1 files changed, 291 insertions, 0 deletions

diff --git a/biology/tRNAscan-SE/files/patch-sqio.c b/biology/tRNAscan-SE/files/patch-sqio.c
new file mode 100644
index 000000000000..62591b3555ba
--- /dev/null
+++ b/biology/tRNAscan-SE/files/patch-sqio.c
@@ -0,0 +1,291 @@
+--- sqio.c.orig	2002-04-12 20:12:04 UTC
++++ sqio.c
+@@ -235,7 +235,7 @@ readline(FILE *f, char *s)
+ }
+ 
+ static void 
+-getline(struct ReadSeqVars *V)
++get_line(struct ReadSeqVars *V)
+ {
+   readline(V->f, V->sbuffer);
+ }
+@@ -306,7 +306,7 @@ readLoop(int addfirst, int (*endTest)(ch
+   V->seqlen = 0;
+   if (addfirst) addseq(V->sbuffer, V);
+   do {
+-    getline(V);
++    get_line(V);
+     done = feof(V->f);
+     done |= (*endTest)(V->sbuffer, &addend);
+     if (addend || !done)
+@@ -332,7 +332,7 @@ readPIR(struct ReadSeqVars *V)
+   char *sptr;
+ 				/* load first line of entry  */
+   while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
+-    getline(V);
++    get_line(V);
+   if (feof(V->f)) return;
+ 
+   if ((sptr = strtok(V->sbuffer + 15, "\n\t ")) != NULL)
+@@ -341,7 +341,7 @@ readPIR(struct ReadSeqVars *V)
+       SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID);
+     }
+   do {
+-    getline(V);
++    get_line(V);
+     if (!feof(V->f) && strncmp(V->sbuffer, "TITLE", 5) == 0)
+       SetSeqinfoString(V->sqinfo, V->sbuffer+15, SQINFO_DESC);
+     else if (!feof(V->f) && strncmp(V->sbuffer, "ACCESSION", 9) == 0)
+@@ -350,7 +350,7 @@ readPIR(struct ReadSeqVars *V)
+ 	  SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC);
+       }
+   } while (! feof(V->f) && (strncmp(V->sbuffer,"SEQUENCE", 8) != 0));
+-  getline(V);			/* skip next line, coords */
++  get_line(V);			/* skip next line, coords */
+ 
+   readLoop(0, endPIR, V);
+ 
+@@ -364,7 +364,7 @@ readPIR(struct ReadSeqVars *V)
+   /* get next line
+    */
+   while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
+-    getline(V);
++    get_line(V);
+ }
+ 
+ 
+@@ -382,7 +382,7 @@ readIG(struct ReadSeqVars *V)
+   char *nm;
+ 				/* position past ';' comments */
+   do {
+-    getline(V);
++    get_line(V);
+   } while (! (feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer != ';')) ));
+ 
+   if (!feof(V->f))
+@@ -394,7 +394,7 @@ readIG(struct ReadSeqVars *V)
+     }
+   
+   while (!(feof(V->f) || ((*V->sbuffer != '\0') && (*V->sbuffer == ';'))))
+-    getline(V);
++    get_line(V);
+ }
+ 
+ static int 
+@@ -416,7 +416,7 @@ readStrider(struct ReadSeqVars *V)
+ 	  if ((nm = strtok(V->sbuffer+16, ",\n\t ")) != NULL)
+ 	    SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME);
+ 	}
+-      getline(V);
++      get_line(V);
+     }
+ 
+   if (! feof(V->f))
+@@ -425,7 +425,7 @@ readStrider(struct ReadSeqVars *V)
+   /* load next line
+    */
+   while ((!feof(V->f)) && (*V->sbuffer != ';')) 
+-    getline(V);
++    get_line(V);
+ }
+ 
+ 
+@@ -443,7 +443,7 @@ readGenBank(struct ReadSeqVars *V)
+   int   in_definition;
+ 
+   while (strncmp(V->sbuffer, "LOCUS", 5) != 0)
+-    getline(V);
++    get_line(V);
+ 
+   if ((sptr = strtok(V->sbuffer+12, "\n\t ")) != NULL)
+     {
+@@ -454,7 +454,7 @@ readGenBank(struct ReadSeqVars *V)
+   in_definition = FALSE;
+   while (! feof(V->f))
+     {
+-      getline(V);
++      get_line(V);
+       if (! feof(V->f) && strstr(V->sbuffer, "DEFINITION") == V->sbuffer)
+ 	{
+ 	  if ((sptr = strtok(V->sbuffer+12, "\n")) != NULL)
+@@ -487,11 +487,11 @@ readGenBank(struct ReadSeqVars *V)
+ 
+ 
+   while (!(feof(V->f) || ((*V->sbuffer!=0) && (strstr(V->sbuffer,"LOCUS") == V->sbuffer))))
+-    getline(V);
++    get_line(V);
+ 				/* SRE: V->s now holds "//", so sequential
+ 				   reads are wedged: fixed Tue Jul 13 1993 */
+   while (!feof(V->f) && strstr(V->sbuffer, "LOCUS  ") != V->sbuffer)
+-    getline(V);
++    get_line(V);
+ }
+ 
+ static int
+@@ -521,12 +521,12 @@ readNBRF(struct ReadSeqVars *V)
+   if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL)
+     SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
+ 
+-  getline(V);   /*skip title-junk line*/
++  get_line(V);   /*skip title-junk line*/
