/*
 * 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.gui;

import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;

import jalview.bin.Cache;
import jalview.bin.Jalview;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.PDBEntry.Type;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.io.FileLoader;
import jalview.io.FormatAdapter;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.PIDColourScheme;
import jalview.structure.StructureSelectionManager;
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 AlignViewportTest
{

  AlignmentI al;

  AlignViewport testee;

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

  @BeforeMethod(alwaysRun = true)
  public void setUp()
  {
    SequenceI seq1 = new Sequence("Seq1", "ABC");
    SequenceI seq2 = new Sequence("Seq2", "ABC");
    SequenceI seq3 = new Sequence("Seq3", "ABC");
    SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3 };
    al = new Alignment(seqs);
    al.setDataset(null);
    testee = new AlignViewport(al);
  }

  @Test(groups = { "Functional" })
  public void testCollateForPdb()
  {
    // JBP: What behaviour is this supposed to test ?
    /*
     * Set up sequence pdb ids
     */
    PDBEntry pdb1 = new PDBEntry("1ABC", "B", Type.PDB, "1ABC.pdb");
    PDBEntry pdb2 = new PDBEntry("2ABC", "C", Type.PDB, "2ABC.pdb");
    PDBEntry pdb3 = new PDBEntry("3ABC", "D", Type.PDB, "3ABC.pdb");

    /*
     * seq1 and seq3 refer to 1abcB, seq2 to 2abcC, none to 3abcD
     */
    al.getSequenceAt(0).getDatasetSequence()
            .addPDBId(new PDBEntry("1ABC", "B", Type.PDB, "1ABC.pdb"));
    al.getSequenceAt(2).getDatasetSequence()
            .addPDBId(new PDBEntry("1ABC", "B", Type.PDB, "1ABC.pdb"));
    al.getSequenceAt(1).getDatasetSequence()
            .addPDBId(new PDBEntry("2ABC", "C", Type.PDB, "2ABC.pdb"));
    /*
     * Add a second chain PDB xref to Seq2 - should not result in a duplicate in
     * the results
     */
    al.getSequenceAt(1).getDatasetSequence()
            .addPDBId(new PDBEntry("2ABC", "D", Type.PDB, "2ABC.pdb"));
    /*
     * Seq3 refers to 3abc - this does not match 3ABC (as the code stands)
     */
    al.getSequenceAt(2).getDatasetSequence()
            .addPDBId(new PDBEntry("3abc", "D", Type.PDB, "3ABC.pdb"));

    /*
     * run method under test
     */
    SequenceI[][] seqs = testee.collateForPDB(new PDBEntry[] { pdb1, pdb2,
        pdb3 });

    // seq1 and seq3 refer to PDBEntry[0]
    assertEquals(2, seqs[0].length);
    assertSame(al.getSequenceAt(0), seqs[0][0]);
    assertSame(al.getSequenceAt(2), seqs[0][1]);

    // seq2 refers to PDBEntry[1]
    assertEquals(1, seqs[1].length);
    assertSame(al.getSequenceAt(1), seqs[1][0]);

    // no sequence refers to PDBEntry[2]
    assertEquals(0, seqs[2].length);
  }

  /**
   * Test that a mapping is not deregistered when a second view is closed but
   * the first still holds a reference to the mapping
   */
  @Test(groups = { "Functional" })
  public void testDeregisterMapping_onCloseView()
  {
    /*
     * alignment with reference to mappings
     */
    AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
            ">Seq1\nCAGT\n", FormatAdapter.PASTE);

    SequenceI s1 = af1.getViewport().getAlignment().getSequenceAt(0);
    AlignedCodonFrame acf1 = new AlignedCodonFrame();
    acf1.addMap(s1, s1, new MapList(new int[] { 1, 4 }, new int[] { 1, 4 },
            1, 1));
    AlignedCodonFrame acf2 = new AlignedCodonFrame();
    acf2.addMap(s1, s1, new MapList(new int[] { 1, 4 }, new int[] { 4, 1 },
            1, 1));

    List<AlignedCodonFrame> mappings = new ArrayList<AlignedCodonFrame>();
    mappings.add(acf1);
    mappings.add(acf2);
    af1.getViewport().getAlignment().setCodonFrames(mappings);
    af1.newView_actionPerformed(null);

