/*
 * 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.structure;

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

import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.gui.JvOptionPane;
import jalview.io.DataSourceType;
import jalview.io.StructureFile;
import jalview.util.MapList;

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

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

public class StructureSelectionManagerTest
{

  @BeforeClass(alwaysRun = true)
  public void setUpJvOptionPane()
  {
    JvOptionPane.setInteractiveMode(false);
    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  }

  private StructureSelectionManager ssm;

  @BeforeMethod(alwaysRun = true)
  public void setUp()
  {
    StructureImportSettings.setShowSeqFeatures(true);
    ssm = new StructureSelectionManager();
  }

  @Test(groups = { "Functional" })
  public void testRegisterMapping()
  {
    AlignedCodonFrame acf1 = new AlignedCodonFrame();
    acf1.addMap(new Sequence("s1", "ttt"), new Sequence("p1", "p"),
            new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1));
    AlignedCodonFrame acf2 = new AlignedCodonFrame();
    acf2.addMap(new Sequence("s2", "ttt"), new Sequence("p2", "p"),
            new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1));

    ssm.registerMapping(acf1);
    assertEquals(1, ssm.getSequenceMappings().size());
    assertTrue(ssm.getSequenceMappings().contains(acf1));

    ssm.registerMapping(acf2);
    assertEquals(2, ssm.getSequenceMappings().size());
    assertTrue(ssm.getSequenceMappings().contains(acf1));
    assertTrue(ssm.getSequenceMappings().contains(acf2));

    /*
     * Re-adding the first mapping does nothing
     */
    ssm.registerMapping(acf1);
    assertEquals(2, ssm.getSequenceMappings().size());
    assertTrue(ssm.getSequenceMappings().contains(acf1));
    assertTrue(ssm.getSequenceMappings().contains(acf2));
  }

  @Test(groups = { "Functional" })
  public void testRegisterMappings()
  {
    AlignedCodonFrame acf1 = new AlignedCodonFrame();
    acf1.addMap(new Sequence("s1", "ttt"), new Sequence("p1", "p"),
            new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1));
    AlignedCodonFrame acf2 = new AlignedCodonFrame();
    acf2.addMap(new Sequence("s2", "ttt"), new Sequence("p2", "p"),
            new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1));
    AlignedCodonFrame acf3 = new AlignedCodonFrame();
    acf3.addMap(new Sequence("s3", "ttt"), new Sequence("p3", "p"),
            new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1));

    List<AlignedCodonFrame> set1 = new ArrayList<AlignedCodonFrame>();
    set1.add(acf1);
    set1.add(acf2);
    List<AlignedCodonFrame> set2 = new ArrayList<AlignedCodonFrame>();
    set2.add(acf2);
    set2.add(acf3);

    /*
     * Add both sets twice; each mapping should be added once only
     */
    ssm.registerMappings(set1);
    ssm.registerMappings(set1);
    ssm.registerMappings(set2);
    ssm.registerMappings(set2);

    assertEquals(3, ssm.getSequenceMappings().size());
    assertTrue(ssm.getSequenceMappings().contains(acf1));
    assertTrue(ssm.getSequenceMappings().contains(acf2));
    assertTrue(ssm.getSequenceMappings().contains(acf3));
  }

  /**
   * Verify that RESNUM sequence features are present after creating a PDB
   * mapping
   */
  @Test(groups = { "Functional" })
  public void testSetMapping_seqFeatures()
  {
    SequenceI seq = new Sequence(
            "1GAQ|B",
            "ATYNVKLITPEGEVELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDVVIETHKEEELTGA");
    StructureSelectionManager sm = new StructureSelectionManager();
    sm.setProcessSecondaryStructure(true);
    sm.setAddTempFacAnnot(true);
    StructureFile pmap = sm.setMapping(true, new SequenceI[] { seq },
            new String[] { null }, "examples/1gaq.txt", DataSourceType.FILE);
    assertTrue(pmap != null);

    assertEquals(3, pmap.getSeqs().size());
    assertEquals("1GAQ|A", pmap.getSeqs().get(0).getName());
    assertEquals("1GAQ|B", pmap.getSeqs().get(1).getName());
    assertEquals("1GAQ|C", pmap.getSeqs().get(2).getName());

    /*
     * Verify a RESNUM sequence feature in the PDBfile sequence
     */
    SequenceFeature sf = pmap.getSeqs().get(0).getSequenceFeatures()[0];
    assertEquals("RESNUM", sf.getType());
    assertEquals("1gaq", sf.getFeatureGroup());
    assertEquals("GLU:  19  1gaqA", sf.getDescription());

    /*
     * Verify a RESNUM sequence feature in the StructureSelectionManager mapped
     * sequence
     */
    StructureMapping map = sm.getMapping("examples/1gaq.txt")[0];
    sf = map.sequence.getSequenceFeatures()[0];
    assertEquals("RESNUM", sf.getType());
    assertEquals("1gaq", sf.getFeatureGroup());
    assertEquals("ALA:   1  1gaqB", sf.getDescription());
  }
}