73b74e92fd0ccbea53939947f6b7d593bc663375
galt
  Wed Aug 15 14:23:42 2012 -0700
fix hgc/encodeClick doEncodePeak to support items and use them to match unique display - even though multiples are now incredibly rare with new item=name matching, the code improves the display of the multiples by separating them with a vertical space
diff --git src/hg/hgc/encodeClick.c src/hg/hgc/encodeClick.c
index 22e7c9f..679f983 100644
--- src/hg/hgc/encodeClick.c
+++ src/hg/hgc/encodeClick.c
@@ -1,281 +1,290 @@
 /* Handle details page for ENCODE tracks. */
 
 #include "common.h"
 #include "cart.h"
 #include "hgc.h"
 #include "hCommon.h"
 #include "hgColors.h"
 #include "customTrack.h"
 #include "web.h"
 #include "encode/encodePeak.h"
 #include "peptideMapping.h"
 
 #ifdef UNUSED
 static boolean pairInList(struct slPair *pair, struct slPair *list)
 /* Return TRUE if pair is in list. */
 {
 struct slPair *el;
 for (el = list; el != NULL; el = el->next)
     if (sameString(pair->name, el->name) && sameString(pair->val, el->val))
         return TRUE;
 return FALSE;
 }
 
 static boolean selGroupListMatch(struct trackDb *tdb, struct slPair *selGroupList)
 /* Return TRUE if tdb has match to every item in selGroupList */
 {
 char *subGroups = trackDbSetting(tdb, "subGroups");
 if (subGroups == NULL)
     return FALSE;
 struct slPair *groupList = slPairFromString(subGroups);
 struct slPair *selGroup;
 for (selGroup = selGroupList; selGroup != NULL; selGroup = selGroup->next)
     {
     if (!pairInList(selGroup, groupList))
         return FALSE;
     }
 return TRUE;
 }
 
 static void rAddMatching(struct trackDb *tdb, struct slPair *selGroupList, struct slName **pList)
 /* Add track and any descendents that match selGroupList to pList */
 {
 if (selGroupListMatch(tdb, selGroupList))
     slNameAddHead(pList, tdb->track);
 struct trackDb *sub;
 for (sub = tdb->subtracks; sub != NULL; sub = sub->next)
     rAddMatching(sub, selGroupList, pList);
 }
 #endif//def UNUSED
 
-void doEncodePeak(struct trackDb *tdb, struct customTrack *ct)
+void doEncodePeak(struct trackDb *tdb, struct customTrack *ct, char *item)
 /*  details for encodePeak type tracks. */
 {
 struct sqlConnection *conn;
 struct sqlResult *sr;
 enum encodePeakType peakType;
 char **row;
 char *db;
 char *table = tdb->table;
 char *chrom = cartString(cart,"c");
 int start = cgiInt("o");
 int end = cgiInt("t");
 int rowOffset;
+boolean firstTime = TRUE;
 /* connect to DB */
 if (ct)
     {
     db = CUSTOM_TRASH;
     table = ct->dbTableName;
     }
 else
     db = database;
 conn = hAllocConn(db);
 peakType = encodePeakInferTypeFromTable(db, table, tdb->type);
 if (peakType == 0)
     errAbort("unrecognized peak type from table %s", tdb->table);
-genericHeader(tdb, NULL);
+genericHeader(tdb, NULL);  // genericClickHandlerPlus gets there first anyway and overrides this which is now moot.
 sr = hOrderedRangeQuery(conn, table, chrom, start, end,
 			NULL, &rowOffset);
 while((row = sqlNextRow(sr)) != NULL)
     {
     char **rowPastOffset = row + rowOffset;
     if ((sqlUnsigned(rowPastOffset[1]) != start) ||  (sqlUnsigned(rowPastOffset[2]) != end))
 	continue;
+    if (!sameString(rowPastOffset[3], item))
+	continue;
 
