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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/
*
* created at Sep 14, 2008
*/
package org.biojava.bio.program.sax;
import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.List;
import java.util.zip.GZIPInputStream;
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.SeqSimilaritySearchHit;
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;
import org.xml.sax.SAXException;
/** a class to test Blast parsing
*
* @author Travis Banks
*
*/
public class BlastTest extends TestCase {
public void testBLASTP2_2_11() throws Exception
{
String filename = "files/org/biojava/bio/program/sax/blastp-2.2.11.txt.gz";
parseBlastFile(filename, 2, 2, 2);
}
public void testBLASTP2_2_15() throws Exception
{
String filename = "files/org/biojava/bio/program/sax/blastp-2.2.15.txt.gz";
parseBlastFile(filename, 2, 2, 2);
}
public void testTBLASTN2_2_18() throws Exception
{
String filename = "files/org/biojava/bio/program/sax/tblastn-2.2.18.txt.gz";
parseBlastFile(filename, 2, 10, 2);
}
public void testSingleBLASTHit2_2_15() throws Exception
{
String filename = "files/org/biojava/bio/program/sax/single-blastp-2.2.15.txt.gz";
parseBlastFile(filename, 2, 2, 1);
}
public void testBug2584() throws Exception {
String filename="files/org/biojava/bio/program/sax/bug-2584-test_file.txt.gz";
InputStream resStream = new GZIPInputStream( getClass().getClassLoader().getResourceAsStream(filename));
assert resStream != null: "Resource " + filename + " could not be located";
InputSource is = new InputSource(resStream);
BlastLikeSAXParser parser = new BlastLikeSAXParser();
parser.setModeStrict();
SeqSimilarityAdapter adapter = new SeqSimilarityAdapter();
parser.setContentHandler(adapter);
List<SeqSimilaritySearchResult> results = new ArrayList<SeqSimilaritySearchResult>();
SearchContentHandler builder = new BlastLikeSearchBuilder(results,new DummySequenceDB("queries"), new DummySequenceDBInstallation());
adapter.setSearchContentHandler(builder);
parser.parse(is);
assertEquals(10, results.size());
for(int i=0;i<results.size();i++) {
SeqSimilaritySearchResult sssr=results.get(i);
String queryId=(String)sssr.getAnnotation().getProperty("queryId");
switch(i) {
case(0):
assertEquals("BmRpP0",queryId);
break;
case(1):
assertEquals("BmRpP1",queryId);
break;
case(2):
assertEquals("BmRpP2",queryId);
break;
case(3):
assertEquals("BmRpL3",queryId);
break;
case(4):
assertEquals("BmRpL4",queryId);
break;
case(5):
assertEquals("BmRpL5",queryId);
break;
case(6):
assertEquals("BmRpL6",queryId);
break;
case(7):
assertEquals("BmRpL7",queryId);
break;
case(8):
assertEquals("BmRpL7A",queryId);
break;
case(9):
assertEquals("BmRpL8",queryId);
break;
};
}
}
private void parseBlastFile(String filename, int numberOfReports, int numberOfHits, int numberOfHsps) throws IOException, SAXException {
String resName = filename;
InputStream resStream = new GZIPInputStream( getClass().getClassLoader().getResourceAsStream(
resName));
assert resStream != null
: "Resource " + resName + " could not be located";
InputSource is = new InputSource(resStream);
BlastLikeSAXParser parser = new BlastLikeSAXParser();
parser.setModeStrict();
SeqSimilarityAdapter adapter = new SeqSimilarityAdapter();
parser.setContentHandler(adapter);
List<SeqSimilaritySearchResult> results = new ArrayList<SeqSimilaritySearchResult>();
SearchContentHandler builder = new BlastLikeSearchBuilder(results,
new DummySequenceDB("queries"), new DummySequenceDBInstallation());
adapter.setSearchContentHandler(builder);
parser.parse(is);
// check that there are the correct numbers of queries
assertEquals(numberOfReports, results.size());
// check that the number of hits is correct
for(SeqSimilaritySearchResult sssr: results) {
assertEquals(numberOfHits,sssr.getHits().size());
}
// check that the number of hsps is correct
for(SeqSimilaritySearchResult sssr: results) {
for(Object o:sssr.getHits()) {
SeqSimilaritySearchHit hit=(SeqSimilaritySearchHit)o;
assertEquals(numberOfHsps,hit.getSubHits().size());
}
}
}
}
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