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/ccdsGeneMap.c src/hg/lib/ccdsGeneMap.c
deleted file mode 100644
index 6b8424c..0000000
--- src/hg/lib/ccdsGeneMap.c
+++ /dev/null
@@ -1,270 +0,0 @@
-/* ccdsGeneMap.c was originally generated by the autoSql program, which also 
- * generated ccdsGeneMap.h and ccdsGeneMap.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 "ccdsGeneMap.h"
-
-
-void ccdsGeneMapStaticLoad(char **row, struct ccdsGeneMap *ret)
-/* Load a row from ccdsGeneMap table into ret.  The contents of ret will
- * be replaced at the next call to this function. */
-{
-
-ret->ccdsId = row[0];
-ret->geneId = row[1];
-ret->chrom = row[2];
-ret->chromStart = sqlUnsigned(row[3]);
-ret->chromEnd = sqlUnsigned(row[4]);
-ret->cdsSimilarity = atof(row[5]);
-}
-
-struct ccdsGeneMap *ccdsGeneMapLoad(char **row)
-/* Load a ccdsGeneMap from row fetched with select * from ccdsGeneMap
- * from database.  Dispose of this with ccdsGeneMapFree(). */
-{
-struct ccdsGeneMap *ret;
-
-AllocVar(ret);
-ret->ccdsId = cloneString(row[0]);
-ret->geneId = cloneString(row[1]);
-ret->chrom = cloneString(row[2]);
-ret->chromStart = sqlUnsigned(row[3]);
-ret->chromEnd = sqlUnsigned(row[4]);
-ret->cdsSimilarity = atof(row[5]);
-return ret;
-}
-
-struct ccdsGeneMap *ccdsGeneMapLoadAll(char *fileName) 
-/* Load all ccdsGeneMap from a whitespace-separated file.
- * Dispose of this with ccdsGeneMapFreeList(). */
-{
-struct ccdsGeneMap *list = NULL, *el;
-struct lineFile *lf = lineFileOpen(fileName, TRUE);
-char *row[6];
-
-while (lineFileRow(lf, row))
-    {
-    el = ccdsGeneMapLoad(row);
-    slAddHead(&list, el);
-    }
-lineFileClose(&lf);
-slReverse(&list);
-return list;
-}
-
-struct ccdsGeneMap *ccdsGeneMapLoadAllByChar(char *fileName, char chopper) 
-/* Load all ccdsGeneMap from a chopper separated file.
- * Dispose of this with ccdsGeneMapFreeList(). */
-{
-struct ccdsGeneMap *list = NULL, *el;
-struct lineFile *lf = lineFileOpen(fileName, TRUE);
-char *row[6];
-
-while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
-    {
-    el = ccdsGeneMapLoad(row);
-    slAddHead(&list, el);
-    }
-lineFileClose(&lf);
-slReverse(&list);
-return list;
-}
-
-struct ccdsGeneMap *ccdsGeneMapCommaIn(char **pS, struct ccdsGeneMap *ret)
-/* Create a ccdsGeneMap out of a comma separated string. 
- * This will fill in ret if non-null, otherwise will
- * return a new ccdsGeneMap */
-{
-char *s = *pS;
-
-if (ret == NULL)
-    AllocVar(ret);
-ret->ccdsId = sqlStringComma(&s);
-ret->geneId = sqlStringComma(&s);
-ret->chrom = sqlStringComma(&s);
-ret->chromStart = sqlUnsignedComma(&s);
-ret->chromEnd = sqlUnsignedComma(&s);
-ret->cdsSimilarity = sqlFloatComma(&s);
-*pS = s;
-return ret;
-}
-
-void ccdsGeneMapFree(struct ccdsGeneMap **pEl)
-/* Free a single dynamically allocated ccdsGeneMap such as created
- * with ccdsGeneMapLoad(). */
-{
-struct ccdsGeneMap *el;
-
-if ((el = *pEl) == NULL) return;
-freeMem(el->ccdsId);
-freeMem(el->geneId);
-freeMem(el->chrom);
-freez(pEl);
-}
-
-void ccdsGeneMapFreeList(struct ccdsGeneMap **pList)
-/* Free a list of dynamically allocated ccdsGeneMap's */
-{
-struct ccdsGeneMap *el, *next;
-
-for (el = *pList; el != NULL; el = next)
-    {
-    next = el->next;
-    ccdsGeneMapFree(&el);
-    }
-*pList = NULL;
-}
-
-void ccdsGeneMapOutput(struct ccdsGeneMap *el, FILE *f, char sep, char lastSep) 
-/* Print out ccdsGeneMap.  Separate fields with sep. Follow last field with lastSep. */
-{
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->ccdsId);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->geneId);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-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);
-fprintf(f, "%g", el->cdsSimilarity);
-fputc(lastSep,f);
-}
-
-/* -------------------------------- End autoSql Generated Code -------------------------------- */
-
-/* template for SQL to create a ccdsGeneMap table */
-static char *createSql =
-    "CREATE TABLE %s ("
-    "    ccdsId varchar(32) not null,"
-    "    geneId varchar(255) not null,"
-    "    chrom varchar(255) not null,"
-    "    chromStart int unsigned not null,"
-    "    chromEnd int unsigned not null,"
-    "    cdsSimilarity float not null,"
-    "    KEY(ccdsId),"
-    "    KEY(geneId)"
-    ")";
-
-char *ccdsGeneMapGetCreateSql(char *table)
-/* Get SQL command to create ccdsGeneMap table. Result should be freed. */
-{
-char sql[1024];
-sqlSafef(sql, sizeof(sql), createSql, table);
-return cloneString(sql);
-}
-
-struct ccdsGeneMap *ccdsGeneMapSelectByCcds(struct sqlConnection *conn, char *mapTable,
-                                            char *ccdsId, char *chrom, float minSimilarity)
-/* select ccdsGeneMap records by ccds and minimum CDS similarity from the
- * specified table. Chrom is required since the same CCDS id is mapped twice in the PAR.
- */
-{
-struct ccdsGeneMap *ccdsGeneList = NULL;
-char query[128];
-struct sqlResult *sr = NULL;
-char **row = NULL;
-
-sqlSafef(query, sizeof(query), "select * from %s where (ccdsId='%s') and (chrom='%s') and (cdsSimilarity >= %f)",
-      mapTable, ccdsId, chrom, minSimilarity);
-sr = sqlGetResult(conn, query);
-while ((row = sqlNextRow(sr)) != NULL)
-    slSafeAddHead(&ccdsGeneList, ccdsGeneMapLoad(row));
-sqlFreeResult(&sr);
-return ccdsGeneList;
-}
-
-struct ccdsGeneMap *ccdsGeneMapSelectByGene(struct sqlConnection *conn, char *mapTable,
-                                            char *geneId, float minSimilarity)
-/* select ccdsGeneMap records by gene id and minimum CDS similarity from the
- * specified table. */
-{
-struct ccdsGeneMap *ccdsGeneList = NULL;
-char query[128], simExpr[64];
-struct sqlResult *sr = NULL;
-char **row = NULL;
-
-simExpr[0] = '\0';
-if (minSimilarity > 0.0)
-    safef(simExpr, sizeof(simExpr), "and cdsSimilarity >= %f", minSimilarity);
-
-sqlSafef(query, sizeof(query), "select * from %s where geneId='%s' %s",
-      mapTable, geneId, simExpr);
-sr = sqlGetResult(conn, query);
-while ((row = sqlNextRow(sr)) != NULL)
-    slSafeAddHead(&ccdsGeneList, ccdsGeneMapLoad(row));
-sqlFreeResult(&sr);
-return ccdsGeneList;
-}
-
-struct ccdsGeneMap *ccdsGeneMapSelectByGeneOver(struct sqlConnection *conn, char *mapTable,
-                                                char *geneId, char *chrom, unsigned chromStart,
-                                                unsigned chromEnd, float minSimilarity)
-/* select ccdsGeneMap records by gene id, location overlap, and minimum CDS
- * similarity from the specified table. */
-{
-struct ccdsGeneMap *ccdsGeneList = ccdsGeneMapSelectByGene(conn, mapTable, geneId, minSimilarity);
-struct ccdsGeneMap *overList = NULL, *gene;
-
-while ((gene = slPopHead(&ccdsGeneList)) != NULL)
-    {
-    if (sameString(gene->chrom, chrom)
-        && (positiveRangeIntersection(gene->chromStart, gene->chromEnd,
-                                      chromStart, chromEnd) > 0))
-        slAddHead(&overList, gene);
-    else
-        ccdsGeneMapFree(&gene);
-    }
-return overList;
-}
-
-int ccdsGeneMapSimilarityCmp(const void *va, const void *vb)
-/* compare based on descending similarity */
-{
-const struct ccdsGeneMap *a = *((struct ccdsGeneMap **)va);
-const struct ccdsGeneMap *b = *((struct ccdsGeneMap **)vb);
-if (a->cdsSimilarity > b->cdsSimilarity)
-    return -1;
-if (a->cdsSimilarity < b->cdsSimilarity)
-    return 1;
-return 0;
-}
-
-int ccdsGeneMapCcdsIdCmp(const void *va, const void *vb)
-/* compare based on gene id */
-{
-const struct ccdsGeneMap *a = *((struct ccdsGeneMap **)va);
-const struct ccdsGeneMap *b = *((struct ccdsGeneMap **)vb);
-/* convert number past "CCDS" as float */
-float aId = sqlFloat(a->ccdsId+4);
-float bId = sqlFloat(b->ccdsId+4);
-
-if (aId > bId)
-    return -1;
-if (aId < bId)
-    return 1;
-return 0;
-}
-
-int ccdsGeneMapGeneIdCmp(const void *va, const void *vb)
-/* compare based on gene id */
-{
-const struct ccdsGeneMap *a = *((struct ccdsGeneMap **)va);
-const struct ccdsGeneMap *b = *((struct ccdsGeneMap **)vb);
-return strcmp(a->geneId, b->geneId);
-}
-