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