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/cgilib/factorSource.c src/hg/cgilib/factorSource.c
new file mode 100644
index 0000000..f6adbb6
--- /dev/null
+++ src/hg/cgilib/factorSource.c
@@ -0,0 +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. */
+
+#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);
+}