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/stsMap.c src/hg/lib/stsMap.c
index e98e8cd..f37973d 100644
--- src/hg/lib/stsMap.c
+++ src/hg/lib/stsMap.c
@@ -1,379 +1,382 @@
 /* stsMap.c was originally generated by the autoSql program, which also 
  * generated stsMap.h and stsMap.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 "stsMarker.h"
 #include "stsMap.h"
 
 
 void stsMapStaticLoad(char **row, struct stsMap *ret)
 /* Load a row from stsMap table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->chrom = row[0];
 ret->chromStart = sqlSigned(row[1]);
 ret->chromEnd = sqlUnsigned(row[2]);
 ret->name = row[3];
 ret->score = sqlUnsigned(row[4]);
 ret->identNo = sqlUnsigned(row[5]);
 ret->ctgAcc = row[6];
 ret->otherAcc = row[7];
 ret->genethonChrom = row[8];
 ret->genethonPos = atof(row[9]);
 ret->marshfieldChrom = row[10];
 ret->marshfieldPos = atof(row[11]);
 ret->gm99Gb4Chrom = row[12];
 ret->gm99Gb4Pos = atof(row[13]);
 ret->shgcTngChrom = row[14];
 ret->shgcTngPos = atof(row[15]);
 ret->shgcG3Chrom = row[16];
 ret->shgcG3Pos = atof(row[17]);
 ret->wiYacChrom = row[18];
 ret->wiYacPos = atof(row[19]);
 ret->wiRhChrom = row[20];
 ret->wiRhPos = atof(row[21]);
 ret->fishChrom = row[22];
 ret->beginBand = row[23];
 ret->endBand = row[24];
 ret->lab = row[25];
 ret->decodeChrom = "0";
 ret->decodePos = 0;
 }
 
 void stsMapStaticLoad28(char **row, struct stsMap *ret)
 /* Load a row from stsMap table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->chrom = row[0];
 ret->chromStart = sqlSigned(row[1]);
 ret->chromEnd = sqlUnsigned(row[2]);
 ret->name = row[3];
 ret->score = sqlUnsigned(row[4]);
 ret->identNo = sqlUnsigned(row[5]);
 ret->ctgAcc = row[6];
 ret->otherAcc = row[7];
 ret->genethonChrom = row[8];
 ret->genethonPos = atof(row[9]);
 ret->marshfieldChrom = row[10];
 ret->marshfieldPos = atof(row[11]);
 ret->gm99Gb4Chrom = row[12];
 ret->gm99Gb4Pos = atof(row[13]);
 ret->shgcTngChrom = row[14];
 ret->shgcTngPos = atof(row[15]);
 ret->shgcG3Chrom = row[16];
 ret->shgcG3Pos = atof(row[17]);
 ret->wiYacChrom = row[18];
 ret->wiYacPos = atof(row[19]);
 ret->wiRhChrom = row[20];
 ret->wiRhPos = atof(row[21]);
 ret->fishChrom = row[22];
 ret->beginBand = row[23];
 ret->endBand = row[24];
 ret->lab = row[25];
 ret->decodeChrom = row[26];
 ret->decodePos = atof(row[27]);
 }
 
 struct stsMap *stsMapLoad(char **row)
 /* Load a stsMap from row fetched with select * from stsMap
  * from database.  Dispose of this with stsMapFree(). */
 {
 struct stsMap *ret;
 
 AllocVar(ret);
 ret->chrom = cloneString(row[0]);
 ret->chromStart = sqlSigned(row[1]);
 ret->chromEnd = sqlUnsigned(row[2]);
 ret->name = cloneString(row[3]);
 ret->score = sqlUnsigned(row[4]);
 ret->identNo = sqlUnsigned(row[5]);
 ret->ctgAcc = cloneString(row[6]);
 ret->otherAcc = cloneString(row[7]);
 ret->genethonChrom = cloneString(row[8]);
 ret->genethonPos = atof(row[9]);
 ret->marshfieldChrom = cloneString(row[10]);
 ret->marshfieldPos = atof(row[11]);
 ret->gm99Gb4Chrom = cloneString(row[12]);
 ret->gm99Gb4Pos = atof(row[13]);
 ret->shgcTngChrom = cloneString(row[14]);
 ret->shgcTngPos = atof(row[15]);
 ret->shgcG3Chrom = cloneString(row[16]);
 ret->shgcG3Pos = atof(row[17]);
 ret->wiYacChrom = cloneString(row[18]);
 ret->wiYacPos = atof(row[19]);
 ret->wiRhChrom = cloneString(row[20]);
 ret->wiRhPos = atof(row[21]);
 ret->fishChrom = cloneString(row[22]);
 ret->beginBand = cloneString(row[23]);
 ret->endBand = cloneString(row[24]);
 ret->lab = cloneString(row[25]);
 ret->decodeChrom = cloneString("0");
 ret->decodePos = 0;
 
 return ret;
 }
 
 struct stsMap *stsMapLoad28(char **row)
 /* Load a stsMap from row fetched with select * from stsMap
  * from database.  Dispose of this with stsMapFree(). */
 {
 struct stsMap *ret;
 
 AllocVar(ret);
 ret->chrom = cloneString(row[0]);
 ret->chromStart = sqlSigned(row[1]);
 ret->chromEnd = sqlUnsigned(row[2]);
 ret->name = cloneString(row[3]);
 ret->score = sqlUnsigned(row[4]);
 ret->identNo = sqlUnsigned(row[5]);
 ret->ctgAcc = cloneString(row[6]);
 ret->otherAcc = cloneString(row[7]);
 ret->genethonChrom = cloneString(row[8]);
 ret->genethonPos = atof(row[9]);
 ret->marshfieldChrom = cloneString(row[10]);
 ret->marshfieldPos = atof(row[11]);
 ret->gm99Gb4Chrom = cloneString(row[12]);
 ret->gm99Gb4Pos = atof(row[13]);
 ret->shgcTngChrom = cloneString(row[14]);
 ret->shgcTngPos = atof(row[15]);
 ret->shgcG3Chrom = cloneString(row[16]);
 ret->shgcG3Pos = atof(row[17]);
 ret->wiYacChrom = cloneString(row[18]);
 ret->wiYacPos = atof(row[19]);
 ret->wiRhChrom = cloneString(row[20]);
 ret->wiRhPos = atof(row[21]);
 ret->fishChrom = cloneString(row[22]);
 ret->beginBand = cloneString(row[23]);
 ret->endBand = cloneString(row[24]);
 ret->lab = cloneString(row[25]);
 ret->decodeChrom = cloneString(row[26]);
 ret->decodePos = atof(row[27]);
 return ret;
 }
 
 struct stsMap *stsMapLoadAll(char *fileName) 
 /* Load all stsMap from a tab-separated file.
  * Dispose of this with stsMapFreeList(). */
 {
 struct stsMap *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[26];
 
 while (lineFileRow(lf, row))
     {
     el = stsMapLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct stsMap *stsMapCommaIn(char **pS, struct stsMap *ret)
 /* Create a stsMap out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new stsMap */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->chrom = sqlStringComma(&s);
 ret->chromStart = sqlSignedComma(&s);
 ret->chromEnd = sqlUnsignedComma(&s);
 ret->name = sqlStringComma(&s);
 ret->score = sqlUnsignedComma(&s);
 ret->identNo = sqlUnsignedComma(&s);
 ret->ctgAcc = sqlStringComma(&s);
 ret->otherAcc = sqlStringComma(&s);
 ret->genethonChrom = sqlStringComma(&s);
 ret->genethonPos = sqlSignedComma(&s);
 ret->marshfieldChrom = sqlStringComma(&s);
 ret->marshfieldPos = sqlSignedComma(&s);
 ret->gm99Gb4Chrom = sqlStringComma(&s);
 ret->gm99Gb4Pos = sqlSignedComma(&s);
 ret->shgcTngChrom = sqlStringComma(&s);
 ret->shgcTngPos = sqlSignedComma(&s);
 ret->shgcG3Chrom = sqlStringComma(&s);
 ret->shgcG3Pos = sqlSignedComma(&s);
 ret->wiYacChrom = sqlStringComma(&s);
 ret->wiYacPos = sqlSignedComma(&s);
 ret->wiRhChrom = sqlStringComma(&s);
 ret->wiRhPos = sqlSignedComma(&s);
 ret->fishChrom = sqlStringComma(&s);
 ret->beginBand = sqlStringComma(&s);
 ret->endBand = sqlStringComma(&s);
 ret->lab = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void stsMapFree(struct stsMap **pEl)
 /* Free a single dynamically allocated stsMap such as created
  * with stsMapLoad(). */
 {
 struct stsMap *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->name);
 freeMem(el->ctgAcc);
 freeMem(el->otherAcc);
 freeMem(el->genethonChrom);
 freeMem(el->marshfieldChrom);
 freeMem(el->gm99Gb4Chrom);
 freeMem(el->shgcTngChrom);
 freeMem(el->shgcG3Chrom);
 freeMem(el->wiYacChrom);
 freeMem(el->wiRhChrom);
 freeMem(el->fishChrom);
 freeMem(el->beginBand);
 freeMem(el->endBand);
 freeMem(el->decodeChrom);
 freez(pEl);
 }
 
 void stsMapFreeList(struct stsMap **pList)
 /* Free a list of dynamically allocated stsMap's */
 {
 struct stsMap *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     stsMapFree(&el);
     }
 *pList = NULL;
 }
 
 void stsMapOutput(struct stsMap *el, FILE *f, char sep, char lastSep) 
 /* Print out stsMap.  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, "%d", 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);
 fprintf(f, "%u", el->identNo);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->ctgAcc);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->otherAcc);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->genethonChrom);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%f", el->genethonPos);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->marshfieldChrom);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%f", el->marshfieldPos);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->gm99Gb4Chrom);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%f", el->gm99Gb4Pos);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->shgcTngChrom);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%f", el->shgcTngPos);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->shgcG3Chrom);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%f", el->shgcG3Pos);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->wiYacChrom);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%f", el->wiYacPos);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->wiRhChrom);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%f", el->wiRhPos);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->fishChrom);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->beginBand);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->endBand);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->lab);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->decodeChrom);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%f", el->decodePos);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 /* ------ End AutoSQL generated Code ------- */
 
 void stsMapFromStsMarker(struct stsMarker *oldEl, struct stsMap *el)
 /* Convert from older stsMarker format to stsMap format. */
 {
 ZeroVar(el);
 el->chrom = oldEl->chrom;
 el->chromStart = oldEl->chromStart;
 el->chromEnd = oldEl->chromEnd;
 el->name = oldEl->name;
 el->score = oldEl->score;
 el->identNo = oldEl->identNo;
 el->ctgAcc = oldEl->ctgAcc;
 el->otherAcc = oldEl->otherAcc;
 el->genethonChrom = oldEl->genethonChrom;
 el->genethonPos = oldEl->genethonPos;
 el->marshfieldChrom = oldEl->marshfieldChrom;
 el->marshfieldPos = oldEl->marshfieldPos;
 el->gm99Gb4Chrom = oldEl->gm99Gb4Chrom;
 el->gm99Gb4Pos = oldEl->gm99Gb4Pos;
 el->shgcG3Chrom = oldEl->shgcG3Chrom;
 el->shgcG3Pos = oldEl->shgcG3Pos;
 el->wiYacChrom = oldEl->wiYacChrom;
 el->wiYacPos = oldEl->wiYacPos;
 el->shgcTngChrom = oldEl->shgcTngChrom;
 el->shgcTngPos = oldEl->shgcTngPos;
 el->fishChrom = oldEl->fishChrom;
 el->beginBand = oldEl->beginBand;
 el->endBand = oldEl->endBand;
 el->wiRhChrom = "0";
 el->wiRhPos = 0;
 el->decodeChrom = "0";
 el->decodePos = 0;
 el->lab = "-";
 }