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("
\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; inext)
{
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("
\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("
\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("
\n");
webPrintIntCell(++displayNo);
if (!invert)
webPrintDoubleCell(signal);
webPrintLinkCell(row[1]);
int i;
for (i=0; ishortLabel);
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("Items in Cluster: %s of %d
\n", cluster->name,
sqlRowCount(conn, inputTrackTable));
printf("Cluster Score (out of 1000): %d
\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("Items in Cluster: %s of %d
\n", cluster->name, slCount(matchTrackList));
- printf("Cluster Score (out of 1000): %d
\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("", hgcPathAndSettings(),
tdb->track);
printf("List all items assayed");
printf("
\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("Factor: %s
\n", factorLink);
printf("Cluster Score (out of 1000): %d
\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("Motif Score #%d: %.2f (max: %.2f)
\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");
}
}