dfd733e82c713d46ceb8c9d14c6421be76c5709b
kate
  Thu May 2 16:56:12 2013 -0700
Remove obsolete code (support for 'inputTracksSubgroupDisplay' tsetting/feature, which poked through a tracks and trackDb in a related composite track for info -- to provide more features ??.  The code was all bracketed with TO_BE_REMOVED.  Alternate approach uses inputTableFieldDisplay setting
diff --git src/hg/hgc/peakClusters.c src/hg/hgc/peakClusters.c
index 09684d9..8ebdf04 100644
--- src/hg/hgc/peakClusters.c
+++ src/hg/hgc/peakClusters.c
@@ -1,708 +1,494 @@
 /* Stuff to display details on tracks that are clusters of peaks (items) in other tracks. 
  * In particular peaks in either ENCODE narrowPeak or broadPeak settings, and residing in
  * composite tracks. 
  *
  * These come in two main forms currently:
  *     DNAse hypersensitive clusters - peaks clustered across cell lines stored in bed 5
  *                                     with no special type
  *     Transcription Factor Binding Sites (TFBS) - peaks from transcription factor ChIP-seq
  *                   across a number of transcription factors and cell lines. Stored in bed 15
  *                   plus sourceTable with type factorSource */
  
-#define TO_BE_REMOVED  /* Some code that is brittle we are phasing out */
-                       /* In particular this code demanded all tracks cluster was built on
-		        * still exist, which isn't realistic given ENCODE data thrash */
-
 #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 "hui.h"
 #include "hgc.h"
 #include "encode/encodePeak.h"
 #include "expRecord.h"
 #include "bed6FloatScore.h"
 #include "ra.h"
 #include "txCluster.h"
 
-#ifdef TO_BE_REMOVED
-char *findGroupTagVal(struct trackDb *tdb, char *tag)
-/* Find value of given tag inside of subgroups field. */ 
-{
-char *subGroups = trackDbSetting(tdb, "subGroups");
-struct slPair *el, *list = slPairFromString(subGroups);
-char *val = NULL;
-for (el = list; el != NULL; el = el->next)
-    {
-    if (sameString(el->name, tag))
-	{
-        val = el->val;
-	break;
-	}
-    }
-return val;
-}
-#endif /* TO_BE_REMOVED */
-
-#ifdef TO_BE_REMOVED
-char *mustFindGroupTagVal(struct trackDb *tdb, char *tag)
-/* Find value of given tag inside of subgroups field or abort with error message. */ 
-{
-char *val = findGroupTagVal(tdb, tag);
-if (val == NULL)
-    errAbort("Couldn't find %s in subGroups tag of %s", tag, tdb->track);
-return val;
-}
-#endif /* TO_BE_REMOVED */
-
-#ifdef TO_BE_REMOVED
-char *findGroupLabel(struct trackDb *tdb, char *group)
-/* Given name of group, ruffle through all subGroupN tags, looking for one that
- * matches group */
-{
-char *groupId = mustFindGroupTagVal(tdb, group);
-return compositeGroupLabel(tdb, group, groupId);
-}
-#endif /* TO_BE_REMOVED */
 
 static void printClusterTableHeader(struct slName *otherCols, 
 	boolean withAbbreviation, boolean withDescription, boolean withSignal)
 /* Print out header fields table of tracks in cluster */
 {
 webPrintLabelCell("#");
 if (withSignal)
     webPrintLabelCell("signal");
 if (withAbbreviation)
     webPrintLabelCell("abr");
 struct slName *col;
 for (col = otherCols; col != NULL; col = col->next)
     webPrintLabelCell(col->name);
 if (withDescription)
     webPrintLabelCell("description");
 webPrintLabelCell("more info");
 }
 
-#ifdef TO_BE_REMOVED
-static void printTableInfo(struct trackDb *tdb, struct trackDb *clusterTdb,
-    struct slName *displayGroupList)
-/* Print out info on table. */
-{
-struct slName *displayGroup;
-for (displayGroup = displayGroupList; displayGroup != NULL; displayGroup = displayGroup->next)
-    {
-    char *label = findGroupLabel(tdb, displayGroup->name);
-    char *linkedLabel = compositeLabelWithVocabLink(database, tdb, tdb, displayGroup->name, label);
-    webPrintLinkCell(linkedLabel);
-    }
-webPrintLinkCell(tdb->longLabel);
-webPrintLinkCellStart();
-compositeMetadataToggle(database, tdb, "metadata", TRUE, FALSE);
-webPrintLinkCellEnd();
-}
-#endif /* TO_BE_REMOVED */
-
-#ifdef TO_BE_REMOVED
-static void showOnePeakOrMiss(struct trackDb *tdb, struct trackDb *clusterTdb,
-	struct encodePeak *peakList, struct slName *displayGroupList, int *pIx)
-/* Show info on track and peak.  Peak may be NULL in which case fewer columns will be printed. */
-{
-struct encodePeak *peak;
-*pIx += 1;
-printf("</TR><TR>\n");
-webPrintIntCell(*pIx);
-if (peakList)
-    {
-    webPrintLinkCellRightStart();
-    printf("%g", peakList->signalValue);
-    for (peak = peakList->next; peak != NULL; peak = peak->next)
-	printf(",%g", peak->signalValue);
-    webPrintLinkCellEnd();
-    }
-printTableInfo(tdb, clusterTdb, displayGroupList);
-}
-#endif /* TO_BE_REMOVED */
-
-#ifdef TO_BE_REMOVED
-static void showMatchingTrack(char *track, struct bed *cluster, struct sqlConnection *conn,
-	struct trackDb *clusterTdb, struct slName *displayGroupList, boolean invert, int *pRowIx)
-/* put out a line in an html table that describes the given track. */ 
-{
-struct trackDb *tdb = hashFindVal(trackHash, track);
-if (tdb != NULL)
-    {
-    char **row;
-    int rowOffset = 0;
-    struct sqlResult *sr = hRangeQuery(conn, tdb->table, 
-	    cluster->chrom, cluster->chromStart, cluster->chromEnd, NULL, &rowOffset);
-    struct encodePeak *peakList = NULL;
-    struct slDouble *slDoubleNew(double x);
-    while ((row = sqlNextRow(sr)) != NULL)
-	{
-	enum encodePeakType pt = encodePeakInferTypeFromTable(database, tdb->table, tdb->type);
-	struct encodePeak *peak = encodePeakGeneralLoad(row + rowOffset, pt);
-	slAddTail(&peakList, peak);
-	}
-    if (invert)
-	{
-	if (!peakList)
-	    showOnePeakOrMiss(tdb, clusterTdb, NULL, displayGroupList, pRowIx);
-	}
-    else
-	{
-	if (peakList)
-	    showOnePeakOrMiss(tdb, clusterTdb, peakList, displayGroupList, pRowIx);
-	}
-    sqlFreeResult(&sr);
-    }
-}
-#endif /* TO_BE_REMOVED */
-
 static double getSignalAt(char *table, struct bed *cluster)
 /* Get (average) signal from table entries that overlap cluster */
 {
 struct sqlConnection *conn = hAllocConn(database);
 int count = 0;
 double sum = 0;
 if (sqlTableExists(conn, table))  // Table might be withdrawn from data thrash
     {
     int rowOffset;
     struct sqlResult *sr = hRangeQuery(conn, table, cluster->chrom, cluster->chromStart, 
 	    cluster->chromEnd, NULL, &rowOffset);
     int signalCol = sqlFieldColumn(sr, "signalValue");
     if (signalCol < 0)
 	internalErr();
     char **row;
     while ((row = sqlNextRow(sr)) != NULL)
 	{
 	count += 1;
 	sum += sqlDouble(row[signalCol]);
 	}
     sqlFreeResult(&sr);
     hFreeConn(&conn);
     }
 
 if (count > 0)
     return sum/count;
 else
     return 0;
 }
 
 static void printControlledVocabFields(char **row, int fieldCount, 
 	struct slName *fieldList, char *vocabFile, struct hash *vocabHash)
 /* Print out fields from row, linking them to controlled vocab if need be. */
 {
 int i;
 struct slName *field;
 for (i=0, field = fieldList; i<fieldCount; ++i, field = field->next)
     {
     char *fieldVal = row[i];
     if (vocabFile && hashLookup(vocabHash, field->name))
 	{
 	char *link = controlledVocabLink(vocabFile, "term", 
 		fieldVal, fieldVal, fieldVal, "");
 	webPrintLinkCell(link);
 	}
     else
 	webPrintLinkCell(fieldVal);
     }
 }
 
