/*
* Copyright (c) 2007-2012 The Broad Institute, Inc.
* SOFTWARE COPYRIGHT NOTICE
* This software and its documentation are the copyright of the Broad Institute, Inc. All rights are reserved.
*
* This software is supplied without any warranty or guaranteed support whatsoever. The Broad Institute is not responsible for its use, misuse, or functionality.
*
* This software is licensed under the terms of the GNU Lesser General Public License (LGPL),
* Version 2.1 which is available at http://www.opensource.org/licenses/lgpl-2.1.php.
*/
package org.broad.igv.dev.db;
import org.apache.log4j.Logger;
import org.broad.igv.data.seg.SegmentedAsciiDataSet;
import org.broad.igv.feature.genome.Genome;
import org.broad.igv.util.ResourceLocator;
import java.sql.ResultSet;
import java.sql.SQLException;
/**
* Reader for Segmented data, from a SQL database. Column names are hardcoded
*
* @author Jim Robinson
* @date 10/14/11
* @deprecated See {@link org.broad.igv.dev.SegmentedReader}
*/
public class SegmentedSQLReader extends WholeTableDBReader<SegmentedAsciiDataSet> {
private static Logger log = Logger.getLogger(SegmentedSQLReader.class);
private Genome genome;
public SegmentedSQLReader(ResourceLocator locator, String tableName, Genome genome) {
super(locator, tableName, null);
this.genome = genome;
}
@Override
protected SegmentedAsciiDataSet processResultSet(ResultSet rs) throws SQLException {
SegmentedAsciiDataSet dataset = new SegmentedAsciiDataSet(genome);
while (rs.next()) {
String sample = rs.getString("Sample");
String chr = rs.getString("chr");
int start = rs.getInt("start");
int end = rs.getInt("end");
float value = rs.getFloat("value");
String description = rs.getString("description");
dataset.addSegment(sample, chr, start, end, value, description);
}
dataset.sortLists();
return dataset;
}
}