+ 
+   readLoop(0, endNBRF, V);
+ 
+   while (!(feof(V->f) || (*V->sbuffer != 0 && *V->sbuffer == '>')))
+-    getline(V);
++    get_line(V);
+ }
+ 
+ 
+@@ -559,7 +559,7 @@ readGCGdata(struct ReadSeqVars *V)
+   } else Die("bogus GCGdata format? %s", V->sbuffer);
+ 
+ 				/* second line contains free text description */
+-  getline(V);
++  get_line(V);
+   SetSeqinfoString(V->sqinfo, V->sbuffer, SQINFO_DESC);
+ 
+   if (binary) {
+@@ -579,7 +579,7 @@ readGCGdata(struct ReadSeqVars *V)
+   else readLoop(0, endGCGdata, V);
+   
+   while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
+-    getline(V);
++    get_line(V);
+ }
+ 
+ static int
+@@ -625,7 +625,7 @@ readPearson(struct ReadSeqVars *V)
+     readLoop(0, endPearson, V);
+ 
+   while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
+-    getline(V);
++    get_line(V);
+ }
+ 
+ 
+@@ -652,7 +652,7 @@ readEMBL(struct ReadSeqVars *V)
+ 
+ 				/* make sure we have first line */
+   while (!feof(V->f) && strncmp(V->sbuffer, "ID  ", 4) != 0)
+-    getline(V);
++    get_line(V);
+ 
+   if ((sptr = strtok(V->sbuffer+5, "\n\t ")) != NULL)
+     {
+@@ -661,7 +661,7 @@ readEMBL(struct ReadSeqVars *V)
+     }
+ 
+   do {
+-    getline(V);
++    get_line(V);
+     if (!feof(V->f) && strstr(V->sbuffer, "AC  ") == V->sbuffer)
+       {
+ 	if ((sptr = strtok(V->sbuffer+5, ";  \t\n")) != NULL)
+@@ -685,7 +685,7 @@ readEMBL(struct ReadSeqVars *V)
+ 
+ 				/* load next record's ID line */
+   while (!feof(V->f) && strncmp(V->sbuffer, "ID  ", 4) != 0)
+-    getline(V);
++    get_line(V);
+ }
+ 
+ 
+@@ -701,7 +701,7 @@ readZuker(struct ReadSeqVars *V)
+ {
+   char *sptr;
+ 
+-  getline(V);  /*s == "seqLen seqid string..."*/
++  get_line(V);  /*s == "seqLen seqid string..."*/
+ 
+   if ((sptr = strtok(V->sbuffer+6, " \t\n")) != NULL)
+     SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
+@@ -712,7 +712,7 @@ readZuker(struct ReadSeqVars *V)
+   readLoop(0, endZuker, V);
+ 
+   while (!(feof(V->f) | ((*V->sbuffer != '\0') & (*V->sbuffer == '('))))
+-    getline(V);
++    get_line(V);
+ }
+ 
+ static void 
+@@ -734,7 +734,7 @@ readUWGCG(struct ReadSeqVars *V)
+ 
+   do {
+     done = feof(V->f);
+-    getline(V);
++    get_line(V);
+     if (! done) addseq(V->sbuffer, V);
+   } while (!done);
+ }
+@@ -746,7 +746,7 @@ readSquid(struct ReadSeqVars *V)
+   char *sptr;
+   int   dostruc = FALSE;
+ 
+-  while (strncmp(V->sbuffer, "NAM ", 4) != 0) getline(V);
++  while (strncmp(V->sbuffer, "NAM ", 4) != 0) get_line(V);
+ 
+   if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL)
+     SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
+@@ -754,7 +754,7 @@ readSquid(struct ReadSeqVars *V)
+   /*CONSTCOND*/
+   while (1)
+     {
+-      getline(V);
++      get_line(V);
+       if (feof(V->f)) {squid_errno = SQERR_FORMAT; return; }
+ 
+       if (strncmp(V->sbuffer, "SRC ", 4) == 0)
+@@ -786,14 +786,14 @@ readSquid(struct ReadSeqVars *V)
+   while (1)
+     {
+ 				/* sequence line */
+-      getline(V);
++      get_line(V);
+       if (feof(V->f) || strncmp(V->sbuffer, "++", 2) == 0) 
+ 	break;
+       addseq(V->sbuffer, V);
+ 				/* structure line */
+       if (dostruc)
+ 	{
+-	  getline(V);
++	  get_line(V);
+ 	  if (feof(V->f)) { squid_errno = SQERR_FORMAT; return; }
+ 	  addstruc(V->sbuffer, V);
+ 	}
+@@ -801,7 +801,7 @@ readSquid(struct ReadSeqVars *V)
+ 
+ 
+   while (!feof(V->f) && strncmp(V->sbuffer, "NAM ", 4) != 0)
+-    getline(V);
++    get_line(V);
+ }
+ 
+ 
+@@ -848,7 +848,7 @@ SeqfileOpen(char *filename, int format, 
+ 
+   /* Load the first line.
+    */
+-  getline(dbfp);
++  get_line(dbfp);
+ 
+   return dbfp;
+ }
+@@ -862,7 +862,7 @@ void
+ SeqfilePosition(SQFILE *sqfp, long offset)
+ {
+   fseek(sqfp->f, offset, SEEK_SET);
+-  getline(sqfp);
++  get_line(sqfp);
+ }
+ 
+ 
+@@ -954,7 +954,7 @@ ReadSeq(SQFILE *V, int format, char **re
+ 	do {			/* skip leading comments on GCG file */
+ 	  gotuw = (strstr(V->sbuffer,"..") != NULL);
+ 	  if (gotuw) readUWGCG(V);
+-	  getline(V);
++	  get_line(V);
+ 	} while (! feof(V->f));
+ 	break;
+