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/peptideMapping.c src/hg/lib/encode/peptideMapping.c
index 1a778e9..3d9158e 100644
--- src/hg/lib/encode/peptideMapping.c
+++ src/hg/lib/encode/peptideMapping.c
@@ -1,171 +1,171 @@
 /* peptideMapping.c was originally generated by the autoSql program, which also 
  * generated peptideMapping.h and peptideMapping.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 "peptideMapping.h"
 
 
 void peptideMappingStaticLoad(char **row, struct peptideMapping *ret)
 /* Load a row from peptideMapping 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]);
 safecpy(ret->strand, sizeof(ret->strand), row[5]);
 ret->rawScore = sqlFloat(row[6]);
 ret->spectrumId = row[7];
 ret->peptideRank = sqlUnsigned(row[8]);
 ret->peptideRepeatCount = sqlUnsigned(row[9]);
 }
 
 struct peptideMapping *peptideMappingLoad(char **row)
 /* Load a peptideMapping from row fetched with select * from peptideMapping
  * from database.  Dispose of this with peptideMappingFree(). */
 {
 struct peptideMapping *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]);
 safecpy(ret->strand, sizeof(ret->strand), row[5]);
 ret->rawScore = sqlFloat(row[6]);
 ret->spectrumId = cloneString(row[7]);
 ret->peptideRank = sqlUnsigned(row[8]);
 ret->peptideRepeatCount = sqlUnsigned(row[9]);
 return ret;
 }
 
 struct peptideMapping *peptideMappingLoadAll(char *fileName) 
 /* Load all peptideMapping from a whitespace-separated file.
  * Dispose of this with peptideMappingFreeList(). */
 {
 struct peptideMapping *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[10];
 
 while (lineFileRow(lf, row))
     {
     el = peptideMappingLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct peptideMapping *peptideMappingLoadAllByChar(char *fileName, char chopper) 
 /* Load all peptideMapping from a chopper separated file.
  * Dispose of this with peptideMappingFreeList(). */
 {
 struct peptideMapping *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[10];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = peptideMappingLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct peptideMapping *peptideMappingCommaIn(char **pS, struct peptideMapping *ret)
 /* Create a peptideMapping out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new peptideMapping */
 {
 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->rawScore = sqlFloatComma(&s);
 ret->spectrumId = sqlStringComma(&s);
 ret->peptideRank = sqlUnsignedComma(&s);
 ret->peptideRepeatCount = sqlUnsignedComma(&s);
 *pS = s;
 return ret;
 }
 
 void peptideMappingFree(struct peptideMapping **pEl)
 /* Free a single dynamically allocated peptideMapping such as created
  * with peptideMappingLoad(). */
 {
 struct peptideMapping *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->name);
 freeMem(el->spectrumId);
 freez(pEl);
 }
 
 void peptideMappingFreeList(struct peptideMapping **pList)
 /* Free a list of dynamically allocated peptideMapping's */
 {
 struct peptideMapping *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     peptideMappingFree(&el);
     }
 *pList = NULL;
 }
 
 void peptideMappingOutput(struct peptideMapping *el, FILE *f, char sep, char lastSep) 
 /* Print out peptideMapping.  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, "%g", el->rawScore);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->spectrumId);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->peptideRank);
 fputc(sep,f);
 fprintf(f, "%u", el->peptideRepeatCount);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */