/*
 * 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.io;

import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;

import org.junit.Assert;
import org.testng.annotations.AfterClass;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;

public class ImportHomologyModelTest
{

  public static String base = "examples/testdata/phyre2/";

  public static String profile_msa = base + "query.jal",
          profile_annot = base + "query.jal.ann";

  public static String templaten[] = new String[] { "c1o1nA_", "c3pt8B_",
      "d1scta_" };

  AlignmentI al;
  AlignFrame af;

  /**
   * Ensure 'process secondary structure from PDB and add annotations' are set
   * in preferences, and load PDB example file 1gaq
   * 
   * @throws Exception
   */
  @BeforeMethod(alwaysRun = true)
  public void setup() throws Exception
  {
    Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
            Boolean.TRUE.toString());
    Cache.applicationProperties.setProperty("ADD_SS_ANN",
            Boolean.TRUE.toString());
    FileLoader loader = new FileLoader(false);
    af = loader.LoadFileWaitTillLoaded(profile_msa,
            jalview.io.DataSourceType.FILE);
    Desktop.addInternalFrame(af, "homology models", 800, 500);
    al = af.getViewport().getAlignment();
    af.loadJalviewDataFile(profile_annot, jalview.io.DataSourceType.FILE,
            null, null);
    // if file was loaded, the view should have a reference sequence set
    Assert.assertTrue(al.hasSeqrep());
  }


  @Test(groups = { "Functional" })
  public void testModelsAssociated()
  {
    for (String template : templaten)
    {
      SequenceI templseq = al.findName(template);
      Assert.assertNotNull("Couldn't find template sequence for "
              + template, templseq);
      PDBEntry querymdl = al.getSeqrep().getPDBEntry(template);
      PDBEntry templmdl = templseq.getPDBEntry(template);
      Assert.assertEquals(querymdl.getFile(), templmdl.getFile());
    }
  }

  /**
   * @throws java.lang.Exception
   */
  @BeforeClass(alwaysRun = true)
  public static void setUpBeforeClass() throws Exception
  {
    jalview.bin.Jalview.main(new String[] { "-props",
        "test/jalview/io/testProps.jvprops" });
  }

  /**
   * @throws java.lang.Exception
   */
  @AfterClass(alwaysRun = true)
  public static void tearDownAfterClass() throws Exception
  {
    jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
  }


}