Changeset 6287 for branches/stable_5.0

Timestamp:

01/12/09 11:10:13 (2 years ago)

Author:

westram

Message:

• backport [6285] [6286]

Location:

branches/stable_5.0

Files:

• AWT/AWT_db_browser.cxx (modified) (1 diff)
• AWT/AWT_file_selection.cxx (modified) (1 diff)
• AWTI/AWTI_import.cxx (modified) (1 diff)
• HELP_SOURCE/arb_help2xml.cxx (modified) (1 diff)
• Makefile (modified) (1 diff)
• NTREE/NT_edconf.cxx (modified) (1 diff)
• PROBE_DESIGN/SaiProbeVisualization.cxx (modified) (1 diff)
• PROBE_DESIGN/probe_design.cxx (modified) (1 diff)
• READSEQ/ureadseq.c (modified) (30 diffs)
• SL/FAST_ALIGNER/ClustalV.cxx (modified) (1 diff)
• SL/FILE_BUFFER/FileBuffer.cxx (modified) (1 diff)
• TOOLS/arb_gene_probe.cxx (modified) (1 diff)

branches/stable_5.0/AWT/AWT_db_browser.cxx

@@ -482 +482 @@
 
 inline void insert_history_selection(AW_window *aww, AW_selection_list *sel, const char *entry, int wanted_db) {
-    char *colon = strchr(entry, ':');
+    const char *colon = strchr(entry, ':');
     if (colon && (atoi(entry) == wanted_db)) {
         aww->insert_selection(sel, colon+1, colon+1);

branches/stable_5.0/AWT/AWT_file_selection.cxx

@@ -143 +143 @@
 
 char *AWT_extract_directory(const char *path) {
-    char *lslash = strrchr(path, '/');
+    const char *lslash = strrchr(path, '/');
     if (!lslash) return 0;
 

branches/stable_5.0/AWTI/AWTI_import.cxx

@@ -20 +20 @@
 
 inline const char *name_only(const char *fullpath) {
-    char *lslash = strrchr(fullpath, '/');
+    const char *lslash = strrchr(fullpath, '/');
     return lslash ? lslash+1 : fullpath;
 }

branches/stable_5.0/HELP_SOURCE/arb_help2xml.cxx

@@ -303 +303 @@
     // otherwise returns position behind keyword and sets value of 'keyword'
 
-    char *space = strchr(line, ' ');
+    const char *space = strchr(line, ' ');
     if (space && space>line) {
         keyword = string(line, 0, space-line);

branches/stable_5.0/Makefile

@@ -59 +59 @@
         4.2.0 4.2.1 4.2.3 4.2.4 \
         4.3 4.3.1 4.3.2 4.3.3 \
+        4.4.1
 
 ALLOWED_GCC_VERSIONS=$(ALLOWED_GCC_3xx_VERSIONS) $(ALLOWED_GCC_4xx_VERSIONS)

branches/stable_5.0/NTREE/NT_edconf.cxx

@@ -250 +250 @@
     struct SAI_string_builder *sai_builder = (struct SAI_string_builder*)cd_sai_builder;
 
-    char *sep = strchr(key,1);
+    const char *sep = strchr(key,1);
     if (!sep) return val;                           // what's wrong
 

branches/stable_5.0/PROBE_DESIGN/SaiProbeVisualization.cxx

@@ -527 +527 @@
                     if (!tok_suffix) {
                         // handle special case where no suffix exists
-                        char *end = strchr(probeRegion, 0);
+                        const char *end = strchr(probeRegion, 0);
                         if (end>probeRegion && end[-1] == '-') tok_suffix = "";
                     }

branches/stable_5.0/PROBE_DESIGN/probe_design.cxx

@@ -1849 +1849 @@
 
         if (!error) { // set pt-server database file to same permissions as pts directory
-            char *dir = strrchr(file,'/');
+            char *dir = const_cast<char*>(strrchr(file,'/'));
             if (dir) {
                 *dir = 0;

branches/stable_5.0/READSEQ/ureadseq.c

@@ -70 +70 @@
 
 #ifndef Local
-# define Local      static    /* local functions */
+# define Local static /* local functions */
 #endif
 
