a44421a79fb36cc2036fe116b97ea3bc9590cd0c
braney
  Fri Dec 2 09:34:39 2011 -0800
removed rcsid (#295)
diff --git src/hg/lib/stsInfo2.c src/hg/lib/stsInfo2.c
index 7721e28..04108eb 100644
--- src/hg/lib/stsInfo2.c
+++ src/hg/lib/stsInfo2.c
@@ -1,485 +1,484 @@
 /* stsInfo2.c was originally generated by the autoSql program, which also 
  * generated stsInfo2.h and stsInfo2.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 "stsInfo2.h"
 
-static char const rcsid[] = "$Id: stsInfo2.c,v 1.3 2005/04/13 06:25:57 markd Exp $";
 
 struct stsInfo2 *stsInfo2Load(char **row)
 /* Load a stsInfo2 from row fetched with select * from stsInfo2
  * from database.  Dispose of this with stsInfo2Free(). */
 {
 struct stsInfo2 *ret;
 int sizeOne;
 
 AllocVar(ret);
 ret->gbCount = sqlUnsigned(row[2]);
 ret->gdbCount = sqlUnsigned(row[4]);
 ret->nameCount = sqlUnsigned(row[6]);
 ret->otherDbstsCount = sqlUnsigned(row[9]);
 ret->otherUCSCcount = sqlUnsigned(row[16]);
 ret->mergeUCSCcount = sqlUnsigned(row[18]);
 ret->identNo = sqlUnsigned(row[0]);
 ret->name = cloneString(row[1]);
 sqlStringDynamicArray(row[3], &ret->genbank, &sizeOne);
 assert(sizeOne == ret->gbCount);
 sqlStringDynamicArray(row[5], &ret->gdb, &sizeOne);
 assert(sizeOne == ret->gdbCount);
 sqlStringDynamicArray(row[7], &ret->otherNames, &sizeOne);
 assert(sizeOne == ret->nameCount);
 ret->dbSTSid = sqlUnsigned(row[8]);
 sqlUnsignedDynamicArray(row[10], &ret->otherDbSTS, &sizeOne);
 assert(sizeOne == ret->otherDbstsCount);
 ret->leftPrimer = cloneString(row[11]);
 ret->rightPrimer = cloneString(row[12]);
 ret->distance = cloneString(row[13]);
 ret->organism = cloneString(row[14]);
 ret->sequence = sqlUnsigned(row[15]);
 sqlUnsignedDynamicArray(row[17], &ret->otherUCSC, &sizeOne);
 assert(sizeOne == ret->otherUCSCcount);
 sqlUnsignedDynamicArray(row[19], &ret->mergeUCSC, &sizeOne);
 assert(sizeOne == ret->mergeUCSCcount);
 ret->genethonName = cloneString(row[20]);
 ret->genethonChr = cloneString(row[21]);
 ret->genethonPos = atof(row[22]);
 ret->genethonLOD = atof(row[23]);
 ret->marshfieldName = cloneString(row[24]);
 ret->marshfieldChr = cloneString(row[25]);
 ret->marshfieldPos = atof(row[26]);
 ret->marshfieldLOD = atof(row[27]);
 ret->wiyacName = cloneString(row[28]);
 ret->wiyacChr = cloneString(row[29]);
 ret->wiyacPos = atof(row[30]);
 ret->wiyacLOD = atof(row[31]);
 ret->wirhName = cloneString(row[32]);
 ret->wirhChr = cloneString(row[33]);
 ret->wirhPos = atof(row[34]);
 ret->wirhLOD = atof(row[35]);
 ret->gm99gb4Name = cloneString(row[36]);
 ret->gm99gb4Chr = cloneString(row[37]);
 ret->gm99gb4Pos = atof(row[38]);
 ret->gm99gb4LOD = atof(row[39]);
 ret->gm99g3Name = cloneString(row[40]);
 ret->gm99g3Chr = cloneString(row[41]);
 ret->gm99g3Pos = atof(row[42]);
 ret->gm99g3LOD = atof(row[43]);
 ret->tngName = cloneString(row[44]);
 ret->tngChr = cloneString(row[45]);
 ret->tngPos = atof(row[46]);
 ret->tngLOD = atof(row[47]);
 ret->decodeName = cloneString(row[48]);
 ret->decodeChr = cloneString(row[49]);
 ret->decodePos = atof(row[50]);
 ret->decodeLOD = atof(row[51]);
 return ret;
 }
 
 struct stsInfo2 *stsInfo2LoadAll(char *fileName) 
 /* Load all stsInfo2 from a tab-separated file.
  * Dispose of this with stsInfo2FreeList(). */
 {
 struct stsInfo2 *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[52];
 
 while (lineFileRow(lf, row))
     {
     el = stsInfo2Load(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct stsInfo2 *stsInfo2LoadWhere(struct sqlConnection *conn, char *table, char *where)
 /* Load all stsInfo2 from table that satisfy where clause. The
  * where clause may be NULL in which case whole table is loaded
  * Dispose of this with stsInfo2FreeList(). */
 {
 struct stsInfo2 *list = NULL, *el;
 struct dyString *query = dyStringNew(256);
 struct sqlResult *sr;
 char **row;
 
