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/zdobnovSynt.c src/hg/lib/zdobnovSynt.c
index 82fcf9e..64a560b 100644
--- src/hg/lib/zdobnovSynt.c
+++ src/hg/lib/zdobnovSynt.c
@@ -1,213 +1,216 @@
 /* zdobnovSynt.c was originally generated by the autoSql program, which also 
  * generated zdobnovSynt.h and zdobnovSynt.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 "zdobnovSynt.h"
 
 
 struct zdobnovSynt *zdobnovSyntLoad(char **row)
 /* Load a zdobnovSynt from row fetched with select * from zdobnovSynt
  * from database.  Dispose of this with zdobnovSyntFree(). */
 {
 struct zdobnovSynt *ret;
 int sizeOne;
 
 AllocVar(ret);
 ret->blockCount = sqlSigned(row[9]);
 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]);
 strcpy(ret->strand, row[5]);
 ret->thickStart = sqlUnsigned(row[6]);
 ret->thickEnd = sqlUnsigned(row[7]);
 ret->reserved = sqlUnsigned(row[8]);
 sqlSignedDynamicArray(row[10], &ret->blockSizes, &sizeOne);
 assert(sizeOne == ret->blockCount);
 sqlSignedDynamicArray(row[11], &ret->chromStarts, &sizeOne);
 assert(sizeOne == ret->blockCount);
 sqlStringDynamicArray(row[12], &ret->geneNames, &sizeOne);
 assert(sizeOne == ret->blockCount);
 return ret;
 }
 
 struct zdobnovSynt *zdobnovSyntLoadAll(char *fileName) 
 /* Load all zdobnovSynt from a whitespace-separated file.
  * Dispose of this with zdobnovSyntFreeList(). */
 {
 struct zdobnovSynt *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[13];
 
 while (lineFileRow(lf, row))
     {
     el = zdobnovSyntLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct zdobnovSynt *zdobnovSyntLoadAllByChar(char *fileName, char chopper) 
 /* Load all zdobnovSynt from a chopper separated file.
  * Dispose of this with zdobnovSyntFreeList(). */
 {
 struct zdobnovSynt *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[13];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = zdobnovSyntLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct zdobnovSynt *zdobnovSyntCommaIn(char **pS, struct zdobnovSynt *ret)
 /* Create a zdobnovSynt out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new zdobnovSynt */
 {
 char *s = *pS;
 int i;
 
 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);
 sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand));
 ret->thickStart = sqlUnsignedComma(&s);
 ret->thickEnd = sqlUnsignedComma(&s);
 ret->reserved = sqlUnsignedComma(&s);
 ret->blockCount = sqlSignedComma(&s);
 s = sqlEatChar(s, '{');
 AllocArray(ret->blockSizes, ret->blockCount);
 for (i=0; i<ret->blockCount; ++i)
     {
     ret->blockSizes[i] = sqlSignedComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 s = sqlEatChar(s, '{');
 AllocArray(ret->chromStarts, ret->blockCount);
 for (i=0; i<ret->blockCount; ++i)
     {
     ret->chromStarts[i] = sqlSignedComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 s = sqlEatChar(s, '{');
 AllocArray(ret->geneNames, ret->blockCount);
 for (i=0; i<ret->blockCount; ++i)
     {
     ret->geneNames[i] = sqlStringComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 *pS = s;
 return ret;
 }
 
 void zdobnovSyntFree(struct zdobnovSynt **pEl)
 /* Free a single dynamically allocated zdobnovSynt such as created
  * with zdobnovSyntLoad(). */
 {
 struct zdobnovSynt *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->name);
 freeMem(el->blockSizes);
 freeMem(el->chromStarts);
 /* All strings in geneNames are allocated at once, so only need to free first. */
 if (el->geneNames != NULL)
     freeMem(el->geneNames[0]);
 freeMem(el->geneNames);
 freez(pEl);
 }
 
 void zdobnovSyntFreeList(struct zdobnovSynt **pList)
 /* Free a list of dynamically allocated zdobnovSynt's */
 {
 struct zdobnovSynt *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     zdobnovSyntFree(&el);
     }
 *pList = NULL;
 }
 
 void zdobnovSyntOutput(struct zdobnovSynt *el, FILE *f, char sep, char lastSep) 
 /* Print out zdobnovSynt.  Separate fields with sep. Follow last field with lastSep. */
 {
 int i;
 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);
 fprintf(f, "%u", el->thickStart);
 fputc(sep,f);
 fprintf(f, "%u", el->thickEnd);
 fputc(sep,f);
 fprintf(f, "%u", el->reserved);
 fputc(sep,f);
 fprintf(f, "%d", el->blockCount);
 fputc(sep,f);
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->blockCount; ++i)
     {
     fprintf(f, "%d", el->blockSizes[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 fputc(sep,f);
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->blockCount; ++i)
     {
     fprintf(f, "%d", el->chromStarts[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 fputc(sep,f);
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->blockCount; ++i)
     {
     if (sep == ',') fputc('"',f);
     fprintf(f, "%s", el->geneNames[i]);
     if (sep == ',') fputc('"',f);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */