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/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
*/
package org.biojava.bio.program.sax.blastxml;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.List;
import junit.framework.TestCase;
import org.biojava.bio.program.ssbind.BlastLikeSearchBuilder;
import org.biojava.bio.program.ssbind.SeqSimilarityAdapter;
import org.biojava.bio.search.SearchContentHandler;
import org.biojava.bio.search.SeqSimilaritySearchResult;
import org.biojava.bio.seq.db.DummySequenceDB;
import org.biojava.bio.seq.db.DummySequenceDBInstallation;
import org.xml.sax.InputSource;
public class BlastXMLTest
extends TestCase
{
private List results;
protected void setUp()
throws Exception
{
// get test input file
String resName = "org/biojava/bio/program/sax/blastxml/input.xml";
InputStream resStream = getClass().getClassLoader().getResourceAsStream(resName);
assert resStream != null
: "Resource " + resName + " could not be located";
InputSource is = new InputSource(resStream);
//make a BlastLikeSAXParser
BlastXMLParserFacade parser = new BlastXMLParserFacade();
//make the SAX event adapter that will pass events to a Handler.
SeqSimilarityAdapter adapter = new SeqSimilarityAdapter();
//set the parsers SAX event adapter
parser.setContentHandler(adapter);
//The list to hold the SeqSimilaritySearchResults
results = new ArrayList();
//create the SearchContentHandler that will build SeqSimilaritySearchResults
//in the results List
SearchContentHandler builder = new BlastLikeSearchBuilder(results,
new DummySequenceDB("queries"), new DummySequenceDBInstallation());
//register builder with adapter
adapter.setSearchContentHandler(builder);
//parse the file, after this the result List will be populated with
//SeqSimilaritySearchResults
parser.parse(is);
}
private static int EXPECTED_QUERY_COUNT = 1;
private static int EXPECTED_HIT_COUNT = 5;
public void testHitCount()
{
// check that there are right numbers of queries
assertEquals(EXPECTED_QUERY_COUNT, results.size());
// check that number of hits is correct
SeqSimilaritySearchResult result =
(SeqSimilaritySearchResult) results.get(0);
assertEquals(EXPECTED_HIT_COUNT, result.getHits().size());
}
}
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