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/ccdsGeneMap.c src/hg/cgilib/ccdsGeneMap.c
new file mode 100644
index 0000000..6b8424c
--- /dev/null
+++ src/hg/cgilib/ccdsGeneMap.c
@@ -0,0 +1,270 @@
+/* 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);
+}
+