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https://github.com/gentoo-mirror/gentoo.git
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sci-biology/wise: remove unused patch
Closes: https://github.com/gentoo/gentoo/pull/3708
This commit is contained in:
Michael Mair-Keimberger (asterix)
committed by
David Seifert
David Seifert
parent
8f462818f9
commit
dda41b33bd
@@ -1,301 +0,0 @@
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diff -ur wise2.2.0.orig/src/HMMer2/sqio.c wise2.2.0/src/HMMer2/sqio.c
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--- wise2.2.0.orig/src/HMMer2/sqio.c 2001-06-18 16:59:51.000000000 +0300
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+++ wise2.2.0/src/HMMer2/sqio.c 2009-08-05 22:39:04.000000000 +0300
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@@ -213,7 +213,7 @@
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}
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}
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-/* Function: getline()
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+/* Function: get_line()
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* Date: SRE, Tue Mar 3 08:30:01 1998 [St. Louis]
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*
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* Purpose: read a line from a sequence file into V->sbuffer.
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@@ -229,7 +229,7 @@
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* Returns: (void)
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*/
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static void
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-getline(struct ReadSeqVars *V)
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+get_line(struct ReadSeqVars *V)
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{
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char *cp;
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@@ -299,7 +299,7 @@
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V->seqlen = 0;
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if (addfirst) addseq(V->sbuffer, V);
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do {
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- getline(V);
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+ get_line(V);
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/* feof() alone is a bug; files not necessarily \n terminated */
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if (*(V->sbuffer) == '\0' && feof(V->f))
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done = TRUE;
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@@ -327,7 +327,7 @@
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char *sptr;
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/* load first line of entry */
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while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
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- getline(V);
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+ get_line(V);
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if (feof(V->f)) return;
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if ((sptr = strtok(V->sbuffer + 15, "\n\t ")) != NULL)
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@@ -336,7 +336,7 @@
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SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID);
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}
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do {
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- getline(V);
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+ get_line(V);
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if (!feof(V->f) && strncmp(V->sbuffer, "TITLE", 5) == 0)
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SetSeqinfoString(V->sqinfo, V->sbuffer+15, SQINFO_DESC);
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else if (!feof(V->f) && strncmp(V->sbuffer, "ACCESSION", 9) == 0)
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@@ -345,7 +345,7 @@
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SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC);
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}
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} while (! feof(V->f) && (strncmp(V->sbuffer,"SEQUENCE", 8) != 0));
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- getline(V); /* skip next line, coords */
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+ get_line(V); /* skip next line, coords */
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readLoop(0, endPIR, V);
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@@ -359,7 +359,7 @@
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/* get next line
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*/
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while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
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- getline(V);
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+ get_line(V);
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}
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@@ -377,7 +377,7 @@
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char *nm;
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/* position past ';' comments */
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do {
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- getline(V);
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+ get_line(V);
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} while (! (feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer != ';')) ));
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if (!feof(V->f))
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@@ -389,7 +389,7 @@
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}
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while (!(feof(V->f) || ((*V->sbuffer != '\0') && (*V->sbuffer == ';'))))
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- getline(V);
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+ get_line(V);
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}
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static int
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@@ -411,7 +411,7 @@
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if ((nm = strtok(V->sbuffer+16, ",\n\t ")) != NULL)
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SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME);
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}
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- getline(V);
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+ get_line(V);
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}
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if (! feof(V->f))
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@@ -420,7 +420,7 @@
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/* load next line
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*/
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while ((!feof(V->f)) && (*V->sbuffer != ';'))
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- getline(V);
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+ get_line(V);
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}
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@@ -438,7 +438,7 @@
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int in_definition;
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while (strncmp(V->sbuffer, "LOCUS", 5) != 0)
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- getline(V);
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+ get_line(V);
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if ((sptr = strtok(V->sbuffer+12, "\n\t ")) != NULL)
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{
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@@ -449,7 +449,7 @@
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in_definition = FALSE;
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while (! feof(V->f))
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{
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- getline(V);
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+ get_line(V);
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if (! feof(V->f) && strstr(V->sbuffer, "DEFINITION") == V->sbuffer)
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{
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if ((sptr = strtok(V->sbuffer+12, "\n")) != NULL)
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@@ -482,11 +482,11 @@
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while (!(feof(V->f) || ((*V->sbuffer!=0) && (strstr(V->sbuffer,"LOCUS") == V->sbuffer))))
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- getline(V);
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+ get_line(V);
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/* SRE: V->s now holds "//", so sequential
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reads are wedged: fixed Tue Jul 13 1993 */
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while (!feof(V->f) && strstr(V->sbuffer, "LOCUS ") != V->sbuffer)
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- getline(V);
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+ get_line(V);
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}
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static int
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@@ -515,7 +515,7 @@
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Die("bogus GCGdata format? %s", V->sbuffer);
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/* second line contains free text description */
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- getline(V);
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+ get_line(V);
