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/visiGene/vgLoadMahoney/mahoney.c src/hg/visiGene/vgLoadMahoney/mahoney.c
index 773b6bb..fa247af 100644
--- src/hg/visiGene/vgLoadMahoney/mahoney.c
+++ src/hg/visiGene/vgLoadMahoney/mahoney.c
@@ -1,259 +1,259 @@
 /* mahoney.c was originally generated by the autoSql program, which also 
  * generated mahoney.h and mahoney.sql.  This module links the database and
  * the RAM representation of objects. */
 
 /* Copyright (C) 2011 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 "dystring.h"
 #include "jksql.h"
 #include "mahoney.h"
 
 
 void mahoneyStaticLoad(char **row, struct mahoney *ret)
 /* Load a row from mahoney table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->empty = row[0];
 ret->mtf = sqlSigned(row[1]);
 ret->sameAs = row[2];
 ret->geneName = row[3];
 ret->domain = row[4];
 ret->genbank = row[5];
 ret->locusId = row[6];
 ret->unigene = row[7];
 ret->fragSize = row[8];
 ret->linzyme = row[9];
 ret->rnaPol = row[10];
 ret->cloneVector = row[11];
 ret->seqVerified = row[12];
 ret->startLoc = row[13];
 ret->endLoc = row[14];
 ret->fPrimer = row[15];
 ret->rPrimer = row[16];
 ret->fAdaptor = row[17];
 ret->rAdaptor = row[18];
 }
 
 struct mahoney *mahoneyLoad(char **row)
 /* Load a mahoney from row fetched with select * from mahoney
  * from database.  Dispose of this with mahoneyFree(). */
 {
 struct mahoney *ret;
 
 AllocVar(ret);
 ret->empty = cloneString(row[0]);
 ret->mtf = sqlSigned(row[1]);
 ret->sameAs = cloneString(row[2]);
 ret->geneName = cloneString(row[3]);
 ret->domain = cloneString(row[4]);
 ret->genbank = cloneString(row[5]);
 ret->locusId = cloneString(row[6]);
 ret->unigene = cloneString(row[7]);
 ret->fragSize = cloneString(row[8]);
 ret->linzyme = cloneString(row[9]);
 ret->rnaPol = cloneString(row[10]);
 ret->cloneVector = cloneString(row[11]);
 ret->seqVerified = cloneString(row[12]);
 ret->startLoc = cloneString(row[13]);
 ret->endLoc = cloneString(row[14]);
 ret->fPrimer = cloneString(row[15]);
 ret->rPrimer = cloneString(row[16]);
 ret->fAdaptor = cloneString(row[17]);
 ret->rAdaptor = cloneString(row[18]);
 return ret;
 }
 
 struct mahoney *mahoneyLoadAll(char *fileName) 
 /* Load all mahoney from a whitespace-separated file.
  * Dispose of this with mahoneyFreeList(). */
 {
 struct mahoney *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[19];
 
 while (lineFileRow(lf, row))
     {
     el = mahoneyLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct mahoney *mahoneyLoadAllByChar(char *fileName, char chopper) 
 /* Load all mahoney from a chopper separated file.
  * Dispose of this with mahoneyFreeList(). */
 {
 struct mahoney *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[19];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = mahoneyLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct mahoney *mahoneyCommaIn(char **pS, struct mahoney *ret)
 /* Create a mahoney out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new mahoney */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->empty = sqlStringComma(&s);
 ret->mtf = sqlSignedComma(&s);
 ret->sameAs = sqlStringComma(&s);
 ret->geneName = sqlStringComma(&s);
 ret->domain = sqlStringComma(&s);
 ret->genbank = sqlStringComma(&s);
 ret->locusId = sqlStringComma(&s);
 ret->unigene = sqlStringComma(&s);
 ret->fragSize = sqlStringComma(&s);
 ret->linzyme = sqlStringComma(&s);
 ret->rnaPol = sqlStringComma(&s);
 ret->cloneVector = sqlStringComma(&s);
 ret->seqVerified = sqlStringComma(&s);
 ret->startLoc = sqlStringComma(&s);
 ret->endLoc = sqlStringComma(&s);
 ret->fPrimer = sqlStringComma(&s);
 ret->rPrimer = sqlStringComma(&s);
 ret->fAdaptor = sqlStringComma(&s);
 ret->rAdaptor = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void mahoneyFree(struct mahoney **pEl)
 /* Free a single dynamically allocated mahoney such as created
  * with mahoneyLoad(). */
 {
 struct mahoney *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->empty);
 freeMem(el->sameAs);
 freeMem(el->geneName);
 freeMem(el->domain);
 freeMem(el->genbank);
 freeMem(el->locusId);
 freeMem(el->unigene);
 freeMem(el->fragSize);
 freeMem(el->linzyme);
 freeMem(el->rnaPol);
 freeMem(el->cloneVector);
 freeMem(el->seqVerified);
 freeMem(el->startLoc);
 freeMem(el->endLoc);
 freeMem(el->fPrimer);
 freeMem(el->rPrimer);
 freeMem(el->fAdaptor);
 freeMem(el->rAdaptor);
 freez(pEl);
 }
 
 void mahoneyFreeList(struct mahoney **pList)
 /* Free a list of dynamically allocated mahoney's */
 {
 struct mahoney *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     mahoneyFree(&el);
     }
 *pList = NULL;
 }
 
 void mahoneyOutput(struct mahoney *el, FILE *f, char sep, char lastSep) 
 /* Print out mahoney.  Separate fields with sep. Follow last field with lastSep. */
 {
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->empty);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%d", el->mtf);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->sameAs);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->geneName);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->domain);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->genbank);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->locusId);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->unigene);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->fragSize);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->linzyme);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->rnaPol);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->cloneVector);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->seqVerified);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->startLoc);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->endLoc);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->fPrimer);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->rPrimer);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->fAdaptor);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->rAdaptor);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */