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/pgSiftPred.c src/hg/cgilib/pgSiftPred.c
new file mode 100644
index 0000000..ab4f9ae
--- /dev/null
+++ src/hg/cgilib/pgSiftPred.c
@@ -0,0 +1,261 @@
+/* pgSiftPred.c was originally generated by the autoSql program, which also 
+ * generated pgSiftPred.h and pgSiftPred.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 "hdb.h"
+#include "pgSiftPred.h"
+
+
+void pgSiftPredStaticLoadWithNull(char **row, struct pgSiftPred *ret)
+/* Load a row from pgSiftPred table into ret.  The contents of ret will
+ * be replaced at the next call to this function. */
+{
+
+ret->chrom = row[0];
+if (row[1] != NULL)
+    {
+    ret->chromStart = needMem(sizeof(*(ret->chromStart)));
+    *(ret->chromStart) = sqlUnsigned(row[1]);
+    }
+else
+    {
+    ret->chromStart = NULL;
+    }
+if (row[2] != NULL)
+    {
+    ret->chromEnd = needMem(sizeof(*(ret->chromEnd)));
+    *(ret->chromEnd) = sqlUnsigned(row[2]);
+    }
+else
+    {
+    ret->chromEnd = NULL;
+    }
+ret->prediction = row[3];
+ret->geneId = row[4];
+ret->geneName = row[5];
+ret->geneDesc = row[6];
+ret->protFamDesc = row[7];
+ret->omimDisease = row[8];
+ret->aveAlleleFreq = row[9];
+ret->ceuAlleleFreq = row[10];
+}
+
+struct pgSiftPred *pgSiftPredLoadWithNull(char **row)
+/* Load a pgSiftPred from row fetched with select * from pgSiftPred
+ * from database.  Dispose of this with pgSiftPredFree(). */
+{
+struct pgSiftPred *ret;
+
+AllocVar(ret);
+ret->chrom = cloneString(row[0]);
+if (row[1] != NULL)
+    {
+    ret->chromStart = needMem(sizeof(*(ret->chromStart)));
+    *(ret->chromStart) = sqlUnsigned(row[1]);
+    }
+else
+    {
+    ret->chromStart = NULL;
+    }
+if (row[2] != NULL)
+    {
+    ret->chromEnd = needMem(sizeof(*(ret->chromEnd)));
+    *(ret->chromEnd) = sqlUnsigned(row[2]);
+    }
+else
+    {
+    ret->chromEnd = NULL;
+    }
+ret->prediction = cloneString(row[3]);
+ret->geneId = cloneString(row[4]);
+ret->geneName = cloneString(row[5]);
+ret->geneDesc = cloneString(row[6]);
+ret->protFamDesc = cloneString(row[7]);
+ret->omimDisease = cloneString(row[8]);
+ret->aveAlleleFreq = cloneString(row[9]);
+ret->ceuAlleleFreq = cloneString(row[10]);
+return ret;
+}
+
+struct pgSiftPred *pgSiftPredLoadAll(char *fileName) 
+/* Load all pgSiftPred from a whitespace-separated file.
+ * Dispose of this with pgSiftPredFreeList(). */
+{
+struct pgSiftPred *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[11];
+
+while (lineFileRow(lf, row))
+    {
+    el = pgSiftPredLoadWithNull(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct pgSiftPred *pgSiftPredLoadAllByChar(char *fileName, char chopper) 
+/* Load all pgSiftPred from a chopper separated file.
+ * Dispose of this with pgSiftPredFreeList(). */
+{
+struct pgSiftPred *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[11];
+
+while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
+    {
+    el = pgSiftPredLoadWithNull(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct pgSiftPred *pgSiftPredCommaIn(char **pS, struct pgSiftPred *ret)
+/* Create a pgSiftPred out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new pgSiftPred */
+{
+char *s = *pS;
+
+if (ret == NULL)
+    AllocVar(ret);
+ret->chrom = sqlStringComma(&s);
+ret->chromStart = needMem(sizeof(unsigned));
+*(ret->chromStart) = sqlUnsignedComma(&s);
+ret->chromEnd = needMem(sizeof(unsigned));
+*(ret->chromEnd) = sqlUnsignedComma(&s);
+ret->prediction = sqlStringComma(&s);
+ret->geneId = sqlStringComma(&s);
+ret->geneName = sqlStringComma(&s);
+ret->geneDesc = sqlStringComma(&s);
+ret->protFamDesc = sqlStringComma(&s);
+ret->omimDisease = sqlStringComma(&s);
+ret->aveAlleleFreq = sqlStringComma(&s);
+ret->ceuAlleleFreq = sqlStringComma(&s);
+*pS = s;
+return ret;
+}
+
+void pgSiftPredFree(struct pgSiftPred **pEl)
+/* Free a single dynamically allocated pgSiftPred such as created
+ * with pgSiftPredLoad(). */
+{
+struct pgSiftPred *el;
+
+if ((el = *pEl) == NULL) return;
+freeMem(el->chrom);
+freeMem(el->prediction);
+freeMem(el->geneId);
+freeMem(el->geneName);
+freeMem(el->geneDesc);
+freeMem(el->protFamDesc);
+freeMem(el->omimDisease);
+freeMem(el->aveAlleleFreq);
+freeMem(el->ceuAlleleFreq);
+freez(pEl);
+}
+
+void pgSiftPredFreeList(struct pgSiftPred **pList)
+/* Free a list of dynamically allocated pgSiftPred's */
+{
+struct pgSiftPred *el, *next;
+
+for (el = *pList; el != NULL; el = next)
+    {
+    next = el->next;
+    pgSiftPredFree(&el);
+    }
+*pList = NULL;
+}
+
+void pgSiftPredOutput(struct pgSiftPred *el, FILE *f, char sep, char lastSep) 
+/* Print out pgSiftPred.  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->prediction);
+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->geneName);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->geneDesc);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->protFamDesc);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->omimDisease);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->aveAlleleFreq);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->ceuAlleleFreq);
+if (sep == ',') fputc('"',f);
+fputc(lastSep,f);
+}
+
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+
+void printPgSiftPred (char *db, char *tableName, struct pgSnp *item)
+/* print the predictions for an hgc item click for a pgSnp track */
+{
+struct pgSiftPred *el;
+struct sqlResult *sr;
+char **row;
+char query[512];
+struct sqlConnection *conn = hAllocConn(db);
+
+sqlSafef(query, sizeof(query), "select * from %s where chrom = '%s' and chromStart = %d and chromEnd = %d",
+    tableName, item->chrom, item->chromStart, item->chromEnd);
+sr = sqlGetResult(conn, query);
+while ((row = sqlNextRow(sr)) != NULL)
+    {
+    el = pgSiftPredLoadWithNull(row);
+    printf("<br><b>SIFT prediction</b>: %s\n", el->prediction);
+    printf("<ul>");
+    if (el->geneId != NULL && differentString(el->geneId, ""))
+        printf("<li>Gene ID: %s</li>\n", el->geneId);
+    if (el->geneName != NULL && differentString(el->geneName, ""))
+        printf("<li>Gene name: %s</li>\n", el->geneName);
+    if (el->geneDesc != NULL && differentString(el->geneDesc, ""))
+        printf("<li>Gene description: %s</li>\n", el->geneDesc);
+    if (el->protFamDesc != NULL && differentString(el->protFamDesc, ""))
+        printf("<li>Protein family description: %s</li>\n", el->protFamDesc);
+    if (el->omimDisease != NULL && differentString(el->omimDisease, ""))
+        printf("<li>OMIM disease: %s</li>\n", el->omimDisease);
+    if (el->aveAlleleFreq != NULL && differentString(el->aveAlleleFreq, ""))
+        printf("<li>Average allele frequency: %s</li>\n", el->aveAlleleFreq);
+    if (el->ceuAlleleFreq != NULL && differentString(el->ceuAlleleFreq, ""))
+	printf("<li>CEU allele frequency: %s</li>\n", el->ceuAlleleFreq);
+    printf("</ul>\n");
+    }
+}