     float signal = -1;
     float pValue = -1;
     float qValue = -1;
+
+    if (firstTime)
+	firstTime = FALSE;
+    else // print separator
+	printf("<BR>\n");
+
     /* Name */
     if (rowPastOffset[3][0] != '.')
 	printf("<B>Name:</B> %s<BR>\n", rowPastOffset[3]);
     /* Position */
     printf("<B>Position:</B> "
        "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">%s:%d-%d</a><BR>\n",
        hgTracksPathAndSettings(), database, chrom, start+1, end, chrom, start+1, end);
     /* Print peak base */
     if ((peakType == narrowPeak) || (peakType == encodePeak))
 	{
 	int peak = sqlSigned(rowPastOffset[9]);
 	if (peak > -1)
 	    printf("<B>Peak point:</B> %d<BR>\n", start + peak + 1); // one based
 	}
     /* Strand, score */
     if (rowPastOffset[5][0] != '.')
 	    printf("<B>Strand:</B> %c<BR>\n", rowPastOffset[5][0]);
     printf("<B>Score:</B> %d<BR>\n", sqlUnsigned(rowPastOffset[4]));
     /* signalVal, pVal */
     if (peakType != gappedPeak)
 	{
 	signal = sqlFloat(rowPastOffset[6]);
 	pValue = sqlFloat(rowPastOffset[7]);
 	qValue = sqlFloat(rowPastOffset[8]);
 	}
     else
 	{
 	signal = sqlFloat(rowPastOffset[12]);
 	pValue = sqlFloat(rowPastOffset[13]);
 	qValue = sqlFloat(rowPastOffset[14]);
 	}
     if (signal >= 0)
 	printf("<B>Signal value:</B> %.3f<BR>\n", signal);
     if (pValue >= 0)
 	printf("<B>P-value (-log10):</B> %.3f<BR>\n", pValue);
     if (qValue >= 0)
 	printf("<B>Q-value (FDR): </B> %.3f<BR>\n", qValue);
     }
 sqlFreeResult(&sr);
 hFreeConn(&conn);
 }
 
 int encodeFiveCInterCmp(const void *va, const void *vb)
 /* reverse sort on bed nine's reserved field which in this */
 /* case is the where the strength of the interaction is stored */
 {
 const struct bed *a = *((struct bed **)va);
 const struct bed *b = *((struct bed **)vb);
 return b->itemRgb - a->itemRgb;
 }
 
 void doEncodeFiveC(struct sqlConnection *conn, struct trackDb *tdb)
 /* Print details for 5C track */
 {
 char *interTable = trackDbRequiredSetting(tdb, "interTable");
 char *interTableKind = trackDbRequiredSetting(tdb, "interTableKind");
 char **row;
 char *chrom = cartString(cart,"c");
 int start = cgiInt("o");
 int end = cgiInt("t");
 int rowOffset;
 int outCount = 0;
 struct sqlResult *sr;
 struct bed *interList = NULL, *inter;
 genericHeader(tdb, NULL);
 sr = hOrderedRangeQuery(conn, interTable, chrom, start, end, NULL, &rowOffset);
 printf("<B>Position:</B> "
        "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">%s:%d-%d</a><BR>\n",
        hgTracksPathAndSettings(), database, chrom, start+1, end, chrom, start+1, end);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     inter = bedLoadN(row + rowOffset, 9);
     slAddHead(&interList, inter);
     }
 slSort(&interList, encodeFiveCInterCmp);
 webNewSection("Top %s interations", interTableKind);
 webPrintLinkTableStart();
 webPrintLabelCell("Position");
 webPrintLabelCell("5C signal");
 webPrintLabelCell("Distance");
 webPrintLinkTableNewRow();
 for (inter = interList; inter != NULL; inter = inter->next)
     {
     char s[1024];
     int distance = 0;
     safef(s, sizeof(s), "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">%s:%d-%d</A>",
        hgTracksPathAndSettings(), database, chrom, inter->thickStart+1, inter->thickEnd, chrom, inter->thickStart+1, inter->thickEnd);
     webPrintLinkCell(s);
     safef(s, sizeof(s), "%d", inter->itemRgb);
     webPrintLinkCell(s);
     if (start > inter->thickStart)
 	distance = inter->thickEnd - start;
     else
 	distance = inter->thickStart - end;
     safef(s, sizeof(s), "%d", distance);
     webPrintLinkCell(s);
     if (++outCount == 50)
 	break;
     if (inter->next != NULL)
 	webPrintLinkTableNewRow();
     }
 webPrintLinkTableEnd();
 sqlFreeResult(&sr);
 }
 
 void doPeptideMapping(struct sqlConnection *conn, struct trackDb *tdb, char *item)
 /* Print details for a peptideMapping track.  */
 {
 char *chrom = cartString(cart,"c");
 int start = cgiInt("o");
 int end = cgiInt("t");
 char query[256];
 char **row;
 struct sqlResult *sr;
 struct peptideMapping pos;
 int rowOffset = 0;  // skip bin field
 int found = 0;
 genericHeader(tdb, NULL);
 
 /* Just get the current item. */
 safef(query, sizeof(query), 
       "select * from %s where name='%s' and chrom='%s' and chromStart=%d and chromEnd=%d", 
       tdb->track, item, chrom, start, end);
 sr = sqlGetResult(conn, query);
 
 if (sqlFieldColumn(sr, "bin") == 0)
     rowOffset = 1;
     
 while ((row = sqlNextRow(sr)) != NULL)
     {
     ++found;
     peptideMappingStaticLoad(row + rowOffset, &pos);
     if (found == 1)
 	{
 	printf("<B>Item:</B> %s<BR>\n", pos.name);
 	printPos(pos.chrom, pos.chromStart, pos.chromEnd, pos.strand, TRUE, item);
 
 	printf("<BR>\n");
 	printf("Additional details for all peptide mappings of %s:<BR>\n", item);
 
 	webPrintLinkTableStart();
 	webPrintLabelCell("Score");
 	webPrintLabelCell("Raw Score");
 	webPrintLabelCell("Spectrum ID");
 	webPrintLabelCell("Peptide Rank");
 	}
     webPrintLinkTableNewRow();
     webPrintIntCell(pos.score);
     webPrintDoubleCell(pos.rawScore);
     webPrintLinkCell(pos.spectrumId);
     webPrintIntCell(pos.peptideRank);
     }
 if (found == 0)
     errAbort("No items in range");
 
 webPrintLinkTableEnd();
 sqlFreeResult(&sr);
 
 /* Draw table of other locations */
 printf("<BR>\n");
 printf("<B>Peptide Repeat Count:</B> %d<BR>\n", pos.peptideRepeatCount);
 if (pos.peptideRepeatCount > 1)
     {
     struct hash *hash = hashNew(8);
     struct peptideMapping anotherPos;
     safef(query, sizeof(query), 
           "select * from %s where name='%s' and not (chrom='%s' and chromStart=%d and chromEnd=%d)", 
 	  tdb->track, item, chrom, start, end);
     printf("<BR>\n");
     webPrintLinkTableStart();
     webPrintLabelCell("Other genomic loci");
     sr = sqlGetResult(conn, query);
     while ((row = sqlNextRow(sr)) != NULL)
 	{
 	char s[1024];
 	peptideMappingStaticLoad(row + rowOffset, &anotherPos);
 	char k[1024];
 	safef(k, sizeof k, "%s.%d.%d", anotherPos.chrom, anotherPos.chromStart, anotherPos.chromEnd);
 	if (!hashLookup(hash, k))
 	    {
 	    hashAdd(hash, k, NULL);
 	    safef(s, sizeof(s), "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">%s:%d-%d</A>",
 		  hgTracksPathAndSettings(), database, anotherPos.chrom, anotherPos.chromStart+1, 
 		  anotherPos.chromEnd, anotherPos.chrom, anotherPos.chromStart+1, anotherPos.chromEnd);
 	    webPrintLinkTableNewRow();
 	    webPrintLinkCell(s);
 	    }
 	}
     webPrintLinkTableEnd();
     sqlFreeResult(&sr);
     freeHash(&hash);
     }    
 
 }