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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.search;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Map;
import junit.framework.TestCase;
import org.biojava.bio.Annotation;
import org.biojava.bio.seq.ProteinTools;
import org.biojava.bio.seq.Sequence;
import org.biojava.bio.seq.db.HashSequenceDB;
import org.biojava.bio.seq.db.SequenceDB;
import org.biojava.bio.seq.impl.SimpleSequence;
import org.biojava.bio.seq.io.SymbolTokenization;
import org.biojava.bio.symbol.SimpleSymbolList;
/**
* <code>SimpleSeqSimilaritySearchResultTest</code> tests the
* behaviour of <code>SimpleSeqSimilaritySearchResult</code>.
*
* @author Keith James
*/
public class SimpleSeqSimilaritySearchResultTest extends TestCase
{
private SeqSimilaritySearchResult r1;
private SeqSimilaritySearchResult r2;
private SequenceDB database;
private Map parameters;
private Sequence query;
private String querySeqTokens = "TRYPASNDEF";
public SimpleSeqSimilaritySearchResultTest(String name)
{
super(name);
}
protected void setUp() throws Exception
{
database = new HashSequenceDB("test");
parameters = new HashMap();
SymbolTokenization tp = ProteinTools.getAlphabet().getTokenization("token");
query = new SimpleSequence(new SimpleSymbolList(tp, querySeqTokens),
"query", "",
Annotation.EMPTY_ANNOTATION);
r1 = new SimpleSeqSimilaritySearchResult(query,
database,
parameters,
new ArrayList(),
Annotation.EMPTY_ANNOTATION);
r2 = new SimpleSeqSimilaritySearchResult(query,
database,
parameters,
new ArrayList(),
Annotation.EMPTY_ANNOTATION);
}
public void testEquals()
{
assertEquals(r1, r1);
assertEquals(r2, r2);
assertEquals(r1, r2);
assertEquals(r2, r1);
}
public void testSequenceDB()
{
assertEquals(r1.getSequenceDB(), database);
}
public void testSearchParameters()
{
assertEquals(r1.getSearchParameters(), parameters);
}
public void testQuerySequence()
{
assertEquals(r1.getQuerySequence(), query);
}
public void testAnnotation()
{
assertEquals(r1.getAnnotation(),
Annotation.EMPTY_ANNOTATION);
}
}
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