 dyStringPrintf(query, "select * from %s", table);
 if (where != NULL)
     dyStringPrintf(query, " where %s", where);
 sr = sqlGetResult(conn, query->string);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = stsInfo2Load(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 dyStringFree(&query);
 return list;
 }
 
 struct stsInfo2 *stsInfo2CommaIn(char **pS, struct stsInfo2 *ret)
 /* Create a stsInfo2 out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new stsInfo2 */
 {
 char *s = *pS;
 int i;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->identNo = sqlUnsignedComma(&s);
 ret->name = sqlStringComma(&s);
 ret->gbCount = sqlUnsignedComma(&s);
 s = sqlEatChar(s, '{');
 AllocArray(ret->genbank, ret->gbCount);
 for (i=0; i<ret->gbCount; ++i)
     {
     ret->genbank[i] = sqlStringComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 ret->gdbCount = sqlUnsignedComma(&s);
 s = sqlEatChar(s, '{');
 AllocArray(ret->gdb, ret->gdbCount);
 for (i=0; i<ret->gdbCount; ++i)
     {
     ret->gdb[i] = sqlStringComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 ret->nameCount = sqlUnsignedComma(&s);
 s = sqlEatChar(s, '{');
 AllocArray(ret->otherNames, ret->nameCount);
 for (i=0; i<ret->nameCount; ++i)
     {
     ret->otherNames[i] = sqlStringComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 ret->dbSTSid = sqlUnsignedComma(&s);
 ret->otherDbstsCount = sqlUnsignedComma(&s);
 s = sqlEatChar(s, '{');
 AllocArray(ret->otherDbSTS, ret->otherDbstsCount);
 for (i=0; i<ret->otherDbstsCount; ++i)
     {
     ret->otherDbSTS[i] = sqlUnsignedComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 ret->leftPrimer = sqlStringComma(&s);
 ret->rightPrimer = sqlStringComma(&s);
 ret->distance = sqlStringComma(&s);
 ret->organism = sqlStringComma(&s);
 ret->sequence = sqlUnsignedComma(&s);
 ret->otherUCSCcount = sqlUnsignedComma(&s);
 s = sqlEatChar(s, '{');
 AllocArray(ret->otherUCSC, ret->otherUCSCcount);
 for (i=0; i<ret->otherUCSCcount; ++i)
     {
     ret->otherUCSC[i] = sqlUnsignedComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 ret->mergeUCSCcount = sqlUnsignedComma(&s);
 s = sqlEatChar(s, '{');
 AllocArray(ret->mergeUCSC, ret->mergeUCSCcount);
 for (i=0; i<ret->mergeUCSCcount; ++i)
     {
     ret->mergeUCSC[i] = sqlUnsignedComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 ret->genethonName = sqlStringComma(&s);
 ret->genethonChr = sqlStringComma(&s);
 ret->genethonPos = sqlFloatComma(&s);
 ret->genethonLOD = sqlFloatComma(&s);
 ret->marshfieldName = sqlStringComma(&s);
 ret->marshfieldChr = sqlStringComma(&s);
 ret->marshfieldPos = sqlFloatComma(&s);
 ret->marshfieldLOD = sqlFloatComma(&s);
 ret->wiyacName = sqlStringComma(&s);
 ret->wiyacChr = sqlStringComma(&s);
 ret->wiyacPos = sqlFloatComma(&s);
 ret->wiyacLOD = sqlFloatComma(&s);
 ret->wirhName = sqlStringComma(&s);
 ret->wirhChr = sqlStringComma(&s);
 ret->wirhPos = sqlFloatComma(&s);
 ret->wirhLOD = sqlFloatComma(&s);
 ret->gm99gb4Name = sqlStringComma(&s);
 ret->gm99gb4Chr = sqlStringComma(&s);
 ret->gm99gb4Pos = sqlFloatComma(&s);
 ret->gm99gb4LOD = sqlFloatComma(&s);
 ret->gm99g3Name = sqlStringComma(&s);
 ret->gm99g3Chr = sqlStringComma(&s);
 ret->gm99g3Pos = sqlFloatComma(&s);
 ret->gm99g3LOD = sqlFloatComma(&s);
 ret->tngName = sqlStringComma(&s);
 ret->tngChr = sqlStringComma(&s);
 ret->tngPos = sqlFloatComma(&s);
 ret->tngLOD = sqlFloatComma(&s);
 ret->decodeName = sqlStringComma(&s);
 ret->decodeChr = sqlStringComma(&s);
 ret->decodePos = sqlFloatComma(&s);
 ret->decodeLOD = sqlFloatComma(&s);
 *pS = s;
 return ret;
 }
 
