a44421a79fb36cc2036fe116b97ea3bc9590cd0c
braney
  Fri Dec 2 09:34:39 2011 -0800
removed rcsid (#295)
diff --git src/hg/lib/txInfo.c src/hg/lib/txInfo.c
index d061b6d..052e908 100644
--- src/hg/lib/txInfo.c
+++ src/hg/lib/txInfo.c
@@ -1,243 +1,242 @@
 /* txInfo.c was originally generated by the autoSql program, which also 
  * generated txInfo.h and txInfo.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 "txInfo.h"
 
-static char const rcsid[] = "$Id: txInfo.c,v 1.6 2007/03/17 22:34:43 kent Exp $";
 
 void txInfoStaticLoad(char **row, struct txInfo *ret)
 /* Load a row from txInfo table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->name = row[0];
 ret->category = row[1];
 ret->sourceAcc = row[2];
 ret->isRefSeq = sqlUnsigned(row[3]);
 ret->sourceSize = sqlSigned(row[4]);
 ret->aliCoverage = sqlDouble(row[5]);
 ret->aliIdRatio = sqlDouble(row[6]);
 ret->genoMapCount = sqlSigned(row[7]);
 ret->exonCount = sqlSigned(row[8]);
 ret->orfSize = sqlSigned(row[9]);
 ret->cdsScore = sqlDouble(row[10]);
 ret->startComplete = sqlUnsigned(row[11]);
 ret->endComplete = sqlUnsigned(row[12]);
 ret->nonsenseMediatedDecay = sqlUnsigned(row[13]);
 ret->retainedIntron = sqlUnsigned(row[14]);
 ret->bleedIntoIntron = sqlSigned(row[15]);
 ret->strangeSplice = sqlSigned(row[16]);
 ret->atacIntrons = sqlSigned(row[17]);
 ret->cdsSingleInIntron = sqlUnsigned(row[18]);
 ret->cdsSingleInUtr3 = sqlUnsigned(row[19]);
 ret->selenocysteine = sqlUnsigned(row[20]);
 ret->genomicFrameShift = sqlUnsigned(row[21]);
 ret->genomicStop = sqlUnsigned(row[22]);
 }
 
 struct txInfo *txInfoLoad(char **row)
 /* Load a txInfo from row fetched with select * from txInfo
  * from database.  Dispose of this with txInfoFree(). */
 {
 struct txInfo *ret;
 
 AllocVar(ret);
 ret->name = cloneString(row[0]);
 ret->category = cloneString(row[1]);
 ret->sourceAcc = cloneString(row[2]);
 ret->isRefSeq = sqlUnsigned(row[3]);
 ret->sourceSize = sqlSigned(row[4]);
 ret->aliCoverage = sqlDouble(row[5]);
 ret->aliIdRatio = sqlDouble(row[6]);
 ret->genoMapCount = sqlSigned(row[7]);
 ret->exonCount = sqlSigned(row[8]);
 ret->orfSize = sqlSigned(row[9]);
 ret->cdsScore = sqlDouble(row[10]);
 ret->startComplete = sqlUnsigned(row[11]);
 ret->endComplete = sqlUnsigned(row[12]);
 ret->nonsenseMediatedDecay = sqlUnsigned(row[13]);
 ret->retainedIntron = sqlUnsigned(row[14]);
 ret->bleedIntoIntron = sqlSigned(row[15]);
 ret->strangeSplice = sqlSigned(row[16]);
 ret->atacIntrons = sqlSigned(row[17]);
 ret->cdsSingleInIntron = sqlUnsigned(row[18]);
 ret->cdsSingleInUtr3 = sqlUnsigned(row[19]);
 ret->selenocysteine = sqlUnsigned(row[20]);
 ret->genomicFrameShift = sqlUnsigned(row[21]);
 ret->genomicStop = sqlUnsigned(row[22]);
 return ret;
 }
 
 struct txInfo *txInfoLoadAll(char *fileName) 
 /* Load all txInfo from a whitespace-separated file.
  * Dispose of this with txInfoFreeList(). */
 {
 struct txInfo *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[23];
 
