src/hg/hgc/peakClusters.c 1.1

Index: src/hg/hgc/peakClusters.c
===================================================================
RCS file: src/hg/hgc/peakClusters.c
diff -N src/hg/hgc/peakClusters.c
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ src/hg/hgc/peakClusters.c	15 May 2010 22:08:41 -0000	1.1
@@ -0,0 +1,200 @@
+/* Stuff to display details on tracks that are clusters of peaks (items) in other tracks. */
+#include "common.h"
+#include "hash.h"
+#include "jksql.h"
+#include "obscure.h"
+#include "hCommon.h"
+#include "hdb.h"
+#include "web.h"
+#include "cart.h"
+#include "trackDb.h"
+#include "hgc.h"
+#include "encode/encodePeak.h"
+
+
+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);
+}
+
+static struct slName *findMatchingSubtracks(struct slName *inTrackList, struct slPair *selGroupList)
+/* Look in track and it's descendents for tracks with groups that match all values 
+ * in selGroupList. */
+{
+struct slName *matchList = NULL;
+struct slName *inTrack;
+for (inTrack = inTrackList; inTrack != NULL; inTrack = inTrack->next)
+    {
+    struct trackDb *tdb = hashFindVal(trackHash, inTrack->name);
+    if (tdb == NULL)
+        errAbort("Can't find track %s which is in inputTracks", inTrack->name);
+    rAddMatching(tdb,  selGroupList, &matchList);
+    }
+return matchList;
+}
+
+static void printTableInfo(struct trackDb *tdb, struct trackDb *clusterTdb,
+    struct slName *displayGroupList)
+/* Print out info on table. */
+{
+webPrintLinkCell(tdb->shortLabel);
+webPrintLinkCell(tdb->longLabel);
+}
+
+static void showOnePeak(struct trackDb *tdb, struct bed *cluster, struct trackDb *clusterTdb,
+	struct encodePeak *peak, struct slName *displayGroupList, int *pIx)
+/* Show info on track and peak.  Peak may be NULL in which case n/a's will be printed
+ * as appropriate. */
+{
+*pIx += 1;
+webPrintIntCell(*pIx);
+if (peak)
+    {
+    webPrintIntCell(peak->score);
+    int overlap = positiveRangeIntersection(peak->chromStart, peak->chromEnd, 
+    	cluster->chromStart, cluster->chromEnd);
+    double overlapRatio = (double)overlap/(cluster->chromEnd - cluster->chromStart);
+    webPrintLinkCellRightStart();
+    printf("%4.1f%%", overlapRatio*100);
+    webPrintLinkCellEnd();
+    }
+printTableInfo(tdb, clusterTdb, displayGroupList);
+}
+
+static boolean showMatchingTrack(char *track, struct bed *cluster, struct sqlConnection *conn,
+	struct trackDb *clusterTdb, struct slName *displayGroupList,
+	boolean showIfTrue, boolean showIfFalse, int *pRowIx)
+/* put out a line in an html table that describes the given track. */ 
+{
+struct trackDb *tdb = hashMustFindVal(trackHash, track);
+boolean result = FALSE;
+char **row;
+int rowOffset = 0;
+struct sqlResult *sr = hRangeQuery(conn, tdb->table, 
+	cluster->chrom, cluster->chromStart, cluster->chromEnd, NULL, &rowOffset);
+boolean gotData = FALSE;
+while ((row = sqlNextRow(sr)) != NULL)
+    {
+    enum encodePeakType pt = encodePeakInferTypeFromTable(database, tdb->table, tdb->type);
+    struct encodePeak *peak = encodePeakGeneralLoad(row + rowOffset, pt);
+    if (showIfTrue)
+	{
+	showOnePeak(tdb, cluster, clusterTdb, peak, displayGroupList, pRowIx);
+	result = TRUE;
+	}
+    gotData = TRUE;
+    }
+if (!gotData)
+    {
+    if (showIfFalse)
+	{
+	showOnePeak(tdb, cluster, clusterTdb, NULL, displayGroupList, pRowIx);
+	result = TRUE;
+	}
+    }
+sqlFreeResult(&sr);
+return result;
+}
+
+void doPeakClusters(struct trackDb *tdb, char *item)
+/* Display detailed info about a cluster of peaks from other tracks. */
+{
+int start = cartInt(cart, "o");
+char *table = tdb->table;
+int rowOffset = hOffsetPastBin(database, seqName, table);
+char query[256];
+struct sqlResult *sr;
+char **row;
+struct bed *cluster = NULL;
+struct sqlConnection *conn = hAllocConn(database);
+
+char title[256];
+safef(title, sizeof(title), "%s item details", tdb->shortLabel);
+cartWebStart(cart, database, title);
+sprintf(query,
+	"select * from %s where  name = '%s' and chrom = '%s' and chromStart = %d",
+	table, item, seqName, start);
+sr = sqlGetResult(conn, query);
+row = sqlNextRow(sr);
+if (row != NULL)
+    cluster = bedLoadN(row + rowOffset, 5);
+sqlFreeResult(&sr);
+
+if (cluster != NULL)
+    {
+    /* Get list of tracks we'll look through for input. */
+    char *inputTracks = trackDbRequiredSetting(tdb, "inputTracks");
+    struct slName *inTrackList = stringToSlNames(inputTracks);
+
+    /* Get list of subgroups to select on */
+    char *inputTracksSubgroupSelect = trackDbRequiredSetting(tdb, "inputTracksSubgroupSelect");
+    struct slPair *selGroupList = slPairFromString(inputTracksSubgroupSelect);
+
+    /* Get list of subgroups to display */
+    char *inputTracksSubgroupDisplay = trackDbRequiredSetting(tdb, "inputTracksSubgroupDisplay");
+    struct slName *displayGroupList = stringToSlNames(inputTracksSubgroupDisplay);
+
+    /* Get list of tracks that match and make a table out of them. */
+    struct slName *matchTrackList = findMatchingSubtracks(inTrackList, selGroupList);
+    struct slName *matchTrack;
+
+    printf("<B>Items in Cluster:</B> %s of %d<BR>\n", cluster->name, slCount(matchTrackList));
+    printf("<B>Maximum Item Score (out of 1000):</B> %d<BR>\n", cluster->score);
+    printPos(cluster->chrom, cluster->chromStart, cluster->chromEnd, NULL, TRUE, NULL);
+
+
+    webPrintLinkTableStart();
+    int rowIx = 0;
+    for (matchTrack = matchTrackList; matchTrack != NULL; matchTrack = matchTrack->next)
+        {
+	if (showMatchingTrack(matchTrack->name, cluster, conn, tdb, displayGroupList,
+		TRUE, FALSE, &rowIx))
+	    printf("</TR><TR>\n");
+	}
+    webPrintLinkTableEnd();
+
+
+    uglyf("<B>inputTracks:</B> %s<BR>\n", inputTracks);
+    uglyf("<B>inputTracksSubgroupSelect:</B> %s<BR>\n", inputTracksSubgroupSelect);
+    uglyf("<B>inputTracksSubgroupDisplay:</B> %s<BR>\n", inputTracksSubgroupDisplay);
+
+    uglyf("<B>matchingTracks:</B> %d<BR>\n", slCount(matchTrackList));
+    uglyf("<B>displayGroupList:</B> %d<BR>\n", slCount(displayGroupList));
+
+
+    }
+printTrackHtml(tdb);
+hFreeConn(&conn);
+}
+