/*
 *                    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.program.indexdb;

import java.io.File;
import java.io.IOException;
import java.net.URI;
import java.net.URL;

import junit.framework.TestCase;

import org.biojava.bio.seq.Sequence;
import org.biojava.bio.seq.db.SequenceDBLite;
import org.biojava.bio.seq.db.flat.FlatSequenceDB;
import org.biojava.bio.seq.io.SeqIOConstants;

/**
 * <code>IndexToolsTest</code> tests indexing of flat files.
 *
 * @author Keith James
 */
public class IndexToolsTest extends TestCase
{
    protected String location;

    public IndexToolsTest(String name)
    {
        super(name);
    }

    protected void setUp() throws IOException
    {
        location = System.getProperty("java.io.tmpdir")
            + System.getProperty("file.separator")
            + "IndexToolsTest."
            + System.currentTimeMillis()
            + ".idx";
    }

    public void testIndexFastaDNA() throws Exception
    {
        File [] files = getDBFiles(new String [] { "dna1.fasta",
                                                   "dna2.fasta" });
        IndexTools.indexFasta("test", new File(location),
                              files, SeqIOConstants.DNA);

        SequenceDBLite db = new FlatSequenceDB(location, "dna");

        Sequence seq1 = db.getSequence("id1");
        assertEquals("gatatcgatt", seq1.seqString());
        Sequence seq2 = db.getSequence("id2");
        assertEquals("ggcgcgcgcg", seq2.seqString());
        Sequence seq3 = db.getSequence("id3");
        assertEquals("ccccccccta", seq3.seqString());
        Sequence seq4 = db.getSequence("id4");
        assertEquals("tttttcgatt", seq4.seqString());
        Sequence seq5 = db.getSequence("id5");
        assertEquals("ggttcgcgcg", seq5.seqString());
        Sequence seq6 = db.getSequence("id6");
        assertEquals("nnnnnnttna", seq6.seqString());
    }

    public void testIndexFastaRNA() throws Exception
    {
        File [] files = getDBFiles(new String [] { "rna1.fasta",
                                                   "rna2.fasta" });
        IndexTools.indexFasta("test", new File(location),
                              files, SeqIOConstants.RNA);

        SequenceDBLite db = new FlatSequenceDB(location, "rna");

        Sequence seq1 = db.getSequence("id1");
        assertEquals("gauaucgauu", seq1.seqString());
        Sequence seq2 = db.getSequence("id2");
        assertEquals("ggcgcgcgcg", seq2.seqString());
        Sequence seq3 = db.getSequence("id3");
        assertEquals("uuuuucgauu", seq3.seqString());
        Sequence seq4 = db.getSequence("id4");
        assertEquals("gguucgcgcg", seq4.seqString());
    }

    public void testIndexFastaProtein() throws Exception
    {
        File [] files = getDBFiles(new String [] { "protein1.fasta",
                                                   "protein2.fasta" });
        IndexTools.indexFasta("test", new File(location),
                              files, SeqIOConstants.AA);

        SequenceDBLite db = new FlatSequenceDB(location, "protein");

        Sequence seq1 = db.getSequence("id1");
        assertEquals("MTTSRGGGGG", seq1.seqString());
        Sequence seq2 = db.getSequence("id2");
        assertEquals("VVLLLLDDTN", seq2.seqString());
        Sequence seq3 = db.getSequence("id3");
        assertEquals("MVVVLNNGGG", seq3.seqString());
        Sequence seq4 = db.getSequence("id4");
        assertEquals("NGGDEEFDTN", seq4.seqString());
    }

    public void testIndexEmblDNA() throws Exception
    {
        File [] files = getDBFiles(new String [] { "part1.embl",
                                                   "part2.embl" });
        IndexTools.indexEmbl("test", new File(location),
                             files, SeqIOConstants.DNA);

        SequenceDBLite db = new FlatSequenceDB(location, "embl");

        Sequence seq1 = db.getSequence("A16SRRNA");
        assertEquals(1497, seq1.length());
        Sequence seq2 = db.getSequence("A16STM112");
        assertEquals(1346, seq2.length());
        Sequence seq3 = db.getSequence("A16STM146");
        assertEquals(1352, seq3.length());

        Sequence seq4 = db.getSequence("AY080928");
        assertEquals(557, seq4.length());
        Sequence seq5 = db.getSequence("AY080929");
        assertEquals(556, seq5.length());
        Sequence seq6 = db.getSequence("AY080930");
        assertEquals(557, seq6.length());
    }

    public void testIndexGenbankDNA() throws Exception
    {
        File [] files = getDBFiles(new String [] { "part1.gb",
                                                   "part2.gb" });
        IndexTools.indexGenbank("test", new File(location),
                                files, SeqIOConstants.DNA);

        SequenceDBLite db = new FlatSequenceDB(location, "genbank");

        Sequence seq1 = db.getSequence("A16SRRNA");
        assertEquals(1497, seq1.length());
        Sequence seq2 = db.getSequence("A16STM112");
        assertEquals(1346, seq2.length());
        Sequence seq3 = db.getSequence("A16STM146");
        assertEquals(1352, seq3.length());

        Sequence seq4 = db.getSequence("AY080928");
        assertEquals(557, seq4.length());
        Sequence seq5 = db.getSequence("AY080929");
        assertEquals(556, seq5.length());
        Sequence seq6 = db.getSequence("AY080930");
        assertEquals(557, seq6.length());
    }

    public void testIndexSwissprot() throws Exception
    {
        File [] files = getDBFiles(new String [] { "part1.swiss",
                                                   "part2.swiss" });
        IndexTools.indexSwissprot("test", new File(location), files);

        SequenceDBLite db = new FlatSequenceDB(location, "swiss");

        Sequence seq1 = db.getSequence("104K_THEPA");
        assertEquals(924, seq1.length());
        Sequence seq2 = db.getSequence("108_LYCES");
        assertEquals(102, seq2.length());
        Sequence seq3 = db.getSequence("10KD_VIGUN");
        assertEquals(75, seq3.length());
        Sequence seq4 = db.getSequence("110K_PLAKN");
        assertEquals(296, seq4.length());
        Sequence seq5 = db.getSequence("11S3_HELAN");
        assertEquals(493, seq5.length());
        Sequence seq6 = db.getSequence("11SB_CUCMA");
        assertEquals(480, seq6.length());
    }

    private File [] getDBFiles(String [] fileNames) throws Exception
    {
        File [] files = new File [fileNames.length];

        for (int i = 0; i < files.length; i++)
        {
            URL seqURL = getClass().getResource("/org/biojava/bio/program/indexdb/"+fileNames[i]);                        
            files[i] = new File(seqURL.toURI());
        }

        return files;
    }            
}

@@ -1405,25 +1405,16 @@
 tem.
-currentTimeMillis
+nanoTime
 ()%0A 

fix for intermittent test failures on windows platform