440d84ee43c6a5f8a22bfe7886681db4ee7cc202
braney
  Thu Aug 28 16:55:27 2014 -0700
adding more support for bigGenePred in hgc and hgTables.
diff --git src/hg/hgc/bigBedClick.c src/hg/hgc/bigBedClick.c
index 8509b59..c55e384 100644
--- src/hg/hgc/bigBedClick.c
+++ src/hg/hgc/bigBedClick.c
@@ -1,146 +1,170 @@
 /* Handle details pages for wiggle tracks. */
 
 /* Copyright (C) 2013 The Regents of the University of California 
  * See README in this or parent directory for licensing information. */
 
 #include "common.h"
 #include "wiggle.h"
 #include "cart.h"
 #include "hgc.h"
 #include "hCommon.h"
 #include "hgColors.h"
 #include "bigBed.h"
 #include "hui.h"
 
+static void bigGenePredLinks(char *track, char *item)
+/* output links to genePred driven sequence dumps */
+{
+printf("<H3>Links to sequence:</H3>\n");
+printf("<UL>\n");
+puts("<LI>\n");
+hgcAnchorSomewhere("htcTranslatedPredMRna", item, "translate", seqName);
+printf("Translated Protein</A> from genomic DNA\n");
+puts("</LI>\n");
+
+puts("<LI>\n");
+hgcAnchorSomewhere("htcGeneMrna", item, track, seqName);
+printf("Predicted mRNA</A> \n");
+puts("</LI>\n");
+
+puts("<LI>\n");
+hgcAnchorSomewhere("htcGeneInGenome", item, track, seqName);
+printf("Genomic Sequence</A> from assembly\n");
+puts("</LI>\n");
+printf("</UL>\n");
+}
+
 static void bigBedClick(char *fileName, struct trackDb *tdb,
                      char *item, int start, int end, int bedSize)
 /* Handle click in generic bigBed track. */
 {
 boolean showUrl = FALSE;
 char *chrom = cartString(cart, "c");
 
 /* Open BigWig file and get interval list. */
 struct bbiFile *bbi = bigBedFileOpen(fileName);
 struct lm *lm = lmInit(0);
 int ivStart = start, ivEnd = end;
 if (start == end)
     {
     // item is an insertion; expand the search range from 0 bases to 2 so we catch it:
     ivStart = max(0, start-1);
     ivEnd++;
     }
 struct bigBedInterval *bbList = bigBedIntervalQuery(bbi, chrom, ivStart, ivEnd, 0, lm);
 
 /* Get bedSize if it's not already defined. */
 if (bedSize == 0)
     {
     bedSize = bbi->definedFieldCount;
     showUrl = TRUE;
     }
 
 
 char *scoreFilter = cartOrTdbString(cart, tdb, "scoreFilter", NULL);
 int minScore = 0;
 if (scoreFilter)
     minScore = atoi(scoreFilter);
 
 /* Find particular item in list - matching start, and item if possible. */
 boolean found = FALSE;
 boolean firstTime = TRUE;
 struct bigBedInterval *bb;
 for (bb = bbList; bb != NULL; bb = bb->next)
     {
     if (!(bb->start == start && bb->end == end))
 	continue;
     if (bedSize > 3)
 	{
 	char *name = cloneFirstWordByTab(bb->rest);
 	boolean match = sameString(name, item);
 	freez(&name);
 	if (!match)
 	    continue;
 	}
 
     found = TRUE;
     if (firstTime)
 	printf("<BR>\n");
     int seq1Seq2Fields = 0;
     // check for seq1 and seq2 in columns 7+8 (eg, pairedTagAlign)
     boolean seq1Seq2 = sameOk(trackDbSetting(tdb, BASE_COLOR_USE_SEQUENCE), "seq1Seq2");
     if (seq1Seq2 && bedSize == 6)
 	seq1Seq2Fields = 2;
     char *fields[bedSize+seq1Seq2Fields];
     char startBuf[16], endBuf[16];
     char *rest = cloneString(bb->rest);
     int bbFieldCount = bigBedIntervalToRow(bb, chrom, startBuf, endBuf, fields,
                                            bedSize+seq1Seq2Fields);
     if (bbFieldCount != bedSize+seq1Seq2Fields)
         {
         errAbort("Disagreement between trackDb field count (%d) and %s fieldCount (%d)",
 		bedSize, fileName, bbFieldCount);
 	}
     struct bed *bed = bedLoadN(fields, bedSize);
     if (bedSize >= 6 && scoreFilter && bed->score < minScore)
 	continue;
     if (showUrl && (bedSize >= 4))
         printCustomUrl(tdb, item, TRUE);
     bedPrintPos(bed, bedSize, tdb);
 
     // display seq1 and seq2
     if (seq1Seq2 && bedSize+seq1Seq2Fields == 8)
         printf("<table><tr><th>Sequence 1</th><th>Sequence 2</th></tr>"
 	       "<tr><td> %s </td><td> %s </td></tr></table>", fields[6], fields[7]);
     else if (isNotEmpty(rest))
 	{
 	char *restFields[256];
 	int restCount = chopTabs(rest, restFields);
 	int restBedFields = bedSize - 3;
 	if (restCount > restBedFields)
 	    {
             if (0 == extraFieldsPrint(tdb,NULL,restFields + restBedFields,restCount - restBedFields))
                 {
                 int i;
                 char label[20];
                 safef(label, sizeof(label), "nonBedFieldsLabel");
                 printf("<B>%s&nbsp;</B>",
                        trackDbSettingOrDefault(tdb, label, "Non-BED fields:"));
                 for (i = restBedFields;  i < restCount;  i++)
                     printf("%s%s", (i > 0 ? "\t" : ""), restFields[i]);
                 printf("<BR>\n");
                 }
 	    }
+	if (sameString(tdb->type, "bigGenePred"))
+	    bigGenePredLinks(tdb->track, item);
 	}
     if (isCustomTrack(tdb->track))
 	{
 	time_t timep = bbiUpdateTime(bbi);
 	printBbiUpdateTime(&timep);
 	}
 
     }
 
 if (!found)
     {
     printf("No item %s starting at %d\n", emptyForNull(item), start);
     }
 
 lmCleanup(&lm);
 bbiFileClose(&bbi);
 }
 
 void genericBigBedClick(struct sqlConnection *conn, struct trackDb *tdb,
                      char *item, int start, int end, int bedSize)
 /* Handle click in generic bigBed track. */
 {
 char *fileName = bbiNameFromSettingOrTable(tdb, conn, tdb->table);
 bigBedClick(fileName, tdb, item, start, end, bedSize);
 }
 
 void bigBedCustomClick(struct trackDb *tdb)
 /* Display details for BigWig custom tracks. */
 {
 char *fileName = trackDbSetting(tdb, "bigDataUrl");
 char *item = cartOptionalString(cart, "i");
 int start = cartInt(cart, "o");
 int end = cartInt(cart, "t");
 bigBedClick(fileName, tdb, item, start, end, 0);
 }