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/alignInfo.c src/hg/lib/alignInfo.c
index 5b9aefe..d490fcf 100644
--- src/hg/lib/alignInfo.c
+++ src/hg/lib/alignInfo.c
@@ -1,179 +1,179 @@
 /* alignInfo.c was originally generated by the autoSql program, which also 
  * generated alignInfo.h and alignInfo.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 "alignInfo.h"
 
 
 void alignInfoStaticLoad(char **row, struct alignInfo *ret)
 /* Load a row from alignInfo 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->hasmatch = sqlUnsigned(row[6]);
 ret->orgn = row[7];
 ret->alignChrom = row[8];
 ret->alignChromStart = sqlUnsigned(row[9]);
 ret->alignChromEnd = sqlUnsigned(row[10]);
 }
 
 struct alignInfo *alignInfoLoad(char **row)
 /* Load a alignInfo from row fetched with select * from alignInfo
  * from database.  Dispose of this with alignInfoFree(). */
 {
 struct alignInfo *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->hasmatch = sqlUnsigned(row[6]);
 ret->orgn = cloneString(row[7]);
 ret->alignChrom = cloneString(row[8]);
 ret->alignChromStart = sqlUnsigned(row[9]);
 ret->alignChromEnd = sqlUnsigned(row[10]);
 return ret;
 }
 
 struct alignInfo *alignInfoLoadAll(char *fileName) 
 /* Load all alignInfo from a whitespace-separated file.
  * Dispose of this with alignInfoFreeList(). */
 {
 struct alignInfo *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[11];
 
 while (lineFileRow(lf, row))
     {
     el = alignInfoLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct alignInfo *alignInfoLoadAllByChar(char *fileName, char chopper) 
 /* Load all alignInfo from a chopper separated file.
  * Dispose of this with alignInfoFreeList(). */
 {
 struct alignInfo *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[11];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = alignInfoLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct alignInfo *alignInfoCommaIn(char **pS, struct alignInfo *ret)
 /* Create a alignInfo out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new alignInfo */
 {
 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->hasmatch = sqlUnsignedComma(&s);
 ret->orgn = sqlStringComma(&s);
 ret->alignChrom = sqlStringComma(&s);
 ret->alignChromStart = sqlUnsignedComma(&s);
 ret->alignChromEnd = sqlUnsignedComma(&s);
 *pS = s;
 return ret;
 }
 
 void alignInfoFree(struct alignInfo **pEl)
 /* Free a single dynamically allocated alignInfo such as created
  * with alignInfoLoad(). */
 {
 struct alignInfo *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->name);
 freeMem(el->orgn);
 freeMem(el->alignChrom);
 freez(pEl);
 }
 
 void alignInfoFreeList(struct alignInfo **pList)
 /* Free a list of dynamically allocated alignInfo's */
 {
 struct alignInfo *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     alignInfoFree(&el);
     }
 *pList = NULL;
 }
 
 void alignInfoOutput(struct alignInfo *el, FILE *f, char sep, char lastSep) 
 /* Print out alignInfo.  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->hasmatch);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->orgn);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->alignChrom);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->alignChromStart);
 fputc(sep,f);
 fprintf(f, "%u", el->alignChromEnd);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */