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/snp132Ext.c src/hg/lib/snp132Ext.c
index 7fab020..a90fe3a 100644
--- src/hg/lib/snp132Ext.c
+++ src/hg/lib/snp132Ext.c
@@ -1,345 +1,348 @@
 /* snp132Ext.c was originally generated by the autoSql program, which also 
  * generated snp132Ext.h and snp132Ext.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 "dystring.h"
 #include "jksql.h"
 #include "snp132Ext.h"
 
 
 struct snp132Ext *snp132ExtLoad(char **row)
 /* Load a snp132Ext from row fetched with select * from snp132Ext
  * from database.  Dispose of this with snp132ExtFree(). */
 {
 struct snp132Ext *ret;
 
 AllocVar(ret);
 ret->submitterCount = sqlSigned(row[18]);
 ret->alleleFreqCount = sqlSigned(row[20]);
 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]);
 ret->strand = cloneString(row[5]);
 ret->refNCBI = cloneString(row[6]);
 ret->refUCSC = cloneString(row[7]);
 ret->observed = cloneString(row[8]);
 ret->molType = cloneString(row[9]);
 ret->class = cloneString(row[10]);
 ret->valid = cloneString(row[11]);
 ret->avHet = sqlFloat(row[12]);
 ret->avHetSE = sqlFloat(row[13]);
 ret->func = cloneString(row[14]);
 ret->locType = cloneString(row[15]);
 ret->weight = sqlUnsigned(row[16]);
 ret->exceptions = cloneString(row[17]);
 {
 int sizeOne;
 sqlStringDynamicArray(row[19], &ret->submitters, &sizeOne);
 assert(sizeOne == ret->submitterCount);
 }
 {
 int sizeOne;
 sqlStringDynamicArray(row[21], &ret->alleles, &sizeOne);
 assert(sizeOne == ret->alleleFreqCount);
 }
 {
 int sizeOne;
 sqlFloatDynamicArray(row[22], &ret->alleleNs, &sizeOne);
 assert(sizeOne == ret->alleleFreqCount);
 }
 {
 int sizeOne;
 sqlFloatDynamicArray(row[23], &ret->alleleFreqs, &sizeOne);
 assert(sizeOne == ret->alleleFreqCount);
 }
 ret->bitfields = cloneString(row[24]);
 return ret;
 }
 
 struct snp132Ext *snp132ExtLoadAll(char *fileName) 
 /* Load all snp132Ext from a whitespace-separated file.
  * Dispose of this with snp132ExtFreeList(). */
 {
 struct snp132Ext *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[25];
 
 while (lineFileRow(lf, row))
     {
     el = snp132ExtLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct snp132Ext *snp132ExtLoadAllByChar(char *fileName, char chopper) 
 /* Load all snp132Ext from a chopper separated file.
  * Dispose of this with snp132ExtFreeList(). */
 {
 struct snp132Ext *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[25];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = snp132ExtLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct snp132Ext *snp132ExtCommaIn(char **pS, struct snp132Ext *ret)
 /* Create a snp132Ext out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new snp132Ext */
 {
 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);
 ret->strand = sqlStringComma(&s);
 ret->refNCBI = sqlStringComma(&s);
 ret->refUCSC = sqlStringComma(&s);
 ret->observed = sqlStringComma(&s);
 ret->molType = sqlStringComma(&s);
 ret->class = sqlStringComma(&s);
 ret->valid = sqlStringComma(&s);
 ret->avHet = sqlFloatComma(&s);
 ret->avHetSE = sqlFloatComma(&s);
 ret->func = sqlStringComma(&s);
 ret->locType = sqlStringComma(&s);
 ret->weight = sqlUnsignedComma(&s);
 ret->exceptions = sqlStringComma(&s);
 ret->submitterCount = sqlSignedComma(&s);
 {
 int i;
 s = sqlEatChar(s, '{');
 AllocArray(ret->submitters, ret->submitterCount);
 for (i=0; i<ret->submitterCount; ++i)
     {
     ret->submitters[i] = sqlStringComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 }
 ret->alleleFreqCount = sqlSignedComma(&s);
 {
 int i;
 s = sqlEatChar(s, '{');
 AllocArray(ret->alleles, ret->alleleFreqCount);
 for (i=0; i<ret->alleleFreqCount; ++i)
     {
     ret->alleles[i] = sqlStringComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 }
 {
 int i;
 s = sqlEatChar(s, '{');
 AllocArray(ret->alleleNs, ret->alleleFreqCount);
 for (i=0; i<ret->alleleFreqCount; ++i)
     {
     ret->alleleNs[i] = sqlFloatComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 }
 {
 int i;
 s = sqlEatChar(s, '{');
 AllocArray(ret->alleleFreqs, ret->alleleFreqCount);
 for (i=0; i<ret->alleleFreqCount; ++i)
     {
     ret->alleleFreqs[i] = sqlFloatComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 }
 ret->bitfields = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void snp132ExtFree(struct snp132Ext **pEl)
 /* Free a single dynamically allocated snp132Ext such as created
  * with snp132ExtLoad(). */
 {
 struct snp132Ext *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->name);
 freeMem(el->strand);
 freeMem(el->refNCBI);
 freeMem(el->refUCSC);
 freeMem(el->observed);
 freeMem(el->molType);
 freeMem(el->class);
 freeMem(el->valid);
 freeMem(el->func);
 freeMem(el->locType);
 freeMem(el->exceptions);
 /* All strings in submitters are allocated at once, so only need to free first. */
 if (el->submitters != NULL)
     freeMem(el->submitters[0]);
 freeMem(el->submitters);
 /* All strings in alleles are allocated at once, so only need to free first. */
 if (el->alleles != NULL)
     freeMem(el->alleles[0]);
 freeMem(el->alleles);
 freeMem(el->alleleNs);
 freeMem(el->alleleFreqs);
 freeMem(el->bitfields);
 freez(pEl);
 }
 
 void snp132ExtFreeList(struct snp132Ext **pList)
 /* Free a list of dynamically allocated snp132Ext's */
 {
 struct snp132Ext *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     snp132ExtFree(&el);
     }
 *pList = NULL;
 }
 
 void snp132ExtOutput(struct snp132Ext *el, FILE *f, char sep, char lastSep) 
 /* Print out snp132Ext.  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->refNCBI);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->refUCSC);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->observed);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->molType);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->class);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->valid);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%g", el->avHet);
 fputc(sep,f);
 fprintf(f, "%g", el->avHetSE);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->func);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->locType);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->weight);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->exceptions);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%d", el->submitterCount);
 fputc(sep,f);
 {
 int i;
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->submitterCount; ++i)
     {
     if (sep == ',') fputc('"',f);
     fprintf(f, "%s", el->submitters[i]);
     if (sep == ',') fputc('"',f);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 }
 fputc(sep,f);
 fprintf(f, "%d", el->alleleFreqCount);
 fputc(sep,f);
 {
 int i;
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->alleleFreqCount; ++i)
     {
     if (sep == ',') fputc('"',f);
     fprintf(f, "%s", el->alleles[i]);
     if (sep == ',') fputc('"',f);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 }
 fputc(sep,f);
 {
 int i;
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->alleleFreqCount; ++i)
     {
     fprintf(f, "%g", el->alleleNs[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 }
 fputc(sep,f);
 {
 int i;
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->alleleFreqCount; ++i)
     {
     fprintf(f, "%g", el->alleleFreqs[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 }
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->bitfields);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */