uk.ac.ebi.interpro.scan.model.ProteinMatchesHolderTest.java Source code

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Here is the source code for uk.ac.ebi.interpro.scan.model.ProteinMatchesHolderTest.java

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/*
 * Copyright 2010 the original author or authors.
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 * http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */

package uk.ac.ebi.interpro.scan.model;

import org.apache.commons.lang.SerializationUtils;
import org.apache.log4j.Logger;
import org.junit.Ignore;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.springframework.test.context.ContextConfiguration;
import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
import org.xml.sax.SAXException;

import java.io.IOException;
import java.text.ParseException;
import java.util.HashSet;
import java.util.Set;

import static org.junit.Assert.assertEquals;

/**
 * Test cases for {@link ProteinMatchesHolder}
 *
 * @author Antony Quinn
 * @version $Id$
 */
@RunWith(SpringJUnit4ClassRunner.class)
@ContextConfiguration
public class ProteinMatchesHolderTest extends AbstractTest<ProteinMatchesHolder> {

    private static final Logger LOGGER = Logger.getLogger(ProteinMatchesHolderTest.class.getName());

    @Test
    public void testEquals() throws IOException, ParseException {
        // Original
        ProteinMatchesHolder original = getPfamObject();
        // Copy
        ProteinMatchesHolder copy = (ProteinMatchesHolder) SerializationUtils.clone(original);
        // Should be equal
        assertEquals("Original and copy should be equal", original, copy);
        // Print
        if (LOGGER.isDebugEnabled()) {
            LOGGER.debug(original);
            LOGGER.debug(super.marshal(original));
        }
    }

    // TODO: Fix UnsupportedOperationException -- the @Ignore annotation was added in June 2011 (http://tinyurl.com/6tq8nz4), yet the comment is not correct -- the SignatureLibraryRelease element does *not* cause the exception  
    @Test
    @Ignore("Round trip does not work.  The embedded SignatureLibraryRelease element is not parsed.")
    public void testXml() throws IOException, SAXException {
        super.testSupportsMarshalling(ProteinMatchesHolder.class);
        super.testXmlRoundTrip();
    }

    private ProteinMatchesHolder getPfamObject() {
        // Create protein
        Protein p = new Protein("MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDI");
        Signature signature = new Signature("PF02310", "B12-binding");
        p.addCrossReference(new ProteinXref("A0A000_9ACTO"));
        Set<Hmmer3Match.Hmmer3Location> locations = new HashSet<Hmmer3Match.Hmmer3Location>();
        locations.add(new Hmmer3Match.Hmmer3Location(3, 107, 3.0, 3.7e-9, 1, 104, 121, 2, 108));
        p.addMatch(new Hmmer3Match(signature, 0.035, 3.7e-9, locations));
        // Create release
        SignatureLibraryRelease release = new SignatureLibraryRelease(SignatureLibrary.PFAM, "23");
        signature.setSignatureLibraryRelease(release);
        // Create holder
        ProteinMatchesHolder holder = new ProteinMatchesHolder();
        holder.addProtein(p);
        return holder;
    }

}