/*
 * 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.assertSame;
import static org.testng.AssertJUnit.assertTrue;

import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.io.DataSourceType;
import jalview.io.FileLoader;
import jalview.schemes.BuriedColourScheme;
import jalview.schemes.HelixColourScheme;
import jalview.schemes.JalviewColourScheme;
import jalview.schemes.StrandColourScheme;
import jalview.schemes.TurnColourScheme;
import jalview.util.MessageManager;

import java.util.List;

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

public class AlignFrameTest
{
  AlignFrame af;

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

  @Test(groups = "Functional")
  public void testHideFeatureColumns()
  {
    SequenceI seq1 = new Sequence("Seq1", "ABCDEFGHIJ");
    SequenceI seq2 = new Sequence("Seq2", "ABCDEFGHIJ");
    seq1.addSequenceFeature(new SequenceFeature("Metal", "", 1, 5,
            Float.NaN, null));
    seq2.addSequenceFeature(new SequenceFeature("Metal", "", 6, 10,
            Float.NaN, null));
    seq1.addSequenceFeature(new SequenceFeature("Turn", "", 2, 4,
            Float.NaN, null));
    seq2.addSequenceFeature(new SequenceFeature("Turn", "", 7, 9,
            Float.NaN, null));
    AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
    AlignFrame af = new AlignFrame(al, al.getWidth(), al.getHeight());

    /*
     * hiding a feature not present does nothing
     */
    assertFalse(af.hideFeatureColumns("exon", true));
    assertTrue(af.getViewport().getColumnSelection().isEmpty());
    assertTrue(af.getViewport().getColumnSelection().getHiddenColumns()
            .isEmpty());
    assertFalse(af.hideFeatureColumns("exon", false));
    assertTrue(af.getViewport().getColumnSelection().isEmpty());
    assertTrue(af.getViewport().getColumnSelection().getHiddenColumns()
            .isEmpty());

    /*
     * hiding a feature in all columns does nothing
     */
    assertFalse(af.hideFeatureColumns("Metal", true));
    assertTrue(af.getViewport().getColumnSelection().isEmpty());
    List<int[]> hidden = af.getViewport().getColumnSelection()
            .getHiddenColumns();
    assertTrue(hidden.isEmpty());

    /*
     * hide a feature present in some columns
     * sequence positions [2-4], [7-9] are column positions
     * [1-3], [6-8] base zero
     */
    assertTrue(af.hideFeatureColumns("Turn", true));
    hidden = af.getViewport().getColumnSelection().getHiddenColumns();
    assertEquals(2, hidden.size());
    assertEquals(1, hidden.get(0)[0]);
    assertEquals(3, hidden.get(0)[1]);
    assertEquals(6, hidden.get(1)[0]);
    assertEquals(8, hidden.get(1)[1]);
  }

  @BeforeMethod
  public void setUp()
  {
    af = new FileLoader().LoadFileWaitTillLoaded("examples/uniref50.fa",
            DataSourceType.FILE);
  }

  /**
   * Test that changing background (alignment) colour scheme
   * <ul>
   * <li>with Apply Colour to All Groups not selected, does not change group
   * colours</li>
   * <li>with Apply Colour to All Groups selected, does change group colours</li>
   * <li>in neither case, changes alignment or group colour thresholds (PID or
   * Conservation)</li>
   * </ul>
   */
  @Test
  public void testChangeColour_background_groupsAndThresholds()
  {
    AlignViewport av = af.getViewport();
    AlignmentI al = av.getAlignment();

    /*
     * Colour alignment by Buried Index
     */
    af.applyToAllGroups_actionPerformed(false);
    af.changeColour_actionPerformed(JalviewColourScheme.Buried.toString());
    assertTrue(av.getGlobalColourScheme() instanceof BuriedColourScheme);
    assertFalse(av.getViewportColourScheme().conservationApplied());
    assertEquals(av.getViewportColourScheme().getThreshold(), 0);

    /*
     * Apply Conservation 20%
     */
    af.conservationMenuItem_actionPerformed(true);
    SliderPanel sp = SliderPanel.getSliderPanel();
    assertEquals(sp.getTitle(), MessageManager.formatMessage(
            "label.conservation_colour_increment",
            new String[] { "Background" }));
    assertTrue(sp.isForConservation());
    sp.valueChanged(20);
    assertTrue(av.getViewportColourScheme().conservationApplied());
    assertEquals(av.getViewportColourScheme().getConservationInc(), 20);

