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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 on Jun 30, 2008
*
*/
package org.biojava.ontology;
import java.io.BufferedReader;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.util.Set;
import org.biojava.ontology.io.OboParser;
import junit.framework.TestCase;
public class ParseOBOFileTest extends TestCase{
public void testsOBOFileParsing(){
OboParser parser = new OboParser();
InputStream inStream = this.getClass().getResourceAsStream("/files/org/biojava/bio/ontology/biosapiens.obo");
assertNotNull("could not find biosapiens.obo file",inStream);
BufferedReader oboFile = new BufferedReader ( new InputStreamReader ( inStream ) );
try {
Ontology ontology = parser.parseOBO(oboFile, "BioSapiens", "the BioSapiens ontology");
Set keys = ontology.getTerms();
assertTrue("did not find the expected nr of Ontology Terms!" , keys.size() > 50 );
String soID = "SO:0001081";
assertTrue("does not contain Term ", ontology.containsTerm(soID));
Term hth = ontology.getTerm(soID);
String soDesc = "helix_turn_helix";
assertTrue("description does not match expectation ("+soDesc + ")", hth.getDescription().equals(soDesc));
}
catch (Exception e){
fail (e.getMessage());
}
}
}
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