 struct hash *getVocabHash(char *fileName)
 /* Get vocabulary term hash */
 {
 struct hash *hash = raTagVals(fileName, "type");
 hashAdd(hash, "cellType", NULL);	/* Will the kludge never end, no, never! */
 return hash;
 }
 
 static void printMetadataForTable(char *table)
 /* If table exists, _and_ tdb associated with it exists, print out
  * a metadata link that expands on click.  Otherwise print "unavailable" */
 {
 webPrintLinkCellStart();
 struct trackDb *tdb = hashFindVal(trackHash, table);
 if (tdb == NULL)
     printf("%s info n/a", table);
 else
     compositeMetadataToggle(database, tdb, "metadata", TRUE, FALSE);
 webPrintLinkCellEnd();
 }
 
 static void queryInputTrackTable(struct dyString *query, char *inputTrackTable,
                                 struct slName *fieldList)
 /* Construct query in dyString to return contents of inputTrackTable ordered appropriately */
 {
 struct dyString *fields = dyStringNew(0);
 struct slName *field;
 dyStringPrintf(query, "select tableName ");
 for (field = fieldList; field != NULL; field = field->next)
     dyStringPrintf(fields, ",%s", field->name);
 dyStringPrintf(query, "%s from %s", fields->string, inputTrackTable);
 if (fieldList != NULL)
     // skip leading comma
     dyStringPrintf(query, " order by %s", fields->string+1);
 dyStringFree(&fields);
 }
 
 static void printPeakClusterTableHits(struct bed *cluster, struct sqlConnection *conn,
 	char *inputTrackTable, struct slName *fieldList, char *vocab)
 /* Put out a lines in an html table that shows assayed sources that have hits in this
  * cluster, or if invert is set, that have misses. */
 {
 char *vocabFile = NULL;
 struct hash *vocabHash = NULL;
 if (vocab)
     {
     vocabFile = cloneFirstWord(vocab);
     vocabHash = getVocabHash(vocabFile);
     }
 
 /* Make the SQL query to get the table and all other fields we want to show
  * from inputTrackTable. */
 struct dyString *query = dyStringNew(0);
 queryInputTrackTable(query, inputTrackTable, fieldList);
 
 int displayNo = 0;
 int fieldCount = slCount(fieldList);
 struct sqlResult *sr = sqlGetResult(conn, query->string);
 char **row;
 while ((row = sqlNextRow(sr)) != NULL)
     {
     char *table = row[0];
     double signal = getSignalAt(table, cluster);
     if (signal != 0)
 	{
 	printf("</TR><TR>\n");
 	webPrintIntCell(++displayNo);
 	webPrintDoubleCell(signal);
 	printControlledVocabFields(row+1, fieldCount, fieldList, vocabFile, vocabHash);
 	printMetadataForTable(table);
 	}
     }
 sqlFreeResult(&sr);
 freez(&vocabFile);
 dyStringFree(&query);
 }
 
 static void printPeakClusterInputs(struct sqlConnection *conn,
 	char *inputTrackTable, struct slName *fieldList, char *vocab)
 /* Print out all input tables for clustering. */
 {
 char *vocabFile = NULL;
 struct hash *vocabHash = NULL;
 if (vocab)
     {
     vocabFile = cloneFirstWord(vocab);
     vocabHash = getVocabHash(vocabFile);
     }
 
 /* Make the SQL query to get the table and all other fields we want to show
  * from inputTrackTable. */
 struct dyString *query = dyStringNew(0);
 queryInputTrackTable(query, inputTrackTable, fieldList);
 
 int displayNo = 0;
 int fieldCount = slCount(fieldList);
 struct sqlResult *sr = sqlGetResult(conn, query->string);
 char **row;
 while ((row = sqlNextRow(sr)) != NULL)
     {
     printf("</TR><TR>\n");
     webPrintIntCell(++displayNo);
     printControlledVocabFields(row+1, fieldCount, fieldList, vocabFile, vocabHash);
     printMetadataForTable(row[0]);
     }
 
 
 sqlFreeResult(&sr);
 freez(&vocabFile);
 dyStringFree(&query);
 }
 
 static void printFactorSourceTableHits(struct bed *cluster, struct sqlConnection *conn,
 	char *sourceTable, char *inputTrackTable, 
 	struct slName *fieldList, boolean invert, char *vocab)
 /* Put out a lines in an html table that shows assayed sources that have hits in this
  * cluster, or if invert is set, that have misses. */
 {
 char *vocabFile = NULL;
 if (vocab)
     {
     vocabFile = cloneFirstWord(vocab);
     }
 
