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ssuominen 09/08/05 19:32:12 |
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|
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Added: qrna-2.0.3c-glibc-2.10.patch |
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Log: |
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Fix building with GLIBC 2.10+ wrt #277098. |
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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/qrna/files/qrna-2.0.3c-glibc-2.10.patch |
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|
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file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/qrna/files/qrna-2.0.3c-glibc-2.10.patch?rev=1.1&view=markup |
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plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/qrna/files/qrna-2.0.3c-glibc-2.10.patch?rev=1.1&content-type=text/plain |
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|
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Index: qrna-2.0.3c-glibc-2.10.patch |
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=================================================================== |
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diff -ur qrna-2.0.3c.orig/squid/sqio.c qrna-2.0.3c/squid/sqio.c |
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--- qrna-2.0.3c.orig/squid/sqio.c 2005-05-11 19:30:51.000000000 +0300 |
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+++ qrna-2.0.3c/squid/sqio.c 2009-08-05 22:27:20.000000000 +0300 |
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@@ -215,7 +215,7 @@ |
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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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@@ -277,7 +277,7 @@ |
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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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@@ -305,7 +305,7 @@ |
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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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@@ -314,7 +314,7 @@ |
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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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@@ -323,7 +323,7 @@ |
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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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@@ -337,7 +337,7 @@ |
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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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@@ -355,7 +355,7 @@ |
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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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@@ -367,7 +367,7 @@ |
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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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@@ -389,7 +389,7 @@ |
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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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@@ -398,7 +398,7 @@ |
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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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@@ -416,7 +416,7 @@ |
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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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@@ -427,7 +427,7 @@ |
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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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@@ -460,11 +460,11 @@ |
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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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@@ -494,12 +494,12 @@ |
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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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@@ -529,7 +529,7 @@ |
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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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@@ -549,7 +549,7 @@ |
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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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@@ -571,7 +571,7 @@ |
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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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@@ -598,7 +598,7 @@ |
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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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@@ -607,7 +607,7 @@ |
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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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@@ -631,7 +631,7 @@ |
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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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@@ -647,7 +647,7 @@ |
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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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@@ -658,7 +658,7 @@ |
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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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@@ -680,7 +680,7 @@ |
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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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@@ -692,7 +692,7 @@ |
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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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@@ -700,7 +700,7 @@ |
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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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@@ -732,14 +732,14 @@ |
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while (1) |
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{ |
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/* sequence line */ |
259 |
- 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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@@ -747,7 +747,7 @@ |
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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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@@ -786,7 +786,7 @@ |
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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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@@ -800,7 +800,7 @@ |
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SeqfilePosition(SQFILE *sqfp, long offset) |
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{ |
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fseek(sqfp->f, offset, SEEK_SET); |
294 |
- 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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@@ -817,7 +817,7 @@ |
300 |
if (sqfp->ali_aseqs != NULL) sqfp->ali_curridx = 0; |
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else { |
302 |
rewind(sqfp->f); |
303 |
- 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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@@ -912,7 +912,7 @@ |
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do { /* skip leading comments on GCG file */ |
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gotuw = (strstr(V->sbuffer,"..") != NULL); |
311 |
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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|
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@@ -991,7 +991,7 @@ |
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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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|
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@@ -1098,7 +1098,7 @@ |
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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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|
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@@ -1204,7 +1204,7 @@ |
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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; |