/*
 * 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.Assert.assertEquals;
import static org.testng.Assert.assertNotEquals;

import jalview.bin.Cache;
import jalview.bin.Jalview;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.io.DataSourceType;
import jalview.io.FileLoader;
import jalview.viewmodel.ViewportRanges;

import java.lang.reflect.InvocationTargetException;

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

@Test(singleThreaded = true)
public class AlignmentPanelTest
{
  SequenceI seq1 = new Sequence(
          "Seq1",
          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");

  SequenceI seq2 = new Sequence(
          "Seq2",
          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");

  SequenceI seq3 = new Sequence(
          "Seq3",
          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");

  SequenceI seq4 = new Sequence(
          "Seq4",
          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");

  SequenceI seq5 = new Sequence(
          "Seq5",
          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");

  SequenceI seq6 = new Sequence(
          "Seq6",
          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");

  SequenceI seq7 = new Sequence(
          "Seq7",
          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");

  SequenceI seq8 = new Sequence(
          "Seq8",
          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");

  SequenceI seq9 = new Sequence(
          "Seq9",
          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");

  SequenceI seq10 = new Sequence(
          "Seq10",
          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");

  SequenceI seq11 = new Sequence(
          "Seq11",
          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");

  SequenceI seq12 = new Sequence(
          "Seq12",
          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");

  SequenceI seq13 = new Sequence(
          "Seq13",
          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");

  SequenceI seq14 = new Sequence(
          "Seq14",
          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");

  SequenceI seq15 = new Sequence(
          "Seq15",
          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");

  SequenceI seq16 = new Sequence(
          "Seq16",
          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");

  SequenceI seq17 = new Sequence(
          "Seq17",
          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");

  SequenceI seq18 = new Sequence(
          "Seq18",
          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");

  SequenceI seq19 = new Sequence(
          "Seq19",
          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");

  SequenceI seq20 = new Sequence(
          "Seq20",
          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");

  SequenceI seq21 = new Sequence(
          "Seq21",
          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");

  SequenceI seq22 = new Sequence(
          "Seq22",
          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");

  SequenceI seq23 = new Sequence(
          "Seq23",
          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");

  AlignFrame af;

  @BeforeMethod(alwaysRun = true)
  public void setUp() throws InvocationTargetException, InterruptedException
  {
    Jalview.setSynchronous(true);
    Jalview.main(new String[] { "-nonews", "-props",
        "test/jalview/testProps.jvprops" });

    Cache.setPropertyNoSave("SHOW_IDENTITY",
            Boolean.TRUE.toString());
    af = new FileLoader().LoadFileWaitTillLoaded("examples/uniref50.fa",
            DataSourceType.FILE);
    
    af.paintImmediately(af.getBounds());

    /*
     * wait for Consensus thread to complete
     */
    synchronized (this)
    {
      while (af.getViewport().getConsensusSeq() == null)
      {
        try
        {
          wait(250); // BH was 50
        } catch (InterruptedException e)
        {
        }
      }
    }
  }


  /**
   * Test side effect that end residue is set correctly by setScrollValues, with
   * or without hidden columns
   */
  @Test(groups = "Functional")
  public void testSetScrollValues()
  {
    ViewportRanges ranges = af.getViewport().getRanges();
    af.alignPanel.setScrollValues(0, 0);

    int oldres = ranges.getEndRes();
    af.alignPanel.setScrollValues(-1, 5);

    // setting -ve x value does not change residue
    assertEquals(ranges.getEndRes(), oldres);

    af.alignPanel.setScrollValues(0, 5);

    // setting 0 as x value does not change residue
    assertEquals(ranges.getEndRes(), oldres);

    af.alignPanel.setScrollValues(5, 5);
    // setting x value to 5 extends endRes by 5 residues
    assertEquals(ranges.getEndRes(), oldres + 5);

    // scroll to position after hidden columns sets endres to oldres (width) +
    // position
    int scrollpos = 60;
    af.getViewport().hideColumns(30, 50);
    af.alignPanel.setScrollValues(scrollpos, 5);

    af.paintImmediately(af.getBounds());
    assertEquals(ranges.getEndRes(), oldres + scrollpos);

    // scroll to position within hidden columns, still sets endres to oldres +
    // position
    // not sure if this is actually correct behaviour but this is what Jalview
    // currently does
    scrollpos = 40;
    af.getViewport().showAllHiddenColumns();
    af.getViewport().hideColumns(30, 50);
    af.alignPanel.setScrollValues(scrollpos, 5);
    assertEquals(ranges.getEndRes(), oldres + scrollpos);

    // scroll to position within <width> distance of the end of the alignment
    // endRes should be set to width of alignment - 1
    scrollpos = 130;
    af.getViewport().showAllHiddenColumns();
    af.alignPanel.setScrollValues(scrollpos, 5);
    af.paintImmediately(af.getBounds());
    assertEquals(ranges.getEndRes(), af.getViewport()
            .getAlignment().getWidth() - 1);

    // now hide some columns, and scroll to position within <width>
    // distance of the end of the alignment
    // endRes should be set to width of alignment - 1 - the number of hidden
    // columns
    af.getViewport().hideColumns(30, 50);
    af.paintImmediately(af.getBounds());
    af.alignPanel.setScrollValues(scrollpos, 5);
    assertEquals(ranges.getEndRes(), af.getViewport()
            .getAlignment().getWidth() - 1 - 21); // 21 is the number of hidden
                                                  // columns
  }

  /**
   * Test that update layout reverts to original (unwrapped) values for endRes
   * when switching from wrapped back to unwrapped mode (JAL-2739)
   */
  @Test(groups = "Functional")
  public void testUpdateLayout_endRes()
  {
    // get details of original alignment dimensions
    ViewportRanges ranges = af.getViewport().getRanges();
    int endres = ranges.getEndRes();

    // System.out.println("APT range end0 " + ranges.getEndRes());
    // wrap
    af.alignPanel.getAlignViewport().setWrapAlignment(true);
    af.alignPanel.updateLayout();
    af.paintImmediately(af.getBounds());
    waitSome();
    // System.out.println("APT range end1 " + ranges.getEndRes());
    // endRes has changed
    assertNotEquals(ranges.getEndRes(), endres);

    // unwrap
    af.alignPanel.getAlignViewport().setWrapAlignment(false);
    af.alignPanel.updateLayout();
    waitSome();
    af.paintImmediately(af.getBounds());

    // System.out.println("APT range end3 " + ranges.getEndRes());

    // endRes back to original value
    assertEquals(ranges.getEndRes(), endres);

  }

  private void waitSome()
  {

    // just a hack
    synchronized (this)
    {
      try
      {
        wait(250);
      } catch (InterruptedException e)
      {
      }
    }
  }
}