 void stsInfo2Free(struct stsInfo2 **pEl)
 /* Free a single dynamically allocated stsInfo2 such as created
  * with stsInfo2Load(). */
 {
 struct stsInfo2 *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->name);
 /* All strings in genbank are allocated at once, so only need to free first. */
 if (el->genbank != NULL)
     freeMem(el->genbank[0]);
 freeMem(el->genbank);
 /* All strings in gdb are allocated at once, so only need to free first. */
 if (el->gdb != NULL)
     freeMem(el->gdb[0]);
 freeMem(el->gdb);
 /* All strings in otherNames are allocated at once, so only need to free first. */
 if (el->otherNames != NULL)
     freeMem(el->otherNames[0]);
 freeMem(el->otherNames);
 freeMem(el->otherDbSTS);
 freeMem(el->leftPrimer);
 freeMem(el->rightPrimer);
 freeMem(el->distance);
 freeMem(el->organism);
 freeMem(el->otherUCSC);
 freeMem(el->mergeUCSC);
 freeMem(el->genethonName);
 freeMem(el->genethonChr);
 freeMem(el->marshfieldName);
 freeMem(el->marshfieldChr);
 freeMem(el->wiyacName);
 freeMem(el->wiyacChr);
 freeMem(el->wirhName);
 freeMem(el->wirhChr);
 freeMem(el->gm99gb4Name);
 freeMem(el->gm99gb4Chr);
 freeMem(el->gm99g3Name);
 freeMem(el->gm99g3Chr);
 freeMem(el->tngName);
 freeMem(el->tngChr);
 freeMem(el->decodeName);
 freeMem(el->decodeChr);
 freez(pEl);
 }
 
 void stsInfo2FreeList(struct stsInfo2 **pList)
 /* Free a list of dynamically allocated stsInfo2's */
 {
 struct stsInfo2 *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     stsInfo2Free(&el);
     }
 *pList = NULL;
 }
 
 void stsInfo2Output(struct stsInfo2 *el, FILE *f, char sep, char lastSep) 
 /* Print out stsInfo2.  Separate fields with sep. Follow last field with lastSep. */
 {
 int i;
 fprintf(f, "%u", el->identNo);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->name);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->gbCount);
 fputc(sep,f);
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->gbCount; ++i)
     {
     if (sep == ',') fputc('"',f);
     fprintf(f, "%s", el->genbank[i]);
     if (sep == ',') fputc('"',f);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 fputc(sep,f);
 fprintf(f, "%u", el->gdbCount);
 fputc(sep,f);
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->gdbCount; ++i)
     {
     if (sep == ',') fputc('"',f);
     fprintf(f, "%s", el->gdb[i]);
     if (sep == ',') fputc('"',f);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 fputc(sep,f);
 fprintf(f, "%u", el->nameCount);
 fputc(sep,f);
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->nameCount; ++i)
     {
     if (sep == ',') fputc('"',f);
     fprintf(f, "%s", el->otherNames[i]);
     if (sep == ',') fputc('"',f);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 fputc(sep,f);
 fprintf(f, "%u", el->dbSTSid);
 fputc(sep,f);
 fprintf(f, "%u", el->otherDbstsCount);
 fputc(sep,f);
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->otherDbstsCount; ++i)
     {
     fprintf(f, "%u", el->otherDbSTS[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->leftPrimer);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->rightPrimer);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->distance);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->organism);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->sequence);
 fputc(sep,f);
 fprintf(f, "%u", el->otherUCSCcount);
 fputc(sep,f);
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->otherUCSCcount; ++i)
     {
     fprintf(f, "%u", el->otherUCSC[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 fputc(sep,f);
 fprintf(f, "%u", el->mergeUCSCcount);
 fputc(sep,f);
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->mergeUCSCcount; ++i)
     {
     fprintf(f, "%u", el->mergeUCSC[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->genethonName);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->genethonChr);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%f", el->genethonPos);
 fputc(sep,f);
 fprintf(f, "%f", el->genethonLOD);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->marshfieldName);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->marshfieldChr);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%f", el->marshfieldPos);
 fputc(sep,f);
 fprintf(f, "%f", el->marshfieldLOD);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->wiyacName);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->wiyacChr);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%f", el->wiyacPos);
 fputc(sep,f);
 fprintf(f, "%f", el->wiyacLOD);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->wirhName);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->wirhChr);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%f", el->wirhPos);
 fputc(sep,f);
 fprintf(f, "%f", el->wirhLOD);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->gm99gb4Name);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->gm99gb4Chr);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%f", el->gm99gb4Pos);
 fputc(sep,f);
 fprintf(f, "%f", el->gm99gb4LOD);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->gm99g3Name);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->gm99g3Chr);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%f", el->gm99g3Pos);
 fputc(sep,f);
 fprintf(f, "%f", el->gm99g3LOD);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->tngName);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->tngChr);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%f", el->tngPos);
 fputc(sep,f);
 fprintf(f, "%f", el->tngLOD);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->decodeName);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->decodeChr);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%f", el->decodePos);
 fputc(sep,f);
 fprintf(f, "%f", el->decodeLOD);
 fputc(lastSep,f);
 }