src/hg/lib/pgPolyphenPred.c 1.1

Index: src/hg/lib/pgPolyphenPred.c
===================================================================
RCS file: src/hg/lib/pgPolyphenPred.c
diff -N src/hg/lib/pgPolyphenPred.c
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ src/hg/lib/pgPolyphenPred.c	8 Mar 2010 17:45:40 -0000	1.1
@@ -0,0 +1,220 @@
+/* pgPolyphenPred.c was originally generated by the autoSql program, which also 
+ * generated pgPolyphenPred.h and pgPolyphenPred.sql.  This module links the database and
+ * the RAM representation of objects. */
+
+#include "common.h"
+#include "linefile.h"
+#include "dystring.h"
+#include "jksql.h"
+#include "pgPolyphenPred.h"
+#include "hdb.h"
+
+static char const rcsid[] = "$Id$";
+
+void pgPolyphenPredStaticLoadWithNull(char **row, struct pgPolyphenPred *ret)
+/* Load a row from pgPolyphenPred 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->basedOn = row[4];
+ret->geneName = row[5];
+ret->aaChange = row[6];
+}
+
+struct pgPolyphenPred *pgPolyphenPredLoadWithNull(char **row)
+/* Load a pgPolyphenPred from row fetched with select * from pgPolyphenPred
+ * from database.  Dispose of this with pgPolyphenPredFree(). */
+{
+struct pgPolyphenPred *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->basedOn = cloneString(row[4]);
+ret->geneName = cloneString(row[5]);
+ret->aaChange = cloneString(row[6]);
+return ret;
+}
+
+struct pgPolyphenPred *pgPolyphenPredLoadAll(char *fileName) 
+/* Load all pgPolyphenPred from a whitespace-separated file.
+ * Dispose of this with pgPolyphenPredFreeList(). */
+{
+struct pgPolyphenPred *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[7];
+
+while (lineFileRow(lf, row))
+    {
+    el = pgPolyphenPredLoadWithNull(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct pgPolyphenPred *pgPolyphenPredLoadAllByChar(char *fileName, char chopper) 
+/* Load all pgPolyphenPred from a chopper separated file.
+ * Dispose of this with pgPolyphenPredFreeList(). */
+{
+struct pgPolyphenPred *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[7];
+
+while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
+    {
+    el = pgPolyphenPredLoadWithNull(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct pgPolyphenPred *pgPolyphenPredCommaIn(char **pS, struct pgPolyphenPred *ret)
+/* Create a pgPolyphenPred out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new pgPolyphenPred */
+{
+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->basedOn = sqlStringComma(&s);
+ret->geneName = sqlStringComma(&s);
+ret->aaChange = sqlStringComma(&s);
+*pS = s;
+return ret;
+}
+
+void pgPolyphenPredFree(struct pgPolyphenPred **pEl)
+/* Free a single dynamically allocated pgPolyphenPred such as created
+ * with pgPolyphenPredLoad(). */
+{
+struct pgPolyphenPred *el;
+
+if ((el = *pEl) == NULL) return;
+freeMem(el->chrom);
+freeMem(el->prediction);
+freeMem(el->basedOn);
+freeMem(el->geneName);
+freeMem(el->aaChange);
+freez(pEl);
+}
+
+void pgPolyphenPredFreeList(struct pgPolyphenPred **pList)
+/* Free a list of dynamically allocated pgPolyphenPred's */
+{
+struct pgPolyphenPred *el, *next;
+
+for (el = *pList; el != NULL; el = next)
+    {
+    next = el->next;
+    pgPolyphenPredFree(&el);
+    }
+*pList = NULL;
+}
+
+void pgPolyphenPredOutput(struct pgPolyphenPred *el, FILE *f, char sep, char lastSep) 
+/* Print out pgPolyphenPred.  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->basedOn);
+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->aaChange);
+if (sep == ',') fputc('"',f);
+fputc(lastSep,f);
+}
+
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+
+void printPgPolyphenPred (char *db, char *tableName, struct pgSnp *item)
+/* print the predictions for an hgc item click for a pgSnp track */
+{
+struct pgPolyphenPred *el;
+struct sqlResult *sr;
+char **row;
+char query[512];
+struct sqlConnection *conn = hAllocConn(db);
+
+safef(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 = pgPolyphenPredLoadWithNull(row);
+    printf("<br><b>Polyphen prediction</b>: %s\n", el->prediction);
+    printf("<ul>");
+    if (el->basedOn != NULL && differentString(el->basedOn, ""))
+        printf("<li>based on: %s</li>\n", el->basedOn);
+    if (el->geneName != NULL && differentString(el->geneName, ""))
+        printf("<li>Protein name: %s</li>\n", el->geneName);
+    if (el->aaChange != NULL && differentString(el->aaChange, ""))
+        printf("<li>Amino acid change: %s</li>\n", el->aaChange);
+    printf("</ul>\n");
+    }
+}
+