org.semanticscience.narf.graphs.lib.CycleSerializerTest.java Source code

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Here is the source code for org.semanticscience.narf.graphs.lib.CycleSerializerTest.java

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/**
 * Copyright (c) 2013  Jose Cruz-Toledo
 * Permission is hereby granted, free of charge, to any person obtaining a copy
 * of this software and associated documentation files (the "Software"), to deal
 * in the Software without restriction, including without limitation the rights
 * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the Software is
 * furnished to do so, subject to the following conditions:
 * 
 * The above copyright notice and this permission notice shall be included in
 * all copies or substantial portions of the Software.
 * 
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 * THE SOFTWARE.
 */
package org.semanticscience.narf.graphs.lib;

import static org.junit.Assert.fail;

import java.io.File;
import java.io.IOException;
import java.net.URL;
import java.util.List;
import java.util.Set;

import org.apache.commons.io.FileUtils;
import org.junit.AfterClass;
import org.junit.BeforeClass;
import org.junit.Test;
import org.semanticscience.narf.graphs.lib.cycles.Cycle;
import org.semanticscience.narf.graphs.lib.cycles.FundamentalCycleBasis;
import org.semanticscience.narf.graphs.nucleicacid.ExtractedNucleicAcid;
import org.semanticscience.narf.graphs.nucleicacid.InteractionEdge;
import org.semanticscience.narf.graphs.nucleicacid.NucleicAcid;
import org.semanticscience.narf.structures.parts.Nucleotide;

import com.hp.hpl.jena.rdf.model.Model;

/**
 * @author  Jose Cruz-Toledo
 *
 */
public class CycleSerializerTest {
    /**
     * The FCB that will be RDFized
     */
    private static FundamentalCycleBasis<Nucleotide, InteractionEdge> fcb = null;
    /**
     * The list of cycles that belong to the FCB
     */
    private static List<Cycle<Nucleotide, InteractionEdge>> cycleBasisList = null;
    /**
     * The PDBId of the file that will be used in this test
     */
    private static String pdbId = "1Y26";
    /**
     * The directory where the pdb files that will be used for this test
     * are stored
     */
    private static File pdbFilesDir = null;
    /**
     * The directory where the output of this test will be stored
     */
    private static File outputDir = null;
    /**
     * The output of X3DNADSSR
     */
    private static Set<NucleicAcid> nucs = null;

    /**
     * @throws java.lang.Exception
     */
    @BeforeClass
    public static void setUpBeforeClass() throws Exception {
        //download a pdb file
        URL aURL = new URL("http://www.rcsb.org/pdb/files/" + pdbId + ".pdb");
        //make a temporary direcotry
        pdbFilesDir = new File(FileUtils.getTempDirectoryPath() + "/pdb_files");
        File aPdbFile = new File(pdbFilesDir + "/" + pdbId + ".pdb");
        FileUtils.copyURLToFile(aURL, aPdbFile);

        outputDir = new File(FileUtils.getTempDirectory() + "/rdfutil_output");
        FileUtils.forceMkdir(outputDir);
        nucs = ExtractedNucleicAcid.x3dnaDssr(aPdbFile);
        //now compute the fundamental cycle basis
        if (nucs.size() == 1) {
            for (NucleicAcid aNuc : nucs) {
                fcb = new FundamentalCycleBasis<Nucleotide, InteractionEdge>(aNuc);
            }
        }
    }

    /**
     * @throws java.lang.Exception
     */
    @AfterClass
    public static void tearDownAfterClass() throws Exception {
        FileUtils.forceDeleteOnExit(pdbFilesDir);
        nucs = null;
        fcb = null;
        cycleBasisList = null;
    }

    /*@Test
    public void testRDFizer() throws IOException {
       List<Cycle<Nucleotide, InteractionEdge>> cycleBasisList = fcb.getCycleBasis();
       Model m = CycleSerializer.createNarfModel(pdbId, cycleBasisList);
       m.write(System.out);   
    }*/

}