freebsd-ports/biology/seqio/files/patch-grepseq

--- grepseq.c.orig	Sat Aug 18 16:19:15 2001
+++ grepseq.c	Sat Aug 18 16:37:58 2001
@@ -18,7 +18,6 @@
 #include <string.h>
 #include "seqio.h"
 
-extern char *sys_errlist[];
 
 #define ASCII 4
 
@@ -475,7 +474,7 @@
         ascii_alpha_mask[num] |= mask;
       }
       else
-        ascii_alpha_mask[*s] |= mask;
+        ascii_alpha_mask[(int) *s] |= mask;
       break;
       
     case '.':
@@ -518,7 +517,7 @@
             ascii_alpha_mask[num] |= mask;
           }
           else
-            ascii_alpha_mask[*s] |= mask;
+            ascii_alpha_mask[(int) *s] |= mask;
         }
         else {
           if (dna_flag) {
@@ -526,17 +525,17 @@
               dna_flag = 0;
             else
               for ( ; *t; t++)
-                dna_alpha_mask[*t] |= mask;
+                dna_alpha_mask[(int) *t] |= mask;
           }
           if (prt_flag) {
             if ((t = prt_expand(*s)) == NULL)
               prt_flag = 0;
             else
               for ( ; *t; t++)
-                prt_alpha_mask[*t] |= mask;
+                prt_alpha_mask[(int) *t] |= mask;
           }
               
-          ascii_alpha_mask[*s] |= mask;
+          ascii_alpha_mask[(int) *s] |= mask;
         }
       }
         
@@ -557,17 +556,17 @@
           dna_flag = 0;
         else
           for ( ; *t; t++)
-            dna_alpha_mask[*t] |= mask;
+            dna_alpha_mask[(int) *t] |= mask;
       }
       if (prt_flag) {
         if ((t = prt_expand(*s)) == NULL)
           prt_flag = 0;
         else
           for ( ; *t; t++)
-            prt_alpha_mask[*t] |= mask;
+            prt_alpha_mask[(int) *t] |= mask;
       }
               
-      ascii_alpha_mask[*s] |= mask;
+      ascii_alpha_mask[(int) *s] |= mask;
     }
 
     /*
@@ -677,16 +676,16 @@
      */
     if (num_errors == 0) {
       score = 0;
-      while ((ch = *s) && table[ch] &&
-             !((masklist0 = ((masklist0 << 1) & alpha_mask[*s]) + 1) &
+      while ((ch = *s) && table[(int) ch] &&
+             !((masklist0 = ((masklist0 << 1) & alpha_mask[(int) *s]) + 1) &
                accept_mask))
         s++;
     }
     else if (num_errors == 1) {
       score = -1;
       if (misonly_flag) {
-        while ((ch = *s) && table[ch]) {
-          chmask = alpha_mask[ch];
+        while ((ch = *s) && table[(int) ch]) {
+          chmask = alpha_mask[(int) ch];
           last_mask = masklist0;
           masklist0 = ((masklist0 << 1) & chmask) + 1;
           masklist1 = ((masklist1 << 1) & chmask) | (last_mask << 1);
@@ -703,8 +702,8 @@
         }
       }
       else {
-        while ((ch = *s) && table[ch]) {
-          chmask = alpha_mask[ch];
+        while ((ch = *s) && table[(int) ch]) {
+          chmask = alpha_mask[(int) ch];
           last_mask = masklist0;
           masklist0 = ((masklist0 << 1) & chmask) + 1;
           masklist1 = ((masklist1 << 1) & chmask) |  /* match */
@@ -727,8 +726,8 @@
     else if (num_errors == 2) {
       score = -1;
       if (misonly_flag) {
-        while ((ch = *s) && table[ch]) {
-          chmask = alpha_mask[ch];
+        while ((ch = *s) && table[(int) ch]) {
+          chmask = alpha_mask[(int) ch];
           last_mask = masklist0;
           masklist0 = ((masklist0 << 1) & chmask) + 1;
           newmask = ((masklist1 << 1) & chmask) | (last_mask << 1);
@@ -752,8 +751,8 @@
         }
       }
       else {
-        while ((ch = *s) && table[ch]) {
-          chmask = alpha_mask[ch];
+        while ((ch = *s) && table[(int) ch]) {
+          chmask = alpha_mask[(int) ch];
           last_mask = masklist0;
           masklist0 = ((masklist0 << 1) & chmask) + 1;
           newmask = ((masklist1 << 1) & chmask) |  /* match */
@@ -785,8 +784,8 @@
     }
     else if (misonly_flag) {
       score = -1;
-      while ((ch = *s) && table[ch]) {
-        chmask = alpha_mask[ch];
+      while ((ch = *s) && table[(int) ch]) {
+        chmask = alpha_mask[(int) ch];
 
         last_mask = masklist[0];
         masklist[0] = ((masklist[0] << 1) & chmask) + 1;
@@ -808,8 +807,8 @@
     }
     else {
       score = -1;
-      while ((ch = *s) && table[ch]) {
-        chmask = alpha_mask[ch];
+      while ((ch = *s) && table[(int) ch]) {
+        chmask = alpha_mask[(int) ch];
 
         last_mask = masklist[0];
         masklist[0] = ((masklist[0] << 1) & chmask) + 1;
@@ -835,7 +834,7 @@
       
     if (!ch)
       break;
-    else if (!table[ch]) {
+    else if (!table[(int) ch]) {
       fprintf(stderr, "%s, entry %d:  Sequence contains invalid characters.\n",
               seqffilename(sfp, 0), seqfentryno(sfp));
       return NULL;