/*
 * 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;

import static org.testng.AssertJUnit.assertTrue;

import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.structure.StructureImportSettings;
import jalview.structure.StructureImportSettings.StructureParser;
import jalview.ws.seqfetcher.DbSourceProxy;

import java.util.List;

import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;

public class PDBSequenceFetcherTest
{

  SequenceFetcher sf;

  @BeforeMethod(alwaysRun = true)
  public void setUp() throws Exception
  {
    Cache.loadProperties("test/jalview/io/testProps.jvprops");
    // ensure 'add annotation from structure' is selected
    Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
            Boolean.TRUE.toString());
    Cache.applicationProperties.setProperty("ADD_SS_ANN",
            Boolean.TRUE.toString());

    sf = new SequenceFetcher(false);
  }

  /**
   * Test that RNA structure can be added by a call to the RNAML service.
   * 
   * Note this test depends on http://arn-ibmc.in2p3.fr/api/compute/2d which is
   * not always reliable.
   * 
   * @throws Exception
   */
  @Test(groups = { "Network" }, enabled = true)
  public void testRnaSeqRetrieve() throws Exception
  {
    Cache.applicationProperties.setProperty("PDB_DOWNLOAD_FORMAT", "PDB");
    List<DbSourceProxy> sps = sf.getSourceProxy("PDB");
    AlignmentI response = sps.get(0).getSequenceRecords("2GIS");
    assertTrue(response != null);
    assertTrue(response.getHeight() == 1);
    for (SequenceI sq : response.getSequences())
    {
      assertTrue("No annotation transfered to sequence.",
              sq.getAnnotation().length > 0);
      assertTrue("No PDBEntry on sequence.",
              sq.getAllPDBEntries().size() > 0);
      assertTrue(
              "No RNA annotation on sequence, possibly http://arn-ibmc.in2p3.fr/api/compute/2d not available?",
              sq.getRNA() != null);
    }
  }

  @Test(groups = { "Network" }, enabled = true)
  public void testPdbSeqRetrieve() throws Exception
  {
    StructureImportSettings.setDefaultStructureFileFormat("PDB");
    StructureImportSettings
            .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER);

    testRetrieveProteinSeqFromPDB();
  }

  @Test(groups = { "Network" }, enabled = true)
  public void testmmCifSeqRetrieve() throws Exception
  {
    StructureImportSettings.setDefaultStructureFileFormat("mmCIF");
    testRetrieveProteinSeqFromPDB();
  }

  private void testRetrieveProteinSeqFromPDB() throws Exception
  {
    List<DbSourceProxy> sps = sf.getSourceProxy("PDB");
    AlignmentI response = sps.get(0).getSequenceRecords("1QIP");
    assertTrue(response != null);
    assertTrue(response.getHeight() == 4);
    for (SequenceI sq : response.getSequences())
    {
      assertTrue("No annotation transfered to sequence.",
              sq.getAnnotation().length > 0);
      assertTrue("No PDBEntry on sequence.",
              sq.getAllPDBEntries().size() > 0);
      org.testng.Assert
              .assertEquals(sq.getEnd() - sq.getStart() + 1,
                      sq.getLength(),
                      "Sequence start/end doesn't match number of residues in sequence");
    }
  }

}