/*
* 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.feature;
import org.broad.igv.AbstractHeadlessTest;
import org.broad.igv.util.TestUtils;
import org.jgrapht.ext.GmlExporter;
import org.junit.Ignore;
import org.junit.Test;
import java.io.FileWriter;
import java.util.ArrayList;
import java.util.List;
import static junit.framework.Assert.assertTrue;
/**
* User: jacob
* Date: 2012/03/28
*/
@Ignore
public class AlternativeSpliceGraphTest extends AbstractHeadlessTest {
@Test
public void initTest() throws Exception {
String nm = "CLIP1";
List<NamedFeature> n_features = FeatureDB.getFeaturesList(nm, Integer.MAX_VALUE, false);
List<IGVFeature> features = new ArrayList<IGVFeature>(n_features.size());
int maxNumExons = -1;
for (NamedFeature feat : n_features) {
if (feat.getName().equals(nm) && feat instanceof IGVFeature) {
IGVFeature iFeat = (IGVFeature) feat;
if (iFeat.getExons().size() > maxNumExons) {
maxNumExons = iFeat.getExons().size();
}
features.add(iFeat);
}
}
AlternativeSpliceGraph graph = new AlternativeSpliceGraph(features);
assertTrue(graph.vertexSet().size() >= maxNumExons);
GmlExporter exporter = new GmlExporter();
String outfile = TestUtils.DATA_DIR + "testas.gml";
FileWriter writer = new FileWriter(outfile);
exporter.export(writer, graph);
}
}