/*
 * 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.ws.seqfetcher;

import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;

import java.util.ArrayList;
import java.util.List;

import org.junit.AfterClass;
import org.junit.BeforeClass;
import org.junit.Test;

import jalview.analysis.CrossRef;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.util.DBRefUtils;
import jalview.ws.SequenceFetcher;

/**
 * @author jimp
 * 
 */
public class DbRefFetcherTest
{

  /**
   * @throws java.lang.Exception
   */
  @BeforeClass
  public static void setUpBeforeClass() throws Exception
  {
    jalview.bin.Cache.initLogger();
  }

  /**
   * @throws java.lang.Exception
   */
  @AfterClass
  public static void tearDownAfterClass() throws Exception
  {
  }

  @Test
  public void testStandardProtDbs()
  {
    String[] defdb = DBRefSource.PROTEINDBS;
    List<DbSourceProxy> srces = new ArrayList<DbSourceProxy>();
    for (String ddb : defdb)
    {
      SequenceFetcher sfetcher = new SequenceFetcher();
      List<DbSourceProxy> srcesfordb = sfetcher.getSourceProxy(ddb);

      if (srcesfordb != null)
      {
        srces.addAll(srcesfordb);
      }
    }
    DbSourceProxy uniprot = null;
    int i = 0;
    // append the selected sequence sources to the default dbs
    for (DbSourceProxy s : srces)
    {
      if (s.getDbSource().equalsIgnoreCase(DBRefSource.UNIPROT))
      {
        i++;
      }

      if (s instanceof jalview.ws.dbsources.Uniprot)
      {
        uniprot = s;
        break;
      }
    }

    assertTrue("Failed to find Uniprot source as first source amongst "
            + srces.size() + " sources (source was at position " + i + ")",
            uniprot != null && i < 2);
  }

  @Test
  public void testEmblUniprotProductRecovery() throws Exception
  {
    String retrievalId = "CAA23748"; // "V00488";
    DbSourceProxy embl = new SequenceFetcher().getSourceProxy(DBRefSource.EMBL).get(0);
    assertNotNull("Couldn't find the EMBL retrieval client", embl);
    verifyProteinNucleotideXref(retrievalId, embl);
  }

  @Test
  public void testEmblCDSUniprotProductRecovery() throws Exception
  {
    String retrievalId = "AAH29712";
    DbSourceProxy embl = new SequenceFetcher().getSourceProxy(
            DBRefSource.EMBLCDS).get(0);
    assertNotNull("Couldn't find the EMBL retrieval client", embl);
    verifyProteinNucleotideXref(retrievalId, embl);
  }

  private void verifyProteinNucleotideXref(String retrievalId,
          DbSourceProxy embl) throws Exception
  {
    AlignmentI alsq = embl.getSequenceRecords(retrievalId);
    assertNotNull("Couldn't find the EMBL record " + retrievalId, alsq);
    assertEquals("Didn't retrieve right number of records", 1, alsq.getHeight());
    DBRefEntry[] dr = DBRefUtils.selectRefs(alsq.getSequenceAt(0).getDBRef(), DBRefSource.PROTEINSEQ);
    assertNotNull(dr);
    assertEquals("Expected a single Uniprot cross reference", 1, dr.length);
    assertEquals("Expected cross refernce map to be one amino acid", dr[0]
            .getMap().getMappedWidth(), 1);
    assertEquals("Expected local refernce map to be 3 nucleotides", dr[0]
            .getMap().getWidth(), 3);
    AlignmentI sprods = CrossRef.findXrefSequences(alsq.getSequencesArray(), true, dr[0].getSource(), alsq.getDataset());
    assertNotNull(
            "Couldn't recover cross reference sequence from dataset. Was it ever added ?",
            sprods);
    
    
  }
}