 /* Make the monster SQL query to get all assays*/
 struct dyString *query = dyStringNew(0);
 dyStringPrintf(query, "select %s.id,%s.name,%s.tableName", sourceTable, sourceTable, 
 	inputTrackTable);
 struct slName *field;
 for (field = fieldList; field != NULL; field = field->next)
     dyStringPrintf(query, ",%s.%s", inputTrackTable, field->name);
 dyStringPrintf(query, " from %s,%s ", inputTrackTable, sourceTable);
 dyStringPrintf(query, " where %s.source = %s.description", inputTrackTable, sourceTable);
 dyStringPrintf(query, " and factor='%s' order by %s.source", cluster->name, inputTrackTable);
 
 int displayNo = 0;
 int fieldCount = slCount(fieldList);
 struct sqlResult *sr = sqlGetResult(conn, query->string);
 char **row;
 while ((row = sqlNextRow(sr)) != NULL)
     {
     int sourceId = sqlUnsigned(row[0]);
     double signal = cluster->expScores[sourceId];
     boolean hit = (signal > 0);
     if (hit ^ invert)
         {
 	printf("</TR><TR>\n");
 	webPrintIntCell(++displayNo);
 	if (!invert)
 	    webPrintDoubleCell(signal);
 	webPrintLinkCell(row[1]);
 	int i;
 	for (i=0; i<fieldCount; ++i)
 	    {
 	    char *fieldVal = row[i+3];
 	    if (vocab)
 	        {
 		char *link = controlledVocabLink(vocabFile, "term", 
 			fieldVal, fieldVal, fieldVal, "");
 		webPrintLinkCell(link);
 		}
 	    else
 		webPrintLinkCell(fieldVal);
 	    }
 	printMetadataForTable(row[2]);
 	}
     }
 sqlFreeResult(&sr);
 freez(&vocabFile);
 dyStringFree(&query);
 }
 
-
-static struct slName *findMatchingSubtracks(struct trackDb *tdb)
-/* Find subtracks that match inputTracks tags. */
-{
-/* Just list look up tableName in inputTrackTable and return the list. */
-char *inputTrackTable = trackDbRequiredSetting(tdb, "inputTrackTable");
-struct sqlConnection *conn = hAllocConn(database);
-char query[256];
-safef(query, sizeof(query), "select tableName from %s order by source", inputTrackTable);
-struct slName *matchTrackList = sqlQuickList(conn, query);
-hFreeConn(&conn);
-return matchTrackList;
-}
-
-
 void doPeakClusterListItemsAssayed()
 /* Put up a page that shows all experiments associated with a cluster track. */
 {
 struct trackDb *clusterTdb = tdbForTableArg();
 cartWebStart(cart, database, "List of items assayed in %s", clusterTdb->shortLabel);
 struct sqlConnection *conn = hAllocConn(database);
 
-char *inputTracksSubgroupDisplay = trackDbSetting(clusterTdb, "inputTracksSubgroupDisplay");
 char *inputTableFieldDisplay = trackDbSetting(clusterTdb, "inputTableFieldDisplay");
 webPrintLinkTableStart();
 if (inputTableFieldDisplay)
     {
     struct slName *fieldList = stringToSlNames(inputTableFieldDisplay);
     printClusterTableHeader(fieldList, FALSE, FALSE, FALSE);
     char *vocab = trackDbSetting(clusterTdb, "controlledVocabulary");
     char *inputTrackTable = trackDbRequiredSetting(clusterTdb, "inputTrackTable");
     printPeakClusterInputs(conn, inputTrackTable, fieldList, vocab);
     }
-#ifdef TO_BE_REMOVED
-else if (inputTracksSubgroupDisplay)
-    {
-    struct slName *matchTrackList = findMatchingSubtracks(clusterTdb);
-    struct slName *matchTrack;
-
-    struct slName *displayGroupList = stringToSlNames(inputTracksSubgroupDisplay);
-    printClusterTableHeader(displayGroupList, FALSE, TRUE, FALSE);
-    int rowIx = 0;
-    for (matchTrack = matchTrackList; matchTrack != NULL; matchTrack = matchTrack->next)
-	{
-	struct trackDb *tdb = hashFindVal(trackHash, matchTrack->name);
-	showOnePeakOrMiss(tdb, clusterTdb, NULL, displayGroupList, &rowIx);
-	}
-    }
-#endif /* TO_BE_REMOVED */
 else
-    errAbort("Missing required trackDb setting %s or %s for track %s",
-	"inputTracksSubgroupDisplay", "inputTableFieldDisplay", clusterTdb->track);
+    errAbort("Missing required trackDb setting %s for track %s", "inputTableFieldDisplay", 
+                clusterTdb->track);
 webPrintLinkTableEnd();
 hFreeConn(&conn);
 cartWebEnd();
 }
 
 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);
 
 cartWebStart(cart, database, "%s item details", tdb->shortLabel);
 safef(query, sizeof(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 subgroups to display */
-    char *inputTracksSubgroupDisplay = trackDbSetting(tdb, "inputTracksSubgroupDisplay");
     char *inputTableFieldDisplay = trackDbSetting(tdb, "inputTableFieldDisplay");
     if (inputTableFieldDisplay != NULL)
         {
 	struct slName *fieldList = stringToSlNames(inputTableFieldDisplay);
 	char *vocab = trackDbSetting(tdb, "controlledVocabulary");
 	char *inputTrackTable = trackDbRequiredSetting(tdb, "inputTrackTable");
 
 	/* Print out some information about the cluster overall. */
 	printf("<B>Items in Cluster:</B> %s of %d<BR>\n", cluster->name, 
 	    sqlRowCount(conn, inputTrackTable));
 	printf("<B>Cluster Score (out of 1000):</B> %d<BR>\n", cluster->score);
 	printPos(cluster->chrom, cluster->chromStart, cluster->chromEnd, NULL, TRUE, NULL);
 
 	/* In a new section put up list of hits. */
 	webNewSection("List of Items in Cluster");
 	webPrintLinkTableStart();
 	printClusterTableHeader(fieldList, FALSE, FALSE, TRUE);
 	printPeakClusterTableHits(cluster, conn, inputTrackTable, fieldList, vocab);
 	}
-#ifdef TO_BE_REMOVED
-    else if (inputTracksSubgroupDisplay != NULL)
-	{
-	struct slName *displayGroupList = stringToSlNames(inputTracksSubgroupDisplay);
-
-	/* Get list of tracks that match criteria. */
-	struct slName *matchTrackList = findMatchingSubtracks(tdb);
-	struct slName *matchTrack;
-
-	/* Print out some information about the cluster overall. */
-	printf("<B>Items in Cluster:</B> %s of %d<BR>\n", cluster->name, slCount(matchTrackList));
-	printf("<B>Cluster Score (out of 1000):</B> %d<BR>\n", cluster->score);
-	printPos(cluster->chrom, cluster->chromStart, cluster->chromEnd, NULL, TRUE, NULL);
-
-	/* In a new section put up list of hits. */
-	webNewSection("List of Items in Cluster");
-	webPrintLinkTableStart();
-	printClusterTableHeader(displayGroupList, FALSE, TRUE, TRUE);
-	int rowIx = 0;
-	for (matchTrack = matchTrackList; matchTrack != NULL; matchTrack = matchTrack->next)
-	    {
-	    showMatchingTrack(matchTrack->name, cluster, conn, tdb, displayGroupList,
-		    FALSE, &rowIx);
-	    }
-	}
-#endif /* TO_BE_REMOVED */
     else
-	errAbort("Missing required trackDb setting %s or %s for track %s",
-	    "inputTracksSubgroupDisplay", "inputTableFieldDisplay", tdb->track);
+	errAbort("Missing required trackDb setting %s for track %s",
+	    "inputTableFieldDisplay", tdb->track);
     webPrintLinkTableEnd();
     }
 printf("<A HREF=\"%s&g=htcListItemsAssayed&table=%s\" TARGET_blank>", hgcPathAndSettings(),
 	tdb->track);
 printf("List all items assayed");
 printf("</A><BR>\n");
 webNewSection("Track Description");
 printTrackHtml(tdb);
 cartWebEnd();
 hFreeConn(&conn);
 }
 
