@Override
public Gene[] getTranscripts(String sessID, GeneSet geneSet)
throws SQLException, SessionExpiredException {
SelectQuery query =
MedSavantDatabase.GeneSetTableSchema.where(
GENOME, geneSet.getReference(), TYPE, geneSet.getType())
.select(NAME, CHROM, START, END, CODING_START, CODING_END, TRANSCRIPT);
LOG.debug(query);
ResultSet rs = ConnectionController.executeQuery(sessID, query.toString());
Gene[] result = new Gene[geneSet.getSize()];
int i = 0;
while (rs.next()) {
result[i++] =
new Gene(
rs.getString(1),
rs.getString(2),
rs.getInt(3),
rs.getInt(4),
rs.getInt(5),
rs.getInt(6),
rs.getString(7));
}
return result;
}
@Override
public Gene[] getGenes(String sessID, GeneSet geneSet)
throws SQLException, SessionExpiredException {
TableSchema table = MedSavantDatabase.GeneSetTableSchema;
SelectQuery query =
MedSavantDatabase.GeneSetTableSchema.where(
GENOME, geneSet.getReference(), TYPE, geneSet.getType())
.groupBy(CHROM)
.groupBy(NAME)
.select(NAME, CHROM, "MIN(start)", "MAX(end)", "MIN(codingStart)", "MAX(codingEnd)");
BinaryCondition dumbChrsCondition =
BinaryConditionMS.notlike(
table.getDBColumn(MedSavantDatabase.GeneSetColumns.CHROM), "%\\_%");
query.addCondition(dumbChrsCondition);
BinaryCondition dumbNameCondition =
BinaryConditionMS.notlike(table.getDBColumn(MedSavantDatabase.GeneSetColumns.NAME), "%-%");
query.addCondition(dumbNameCondition);
System.out.println(query.toString());
LOG.info(query);
ResultSet rs = ConnectionController.executeQuery(sessID, query.toString());
Gene[] result = new Gene[geneSet.getSize()];
int i = 0;
while (rs.next()) {
Gene g =
new Gene(
rs.getString(1),
rs.getString(2),
rs.getInt(3),
rs.getInt(4),
rs.getInt(5),
rs.getInt(6),
null);
result[i++] = g;
}
if (i != result.length) {
LOG.info("There were " + result.length + " genes, but only " + i + " were loaded.");
}
result = Arrays.copyOf(result, i);
return result;
}