e70152e44cc66cc599ff6b699eb8adc07f3e656a
kent
  Sat May 24 21:09:34 2014 -0700
Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
diff --git src/hg/lib/stsInfo.c src/hg/lib/stsInfo.c
index 901d486..833516d 100644
--- src/hg/lib/stsInfo.c
+++ src/hg/lib/stsInfo.c
@@ -1,436 +1,439 @@
 /* stsInfo.c was originally generated by the autoSql program, which also 
  * generated stsInfo.h and stsInfo.sql.  This module links the database and
  * the RAM representation of objects. */
 
+/* Copyright (C) 2014 The Regents of the University of California 
+ * See README in this or parent directory for licensing information. */
+
 #include "common.h"
 #include "linefile.h"
 #include "jksql.h"
 #include "stsInfo.h"
 
 
 struct stsInfo *stsInfoLoad(char **row)
 /* Load a stsInfo from row fetched with select * from stsInfo
  * from database.  Dispose of this with stsInfoFree(). */
 {
 struct stsInfo *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]);
 return ret;
 }
 
 struct stsInfo *stsInfoLoadAll(char *fileName) 
 /* Load all stsInfo from a tab-separated file.
  * Dispose of this with stsInfoFreeList(). */
 {
 struct stsInfo *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[48];
 
 while (lineFileRow(lf, row))
     {
     el = stsInfoLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct stsInfo *stsInfoCommaIn(char **pS, struct stsInfo *ret)
 /* Create a stsInfo out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new stsInfo */
 {
 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 = sqlSignedComma(&s);
 ret->genethonLOD = sqlSignedComma(&s);
 ret->marshfieldName = sqlStringComma(&s);
 ret->marshfieldChr = sqlStringComma(&s);
 ret->marshfieldPos = sqlSignedComma(&s);
 ret->marshfieldLOD = sqlSignedComma(&s);
 ret->wiyacName = sqlStringComma(&s);
 ret->wiyacChr = sqlStringComma(&s);
 ret->wiyacPos = sqlSignedComma(&s);
 ret->wiyacLOD = sqlSignedComma(&s);
 ret->wirhName = sqlStringComma(&s);
 ret->wirhChr = sqlStringComma(&s);
 ret->wirhPos = sqlSignedComma(&s);
 ret->wirhLOD = sqlSignedComma(&s);
 ret->gm99gb4Name = sqlStringComma(&s);
 ret->gm99gb4Chr = sqlStringComma(&s);
 ret->gm99gb4Pos = sqlSignedComma(&s);
 ret->gm99gb4LOD = sqlSignedComma(&s);
 ret->gm99g3Name = sqlStringComma(&s);
 ret->gm99g3Chr = sqlStringComma(&s);
 ret->gm99g3Pos = sqlSignedComma(&s);
 ret->gm99g3LOD = sqlSignedComma(&s);
 ret->tngName = sqlStringComma(&s);
 ret->tngChr = sqlStringComma(&s);
 ret->tngPos = sqlSignedComma(&s);
 ret->tngLOD = sqlSignedComma(&s);
 *pS = s;
 return ret;
 }
 
 void stsInfoFree(struct stsInfo **pEl)
 /* Free a single dynamically allocated stsInfo such as created
  * with stsInfoLoad(). */
 {
 struct stsInfo *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);
 freez(pEl);
 }
 
 void stsInfoFreeList(struct stsInfo **pList)
 /* Free a list of dynamically allocated stsInfo's */
 {
 struct stsInfo *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     stsInfoFree(&el);
     }
 *pList = NULL;
 }
 
 void stsInfoOutput(struct stsInfo *el, FILE *f, char sep, char lastSep) 
 /* Print out stsInfo.  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(lastSep,f);
 }