 void doFactorSource(struct sqlConnection *conn, struct trackDb *tdb, char *item, int start)
 /* Display detailed info about a cluster of peaks from other tracks. */
 {
 int rowOffset = hOffsetPastBin(database, seqName, tdb->table);
 char **row;
 struct sqlResult *sr;
 char query[256];
 char *motifTable = NULL;
 #ifdef TXCLUSTER_MOTIFS_TABLE
 motifTable = TXCLUSTER_MOTIFS_TABLE;
 #endif
 
 safef(query, sizeof(query),
 	"select * from %s where  name = '%s' and chrom = '%s' and chromStart = %d",
 	tdb->table, item, seqName, start);
 sr = sqlGetResult(conn, query);
 row = sqlNextRow(sr);
 struct bed *cluster = NULL;
 if (row != NULL)
     cluster = bedLoadN(row + rowOffset, 15);
 sqlFreeResult(&sr);
 
 if (cluster != NULL)
     {
     char *sourceTable = trackDbRequiredSetting(tdb, "sourceTable");
     struct dnaMotif *motif = NULL;
     struct dnaSeq **seqs = NULL;
     struct bed6FloatScore *hits = NULL;
 
     if(motifTable != NULL && sqlTableExists(conn, motifTable))
         {
         struct sqlResult *sr;
         int rowOffset;
         char where[256];
 
         motif = loadDnaMotif(item, "transRegCodeMotif");
         safef(where, sizeof(where), "name = '%s'", item);
         sr = hRangeQuery(conn, "wgEncodeRegTfbsClusteredMotifs", cluster->chrom, cluster->chromStart,
                          cluster->chromEnd, where, &rowOffset);
         while ((row = sqlNextRow(sr)) != NULL)
             {
             struct bed6FloatScore *hit = NULL;
             AllocVar(hit);
             hit->chromStart = sqlUnsigned(row[rowOffset + 1]);
             hit->chromEnd = sqlUnsigned(row[rowOffset + 2]);
             hit->score = sqlFloat(row[rowOffset + 4]);
             hit->strand[0] = row[rowOffset + 5][0];
             slAddHead(&hits, hit);
             }
         sqlFreeResult(&sr);
         }
     
     char *factorLink = cluster->name;
     char *vocab = trackDbSetting(tdb, "controlledVocabulary");
     if (vocab != NULL)
 	{
 	char *file = cloneFirstWord(vocab);
 	factorLink = controlledVocabLink(file, "term", factorLink, factorLink, factorLink, "");
 	}
     printf("<B>Factor:</B> %s<BR>\n", factorLink);
     printf("<B>Cluster Score (out of 1000):</B> %d<BR>\n", cluster->score);
     if(motif != NULL && hits != NULL)
         {
         struct bed6FloatScore *hit = NULL;
         int i;
         seqs = needMem(sizeof(struct dnaSeq *) * slCount(hits));
         for (hit = hits, i = 0; hit != NULL; hit = hit->next, i++)
             {
             char query[256];
             float maxScore = -1;
 
             safef(query, sizeof(query), 
 	    	"select max(score) from %s where name = '%s'", 
 		"wgEncodeRegTfbsClusteredMotifs", item);
             sr = sqlGetResult(conn, query);
             if ((row = sqlNextRow(sr)) != NULL)
                 {
                 if(!isEmpty(row[0]))
                     {
                     maxScore = sqlFloat(row[0]);
                     }
                 }
             sqlFreeResult(&sr);
 
             struct dnaSeq *seq = hDnaFromSeq(database, 
 	    	seqName, hit->chromStart, hit->chromEnd, dnaLower);
             if(hit->strand[0] == '-')
                 reverseComplement(seq->dna, seq->size);
             seqs[i] = seq;
             printf("<B>Motif Score #%d:</B>  %.2f (max: %.2f)<BR>\n", i + 1, hit->score, maxScore);
             }
         }
     printPos(cluster->chrom, cluster->chromStart, cluster->chromEnd, NULL, TRUE, NULL);
 
     if(seqs != NULL)
         {
         motifMultipleHitsSection(seqs, slCount(hits), motif);
         }
 
