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ssuominen 09/08/05 18:45:47 |
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|
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Added: trnascan-se-1.23-glibc-2.10.patch |
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Log: |
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Fix building with GLIBC 2.10+ wrt #279574. |
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(Portage version: 2.2_rc36/cvs/Linux x86_64) |
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|
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Revision Changes Path |
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1.1 sci-biology/trnascan-se/files/trnascan-se-1.23-glibc-2.10.patch |
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|
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file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/trnascan-se/files/trnascan-se-1.23-glibc-2.10.patch?rev=1.1&view=markup |
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plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/trnascan-se/files/trnascan-se-1.23-glibc-2.10.patch?rev=1.1&content-type=text/plain |
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|
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Index: trnascan-se-1.23-glibc-2.10.patch |
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=================================================================== |
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diff -ur trnascan-se-1.23.orig/sqio.c trnascan-se-1.23/sqio.c |
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--- trnascan-se-1.23.orig/sqio.c 2002-04-12 23:12:04.000000000 +0300 |
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+++ trnascan-se-1.23/sqio.c 2009-08-05 21:45:53.000000000 +0300 |
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@@ -235,7 +235,7 @@ |
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} |
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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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readline(V->f, V->sbuffer); |
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} |
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@@ -306,7 +306,7 @@ |
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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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done = feof(V->f); |
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done |= (*endTest)(V->sbuffer, &addend); |
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if (addend || !done) |
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@@ -332,7 +332,7 @@ |
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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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|
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if ((sptr = strtok(V->sbuffer + 15, "\n\t ")) != NULL) |
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@@ -341,7 +341,7 @@ |
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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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@@ -350,7 +350,7 @@ |
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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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|
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readLoop(0, endPIR, V); |
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|
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@@ -364,7 +364,7 @@ |
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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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|
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|
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@@ -382,7 +382,7 @@ |
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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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|
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if (!feof(V->f)) |
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@@ -394,7 +394,7 @@ |
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} |
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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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|
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static int |
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@@ -416,7 +416,7 @@ |
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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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|
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if (! feof(V->f)) |
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@@ -425,7 +425,7 @@ |
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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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|
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|
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@@ -443,7 +443,7 @@ |
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int in_definition; |
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|
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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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|
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if ((sptr = strtok(V->sbuffer+12, "\n\t ")) != NULL) |
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{ |
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@@ -454,7 +454,7 @@ |
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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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@@ -487,11 +487,11 @@ |
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|
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|
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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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|
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static int |
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@@ -521,12 +521,12 @@ |
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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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|
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- getline(V); /*skip title-junk line*/ |
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+ get_line(V); /*skip title-junk line*/ |
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|
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readLoop(0, endNBRF, V); |
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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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|
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|
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@@ -559,7 +559,7 @@ |
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} else Die("bogus GCGdata format? %s", V->sbuffer); |
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|
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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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|
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if (binary) { |
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@@ -579,7 +579,7 @@ |
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else readLoop(0, endGCGdata, V); |
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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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|
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static int |
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@@ -625,7 +625,7 @@ |
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readLoop(0, endPearson, V); |
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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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|
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|
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@@ -652,7 +652,7 @@ |
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|
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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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|
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if ((sptr = strtok(V->sbuffer+5, "\n\t ")) != NULL) |
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{ |
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@@ -661,7 +661,7 @@ |
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} |
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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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@@ -685,7 +685,7 @@ |
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|
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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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|
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|
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@@ -701,7 +701,7 @@ |
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{ |
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char *sptr; |
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|
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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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|
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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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@@ -712,7 +712,7 @@ |
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readLoop(0, endZuker, V); |
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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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|
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static void |
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@@ -734,7 +734,7 @@ |
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|
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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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@@ -746,7 +746,7 @@ |
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char *sptr; |
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int dostruc = FALSE; |
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|
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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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|
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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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@@ -754,7 +754,7 @@ |
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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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|
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if (strncmp(V->sbuffer, "SRC ", 4) == 0) |
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@@ -786,14 +786,14 @@ |
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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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@@ -801,7 +801,7 @@ |
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|
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|
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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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|
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|
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@@ -848,7 +848,7 @@ |
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|
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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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|
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return dbfp; |
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} |
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@@ -862,7 +862,7 @@ |
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SeqfilePosition(SQFILE *sqfp, long offset) |
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{ |
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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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|
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|
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@@ -954,7 +954,7 @@ |
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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; |