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/lib/encode/encodeStanfordPromoters.c src/hg/lib/encode/encodeStanfordPromoters.c
index 98c6ad9..8b732d6 100644
--- src/hg/lib/encode/encodeStanfordPromoters.c
+++ src/hg/lib/encode/encodeStanfordPromoters.c
@@ -1,214 +1,214 @@
 /* encodeStanfordPromoters.c was originally generated by the autoSql program, which also 
  * generated encodeStanfordPromoters.h and encodeStanfordPromoters.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 "encode/encodeStanfordPromoters.h"
 
 
 void encodeStanfordPromotersStaticLoad(char **row, struct encodeStanfordPromoters *ret)
 /* Load a row from encodeStanfordPromoters table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->chrom = row[0];
 ret->chromStart = sqlUnsigned(row[1]);
 ret->chromEnd = sqlUnsigned(row[2]);
 ret->name = 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]);
 ret->geneModel = row[9];
 ret->description = row[10];
 ret->lucA = sqlSigned(row[11]);
 ret->renA = sqlSigned(row[12]);
 ret->lucB = sqlSigned(row[13]);
 ret->renB = sqlSigned(row[14]);
 ret->avgRatio = atof(row[15]);
 ret->normRatio = atof(row[16]);
 ret->normLog2Ratio = atof(row[17]);
 }
 
 struct encodeStanfordPromoters *encodeStanfordPromotersLoad(char **row)
 /* Load a encodeStanfordPromoters from row fetched with select * from encodeStanfordPromoters
  * from database.  Dispose of this with encodeStanfordPromotersFree(). */
 {
 struct encodeStanfordPromoters *ret;
 
 AllocVar(ret);
 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]);
 ret->geneModel = cloneString(row[9]);
 ret->description = cloneString(row[10]);
 ret->lucA = sqlSigned(row[11]);
 ret->renA = sqlSigned(row[12]);
 ret->lucB = sqlSigned(row[13]);
 ret->renB = sqlSigned(row[14]);
 ret->avgRatio = atof(row[15]);
 ret->normRatio = atof(row[16]);
 ret->normLog2Ratio = atof(row[17]);
 return ret;
 }
 
 struct encodeStanfordPromoters *encodeStanfordPromotersLoadAll(char *fileName) 
 /* Load all encodeStanfordPromoters from a whitespace-separated file.
  * Dispose of this with encodeStanfordPromotersFreeList(). */
 {
 struct encodeStanfordPromoters *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[18];
 
 while (lineFileRow(lf, row))
     {
     el = encodeStanfordPromotersLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct encodeStanfordPromoters *encodeStanfordPromotersLoadAllByChar(char *fileName, char chopper) 
 /* Load all encodeStanfordPromoters from a chopper separated file.
  * Dispose of this with encodeStanfordPromotersFreeList(). */
 {
 struct encodeStanfordPromoters *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[18];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = encodeStanfordPromotersLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct encodeStanfordPromoters *encodeStanfordPromotersCommaIn(char **pS, struct encodeStanfordPromoters *ret)
 /* Create a encodeStanfordPromoters out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new encodeStanfordPromoters */
 {
 char *s = *pS;
 
 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->geneModel = sqlStringComma(&s);
 ret->description = sqlStringComma(&s);
 ret->lucA = sqlSignedComma(&s);
 ret->renA = sqlSignedComma(&s);
 ret->lucB = sqlSignedComma(&s);
 ret->renB = sqlSignedComma(&s);
 ret->avgRatio = sqlFloatComma(&s);
 ret->normRatio = sqlFloatComma(&s);
 ret->normLog2Ratio = sqlFloatComma(&s);
 *pS = s;
 return ret;
 }
 
 void encodeStanfordPromotersFree(struct encodeStanfordPromoters **pEl)
 /* Free a single dynamically allocated encodeStanfordPromoters such as created
  * with encodeStanfordPromotersLoad(). */
 {
 struct encodeStanfordPromoters *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->name);
 freeMem(el->geneModel);
 freeMem(el->description);
 freez(pEl);
 }
 
 void encodeStanfordPromotersFreeList(struct encodeStanfordPromoters **pList)
 /* Free a list of dynamically allocated encodeStanfordPromoters's */
 {
 struct encodeStanfordPromoters *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     encodeStanfordPromotersFree(&el);
     }
 *pList = NULL;
 }
 
 void encodeStanfordPromotersOutput(struct encodeStanfordPromoters *el, FILE *f, char sep, char lastSep) 
 /* Print out encodeStanfordPromoters.  Separate fields with sep. Follow last field with lastSep. */
 {
 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);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->geneModel);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->description);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%d", el->lucA);
 fputc(sep,f);
 fprintf(f, "%d", el->renA);
 fputc(sep,f);
 fprintf(f, "%d", el->lucB);
 fputc(sep,f);
 fprintf(f, "%d", el->renB);
 fputc(sep,f);
 fprintf(f, "%g", el->avgRatio);
 fputc(sep,f);
 fprintf(f, "%g", el->normRatio);
 fputc(sep,f);
 fprintf(f, "%g", el->normLog2Ratio);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */