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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.ssbind;
import java.io.BufferedInputStream;
import java.io.InputStream;
import java.util.zip.GZIPInputStream;
import org.biojava.bio.program.sax.BlastLikeSAXParser;
import org.biojava.bio.search.SeqSimilaritySearchResult;
import org.biojava.bio.seq.StrandedFeature;
import org.xml.sax.InputSource;
import org.xml.sax.XMLReader;
/**
* <code>SSBindNCBItblastx2_2_3Test</code> tests object bindings for
* Blast-like SAX events.
*
* @author Keith James
* @since 1.2
*/
public class SSBindNCBItblastx2_2_3Test extends SSBindCase
{
public SSBindNCBItblastx2_2_3Test(String name)
{
super(name);
}
protected void setUp() throws Exception
{
super.setUp();
setTopHitValues(1037D, "ECGLTA01",
1, 1284, StrandedFeature.UNKNOWN,
1091, 2374, StrandedFeature.UNKNOWN);
setBotHitValues(135D, "AF110311",
801, 1131, StrandedFeature.UNKNOWN,
1, 334, StrandedFeature.UNKNOWN);
String resName = "org/biojava/bio/program/ssbind/ncbi_tblastx_2.2.3.out.gz";
InputStream resStream = getClass().getClassLoader().getResourceAsStream(
resName);
assert resStream != null
: "Resource " + resName + " could not be located";
searchStream =
new GZIPInputStream(new BufferedInputStream(resStream));
// XMLReader -> (SAX events) -> adapter -> builder -> objects
XMLReader reader = (XMLReader) new BlastLikeSAXParser();
reader.setContentHandler(adapter);
reader.parse(new InputSource(searchStream));
}
public void testBlastResultHitCount()
{
SeqSimilaritySearchResult result =
(SeqSimilaritySearchResult) searchResults.get(0);
assertEquals(250, result.getHits().size());
}
}
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