void doPeakClusters(struct trackDb *tdb, char *item)
/* Display detailed info about a cluster of DNase 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);
sqlSafef(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 *inputTableFieldDisplay = trackDbSetting(tdb, "inputTableFieldDisplay");
if (inputTableFieldDisplay != NULL)
{
struct slName *fieldList = stringToSlNames(inputTableFieldDisplay);
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, sqlCheckIdentifier(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);
printPeakClusterInfo(tdb, cart, conn, inputTrackTable, fieldList, cluster);
}
else
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);
hFreeConn(&conn);
}
void expRestoreTable(char *file)
/* Fill empty table with experiments in .ra file with id's */
{
struct hash *ra = NULL;
struct lineFile *lf = lineFileOpen(file, TRUE);
struct encodeExp *exp;
int ix = 1;
int expId;
char *accession;
char *key;
verbose(1, "Restoring experiments from file \'%s\' to table \'%s\'\n", file, table);
if (sqlRowCount(connExp, sqlCheckIdentifier(table)) != 0)
errAbort("ERROR: table for restore must exist and be empty");
while ((ra = raNextRecord(lf)) != NULL)
{
exp = encodeExpFromRa(ra);
/* save accession and id as we may stomp on these for to-delete experiments */
accession = cloneString(exp->lab);
expId = exp->ix;
key = encodeExpKey(exp);
while (ix < expId)
{
exp->accession = "DELETED";
exp->ix = ix;
verbose(3, "Adding row for deleted experiment %d\n", ix);
encodeExpAdd(connExp, table, exp);
ix++;
}
/* restore accession and id */
exp->accession = accession;
exp->ix = expId;
encodeExpAdd(connExp, table, exp);
verbose(3, "Adding row for experiment %d: %s\n", ix, key);
ix++;
}
verbose(1, "To complete restore, delete rows where accession=DELETED\n");
}
SQLRETURN SQL_API SQLRowCount(SQLHSTMT StatementHandle, SQLLEN *RowCount)
{
o::SQLRowCount sqlRowCount(StatementHandle, RowCount);
return sqlRowCount();
}