     /* Get list of tracks we'll look through for input. */
     char *inputTrackTable = trackDbRequiredSetting(tdb, "inputTrackTable");
     safef(query, sizeof(query), 
     	"select tableName from %s where factor='%s' order by source", inputTrackTable, 
 	cluster->name);
-    struct slName *matchTrackList = sqlQuickList(conn, query);
-    struct slName *matchTrack;
 
     /* Next do the lists of hits and misses.  We have the hits from the non-zero signals in
      * cluster->expScores.  We need to figure out the sources actually assayed though
-     * some other way.  We'll do this by one of two techniques.
-     * If the inputTracksSubgroupDisplay is set, we'll try and figure out what was
-     * assayed by looking at the subgroup stuff in trackDb, which works if everythings
-     * part of a composite.  If not, we'll use the inputTrackTable. */
-    /* Get list of subgroups to display */
-    char *inputTracksSubgroupDisplay = trackDbSetting(tdb, "inputTracksSubgroupDisplay");
+     * some other way.  We'll do this by one of two techniques. */
     char *inputTableFieldDisplay = trackDbSetting(tdb, "inputTableFieldDisplay");
     if (inputTableFieldDisplay != NULL)
         {
 	struct slName *fieldList = stringToSlNames(inputTableFieldDisplay);
 	char *vocab = trackDbSetting(tdb, "controlledVocabulary");
 
 	/* In a new section put up list of hits. */
 	webNewSection("List of %s Items in Cluster", cluster->name);
 	webPrintLinkTableStart();
 	printClusterTableHeader(fieldList, TRUE, FALSE, TRUE);
 	printFactorSourceTableHits(cluster, conn, sourceTable, 
 		inputTrackTable, fieldList, FALSE, vocab);
 	webPrintLinkTableEnd();
 
 	webNewSection("List of cells assayed with %s but without hits in cluster", cluster->name);
 	webPrintLinkTableStart();
 	printClusterTableHeader(fieldList, TRUE, FALSE, FALSE);
 	printFactorSourceTableHits(cluster, conn, sourceTable, 
 		inputTrackTable, fieldList, TRUE, vocab);
 	webPrintLinkTableEnd();
 	}
-#ifdef TO_BE_REMOVED
-    else if (inputTracksSubgroupDisplay != NULL)
-	{
-	struct slName *displayGroupList = stringToSlNames(inputTracksSubgroupDisplay);
-
-	/* In a new section put up list of hits. */
-	webNewSection("List of %s Items in Cluster", cluster->name);
-	webPrintLinkTableStart();
-	printClusterTableHeader(displayGroupList, FALSE, TRUE, TRUE);
-	int rowIx = 0;
-	for (matchTrack = matchTrackList; matchTrack != NULL; matchTrack = matchTrack->next)
-	    {
-	    showMatchingTrack(matchTrack->name, cluster, conn, tdb, displayGroupList,
-		    FALSE, &rowIx);
-	    }
-	webPrintLinkTableEnd();
-
-
-	webNewSection("List of cells assayed with %s but without hits in cluster", cluster->name);
-	webPrintLinkTableStart();
-	printClusterTableHeader(displayGroupList, FALSE, TRUE, FALSE);
-	rowIx = 0;
-	for (matchTrack = matchTrackList; matchTrack != NULL; matchTrack = matchTrack->next)
-	    {
-	    showMatchingTrack(matchTrack->name, cluster, conn, tdb, displayGroupList,
-		    TRUE, &rowIx);
-	    }
-	webPrintLinkTableEnd();
-	}
-#endif /* TO_BE_REMOVED */
     else
         {
-	errAbort("Missing required trackDb setting %s or %s for track %s",
-	    "inputTracksSubgroupDisplay", "inputTableFieldDisplay", tdb->track);
+	errAbort("Missing required trackDb setting %s for track %s",
+	    "inputTableFieldDisplay", tdb->track);
 	}
 
     webNewSection("Table of abbreviations for cells");
     hPrintAbbreviationTable(conn, sourceTable, "Cell Type");
 
     webNewSection("Track Description");
     }
 }