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/factorSource.c src/hg/cgilib/factorSource.c
index f6adbb6..089cd17 100644
--- src/hg/cgilib/factorSource.c
+++ src/hg/cgilib/factorSource.c
@@ -1,222 +1,222 @@
 /* factorSource.c was originally generated by the autoSql program, which also 
  * generated factorSource.h and factorSource.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 "basicBed.h"
 #include "factorSource.h"
 
 
 char *factorSourceCommaSepFieldNames = "chrom,chromStart,chromEnd,name,score,expCount,expNums,expScores";
 
 struct factorSource *factorSourceLoad(char **row);
 
 struct factorSource *factorSourceLoadAll(char *fileName) 
 /* Load all factorSource from a whitespace-separated file.
  * Dispose of this with factorSourceFreeList(). */
 {
 struct factorSource *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[8];
 
 while (lineFileRow(lf, row))
     {
     el = factorSourceLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct factorSource *factorSourceLoadAllByChar(char *fileName, char chopper) 
 /* Load all factorSource from a chopper separated file.
  * Dispose of this with factorSourceFreeList(). */
 {
 struct factorSource *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[8];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = factorSourceLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 void factorSourceFree(struct factorSource **pEl)
 /* Free a single dynamically allocated factorSource such as created
  * with factorSourceLoad(). */
 {
 struct factorSource *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->name);
 freeMem(el->expNums);
 freeMem(el->expScores);
 freez(pEl);
 }
 
 void factorSourceFreeList(struct factorSource **pList)
 /* Free a list of dynamically allocated factorSource's */
 {
 struct factorSource *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     factorSourceFree(&el);
     }
 *pList = NULL;
 }
 
 void factorSourceOutput(struct factorSource *el, FILE *f, char sep, char lastSep) 
 /* Print out factorSource.  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);
 fprintf(f, "%u", el->expCount);
 fputc(sep,f);
 {
 int i;
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->expCount; ++i)
     {
     fprintf(f, "%u", el->expNums[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 }
 fputc(sep,f);
 {
 int i;
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->expCount; ++i)
     {
     fprintf(f, "%g", el->expScores[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 }
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
 // NOTE:  Removed factorSourceCommaIn() from autoSql gened code, as it is unneeded and 
 // would need customizing for the two schemas
 
 // NOTE: make loader able to handle V2 (BED15) and V3 (factorSource) schemas.  
 
 boolean isStrandField(char *field)
 /* Check for '.' strand field */
 {
 if (field[0] == '.')
     return TRUE;
 return FALSE;
 }
 
 struct factorSource *factorSourceLoad(char **row)
 /* Load a factorSource from row fetched with select * from factorSource
  * from database.  Dispose of this with factorSourceFree(). */
 {
 struct factorSource *ret;
 int sizeOne; // autoSql
 
 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]);
 if (isStrandField(row[5]))
     {
     // V2 format (BED15) has sparse info -- filter out zero-scored experiments
     struct bed *bed;
     AllocVar(bed);
     ret->expCount = sqlUnsigned(row[12]);
     sqlSignedDynamicArray(row[13], &bed->expIds, &sizeOne);
     assert(sizeOne == ret->expCount);
     sqlFloatDynamicArray(row[14], &bed->expScores, &sizeOne);
     assert(sizeOne == ret->expCount);
 
     // count non-zero experiments
     ret->expCount = 0;
     int i;
     for (i=0; i<sizeOne; i++)
         {
         float score = bed->expScores[i];
         if (score > 0.0)
             ret->expCount++;
         }
     // populate arrays with non-zero experiments
     AllocArray(ret->expNums, ret->expCount);
     AllocArray(ret->expScores, ret->expCount);
     int j = 0;
     for (i=0; i<sizeOne; i++)
         {
         float score = bed->expScores[i];
         if (score > 0.0)
             {
             ret->expNums[j] = bed->expIds[i];
             ret->expScores[j] = bed->expScores[i];
             j++;
             }
         }
     }
 else
     {
     // V3 format
     ret->expCount = sqlUnsigned(row[5]);
     sqlUnsignedDynamicArray(row[6], &ret->expNums, &sizeOne);
     assert(sizeOne == ret->expCount);
     sqlFloatDynamicArray(row[7], &ret->expScores, &sizeOne);
     assert(sizeOne == ret->expCount);
 }
 return ret;
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
 static char *factorSourceAutoSqlString =
 "table factorSource"
 "\"BED5+ with two fields having variable number of experiment IDs and values (none zero-valued)\""
 "    ("
 "    string chrom;      \"Reference sequence chromosome or scaffold\""
 "    uint   chromStart; \"Start position in chromosome\""
 "    uint   chromEnd;   \"End position in chromosome\""
 "    string name;       \"Name of item\""
 "    uint   score;      \"Score from 0-1000\""
 "    uint expCount;     \"Number of experiment values\""
 "    uint[expCount] expNums; \"Comma separated list of experiment numbers\""
 "    float[expCount] expScores; \"Comma separated list of experiment scores\""
 "    )"
     ;
 
 struct asObject *factorSourceAsObj()
 /* Return asObject describing fields of factorSource */
 {
 return asParseText(factorSourceAutoSqlString);
 }