncbiopt.h
+++ b/corelib/ncbiopt.h
@@ -1,7 +1,7 @@
 #ifndef _NCBIOPT_
 #define _NCBIOPT_
 
-/*  $Id: ncbiopt.h,v 6.14 2004/03/25 17:10:57 lebedev Exp $
+/*  $Id: ncbiopt.h,v 6.15 2004/07/15 15:11:45 ucko Exp $
 * ==========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -34,6 +34,9 @@
 *
 * --------------------------------------------------------------------------
 * $Log: ncbiopt.h,v $
+* Revision 6.15  2004/07/15 15:11:45  ucko
+* Disable workaround for Linux distributions (RH7?) that misdefine LONG_BIT.
+*
 * Revision 6.14  2004/03/25 17:10:57  lebedev
 * Include stdint.h for Darwin, so undef will work for UINT8_MAX
 *
@@ -132,7 +135,7 @@ by including it first.
 #  endif
 
    /* on 64-bit operating systems, the long data type is already 8 bytes */
-#  if LONG_BIT==64  &&  !defined(OS_UNIX_LINUX)
+#  if LONG_BIT==64 /* &&  !defined(OS_UNIX_LINUX) */
 #    define Int8  long
 #    define Uint8 unsigned long