    /*
     * Verify that creating the alignment for the new View has registered the
     * mappings
     */
    StructureSelectionManager ssm = StructureSelectionManager
            .getStructureSelectionManager(Desktop.instance);
    assertEquals(2, ssm.getSequenceMappings().size());
    assertTrue(ssm.getSequenceMappings().contains(acf1));
    assertTrue(ssm.getSequenceMappings().contains(acf2));

    /*
     * Close the second view. Verify that mappings are not removed as the first
     * view still holds a reference to them.
     */
    af1.closeMenuItem_actionPerformed(false);
    assertEquals(2, ssm.getSequenceMappings().size());
    assertTrue(ssm.getSequenceMappings().contains(acf1));
    assertTrue(ssm.getSequenceMappings().contains(acf2));
  }

  /**
   * Test that a mapping is deregistered if no alignment holds a reference to it
   */
  @Test(groups = { "Functional" })
  public void testDeregisterMapping_withNoReference()
  {
    Desktop d = Desktop.instance;
    assertNotNull(d);
    StructureSelectionManager ssm = StructureSelectionManager
            .getStructureSelectionManager(Desktop.instance);
    ssm.resetAll();

    AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
            ">Seq1\nRSVQ\n", FormatAdapter.PASTE);
    AlignFrame af2 = new FileLoader().LoadFileWaitTillLoaded(
            ">Seq2\nDGEL\n", FormatAdapter.PASTE);
    SequenceI cs1 = new Sequence("cseq1", "CCCGGGTTTAAA");
    SequenceI cs2 = new Sequence("cseq2", "CTTGAGTCTAGA");
    SequenceI s1 = af1.getViewport().getAlignment().getSequenceAt(0);
    SequenceI s2 = af2.getViewport().getAlignment().getSequenceAt(0);
    // need to be distinct
    AlignedCodonFrame acf1 = new AlignedCodonFrame();
    acf1.addMap(cs1, s1, new MapList(new int[] { 1, 4 },
            new int[] { 1, 12 }, 1, 3));
    AlignedCodonFrame acf2 = new AlignedCodonFrame();
    acf2.addMap(cs2, s2, new MapList(new int[] { 1, 4 },
            new int[] { 1, 12 }, 1, 3));
    AlignedCodonFrame acf3 = new AlignedCodonFrame();
    acf3.addMap(cs2, cs2, new MapList(new int[] { 1, 12 }, new int[] { 1,
        12 }, 1, 1));

    List<AlignedCodonFrame> mappings1 = new ArrayList<AlignedCodonFrame>();
    mappings1.add(acf1);
    af1.getViewport().getAlignment().setCodonFrames(mappings1);

    List<AlignedCodonFrame> mappings2 = new ArrayList<AlignedCodonFrame>();
    mappings2.add(acf2);
    mappings2.add(acf3);
    af2.getViewport().getAlignment().setCodonFrames(mappings2);

    /*
     * AlignFrame1 has mapping acf1, AlignFrame2 has acf2 and acf3
     */

    List<AlignedCodonFrame> ssmMappings = ssm.getSequenceMappings();
    assertEquals(0, ssmMappings.size());
    ssm.registerMapping(acf1);
    assertEquals(1, ssmMappings.size());
    ssm.registerMapping(acf2);
    assertEquals(2, ssmMappings.size());
    ssm.registerMapping(acf3);
    assertEquals(3, ssmMappings.size());

    /*
     * Closing AlignFrame2 should remove its mappings from
     * StructureSelectionManager, since AlignFrame1 has no reference to them
     */
    af2.closeMenuItem_actionPerformed(true);
    assertEquals(1, ssmMappings.size());
    assertTrue(ssmMappings.contains(acf1));
  }

  /**
   * Test that a mapping is not deregistered if another alignment holds a
   * reference to it
   */
  @Test(groups = { "Functional" })
  public void testDeregisterMapping_withReference()
  {
    Desktop d = Desktop.instance;
    assertNotNull(d);
    StructureSelectionManager ssm = StructureSelectionManager
            .getStructureSelectionManager(Desktop.instance);
    ssm.resetAll();

    AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
            ">Seq1\nRSVQ\n", FormatAdapter.PASTE);
    AlignFrame af2 = new FileLoader().LoadFileWaitTillLoaded(
            ">Seq2\nDGEL\n", FormatAdapter.PASTE);
    SequenceI cs1 = new Sequence("cseq1", "CCCGGGTTTAAA");
    SequenceI cs2 = new Sequence("cseq2", "CTTGAGTCTAGA");
    SequenceI s1 = af1.getViewport().getAlignment().getSequenceAt(0);
    SequenceI s2 = af2.getViewport().getAlignment().getSequenceAt(0);
    // need to be distinct
    AlignedCodonFrame acf1 = new AlignedCodonFrame();
    acf1.addMap(cs1, s1, new MapList(new int[] { 1, 4 },
            new int[] { 1, 12 }, 1, 3));
    AlignedCodonFrame acf2 = new AlignedCodonFrame();
    acf2.addMap(cs2, s2, new MapList(new int[] { 1, 4 },
            new int[] { 1, 12 }, 1, 3));
    AlignedCodonFrame acf3 = new AlignedCodonFrame();
    acf3.addMap(cs2, cs2, new MapList(new int[] { 1, 12 }, new int[] { 1,
        12 }, 1, 1));

    List<AlignedCodonFrame> mappings1 = new ArrayList<AlignedCodonFrame>();
    mappings1.add(acf1);
    mappings1.add(acf2);
    af1.getViewport().getAlignment().setCodonFrames(mappings1);

    List<AlignedCodonFrame> mappings2 = new ArrayList<AlignedCodonFrame>();
    mappings2.add(acf2);
    mappings2.add(acf3);
    af2.getViewport().getAlignment().setCodonFrames(mappings2);

    /*
     * AlignFrame1 has mappings acf1 and acf2, AlignFrame2 has acf2 and acf3
     */

    List<AlignedCodonFrame> ssmMappings = ssm.getSequenceMappings();
    assertEquals(0, ssmMappings.size());
    ssm.registerMapping(acf1);
    assertEquals(1, ssmMappings.size());
    ssm.registerMapping(acf2);
    assertEquals(2, ssmMappings.size());
    ssm.registerMapping(acf3);
    assertEquals(3, ssmMappings.size());

    /*
     * Closing AlignFrame2 should remove mapping acf3 from
     * StructureSelectionManager, but not acf2, since AlignFrame1 still has a
     * reference to it
     */
    af2.closeMenuItem_actionPerformed(true);
    assertEquals(2, ssmMappings.size());
    assertTrue(ssmMappings.contains(acf1));
    assertTrue(ssmMappings.contains(acf2));
    assertFalse(ssmMappings.contains(acf3));
  }

  /**
   * Test for JAL-1306 - conservation thread should run even when only Quality
   * (and not Conservation) is enabled in Preferences
   */
  @Test(groups = { "Functional" })
  public void testUpdateConservation_qualityOnly()
  {
    Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
            Boolean.TRUE.toString());
    Cache.applicationProperties.setProperty("SHOW_QUALITY",
            Boolean.TRUE.toString());
    Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
            Boolean.FALSE.toString());
    Cache.applicationProperties.setProperty("SHOW_IDENTITY",
            Boolean.FALSE.toString());
    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
            "examples/uniref50.fa", FormatAdapter.FILE);
    AlignmentAnnotation[] anns = af.viewport.getAlignment()
            .getAlignmentAnnotation();
    assertNotNull("No annotations found", anns);
    assertEquals("More than one annotation found", 1, anns.length);
    assertTrue("Annotation is not Quality",
            anns[0].description.startsWith("Alignment Quality"));
    Annotation[] annotations = anns[0].annotations;
    assertNotNull("Quality annotations are null", annotations);
    assertNotNull("Quality in column 1 is null", annotations[0]);
    assertTrue("No quality value in column 1", annotations[0].value > 10f);
  }

  @Test(groups = { "Functional" })
  public void testSetGlobalColourScheme()
  {
    /*
     * test for JAL-2283 don't inadvertently turn on colour by conservation
     */
    Cache.applicationProperties.setProperty("DEFAULT_COLOUR_PROT", "NONE");
    Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
            Boolean.TRUE.toString());
    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
            "examples/uniref50.fa", FormatAdapter.FILE);
    ColourSchemeI cs = new PIDColourScheme();
    af.getViewport().setGlobalColourScheme(cs);
    assertFalse(cs.conservationApplied());
  }
}