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/snp125CodingCoordless.c src/hg/cgilib/snp125CodingCoordless.c
index 4e92475..be668b8 100644
--- src/hg/cgilib/snp125CodingCoordless.c
+++ src/hg/cgilib/snp125CodingCoordless.c
@@ -1,258 +1,258 @@
 /* snp125CodingCoordless.c was originally generated by the autoSql program, which also 
  * generated snp125CodingCoordless.h and snp125CodingCoordless.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 "dystring.h"
 #include "jksql.h"
 #include "snp125CodingCoordless.h"
 
 
 /* definitions for frame column */
 static char *values_frame[] = {"1", "2", "3", "n/a", NULL};
 static struct hash *valhash_frame = NULL;
 
 struct snp125CodingCoordless *snp125CodingCoordlessLoad(char **row)
 /* Load a snp125CodingCoordless from row fetched with select * from snp125CodingCoordless
  * from database.  Dispose of this with snp125CodingCoordlessFree(). */
 {
 struct snp125CodingCoordless *ret;
 
 AllocVar(ret);
 ret->alleleCount = sqlSigned(row[3]);
 ret->name = cloneString(row[0]);
 ret->transcript = cloneString(row[1]);
 ret->frame = sqlEnumParse(row[2], values_frame, &valhash_frame);
 {
 int sizeOne;
 sqlUshortDynamicArray(row[4], &ret->funcCodes, &sizeOne);
 assert(sizeOne == ret->alleleCount);
 }
 {
 int sizeOne;
 sqlStringDynamicArray(row[5], &ret->alleles, &sizeOne);
 assert(sizeOne == ret->alleleCount);
 }
 {
 int sizeOne;
 sqlStringDynamicArray(row[6], &ret->codons, &sizeOne);
 assert(sizeOne == ret->alleleCount);
 }
 {
 int sizeOne;
 sqlStringDynamicArray(row[7], &ret->peptides, &sizeOne);
 assert(sizeOne == ret->alleleCount);
 }
 return ret;
 }
 
 struct snp125CodingCoordless *snp125CodingCoordlessLoadAll(char *fileName) 
 /* Load all snp125CodingCoordless from a whitespace-separated file.
  * Dispose of this with snp125CodingCoordlessFreeList(). */
 {
 struct snp125CodingCoordless *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[8];
 
 while (lineFileRow(lf, row))
     {
     el = snp125CodingCoordlessLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct snp125CodingCoordless *snp125CodingCoordlessLoadAllByChar(char *fileName, char chopper) 
 /* Load all snp125CodingCoordless from a chopper separated file.
  * Dispose of this with snp125CodingCoordlessFreeList(). */
 {
 struct snp125CodingCoordless *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[8];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = snp125CodingCoordlessLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct snp125CodingCoordless *snp125CodingCoordlessCommaIn(char **pS, struct snp125CodingCoordless *ret)
 /* Create a snp125CodingCoordless out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new snp125CodingCoordless */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->name = sqlStringComma(&s);
 ret->transcript = sqlStringComma(&s);
 ret->frame = sqlEnumComma(&s, values_frame, &valhash_frame);
 ret->alleleCount = sqlSignedComma(&s);
 {
 int i;
 s = sqlEatChar(s, '{');
 AllocArray(ret->funcCodes, ret->alleleCount);
 for (i=0; i<ret->alleleCount; ++i)
     {
     ret->funcCodes[i] = sqlUnsignedComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 }
 {
 int i;
 s = sqlEatChar(s, '{');
 AllocArray(ret->alleles, ret->alleleCount);
 for (i=0; i<ret->alleleCount; ++i)
     {
     ret->alleles[i] = sqlStringComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 }
 {
 int i;
 s = sqlEatChar(s, '{');
 AllocArray(ret->codons, ret->alleleCount);
 for (i=0; i<ret->alleleCount; ++i)
     {
     ret->codons[i] = sqlStringComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 }
 {
 int i;
 s = sqlEatChar(s, '{');
 AllocArray(ret->peptides, ret->alleleCount);
 for (i=0; i<ret->alleleCount; ++i)
     {
     ret->peptides[i] = sqlStringComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 }
 *pS = s;
 return ret;
 }
 
 void snp125CodingCoordlessFree(struct snp125CodingCoordless **pEl)
 /* Free a single dynamically allocated snp125CodingCoordless such as created
  * with snp125CodingCoordlessLoad(). */
 {
 struct snp125CodingCoordless *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->name);
 freeMem(el->transcript);
 freeMem(el->funcCodes);
 /* All strings in alleles are allocated at once, so only need to free first. */
 if (el->alleles != NULL)
     freeMem(el->alleles[0]);
 freeMem(el->alleles);
 /* All strings in codons are allocated at once, so only need to free first. */
 if (el->codons != NULL)
     freeMem(el->codons[0]);
 freeMem(el->codons);
 /* All strings in peptides are allocated at once, so only need to free first. */
 if (el->peptides != NULL)
     freeMem(el->peptides[0]);
 freeMem(el->peptides);
 freez(pEl);
 }
 
 void snp125CodingCoordlessFreeList(struct snp125CodingCoordless **pList)
 /* Free a list of dynamically allocated snp125CodingCoordless's */
 {
 struct snp125CodingCoordless *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     snp125CodingCoordlessFree(&el);
     }
 *pList = NULL;
 }
 
 void snp125CodingCoordlessOutput(struct snp125CodingCoordless *el, FILE *f, char sep, char lastSep) 
 /* Print out snp125CodingCoordless.  Separate fields with sep. Follow last field with lastSep. */
 {
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->name);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->transcript);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 sqlEnumPrint(f, el->frame, values_frame);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%d", el->alleleCount);
 fputc(sep,f);
 {
 int i;
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->alleleCount; ++i)
     {
     fprintf(f, "%u", el->funcCodes[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 }
 fputc(sep,f);
 {
 int i;
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->alleleCount; ++i)
     {
     if (sep == ',') fputc('"',f);
     fprintf(f, "%s", el->alleles[i]);
     if (sep == ',') fputc('"',f);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 }
 fputc(sep,f);
 {
 int i;
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->alleleCount; ++i)
     {
     if (sep == ',') fputc('"',f);
     fprintf(f, "%s", el->codons[i]);
     if (sep == ',') fputc('"',f);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 }
 fputc(sep,f);
 {
 int i;
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->alleleCount; ++i)
     {
     if (sep == ',') fputc('"',f);
     fprintf(f, "%s", el->peptides[i]);
     if (sep == ',') fputc('"',f);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 }
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */