/*
 *                    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.nbio.core.sequence.loader;

import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
import org.biojava.nbio.core.sequence.ProteinSequence;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
import org.biojava.nbio.core.sequence.features.FeatureInterface;
import org.biojava.nbio.core.sequence.template.AbstractSequence;
import org.junit.Assert;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.junit.runners.Parameterized;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import org.biojava.nbio.core.sequence.features.AbstractFeature;
import org.biojava.nbio.core.sequence.features.Qualifier;

/**
 * Testing example for issue #834
 *
 * @author Jacek Grzebyta
 * @author Paolo Pavan
 * @see InfoTask
 */
@RunWith(Parameterized.class)
public class GenbankProxySequenceReaderTest {

    private String gi;
    private final static Logger logger = LoggerFactory.getLogger(GenbankProxySequenceReaderTest.class);

    public GenbankProxySequenceReaderTest(String gi) {
        this.gi = gi;
    }

    @Parameterized.Parameters
    public static Collection<String[]> getExamples() {
        String[][] out = new String[][]{
            {"399235158"},
            {"7525057"},
            {"379015144"},
            {"381353147"},
            {"381353148"},
            {"152970917"},
            {"381353149"},
            {"254839678"}
        };

        return Arrays.asList(out);
    }

    @Test
    public void testFeatures() throws IOException, InterruptedException, CompoundNotFoundException {
        logger.info("run test for protein: {}", gi);
        GenbankProxySequenceReader<AminoAcidCompound> genbankReader
                = new GenbankProxySequenceReader<AminoAcidCompound>(System.getProperty("java.io.tmpdir"),
                        this.gi,
                        AminoAcidCompoundSet.getAminoAcidCompoundSet());

        // why only tests on protein sequences?
        ProteinSequence seq = new ProteinSequence(genbankReader);

        Assert.assertNotNull("protein sequence is null", seq);

        /*
         parse description from header. There is no separate interface/abstract class for method getHeader()
         so it should be done here (manualy).
         */
        genbankReader.getHeaderParser().parseHeader(genbankReader.getHeader(), seq);

        // test description
        Assert.assertTrue(seq.getDescription() != null);

        // test accession Id
        logger.info("accession id: {}", seq.getAccession().getID());
        Assert.assertNotNull(seq.getAccession().getID());

        // test taxonomy id
        logger.info("taxonomy id: {}", seq.getTaxonomy().getID());
        Assert.assertNotNull(seq.getTaxonomy().getID());
        Assert.assertNotNull(Integer.decode(seq.getTaxonomy().getID().split(":")[1]));

        // test taxonomy name
        String taxonName = seq.getFeaturesByType("source").get(0).getQualifiers().get("organism").getValue();
        logger.info("taxonomy name '{}'", taxonName);
        Assert.assertNotNull(taxonName);

        if (seq.getFeaturesByType("CDS").size() > 0) {
            FeatureInterface<AbstractSequence<AminoAcidCompound>, AminoAcidCompound> CDS = seq.getFeaturesByType("CDS").get(0);
            logger.info("CDS: {}", CDS);
            String codedBy = CDS.getQualifiers().get("coded_by").getValue();
            Assert.assertNotNull(codedBy);
            Assert.assertTrue(!codedBy.isEmpty());
            logger.info("\t\tcoded_by: {}", codedBy);
        }
    }

    @Test
    public void testProteinSequenceFactoring() throws Exception {
        logger.info("create protein sequence test for target {}", gi);

        GenbankProxySequenceReader<AminoAcidCompound> genbankReader
                = new GenbankProxySequenceReader<AminoAcidCompound>(System.getProperty("java.io.tmpdir"),
                        this.gi,
                        AminoAcidCompoundSet.getAminoAcidCompoundSet());

        ProteinSequence seq = new ProteinSequence(genbankReader);

        // if target protein contain CDS/coded_by than it should contain parent nucleotide seq
        ArrayList<AbstractFeature> CDSs = genbankReader.getFeatures().get("CDS");

        if (CDSs != null) {
            if (CDSs.size() == 1) {
                Qualifier codedBy = (Qualifier) CDSs.get(0).getQualifiers().get("coded_by");
                if (codedBy != null) {

                    AbstractSequence<?> parentSeq = seq.getParentSequence();
                    Assert.assertNotNull(parentSeq);

                    /* 
                     Sometimes protein might have many 'parents' with different accessions
                     so accession is not set.
                
                     That test is always failed
                     */
                    //Assert.assertTrue(parentSeq.getAccession()); 
                    Assert.assertTrue(!parentSeq.getSequenceAsString().isEmpty());
                }
            }
        } else {
            logger.info("target {} has no CDS", gi);
        }

    }
}

@@ -3357,24 +3357,202 @@
 ().getID());
+%0A        // test GID number%0A        Assert.assertEquals(gi, seq.getAccession().getIdentifier());%0A        logger.info(%22found identifier '%7B%7D'%22, seq.getAccession().getIdentifier());
 %0A%0A        //

add identifier alias GID test