Index: src/hg/lib/tRNAs.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/lib/tRNAs.c,v
retrieving revision 1.1
retrieving revision 1.2
diff -b -B -U 1000000 -r1.1 -r1.2
--- src/hg/lib/tRNAs.c	1 Dec 2005 01:32:38 -0000	1.1
+++ src/hg/lib/tRNAs.c	7 Jan 2010 02:54:53 -0000	1.2
@@ -1,175 +1,191 @@
 /* tRNAs.c was originally generated by the autoSql program, which also 
  * generated tRNAs.h and tRNAs.sql.  This module links the database and
  * the RAM representation of objects. */
 
 #include "common.h"
 #include "linefile.h"
 #include "dystring.h"
 #include "jksql.h"
 #include "tRNAs.h"
 
 static char const rcsid[] = "$Id$";
 
 void tRNAsStaticLoad(char **row, struct tRNAs *ret)
 /* Load a row from tRNAs table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->chrom = row[0];
 ret->chromStart = sqlUnsigned(row[1]);
 ret->chromEnd = sqlUnsigned(row[2]);
 ret->name = row[3];
 ret->score = sqlUnsigned(row[4]);
-strcpy(ret->strand, row[5]);
+safecpy(ret->strand, sizeof(ret->strand), row[5]);
 ret->aa = row[6];
 ret->ac = row[7];
 ret->intron = row[8];
-ret->trnaScore = atof(row[9]);
+ret->trnaScore = sqlFloat(row[9]);
+ret->genomeUrl = row[10];
+ret->trnaUrl = row[11];
 }
 
 struct tRNAs *tRNAsLoad(char **row)
 /* Load a tRNAs from row fetched with select * from tRNAs
  * from database.  Dispose of this with tRNAsFree(). */
 {
 struct tRNAs *ret;
 
 AllocVar(ret);
 ret->chrom = cloneString(row[0]);
 ret->chromStart = sqlUnsigned(row[1]);
 ret->chromEnd = sqlUnsigned(row[2]);
 ret->name = cloneString(row[3]);
 ret->score = sqlUnsigned(row[4]);
-strcpy(ret->strand, row[5]);
+safecpy(ret->strand, sizeof(ret->strand), row[5]);
 ret->aa = cloneString(row[6]);
 ret->ac = cloneString(row[7]);
 ret->intron = cloneString(row[8]);
-ret->trnaScore = atof(row[9]);
+ret->trnaScore = sqlFloat(row[9]);
+ret->genomeUrl = cloneString(row[10]);
+ret->trnaUrl = cloneString(row[11]);
 return ret;
 }
 
 struct tRNAs *tRNAsLoadAll(char *fileName) 
 /* Load all tRNAs from a whitespace-separated file.
  * Dispose of this with tRNAsFreeList(). */
 {
 struct tRNAs *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
-char *row[10];
+char *row[12];
 
 while (lineFileRow(lf, row))
     {
     el = tRNAsLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct tRNAs *tRNAsLoadAllByChar(char *fileName, char chopper) 
 /* Load all tRNAs from a chopper separated file.
  * Dispose of this with tRNAsFreeList(). */
 {
 struct tRNAs *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
-char *row[10];
+char *row[12];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = tRNAsLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct tRNAs *tRNAsCommaIn(char **pS, struct tRNAs *ret)
 /* Create a tRNAs out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new tRNAs */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->chrom = sqlStringComma(&s);
 ret->chromStart = sqlUnsignedComma(&s);
 ret->chromEnd = sqlUnsignedComma(&s);
 ret->name = sqlStringComma(&s);
 ret->score = sqlUnsignedComma(&s);
 sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand));
 ret->aa = sqlStringComma(&s);
 ret->ac = sqlStringComma(&s);
 ret->intron = sqlStringComma(&s);
 ret->trnaScore = sqlFloatComma(&s);
+ret->genomeUrl = sqlStringComma(&s);
+ret->trnaUrl = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void tRNAsFree(struct tRNAs **pEl)
 /* Free a single dynamically allocated tRNAs such as created
  * with tRNAsLoad(). */
 {
 struct tRNAs *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->name);
 freeMem(el->aa);
 freeMem(el->ac);
 freeMem(el->intron);
+freeMem(el->genomeUrl);
+freeMem(el->trnaUrl);
 freez(pEl);
 }
 
 void tRNAsFreeList(struct tRNAs **pList)
 /* Free a list of dynamically allocated tRNAs's */
 {
 struct tRNAs *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     tRNAsFree(&el);
     }
 *pList = NULL;
 }
 
 void tRNAsOutput(struct tRNAs *el, FILE *f, char sep, char lastSep) 
 /* Print out tRNAs.  Separate fields with sep. Follow last field with lastSep. */
 {
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->chrom);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->chromStart);
 fputc(sep,f);
 fprintf(f, "%u", el->chromEnd);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->name);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->score);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->strand);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->aa);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->ac);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->intron);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%g", el->trnaScore);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->genomeUrl);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->trnaUrl);
+if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 