@@ -144 +144 @@
 }
 
-Local void getline(struct ReadSeqVars *V)
+Local void GetLine(struct ReadSeqVars *V)
 {
   readline(V->f, V->s, &V->linestart);
 }
 
-Local void ungetline(struct ReadSeqVars *V)
+Local void unGetLine(struct ReadSeqVars *V)
 {
   fseek(V->f, V->linestart, 0);
@@ -227 +227 @@
   if (addfirst) addseq(V->s, V);
   do {
-    getline(V);
+    GetLine(V);
     V->done = feof(V->f);
     V->done |= (*endTest)( &addend, &ungetend, V);
@@ -238 +238 @@
   else {
     V->allDone = (V->nseq >= V->choice);
-    if (V->allDone && ungetend) ungetline(V);
+    if (V->allDone && ungetend) unGetLine(V);
     }
 }
@@ -258 +258 @@
   while (!V->allDone) {
     do {
-      getline(V);
+      GetLine(V);
       for (si= V->s; *si != 0 && *si < ' '; si++) *si= ' '; /* drop controls */
       if (*si == 0) *V->s= 0; /* chop line to empty */
@@ -284 +284 @@
 
   while (!V->allDone) {
-    getline(V);
+    GetLine(V);
     if (strstr(V->s,"; DNA sequence  ") == V->s)
       strcpy(V->seqid, (V->s)+16);
@@ -290 +290 @@
       strcpy(V->seqid, (V->s)+1);
     while ((!feof(V->f)) && (*V->s == ';')) {
-      getline(V);
+      GetLine(V);
       }
     if (feof(V->f)) V->allDone = true;
@@ -310 +310 @@
   while (!V->allDone) {
     while (! (feof(V->f) || strstr(V->s,"ENTRY")  || strstr(V->s,"SEQUENCE")) )
-      getline(V);
+      GetLine(V);
     strcpy(V->seqid, (V->s)+16);
     while (! (feof(V->f) || strstr(V->s,"SEQUENCE") == V->s))
-      getline(V);
+      GetLine(V);
     readLoop(0, false, endPIR, V);
 
@@ -319 +319 @@
      while (! (feof(V->f) || ((*V->s != 0)
        && (strstr( V->s,"ENTRY") == V->s))))
-        getline(V);
+        GetLine(V);
       }
     if (feof(V->f)) V->allDone = true;
@@ -342 +342 @@
     strcpy(V->seqid, (V->s)+12);
     while (! (feof(V->f) || strstr(V->s,"ORIGIN") == V->s))
-      getline(V);
+      GetLine(V);
     readLoop(0, false, endGB, V);
 
@@ -348 +348 @@
      while (! (feof(V->f) || ((*V->s != 0)
        && (strstr( V->s, "LOCUS") == V->s))))
-        getline(V);
+        GetLine(V);
       }
     if (feof(V->f)) V->allDone = true;
@@ -382 +382 @@
   while (!V->allDone) {
     strcpy(V->seqid, (V->s)+4);
-    getline(V);   /*skip title-junk line*/
+    GetLine(V);   /*skip title-junk line*/
     readLoop(0, false, endNBRF, V);
     if (!V->allDone) {
      while (!(feof(V->f) || (*V->s != 0 && *V->s == '>')))
-        getline(V);
+        GetLine(V);
       }
     if (feof(V->f)) V->allDone = true;
@@ -408 +408 @@
     if (!V->allDone) {
      while (!(feof(V->f) || ((*V->s != 0) && (*V->s == '>'))))
-        getline(V);
+        GetLine(V);
       }
     if (feof(V->f)) V->allDone = true;
@@ -428 +428 @@
     strcpy(V->seqid, (V->s)+5);
     do {
-      getline(V);
+      GetLine(V);
     } while (!(feof(V->f) | (strstr(V->s,"SQ   ") == V->s)));
 
@@ -435 +435 @@
       while (!(feof(V->f) |
          ((*V->s != '\0') & (strstr(V->s,"ID   ") == V->s))))
-      getline(V);
+      GetLine(V);
     }
     if (feof(V->f)) V->allDone = true;
@@ -455 +455 @@
 
   while (!V->allDone) {
-    getline(V);  /*s == "seqLen seqid string..."*/
+    GetLine(V);  /*s == "seqLen seqid string..."*/
     strcpy(V->seqid, (V->s)+6);
     readLoop(0, false, endZuker, V);
@@ -461 +461 @@
       while (!(feof(V->f) |
         ((*V->s != '\0') & (*V->s == '('))))
-          getline(V);
+          GetLine(V);
       }
     if (feof(V->f)) V->allDone = true;
@@ -504 +504 @@
     addseq(V->s, V);
     V->done = feof(V->f);
-    getline(V);
+    GetLine(V);
   } while (!V->done);
   if (V->choice == kListSequences) addinfo(V->seqid, V);
@@ -516 +516 @@
 10nov91: Reading GCG files casued duplication of last line when
          EOF followed that line !!!
-    fix: getline now sets *V->s = 0
+    fix: GetLine now sets *V->s = 0
 */
   char  *si;
@@ -530 +530 @@
   do {
     V->done = feof(V->f);
-    getline(V);
+    GetLine(V);
     if (!V->done) addseq((V->s), V);
   } while (!V->done);
@@ -549 +549 @@
   rewind(V->f); V->nseq= 0;
   do {
-    getline(V);
+    GetLine(V);
     V->done = feof(V->f);
 
@@ -632 +632 @@
   rewind(V->f); V->nseq= 0;
   do {
-    getline(V);
+    GetLine(V);
     V->done = feof(V->f);
 
@@ -703 +703 @@
 
   do {
-    getline(V);
+    GetLine(V);
     V->done = feof(V->f);
 
@@ -784 +784 @@
   indata= true; /* call here after we find "matrix" */
   do {
-    getline(V);
+    GetLine(V);
     V->done = feof(V->f);
 
@@ -869 +869 @@
 
   do {
-    getline(V);
+    GetLine(V);
     V->done = feof(V->f);
 
@@ -922 +922 @@
   skipwhitespace(si);
   V->topseqlen= atol(si);
-  getline(V);
+  GetLine(V);
   while (!V->allDone) {
     V->seqlencount= 0;
@@ -953 +953 @@
   else {
 
-    for (l = skiplines_; l > 0; l--) getline( V);
+    for (l = skiplines_; l > 0; l--) GetLine( V);
 
     do {
-      getline( V);
+      GetLine( V);
       for (l= strlen(V->s); (l > 0) && (V->s[l] == ' '); l--) ;
     } while ((l == 0) && !feof(V->f));
@@ -981 +981 @@
         /* rewind(V->f); V->nseq= 0; ?? assume it is at top ?? skiplines ... */
         while (!done) {
-          getline( V);
+          GetLine( V);
           tolowerstr( V->s);
           if (strstr( V->s, "matrix")) done= true;
@@ -1013 +1013 @@
 
       case kFitch :
-        strcpy(V->seqid, V->s); getline(V);
+        strcpy(V->seqid, V->s); GetLine(V);
         readFitch(V);
         break;
@@ -1021 +1021 @@
           gotuw = (strstr(V->s,"..") != NULL);
           if (gotuw) readUWGCG(V);
-          getline(V);
+          GetLine(V);
         } while (!(feof(V->f) || V->allDone));
         break;

branches/stable_5.0/SL/FAST_ALIGNER/ClustalV.cxx

@@ -287 +287 @@
 //          -1 if one char is illegal
 {
-    char *p1 = strchr(nucleic_acid_order, c1);
-    char *p2 = strchr(nucleic_acid_order, c2);
+    const char *p1 = strchr(nucleic_acid_order, c1);
+    const char *p2 = strchr(nucleic_acid_order, c2);
 
     awtc_assert(c1);

branches/stable_5.0/SL/FILE_BUFFER/FileBuffer.cxx

@@ -13 +13 @@
 #include <cstdlib>
 #include <cstring>
+#include <cstdio>
 #include <errno.h>
 

branches/stable_5.0/TOOLS/arb_gene_probe.cxx

@@ -216 +216 @@
 
 #if defined(DEBUG)
-    char *firstSem = strchr(long_name, ';');
+    const char *firstSem = strchr(long_name, ';');
     gp_assert(firstSem);
     CHECK_SEMI_ESCAPED(firstSem+1);