4898794edd81be5285ea6e544acbedeaeb31bf78
max
  Tue Nov 23 08:10:57 2021 -0800
Fixing pointers to README file for license in all source code files. refs #27614

diff --git src/hg/cgilib/fishClones.c src/hg/cgilib/fishClones.c
index 29f535c..11727c5 100644
--- src/hg/cgilib/fishClones.c
+++ src/hg/cgilib/fishClones.c
@@ -1,278 +1,278 @@
 /* fishClones.c was originally generated by the autoSql program, which also 
  * generated fishClones.h and fishClones.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. */
+ * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 
 #include "common.h"
 #include "linefile.h"
 #include "jksql.h"
 #include "fishClones.h"
 
 
 struct fishClones *fishClonesLoad(char **row)
 /* Load a fishClones from row fetched with select * from fishClones
  * from database.  Dispose of this with fishClonesFree(). */
 {
 struct fishClones *ret;
 int sizeOne;
 
 AllocVar(ret);
 ret->placeCount = sqlUnsigned(row[5]);
 ret->accCount = sqlUnsigned(row[10]);
 ret->stsCount = sqlUnsigned(row[12]);
 ret->beCount = sqlUnsigned(row[14]);
 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]);
 sqlStringDynamicArray(row[6], &ret->bandStarts, &sizeOne);
 assert(sizeOne == ret->placeCount);
 sqlStringDynamicArray(row[7], &ret->bandEnds, &sizeOne);
 assert(sizeOne == ret->placeCount);
 sqlStringDynamicArray(row[8], &ret->labs, &sizeOne);
 assert(sizeOne == ret->placeCount);
 ret->placeType = cloneString(row[9]);
 sqlStringDynamicArray(row[11], &ret->accNames, &sizeOne);
 assert(sizeOne == ret->accCount);
 sqlStringDynamicArray(row[13], &ret->stsNames, &sizeOne);
 assert(sizeOne == ret->stsCount);
 sqlStringDynamicArray(row[15], &ret->beNames, &sizeOne);
 assert(sizeOne == ret->beCount);
 return ret;
 }
 
 struct fishClones *fishClonesLoadAll(char *fileName) 
 /* Load all fishClones from a tab-separated file.
  * Dispose of this with fishClonesFreeList(). */
 {
 struct fishClones *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[16];
 
 while (lineFileRow(lf, row))
     {
     el = fishClonesLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct fishClones *fishClonesCommaIn(char **pS, struct fishClones *ret)
 /* Create a fishClones out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new fishClones */
 {
 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);
 ret->placeCount = sqlUnsignedComma(&s);
 s = sqlEatChar(s, '{');
 AllocArray(ret->bandStarts, ret->placeCount);
 for (i=0; i<ret->placeCount; ++i)
     {
     ret->bandStarts[i] = sqlStringComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 s = sqlEatChar(s, '{');
 AllocArray(ret->bandEnds, ret->placeCount);
 for (i=0; i<ret->placeCount; ++i)
     {
     ret->bandEnds[i] = sqlStringComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 s = sqlEatChar(s, '{');
 AllocArray(ret->labs, ret->placeCount);
 for (i=0; i<ret->placeCount; ++i)
     {
     ret->labs[i] = sqlStringComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 ret->placeType = sqlStringComma(&s);
 ret->accCount = sqlUnsignedComma(&s);
 s = sqlEatChar(s, '{');
 AllocArray(ret->accNames, ret->accCount);
 for (i=0; i<ret->accCount; ++i)
     {
     ret->accNames[i] = sqlStringComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 ret->stsCount = sqlUnsignedComma(&s);
 s = sqlEatChar(s, '{');
 AllocArray(ret->stsNames, ret->stsCount);
 for (i=0; i<ret->stsCount; ++i)
     {
     ret->stsNames[i] = sqlStringComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 ret->beCount = sqlUnsignedComma(&s);
 s = sqlEatChar(s, '{');
 AllocArray(ret->beNames, ret->beCount);
 for (i=0; i<ret->beCount; ++i)
     {
     ret->beNames[i] = sqlStringComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 *pS = s;
 return ret;
 }
 
 void fishClonesFree(struct fishClones **pEl)
 /* Free a single dynamically allocated fishClones such as created
  * with fishClonesLoad(). */
 {
 struct fishClones *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->name);
 /* All strings in bandStarts are allocated at once, so only need to free first. */
 if (el->bandStarts != NULL)
     freeMem(el->bandStarts[0]);
 freeMem(el->bandStarts);
 /* All strings in bandEnds are allocated at once, so only need to free first. */
 if (el->bandEnds != NULL)
     freeMem(el->bandEnds[0]);
 freeMem(el->bandEnds);
 /* All strings in labs are allocated at once, so only need to free first. */
 if (el->labs != NULL)
     freeMem(el->labs[0]);
 freeMem(el->labs);
 freeMem(el->placeType);
 /* All strings in accNames are allocated at once, so only need to free first. */
 if (el->accNames != NULL)
     freeMem(el->accNames[0]);
 freeMem(el->accNames);
 /* All strings in stsNames are allocated at once, so only need to free first. */
 if (el->stsNames != NULL)
     freeMem(el->stsNames[0]);
 freeMem(el->stsNames);
 /* All strings in beNames are allocated at once, so only need to free first. */
 if (el->beNames != NULL)
     freeMem(el->beNames[0]);
 freeMem(el->beNames);
 freez(pEl);
 }
 
 void fishClonesFreeList(struct fishClones **pList)
 /* Free a list of dynamically allocated fishClones's */
 {
 struct fishClones *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     fishClonesFree(&el);
     }
 *pList = NULL;
 }
 
 void fishClonesOutput(struct fishClones *el, FILE *f, char sep, char lastSep) 
 /* Print out fishClones.  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);
 fprintf(f, "%u", el->placeCount);
 fputc(sep,f);
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->placeCount; ++i)
     {
     if (sep == ',') fputc('"',f);
     fprintf(f, "%s", el->bandStarts[i]);
     if (sep == ',') fputc('"',f);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 fputc(sep,f);
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->placeCount; ++i)
     {
     if (sep == ',') fputc('"',f);
     fprintf(f, "%s", el->bandEnds[i]);
     if (sep == ',') fputc('"',f);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 fputc(sep,f);
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->placeCount; ++i)
     {
     if (sep == ',') fputc('"',f);
     fprintf(f, "%s", el->labs[i]);
     if (sep == ',') fputc('"',f);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->placeType);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->accCount);
 fputc(sep,f);
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->accCount; ++i)
     {
     if (sep == ',') fputc('"',f);
     fprintf(f, "%s", el->accNames[i]);
     if (sep == ',') fputc('"',f);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 fputc(sep,f);
 fprintf(f, "%u", el->stsCount);
 fputc(sep,f);
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->stsCount; ++i)
     {
     if (sep == ',') fputc('"',f);
     fprintf(f, "%s", el->stsNames[i]);
     if (sep == ',') fputc('"',f);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 fputc(sep,f);
 fprintf(f, "%u", el->beCount);
 fputc(sep,f);
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->beCount; ++i)
     {
     if (sep == ',') fputc('"',f);
     fprintf(f, "%s", el->beNames[i]);
     if (sep == ',') fputc('"',f);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 fputc(lastSep,f);
 }