    /*
     * Apply PID threshold 10% (conservation still applies as well)
     */
    af.abovePIDThreshold_actionPerformed(true);
    sp = SliderPanel.getSliderPanel();
    assertFalse(sp.isForConservation());
    assertEquals(sp.getTitle(), MessageManager.formatMessage(
            "label.percentage_identity_threshold",
            new String[] { "Background" }));
    sp.valueChanged(10);
    assertEquals(av.getViewportColourScheme().getThreshold(), 10);
    assertTrue(av.getViewportColourScheme().conservationApplied());
    assertEquals(av.getViewportColourScheme().getConservationInc(), 20);

    /*
     * create a group with Strand colouring, 30% Conservation
     * and 40% PID threshold
     */
    SequenceGroup sg = new SequenceGroup();
    sg.addSequence(al.getSequenceAt(0), false);
    sg.setStartRes(15);
    sg.setEndRes(25);
    av.setSelectionGroup(sg);

    /*
     * apply 30% Conservation to group
     */
    PopupMenu popupMenu = new PopupMenu(af.alignPanel, null, null);
    popupMenu.changeColour_actionPerformed(JalviewColourScheme.Strand
            .toString());
    assertTrue(sg.getColourScheme() instanceof StrandColourScheme);
    assertEquals(al.getGroups().size(), 1);
    assertSame(al.getGroups().get(0), sg);
    popupMenu.conservationMenuItem_actionPerformed(true);
    sp = SliderPanel.getSliderPanel();
    assertTrue(sp.isForConservation());
    assertEquals(sp.getTitle(), MessageManager.formatMessage(
            "label.conservation_colour_increment",
            new String[] { sg.getName() }));
    sp.valueChanged(30);
    assertTrue(sg.getGroupColourScheme().conservationApplied());
    assertEquals(sg.getGroupColourScheme().getConservationInc(), 30);

    /*
     * apply 40% PID threshold to group
     */
    popupMenu.abovePIDColour_actionPerformed(true);
    sp = SliderPanel.getSliderPanel();
    assertFalse(sp.isForConservation());
    assertEquals(sp.getTitle(), MessageManager.formatMessage(
            "label.percentage_identity_threshold",
            new String[] { sg.getName() }));
    sp.valueChanged(40);
    assertEquals(sg.getGroupColourScheme().getThreshold(), 40);
    // conservation threshold is unchanged:
    assertTrue(sg.getGroupColourScheme().conservationApplied());
    assertEquals(sg.getGroupColourScheme().getConservationInc(), 30);

    /*
     * change alignment colour - group colour, and all thresholds,
     * should be unaffected
     */
    af.changeColour_actionPerformed(JalviewColourScheme.Turn.toString());
    assertTrue(av.getGlobalColourScheme() instanceof TurnColourScheme);
    assertTrue(av.getViewportColourScheme().conservationApplied());
    assertEquals(av.getViewportColourScheme().getConservationInc(), 20);
    assertEquals(av.getViewportColourScheme().getThreshold(), 10);
    assertTrue(sg.getColourScheme() instanceof StrandColourScheme);
    assertTrue(sg.getGroupColourScheme().conservationApplied());
    assertEquals(sg.getGroupColourScheme().getConservationInc(), 30);
    assertEquals(sg.getGroupColourScheme().getThreshold(), 40);

    /*
     * Now change alignment colour with Apply Colour To All Groups
     * - group colour should change, but not colour thresholds
     */
    af.applyToAllGroups_actionPerformed(true);
    af.changeColour_actionPerformed(JalviewColourScheme.Helix.toString());
    assertTrue(av.getGlobalColourScheme() instanceof HelixColourScheme);
    assertTrue(av.getViewportColourScheme().conservationApplied());
    assertEquals(av.getViewportColourScheme().getConservationInc(), 20);
    assertEquals(av.getViewportColourScheme().getThreshold(), 10);
    assertTrue(sg.getColourScheme() instanceof HelixColourScheme);
    assertTrue(sg.getGroupColourScheme().conservationApplied());
    assertEquals(sg.getGroupColourScheme().getConservationInc(), 30);
    assertEquals(sg.getGroupColourScheme().getThreshold(), 40);
  }
}