 while (lineFileRow(lf, row))
     {
     el = txInfoLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct txInfo *txInfoLoadAllByChar(char *fileName, char chopper) 
 /* Load all txInfo from a chopper separated file.
  * Dispose of this with txInfoFreeList(). */
 {
 struct txInfo *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[23];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = txInfoLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct txInfo *txInfoCommaIn(char **pS, struct txInfo *ret)
 /* Create a txInfo out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new txInfo */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->name = sqlStringComma(&s);
 ret->category = sqlStringComma(&s);
 ret->sourceAcc = sqlStringComma(&s);
 ret->isRefSeq = sqlUnsignedComma(&s);
 ret->sourceSize = sqlSignedComma(&s);
 ret->aliCoverage = sqlDoubleComma(&s);
 ret->aliIdRatio = sqlDoubleComma(&s);
 ret->genoMapCount = sqlSignedComma(&s);
 ret->exonCount = sqlSignedComma(&s);
 ret->orfSize = sqlSignedComma(&s);
 ret->cdsScore = sqlDoubleComma(&s);
 ret->startComplete = sqlUnsignedComma(&s);
 ret->endComplete = sqlUnsignedComma(&s);
 ret->nonsenseMediatedDecay = sqlUnsignedComma(&s);
 ret->retainedIntron = sqlUnsignedComma(&s);
 ret->bleedIntoIntron = sqlSignedComma(&s);
 ret->strangeSplice = sqlSignedComma(&s);
 ret->atacIntrons = sqlSignedComma(&s);
 ret->cdsSingleInIntron = sqlUnsignedComma(&s);
 ret->cdsSingleInUtr3 = sqlUnsignedComma(&s);
 ret->selenocysteine = sqlUnsignedComma(&s);
 ret->genomicFrameShift = sqlUnsignedComma(&s);
 ret->genomicStop = sqlUnsignedComma(&s);
 *pS = s;
 return ret;
 }
 
 void txInfoFree(struct txInfo **pEl)
 /* Free a single dynamically allocated txInfo such as created
  * with txInfoLoad(). */
 {
 struct txInfo *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->name);
 freeMem(el->category);
 freeMem(el->sourceAcc);
 freez(pEl);
 }
 
 void txInfoFreeList(struct txInfo **pList)
 /* Free a list of dynamically allocated txInfo's */
 {
 struct txInfo *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     txInfoFree(&el);
     }
 *pList = NULL;
 }
 
 void txInfoOutput(struct txInfo *el, FILE *f, char sep, char lastSep) 
 /* Print out txInfo.  Separate fields with sep. Follow last field with lastSep. */
 {
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->name);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->category);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->sourceAcc);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->isRefSeq);
 fputc(sep,f);
 fprintf(f, "%d", el->sourceSize);
 fputc(sep,f);
 fprintf(f, "%g", el->aliCoverage);
 fputc(sep,f);
 fprintf(f, "%g", el->aliIdRatio);
 fputc(sep,f);
 fprintf(f, "%d", el->genoMapCount);
 fputc(sep,f);
 fprintf(f, "%d", el->exonCount);
 fputc(sep,f);
 fprintf(f, "%d", el->orfSize);
 fputc(sep,f);
 fprintf(f, "%g", el->cdsScore);
 fputc(sep,f);
 fprintf(f, "%u", el->startComplete);
 fputc(sep,f);
 fprintf(f, "%u", el->endComplete);
 fputc(sep,f);
 fprintf(f, "%u", el->nonsenseMediatedDecay);
 fputc(sep,f);
 fprintf(f, "%u", el->retainedIntron);
 fputc(sep,f);
 fprintf(f, "%d", el->bleedIntoIntron);
 fputc(sep,f);
 fprintf(f, "%d", el->strangeSplice);
 fputc(sep,f);
 fprintf(f, "%d", el->atacIntrons);
 fputc(sep,f);
 fprintf(f, "%u", el->cdsSingleInIntron);
 fputc(sep,f);
 fprintf(f, "%u", el->cdsSingleInUtr3);
 fputc(sep,f);
 fprintf(f, "%u", el->selenocysteine);
 fputc(sep,f);
 fprintf(f, "%u", el->genomicFrameShift);
 fputc(sep,f);
 fprintf(f, "%u", el->genomicStop);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
 double txInfoCodingScore(struct txInfo *info, boolean boostRefSeq)
 /* Return coding score for info.  This is just the cdsScore score,
  * plus another 1000 if it's a refSeq.  1000 is quite a bit for a
  * cdsScore score, equivalent to another 1000 bases in the coding region. */
 {
 double score = info->cdsScore;
 if (boostRefSeq && info->isRefSeq)
     score += 1000;
 return score;
 }