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/synMap.c src/hg/lib/synMap.c
index bf1c2ac..5ca13bd 100644
--- src/hg/lib/synMap.c
+++ src/hg/lib/synMap.c
@@ -1,175 +1,178 @@
 /* synMap.c was originally generated by the autoSql program, which also 
  * generated synMap.h and synMap.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 "synMap.h"
 
 
 void synMapStaticLoad(char **row, struct synMap *ret)
 /* Load a row from synMap table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->chromA = row[0];
 ret->chromStartA = sqlUnsigned(row[1]);
 ret->chromEndA = sqlUnsigned(row[2]);
 ret->strandA = row[3];
 ret->chromB = row[4];
 ret->chromStartB = sqlUnsigned(row[5]);
 ret->chromEndB = sqlUnsigned(row[6]);
 }
 
 struct synMap *synMapLoad(char **row)
 /* Load a synMap from row fetched with select * from synMap
  * from database.  Dispose of this with synMapFree(). */
 {
 struct synMap *ret;
 
 AllocVar(ret);
 ret->chromA = cloneString(row[0]);
 ret->chromStartA = sqlUnsigned(row[1]);
 ret->chromEndA = sqlUnsigned(row[2]);
 ret->strandA = cloneString(row[3]);
 ret->chromB = cloneString(row[4]);
 ret->chromStartB = sqlUnsigned(row[5]);
 ret->chromEndB = sqlUnsigned(row[6]);
 return ret;
 }
 
 struct synMap *synMapNoStrandLoad(char **row)
 /* Load a synMap from row fetched with select * from synMap
  * from database.  Dispose of this with synMapFree(). */
 {
 struct synMap *ret;
 
 AllocVar(ret);
 ret->chromA = cloneString(row[0]);
 ret->chromStartA = sqlUnsigned(row[1]);
 ret->chromEndA = sqlUnsigned(row[2]);
 
 ret->chromB = cloneString(row[3]);
 ret->chromStartB = sqlUnsigned(row[4]);
 ret->chromEndB = sqlUnsigned(row[5]);
 return ret;
 }
 
 
 struct synMap *synMapLoadAll(char *fileName) 
 /* Load all synMap from a tab-separated file.
  * Dispose of this with synMapFreeList(). */
 {
 struct synMap *list = NULL, *el=NULL;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char **row;
 char *words[32];
 char *line = NULL;
 int lineSize = 1024;
 int wordCount = 0;
 int lineWCount = 0;
 int count =0;
 
 wordCount = lineFileChop(lf, words);
 if (wordCount == 0)
     errAbort("%s appears to be empty", fileName);
 lineFileClose(&lf);
 lf = lineFileOpen(fileName, TRUE);
 row = needMem(sizeof(char *) * wordCount);
 while (lineFileNext(lf, &line, &lineSize))
     {
     count++;
     if(strstr(line, "?") == NULL)
 	{
 	lineWCount = chopByWhite(line, row, wordCount);
 	if(wordCount != lineWCount)
 	    errAbort("Expecting %d words got %d at line %d\n",  wordCount, lineWCount, count);
 	if(lineWCount == 7)
 	    el = synMapLoad(row);
 	else if(lineWCount >= 10)
 	    el = synMapNoStrandLoad(row);
 	else 
 	    errAbort("synMap::synMapLoadAll() - expecting 7 or greater than 10 fields got %d", lineWCount);
 	slAddHead(&list, el);
 	}
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct synMap *synMapCommaIn(char **pS, struct synMap *ret)
 /* Create a synMap out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new synMap */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->chromA = sqlStringComma(&s);
 ret->chromStartA = sqlUnsignedComma(&s);
 ret->chromEndA = sqlUnsignedComma(&s);
 ret->strandA = sqlStringComma(&s);
 ret->chromB = sqlStringComma(&s);
 ret->chromStartB = sqlUnsignedComma(&s);
 ret->chromEndB = sqlUnsignedComma(&s);
 *pS = s;
 return ret;
 }
 
 void synMapFree(struct synMap **pEl)
 /* Free a single dynamically allocated synMap such as created
  * with synMapLoad(). */
 {
 struct synMap *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chromA);
 freeMem(el->strandA);
 freeMem(el->chromB);
 freez(pEl);
 }
 
 void synMapFreeList(struct synMap **pList)
 /* Free a list of dynamically allocated synMap's */
 {
 struct synMap *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     synMapFree(&el);
     }
 *pList = NULL;
 }
 
 void synMapOutput(struct synMap *el, FILE *f, char sep, char lastSep) 
 /* Print out synMap.  Separate fields with sep. Follow last field with lastSep. */
 {
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->chromA);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->chromStartA);
 fputc(sep,f);
 fprintf(f, "%u", el->chromEndA);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->strandA);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->chromB);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->chromStartB);
 fputc(sep,f);
 fprintf(f, "%u", el->chromEndB);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */