533112afe2a2005e80cdb1f82904ea65032d4302
braney
  Sat Oct 2 11:37:34 2021 -0700
split hg/lib into two separate libaries, one only used by the cgis

diff --git src/hg/lib/factorSource.c src/hg/lib/factorSource.c
deleted file mode 100644
index f6adbb6..0000000
--- src/hg/lib/factorSource.c
+++ /dev/null
@@ -1,222 +0,0 @@
-/* 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. */
-
-#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);
-}