Load ncbi (6.1.20021119) into ncbi-tools6/branches/upstream/current.

8 files changed, 120 insertions, 24 deletions

diff --git a/corelib/ncbiargs.c b/corelib/ncbiargs.c
index 01ab1c8a..d71e4f59 100644
--- a/corelib/ncbiargs.c
+++ b/corelib/ncbiargs.c
@@ -35,6 +35,9 @@
 * Modifications:  
 * --------------------------------------------------------------------------
 * $Log: ncbiargs.c,v $
+* Revision 6.7  2002/11/06 21:22:32  ucko
+* Accept "--help" as a synonym for the less intuitive "-"
+*
 * Revision 6.6  2001/07/03 20:03:11  juran
 * Don't corruptly parse argv in Mac OS.
 *
@@ -165,7 +168,8 @@ NLM_EXTERN Nlm_Boolean Nlm_GetArgs(const char* progname,
       return TRUE;
     }
 
-  if (xx_argc == 1  ||  *(xx_argv[1]+1) == '\0')
+  if (xx_argc == 1  ||  *(xx_argv[1]+1) == '\0'
+      ||  !strcmp(xx_argv[1], "--help"))
     {
       printf("\n%s   arguments:\n\n", progname);
       curarg = ap;
diff --git a/corelib/ncbienv.c b/corelib/ncbienv.c
index 4f646909..5181337a 100644
--- a/corelib/ncbienv.c
+++ b/corelib/ncbienv.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   7/7/91
 *
-* $Revision: 6.26 $
+* $Revision: 6.27 $
 *
 * File Description:
 *       portable environment functions, companions for ncbimain.c
@@ -37,6 +37,9 @@
 * Modifications:
 * --------------------------------------------------------------------------
 * $Log: ncbienv.c,v $
+* Revision 6.27  2002/10/03 16:22:03  kans
+* changed fgets to Nlm_FileGets
+*
 * Revision 6.26  2002/03/28 13:29:08  kans
 * checks for OS_UNIX_DARWIN (EN)
 *
@@ -1036,7 +1039,7 @@ static Nlm_Boolean Nlm_ReadConfigFile(FILE* fp)
     eip = NULL;
     lastEip = NULL;
     comment = NULL;
-    while (fgets (str, sizeof (str), fp)) {
+    while (Nlm_FileGets (str, sizeof (str), fp)) {
       ch = *str;
       if (ch != '\n' && ch != '\r') {
         if (ch == ';') { /* comment */
diff --git a/corelib/ncbierr.c b/corelib/ncbierr.c
index a66b2844..d698e441 100644
--- a/corelib/ncbierr.c
+++ b/corelib/ncbierr.c
@@ -23,9 +23,9 @@
 *
 * ===========================================================================
 *
-* $Id: ncbierr.c,v 6.19 2002/08/13 20:44:19 lavr Exp $
+* $Id: ncbierr.c,v 6.20 2002/10/03 16:22:03 kans Exp $
 *
-* $Revision: 6.19 $
+* $Revision: 6.20 $
 *
 * Authors:  Schuler, Sirotkin (UserErr stuff)
 *
@@ -71,6 +71,9 @@
 * 03-06-95 Schuler     Fixed problem with ErrMsgRoot_fopen
 *
 * $Log: ncbierr.c,v $
+* Revision 6.20  2002/10/03 16:22:03  kans
+* changed fgets to Nlm_FileGets
+*
 * Revision 6.19  2002/08/13 20:44:19  lavr
 * Force logging to stderr/stdout if DEBUG_PRINTOUT env.var. is set as follows:
 * STDOUT (case-insensitively) - log to stdout; anything else - log to stderr.
@@ -1005,7 +1008,7 @@ static int ErrMsgRoot_Read (ErrMsgRoot *idx)
     int any_comt;
 
     /* ----- Look for MODULE line ----- */
-    while (fgets(line,sizeof line,fd))
+    while (Nlm_FileGets(line,sizeof line,fd))
       {
         linenum++;
         if ( strchr("#\r\n", line[0]) )
@@ -1032,7 +1035,7 @@ static int ErrMsgRoot_Read (ErrMsgRoot *idx)
     lev1 = lev2 = NULL;
     tmpofs = ftell(fd);
 
-    while (fgets(line,sizeof line,fd))
+    while (Nlm_FileGets(line,sizeof line,fd))
       {
         linenum++;
 
diff --git a/corelib/ncbifile.c b/corelib/ncbifile.c
index 975a5671..7a371a67 100644
--- a/corelib/ncbifile.c
+++ b/corelib/ncbifile.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   3/4/91
 *
-* $Revision: 6.25 $
+* $Revision: 6.28 $
 *
 * File Description: 
 *     portable file routines
@@ -43,6 +43,15 @@
 * 11-27-94 Ostell      moved includes to ncbiwin.h to avoid conflict MSC
 *
 * $Log: ncbifile.c,v $
+* Revision 6.28  2002/11/06 21:23:04  ucko
+* Don't assume MIPS is IRIX; allow Linux too.
+*
+* Revision 6.27  2002/10/03 17:22:29  kans
+* for OS_MAC or OS_UNIX_DARWIN, Nlm_FileGets does fgetc loop, stopping at the first \n or \r character, and leaving a \n as the last character before the null byte
+*
+* Revision 6.26  2002/10/02 14:34:17  kans
+* Nlm_GetOSType and Nlm_FileCreate have ifdef OS_MAC, not WIN_MAC
+*
 * Revision 6.25  2002/06/13 16:14:07  kans
 * fix includes for OS_UNIX_DARWIN with WIN_MAC (EN)
 *
@@ -183,7 +192,7 @@ Removed disabled CD routines.
 #define DEFAULT_RAW_CDROM "/dev/rsr0"
 #endif
 
-#ifdef PROC_MIPS
+#if defined(PROC_MIPS) && !defined(OS_UNIX_LINUX)
 #define DEFAULT_CDROM "/dev/scsi/sc0d4l0"
 #endif
 
@@ -722,9 +731,36 @@ NLM_EXTERN int LIBCALL  Nlm_FilePuts (const char *ptr, FILE *fp)
 *****************************************************************************/
 NLM_EXTERN char * LIBCALL  Nlm_FileGets (Nlm_CharPtr ptr, size_t size, FILE *fp)
 {
-	if ((ptr == NULL) || (size <= 0) || (fp == NULL))
+#if defined(OS_MAC) || defined (OS_UNIX_DARWIN)
+    int         ch;
+	int         count;
+	Nlm_CharPtr tmp;
+#endif
+
+	if ((ptr == NULL) || (size < 1) || (fp == NULL))
 		return NULL;
+#if defined(OS_MAC) || defined (OS_UNIX_DARWIN)
+	ch = fgetc (fp);
+	count = 0;
+	tmp = ptr;
+	while (ch != EOF && ch != '\0' && ch != '\n' && ch != '\r' && count < size - 1) {
+	  *tmp = ch;
+	  tmp++;
+	  count++;
+	  ch = fgetc (fp);
+	}
+	if (ch == '\n' || ch == '\r') {
+	  *tmp = '\n';
+	  tmp++;
+	  count++;
+	}
+	*tmp = '\0';
+	if (count < 1)
+		return NULL;
+	return ptr;
+#else
 	return fgets(ptr,size,fp);
+#endif
 }
 
 
@@ -939,7 +975,7 @@ NLM_EXTERN Nlm_Boolean LIBCALL Nlm_FileRename (Nlm_CharPtr oldFileName, Nlm_Char
 *   FileCreate()
 *
 *****************************************************************************/
-#ifdef WIN_MAC
+#ifdef OS_MAC
 static OSType Nlm_GetOSType (Nlm_CharPtr str, OSType dfault)
 
 {
@@ -956,7 +992,7 @@ static OSType Nlm_GetOSType (Nlm_CharPtr str, OSType dfault)
 NLM_EXTERN void LIBCALL Nlm_FileCreate (Nlm_CharPtr fileName, Nlm_CharPtr type, Nlm_CharPtr creator)
 
 {
-#ifdef WIN_MAC
+#ifdef OS_MAC
   Nlm_Int2  fError;
   Nlm_Char  temp [256];
   OSType    fType;
@@ -968,7 +1004,7 @@ NLM_EXTERN void LIBCALL Nlm_FileCreate (Nlm_CharPtr fileName, Nlm_CharPtr type,
 
   if (fileName != NULL && fileName [0] != '\0') {
 
-#ifdef WIN_MAC
+#ifdef OS_MAC
     // note: the following assumes either full pathname or that the current
     // directory is the proper location to find/create the file
 
diff --git a/corelib/ncbilcl.lnx b/corelib/ncbilcl.lnx
index af65e198..e0cd2a52 100644
--- a/corelib/ncbilcl.lnx
+++ b/corelib/ncbilcl.lnx
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   8/1/94
 *
-* $Revision: 6.6 $
+* $Revision: 6.7 $
 *
 * File Description:
 *		system dependent header
@@ -38,6 +38,10 @@
 * Modifications:
 * --------------------------------------------------------------------------
 * $Log: ncbilcl.lnx,v $
+* Revision 6.7  2002/11/06 21:23:47  ucko
+* Handle non-i386 platforms.
+* Enable large file support here, to ensure consistency.
+*
 * Revision 6.6  2002/07/11 22:13:06  vakatov
 * #define MMAP_AVAIL
 *
@@ -71,7 +75,31 @@
 #define COMP_SYSV
 #define OS_UNIX
 #define OS_UNIX_LINUX
+#if defined(__alpha__) || #cpu(alpha) || #machine(alpha)
+#define PROC_ALPHA
+#elif defined(__arm__) || #cpu(arm) || #machine(arm)
+#define PROC_ARM /* ? (only occurrence) */
+#elif defined(__hppa__) || #cpu(hppa) || #machine(hppa)
+#define PROC_HPPA
+#elif defined(__i386__) || #cpu(i386) || #machine(i386)
 #define PROC_I80X86
+#elif defined(__ia64__) || #cpu(ia64) || #machine(ia64)
+#define PROC_IA64 /* ? */
+#elif defined(m68k) || defined(mc68000) || #cpu(m68k) || #machine(m68k)
+#define PROC_MC680X0
+#elif defined(__mips__) || defined(_mips) || #cpu(mips) || #machine(mips)
+#define PROC_MIPS
+#elif defined(__powerpc__) || defined(__PPC__) || #cpu(powerpc) || #machine(powerpc)
+#define PROC_PPC
+#elif defined(__s390__) || #cpu(s390) || #machine(s390)
+#define PROC_S390 /* ? */
+#elif defined(__sh__) || #cpu(sh) || #machine(sh)
+#define PROC_SH /* ? */
+#elif defined(__sparc__) || #cpu(sparc) || #cpu(sparc64) || #machine(sparc) || #machine(sparc64)
+#define PROC_SPARC
+#else
+#warning Unknown processor type.  Please define something appropriate.
+#endif
 #define WIN_DUMB
 
 /*----------------------------------------------------------------------*/
@@ -86,6 +114,11 @@
 #define _POSIX_C_SOURCE 199309L
 #define _XOPEN_SOURCE	500
 
+/* Only effective on glibc 2.1 and newer. */
+#define _LARGEFILE_SOURCE 1
+#define _LARGEFILE64_SOURCE 1
+#define _FILE_OFFSET_BITS 64 /* Should be safe, I think... */
+
 #ifndef _REENTRANT
 #define _REENTRANT
 #endif
@@ -148,7 +181,12 @@
 #define KBYTE           (1024)
 #define MBYTE           (1048576)
 
+#include <endian.h>
+#if __BYTE_ORDER == __LITTLE_ENDIAN
 #define IS_LITTLE_ENDIAN
+#else
+#define IS_BIG_ENDIAN
+#endif
 #define TEMPNAM_AVAIL
 #define HAVE_MADVISE
 
diff --git a/corelib/ncbimem.c b/corelib/ncbimem.c
index fb4af3f1..af2dec13 100644
--- a/corelib/ncbimem.c
+++ b/corelib/ncbimem.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   6/4/91
 *
-* $Revision: 6.22 $
+* $Revision: 6.24 $
 *
 * File Description:
 *   	portable memory handlers for Mac, PC, Unix
@@ -37,6 +37,12 @@
 * Modifications:
 * --------------------------------------------------------------------------
 * $Log: ncbimem.c,v $
+* Revision 6.24  2002/11/06 21:24:35  ucko
+* Make sure MADV_NORMAL is actually defined before trying to use madvise.
+*
+* Revision 6.23  2002/10/28 20:19:56  kans
+* removed C++ style comment
+*
 * Revision 6.22  2002/07/11 22:14:31  vakatov
 * [LINUX, MMAP_AVAIL]  #define __USE_BSD to get MADV_*** constants
 *
@@ -922,7 +928,7 @@ NLM_EXTERN void Nlm_MemMapFini(Nlm_MemMapPtr mem_mapp)
 
 NLM_EXTERN Nlm_Boolean Nlm_MemMapAdvise(void* addr, size_t len, EMemMapAdvise advise)
 {
-#if defined(HAVE_MADVISE)
+#if defined(HAVE_MADVISE) && defined(MADV_NORMAL)
   int adv;
   if (!addr || !len) {
     return FALSE;
@@ -939,7 +945,7 @@ NLM_EXTERN Nlm_Boolean Nlm_MemMapAdvise(void* addr, size_t len, EMemMapAdvise ad
 	default:
 	  adv = MADV_NORMAL;
   }
-  // Conversion type of "addr" to char* -- Sun Solaris fix
+  /* Conversion type of "addr" to char* -- Sun Solaris fix */
   return madvise((char*)addr, len, adv) == 0;
 #else
   return TRUE;
@@ -949,7 +955,7 @@ NLM_EXTERN Nlm_Boolean Nlm_MemMapAdvise(void* addr, size_t len, EMemMapAdvise ad
 
 NLM_EXTERN Nlm_Boolean Nlm_MemMapAdvisePtr(Nlm_MemMapPtr ptr, EMemMapAdvise advise)
 {
-#if defined(HAVE_MADVISE)
+#if defined(HAVE_MADVISE) && defined(MADV_NORMAL)
   return ptr ? Nlm_MemMapAdvise(ptr->mmp_begin, ptr->file_size, advise) : FALSE;
 #else
   return TRUE;
diff --git a/corelib/ncbimisc.c b/corelib/ncbimisc.c
index 56e8f06c..2ff56458 100644
--- a/corelib/ncbimisc.c
+++ b/corelib/ncbimisc.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   10/23/91
 *
-* $Revision: 6.22 $
+* $Revision: 6.23 $
 *
 * File Description: 
 *   	miscellaneous functions
@@ -43,6 +43,9 @@
 * 02-16-94 Epstein     Retired Gestalt functions and definitions
 *
 * $Log: ncbimisc.c,v $
+* Revision 6.23  2002/11/06 21:25:10  ucko
+* Don't assume MIPS is IRIX, or HPPA is HP/UX; allow Linux too, for both.
+*
 * Revision 6.22  2002/06/13 16:14:07  kans
 * fix includes for OS_UNIX_DARWIN with WIN_MAC (EN)
 *
@@ -1692,11 +1695,11 @@ NLM_EXTERN const Nlm_Char* Nlm_PlatformName(void)
   return "Cray";
 #  elif defined(PROC_CONVEX)
   return "Convex";
-#  elif defined(PROC_HPPA)
+#  elif defined(PROC_HPPA) && !defined(OS_UNIX_LINUX)
   return "HPUX";
 #  elif defined(OS_UNIX_NEXT)
   return "NEXT";
-#  elif defined(PROC_MIPS)
+#  elif defined(PROC_MIPS) && !defined(OS_UNIX_LINUX)
   return "SGI_MIPS";
 #  elif defined(OS_UNIX_ULTRIX)
   return "ULTRIX";
diff --git a/corelib/ncbisgml.c b/corelib/ncbisgml.c
index df47c50f..e9d8dce5 100644
--- a/corelib/ncbisgml.c
+++ b/corelib/ncbisgml.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   10/23/91
 *
-* $Revision: 6.1 $
+* $Revision: 6.2 $
 *
 * File Description: 
 *   	miscellaneous functions
@@ -43,6 +43,9 @@
 *
 *
 * $Log: ncbisgml.c,v $
+* Revision 6.2  2002/10/03 16:22:04  kans
+* changed fgets to Nlm_FileGets
+*
 * Revision 6.1  1997/10/29 02:44:35  vakatov
 * Type castings to pass through the C++ compiler
 *
@@ -103,7 +106,7 @@ NLM_EXTERN int LIBCALL  Nlm_SgmlLoadTable (void)
 	if ((fp = FileOpen(buf,"r")) ==NULL)
 		return FALSE;
 	
-	if (!fgets(buf,sizeof buf,fp))
+	if (!Nlm_FileGets(buf,sizeof buf,fp))
 	{
 		ErrPostEx(SEV_WARNING,E_SGML,1,"Error reading file [sgmlbb.ent]");
 		return FALSE;
@@ -113,7 +116,7 @@ NLM_EXTERN int LIBCALL  Nlm_SgmlLoadTable (void)
 	sgml_ascii  = (char**) MemNew(x * sizeof(char*));
 	for (i = 0; i < x; i++)
 	{
-		if ((p1 = fgets(buf,sizeof buf,fp)) == NULL) break;
+		if ((p1 = Nlm_FileGets(buf,sizeof buf,fp)) == NULL) break;
 		while ((*p1 < ' ') && (*p1 != '\0')) p1++;  /* skip any leading junk */
 		if (*p1 == '\0') break;
 		if ( (p2 = strchr(p1,'\t')) == NULL )   break;