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SetSeqinfoString(V->sqinfo, V->sbuffer, SQINFO_DESC);
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if (binary) {
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@@ -535,7 +535,7 @@
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else readLoop(0, endGCGdata, V);
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while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
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- getline(V);
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+ get_line(V);
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}
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static int
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@@ -555,12 +555,12 @@
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if ((sptr = strtok(NULL, "\n")) != NULL)
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SetSeqinfoString(V->sqinfo, sptr, SQINFO_DESC);
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/* workaround for long NCBI NR lines */
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- while (V->longline && ! feof(V->f)) getline(V);
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+ while (V->longline && ! feof(V->f)) get_line(V);
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readLoop(0, endPearson, V);
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while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
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- getline(V);
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+ get_line(V);
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}
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@@ -587,7 +587,7 @@
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/* make sure we have first line */
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while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0)
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- getline(V);
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+ get_line(V);
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if ((sptr = strtok(V->sbuffer+5, "\n\t ")) != NULL)
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{
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@@ -596,7 +596,7 @@
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}
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do {
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- getline(V);
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+ get_line(V);
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if (!feof(V->f) && strstr(V->sbuffer, "AC ") == V->sbuffer)
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{
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if ((sptr = strtok(V->sbuffer+5, "; \t\n")) != NULL)
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@@ -620,7 +620,7 @@
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/* load next record's ID line */
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while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0)
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- getline(V);
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+ get_line(V);
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}
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@@ -636,7 +636,7 @@
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{
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char *sptr;
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- getline(V); /*s == "seqLen seqid string..."*/
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+ get_line(V); /*s == "seqLen seqid string..."*/
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if ((sptr = strtok(V->sbuffer+6, " \t\n")) != NULL)
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SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
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@@ -647,7 +647,7 @@
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readLoop(0, endZuker, V);
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while (!(feof(V->f) | ((*V->sbuffer != '\0') & (*V->sbuffer == '('))))
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- getline(V);
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+ get_line(V);
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}
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static void
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@@ -669,7 +669,7 @@
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do {
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done = feof(V->f);
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- getline(V);
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+ get_line(V);
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if (! done) addseq(V->sbuffer, V);
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} while (!done);
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}
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@@ -681,7 +681,7 @@
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char *sptr;
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int dostruc = FALSE;
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- while (strncmp(V->sbuffer, "NAM ", 4) != 0) getline(V);
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+ while (strncmp(V->sbuffer, "NAM ", 4) != 0) get_line(V);
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if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL)
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SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
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@@ -689,7 +689,7 @@
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/*CONSTCOND*/
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while (1)
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{
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- getline(V);
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+ get_line(V);
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if (feof(V->f)) {squid_errno = SQERR_FORMAT; return; }
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if (strncmp(V->sbuffer, "SRC ", 4) == 0)
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@@ -721,14 +721,14 @@
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while (1)
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{
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/* sequence line */
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- getline(V);
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+ get_line(V);
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if (feof(V->f) || strncmp(V->sbuffer, "++", 2) == 0)
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break;
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addseq(V->sbuffer, V);
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/* structure line */
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if (dostruc)
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{
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- getline(V);
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+ get_line(V);
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if (feof(V->f)) { squid_errno = SQERR_FORMAT; return; }
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addstruc(V->sbuffer, V);
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}
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@@ -736,7 +736,7 @@
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while (!feof(V->f) && strncmp(V->sbuffer, "NAM ", 4) != 0)
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- getline(V);
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+ get_line(V);
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}
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@@ -816,7 +816,7 @@
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/* Load the first line.
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*/
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- getline(dbfp);
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+ get_line(dbfp);
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return dbfp;
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}
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@@ -833,7 +833,7 @@
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Die("SeqfilePosition() failed: in a nonrewindable data file or stream");
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fseek(sqfp->f, offset, SEEK_SET);
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- getline(sqfp);
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+ get_line(sqfp);
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}
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@@ -853,7 +853,7 @@
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if (sqfp->ali_aseqs != NULL) sqfp->ali_curridx = 0;
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else {
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rewind(sqfp->f);
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- getline(sqfp);
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+ get_line(sqfp);
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}
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}
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@@ -949,7 +949,7 @@
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do { /* skip leading comments on GCG file */
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gotuw = (strstr(V->sbuffer,"..") != NULL);
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if (gotuw) readUWGCG(V);
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- getline(V);
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+ get_line(V);
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} while (! feof(V->f));
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break;
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