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/*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
*/
/*
* AAindexStreamReaderTest.java
* Copyright (C) 2005 BioWeka.org
*/
package org.biojava.bio.proteomics.aaindex;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.util.Iterator;
import java.util.Map;
import junit.framework.TestCase;
import org.biojava.bio.BioException;
import org.biojava.bio.seq.ProteinTools;
import org.biojava.bio.symbol.SymbolList;
/**
* Test class for {@link org.biojava.bio.proteomics.aaindex.AAindexStreamReader}.
* @author <a href="mailto:Martin.Szugat@GMX.net">Martin Szugat</a>
* @version $Revision: 4023 $
*/
public class AAindexStreamReaderTest extends TestCase {
/**
* Main entry point.
* @param args command line arguments
*/
public static void main(String[] args) {
junit.textui.TestRunner.run(AAindexStreamReaderTest.class);
}
/**
* Test for reading AAindex files.
* @throws IOException if aaindex1 file could not be loaded.
* @throws BioException if the format of the file is invalid.
*/
public void testReading() throws IOException, BioException {
InputStream input = getClass().getClassLoader().getResourceAsStream(
"org/biojava/bio/proteomics/aaindex/aaindex1");
AAindexStreamReader reader = new AAindexStreamReader(
new InputStreamReader(input));
while (reader.hasNext()) {
AAindex aaindex = (AAindex) reader.nextTable();
SymbolList symbols = ProteinTools.createProtein(
"ARNDCEQGHILKMFPSTWYV");
for (int i = 1; i <= symbols.length(); i++) {
aaindex.getDoubleValue(symbols.symbolAt(i));
}
assertNotNull(aaindex.accessionNumber());
assertEquals(ProteinTools.getAlphabet(), aaindex.getAlphabet());
assertNotNull(aaindex.getArticleAuthors());
assertNotNull(aaindex.getArticleTitle());
assertNotNull(aaindex.getDescription());
assertNotNull(aaindex.getJournalReference());
assertTrue(aaindex.getLITDBEntryNumbers().length > 0);
assertNotNull(aaindex.getName());
Map entries = aaindex.similarEntries();
Iterator keys = entries.keySet().iterator();
while (keys.hasNext()) {
String key = (String) keys.next();
assertTrue(Double.class.isInstance(entries.get(key)));
}
}
assertTrue(reader.eof());
}
}
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