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/mrnaMisMatch.c src/hg/lib/mrnaMisMatch.c
index b579984..4de2d73 100644
--- src/hg/lib/mrnaMisMatch.c
+++ src/hg/lib/mrnaMisMatch.c
@@ -1,267 +1,270 @@
 /* mrnaMisMatch.c was originally generated by the autoSql program, which also 
  * generated mrnaMisMatch.h and mrnaMisMatch.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 "mrnaMisMatch.h"
 
 
 struct mrnaMisMatch *mrnaMisMatchLoad(char **row)
 /* Load a mrnaMisMatch from row fetched with select * from mrnaMisMatch
  * from database.  Dispose of this with mrnaMisMatchFree(). */
 {
 struct mrnaMisMatch *ret;
 
 AllocVar(ret);
 ret->misMatchCount = sqlSigned(row[3]);
 ret->snpCount = sqlSigned(row[9]);
 ret->name = cloneString(row[0]);
 ret->mrnaBase = row[1][0];
 ret->mrnaLoc = sqlSigned(row[2]);
 ret->bases = cloneString(row[4]);
 {
 int sizeOne;
 sqlStringDynamicArray(row[5], &ret->chroms, &sizeOne);
 assert(sizeOne == ret->misMatchCount);
 }
 {
 int sizeOne;
 sqlUnsignedDynamicArray(row[6], &ret->tStarts, &sizeOne);
 assert(sizeOne == ret->misMatchCount);
 }
 ret->strands = cloneString(row[7]);
 {
 int sizeOne;
 sqlUnsignedDynamicArray(row[8], &ret->loci, &sizeOne);
 assert(sizeOne == ret->misMatchCount);
 }
 {
 int sizeOne;
 sqlStringDynamicArray(row[10], &ret->snps, &sizeOne);
 assert(sizeOne == ret->snpCount);
 }
 return ret;
 }
 
 struct mrnaMisMatch *mrnaMisMatchLoadAll(char *fileName) 
 /* Load all mrnaMisMatch from a whitespace-separated file.
  * Dispose of this with mrnaMisMatchFreeList(). */
 {
 struct mrnaMisMatch *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[11];
 
 while (lineFileRow(lf, row))
     {
     el = mrnaMisMatchLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct mrnaMisMatch *mrnaMisMatchLoadAllByChar(char *fileName, char chopper) 
 /* Load all mrnaMisMatch from a chopper separated file.
  * Dispose of this with mrnaMisMatchFreeList(). */
 {
 struct mrnaMisMatch *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[11];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = mrnaMisMatchLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct mrnaMisMatch *mrnaMisMatchCommaIn(char **pS, struct mrnaMisMatch *ret)
 /* Create a mrnaMisMatch out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new mrnaMisMatch */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->name = sqlStringComma(&s);
 sqlFixedStringComma(&s, &(ret->mrnaBase), sizeof(ret->mrnaBase));
 ret->mrnaLoc = sqlSignedComma(&s);
 ret->misMatchCount = sqlSignedComma(&s);
 ret->bases = sqlStringComma(&s);
 {
 int i;
 s = sqlEatChar(s, '{');
 AllocArray(ret->chroms, ret->misMatchCount);
 for (i=0; i<ret->misMatchCount; ++i)
     {
     ret->chroms[i] = sqlStringComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 }
 {
 int i;
 s = sqlEatChar(s, '{');
 AllocArray(ret->tStarts, ret->misMatchCount);
 for (i=0; i<ret->misMatchCount; ++i)
     {
     ret->tStarts[i] = sqlUnsignedComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 }
 ret->strands = sqlStringComma(&s);
 {
 int i;
 s = sqlEatChar(s, '{');
 AllocArray(ret->loci, ret->misMatchCount);
 for (i=0; i<ret->misMatchCount; ++i)
     {
     ret->loci[i] = sqlUnsignedComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 }
 ret->snpCount = sqlSignedComma(&s);
 {
 int i;
 s = sqlEatChar(s, '{');
 AllocArray(ret->snps, ret->snpCount);
 for (i=0; i<ret->snpCount; ++i)
     {
     ret->snps[i] = sqlStringComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 }
 *pS = s;
 return ret;
 }
 
 void mrnaMisMatchFree(struct mrnaMisMatch **pEl)
 /* Free a single dynamically allocated mrnaMisMatch such as created
  * with mrnaMisMatchLoad(). */
 {
 struct mrnaMisMatch *el;
 int i;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->name);
 freeMem(el->bases);
 for (i = 0 ; i < el->misMatchCount; i++)
     if (el->chroms[i] != NULL)
         freeMem(el->chroms[i]);
 freeMem(el->chroms);
 freeMem(el->tStarts);
 freeMem(el->strands);
 freeMem(el->loci);
 for (i = 0 ; i < el->misMatchCount; i++)
     if (el->snps[i] != NULL)
         freeMem(el->snps[i]);
 freeMem(el->snps);
 freez(pEl);
 }
 
 void mrnaMisMatchFreeList(struct mrnaMisMatch **pList)
 /* Free a list of dynamically allocated mrnaMisMatch's */
 {
 struct mrnaMisMatch *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     mrnaMisMatchFree(&el);
     }
 *pList = NULL;
 }
 
 void mrnaMisMatchOutput(struct mrnaMisMatch *el, FILE *f, char sep, char lastSep) 
 /* Print out mrnaMisMatch.  Separate fields with sep. Follow last field with lastSep. */
 {
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->name);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%c", el->mrnaBase);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%d", el->mrnaLoc);
 fputc(sep,f);
 fprintf(f, "%d", el->misMatchCount);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->bases);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 {
 int i;
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->misMatchCount; ++i)
     {
     if (sep == ',') fputc('"',f);
     fprintf(f, "%s", el->chroms[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->misMatchCount; ++i)
     {
     fprintf(f, "%u", el->tStarts[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 }
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->strands);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 {
 int i;
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->misMatchCount; ++i)
     {
     fprintf(f, "%u", el->loci[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 }
 fputc(sep,f);
 fprintf(f, "%d", el->snpCount);
 fputc(sep,f);
 {
 int i;
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->misMatchCount; i++)
     {
     if (sep == ',') fputc('"',f);
 //        printf("bad snp %s i=%d cnt=%d\n",el->name, i, el->snpCount);
 //    assert(el->snps[i] != NULL);
     if(el->snps[i] != NULL)
         {
         fprintf(f, "%s", el->snps[i]);
         }
     if (sep == ',') fputc('"',f);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 }
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */