/*
 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
 * Copyright (C) $$Year-Rel$$ The Jalview Authors
 * 
 * This file is part of Jalview.
 * 
 * Jalview 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 3
 * of the License, or (at your option) any later version.
 *  
 * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
 * The Jalview Authors are detailed in the 'AUTHORS' file.
 */
package jalview.datamodel.xdb.embl;

import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertNull;

import jalview.datamodel.DBRefEntry;

import java.util.Vector;

import org.testng.annotations.Test;

public class EmblFileTest
{

  @Test(groups = { "Functional" })
  public void testGetEmblFile()
  {
    Vector<EmblEntry> entries = EmblTestHelper.getEmblFile().getEntries();
    assertEquals(1, entries.size());
    EmblEntry entry = entries.get(0);

    assertEquals("X07547", entry.getAccession());
    assertEquals("C. trachomatis plasmid", entry.getDescription());
    assertEquals("STD", entry.getDataClass());
    assertEquals("PRO", entry.getTaxonomicDivision());
    assertEquals("1999-02-10", entry.getLastUpdatedDate());
    assertEquals("58", entry.getLastUpdatedRelease());
    assertEquals("1988-11-10", entry.getFirstPublicDate());
    assertEquals("18", entry.getFirstPublicRelease());
    assertEquals("genomic DNA", entry.getMoleculeType());
    assertEquals("1", entry.getSequenceVersion());
    assertEquals("8", entry.getEntryVersion());
    assertEquals("linear", entry.getTopology());
    assertEquals("7499", entry.getSequenceLength());

    /*
     * FIXME these assertions fail - values are null - why?? Adding or removing
     * attributes in the test XML modifies behaviour. eg. inserting an attribute
     * _before_ lastUpdated results in a null value in this field.
     */
    assertEquals("1988-11-10", entry.getFirstPublicDate());
    assertEquals("18", entry.getFirstPublicRelease());

    assertEquals(2, entry.getKeywords().size());
    assertEquals("plasmid", entry.getKeywords().get(0));
    assertEquals("unidentified reading frame", entry.getKeywords().get(1));

    /*
     * dbrefs
     */
    assertEquals(2, entry.getDbRefs().size());
    DBRefEntry dbref = entry.getDbRefs().get(0);
    assertEquals("EuropePMC", dbref.getSource());
    assertEquals("PMC107176", dbref.getAccessionId());
    assertEquals("9573186", dbref.getVersion());
    dbref = entry.getDbRefs().get(1);
    assertEquals("MD5", dbref.getSource());
    assertEquals("ac73317", dbref.getAccessionId());
    // blank version has been converted to "0"
    assertEquals("0", dbref.getVersion());

    /*
     * three sequence features for CDS
     */
    assertEquals(3, entry.getFeatures().size());
    /*
     * first CDS
     */
    EmblFeature ef = entry.getFeatures().get(0);
    assertEquals("CDS", ef.getName());
    assertEquals("complement(46..57)", ef.getLocation());
    assertEquals(2, ef.getDbRefs().size());
    dbref = ef.getDbRefs().get(0);
    assertEquals("UniProtKB/Swiss-Prot", dbref.getSource());
    assertEquals("B0BCM4", dbref.getAccessionId());
    assertEquals("2.1", dbref.getVersion());
    dbref = ef.getDbRefs().get(1);
    assertEquals("UniProtKB/Swiss-Prot", dbref.getSource());
    assertEquals("P0CE20", dbref.getAccessionId());
    // blank version gets converted to "0":
    assertEquals("0", dbref.getVersion());
    // CDS feature qualifiers
    assertEquals(3, ef.getQualifiers().size());
    Qualifier q = ef.getQualifiers().get(0);
    assertEquals("note", q.getName());
    assertEquals(2, q.getValues().length);
    assertEquals("ORF 8 (AA 1-330)", q.getValues()[0]);
    assertEquals("pickle", q.getValues()[1]);
    assertNull(q.getEvidence());
    q = ef.getQualifiers().get(1);
    assertEquals("protein_id", q.getName());
    assertEquals(1, q.getValues().length);
    assertEquals("CAA30420.1", q.getValues()[0]);
    q = ef.getQualifiers().get(2);
    assertEquals("translation", q.getName());
    assertEquals(1, q.getValues().length);
    assertEquals("MLCF", q.getValues()[0]);
    assertEquals(1, q.getEvidence().length);
    assertEquals("Keith", q.getEvidence()[0]);

    /*
     * second CDS
     */
    ef = entry.getFeatures().get(1);
    assertEquals("CDS", ef.getName());
    assertEquals("4..15", ef.getLocation());
    assertEquals(1, ef.getDbRefs().size());
    dbref = ef.getDbRefs().get(0);
    assertEquals("UniProtKB/Swiss-Prot", dbref.getSource());
    assertEquals("B0BCM3", dbref.getAccessionId());
    assertEquals("0", dbref.getVersion());
    assertEquals(2, ef.getQualifiers().size());
    q = ef.getQualifiers().get(0);
    assertEquals("protein_id", q.getName());
    assertEquals(1, q.getValues().length);
    assertEquals("CAA30421.1", q.getValues()[0]);
    q = ef.getQualifiers().get(1);
    assertEquals("translation", q.getName());
    assertEquals(1, q.getValues().length);
    assertEquals("MSSS", q.getValues()[0]);

    /*
     * third CDS
     */
    ef = entry.getFeatures().get(2);
    assertEquals("CDS", ef.getName());
    assertEquals("join(4..6,10..15)", ef.getLocation());
    assertNull(ef.getDbRefs());
    assertEquals(2, ef.getQualifiers().size());
    q = ef.getQualifiers().get(0);
    assertEquals("protein_id", q.getName());
    assertEquals(1, q.getValues().length);
    assertEquals("CAA12345.6", q.getValues()[0]);
    q = ef.getQualifiers().get(1);
    assertEquals("translation", q.getName());
    assertEquals(1, q.getValues().length);
    assertEquals("MSS", q.getValues()[0]);

    /*
     * Sequence - verify newline not converted to space (JAL-2029)
     */
    EmblSequence seq = entry.getSequence();
    assertEquals(
            "GGTATGTCCTCTAGTACAAACACCCCCAATATTGTGATATAATTAAAAACATAGCAT",
            seq.getSequence());

    /*
     * getSequence() converts empty DBRefEntry.version to "0"
     */
    assertEquals("0", entry.getDbRefs().get(1).getVersion());
    assertEquals("0", entry.getFeatures().get(0).getDbRefs().get(1)
            .getVersion());
  }
}