/*
 * 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.viewmodel;

import static org.testng.Assert.assertEquals;

import jalview.bin.Cache;
import jalview.bin.Jalview;
import jalview.datamodel.Alignment;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.AlignViewport;
import jalview.gui.Desktop;
import jalview.gui.JvOptionPane;
import jalview.io.DataSourceType;
import jalview.io.FileLoader;

import java.util.List;

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

@Test(singleThreaded = true)
public class OverviewDimensionsTest {

  boolean showConservationSetting;

  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");

  AlignFrame af;
  AlignViewport av;
  OverviewDimensions od;

  float scalew;
  float scaleh;
  int boxWidth;
  int boxHeight;

  int viewHeight;

  int viewWidth;

  int alheight;

  int alwidth;

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

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

    Cache.applicationProperties.setProperty("SHOW_IDENTITY",
            Boolean.TRUE.toString());
    af = new FileLoader().LoadFileWaitTillLoaded(
            "examples/testdata/bigal.fa",
            DataSourceType.FILE);

    /*
     * Wait for viewport to initialise
     */
    synchronized (this)
    {
      while (af.getViewport().getEndRes() == 0)
      {
        try
        {
          wait(50);
        } catch (InterruptedException e)
        {
        }
      }
    }

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

    // get cached setting for showConservation
    // reset it in AfterClass!
    showConservationSetting = Cache.getDefault("SHOW_CONSERVATION", true);
    
    av = af.getViewport();

    od = new OverviewDimensions(av);

    while (av.isCalcInProgress())
    {
      try
      {
        Thread.sleep(50);
      } catch (InterruptedException e)
      {

      }
    }

    // Initial box sizing - default path through code
    od.setBoxPosition();

    init();
  }

  private void init()
  {
    av.showAllHiddenColumns();
    av.showAllHiddenSeqs();
    av.setSelectionGroup(null);
    // o/w hidden seqs retain selection group, causes problems later when hiding
    // sequences

    // wait for conservation calc to complete
    while (av.isCalcInProgress())
    {
      try
      {
        Thread.sleep(50);
      } catch (InterruptedException e)
      {

      }
    }

    mouseClick(od, 0, 0);
    moveViewport(0, 0);

    viewHeight = av.getEndSeq() - av.getStartSeq();
    viewWidth = av.getEndRes() - av.getStartRes();

    // wait for gui to get set up
    while (viewHeight != 17 || viewWidth != 59)
    {
      try
      {
        Thread.sleep(50);
        viewHeight = av.getEndSeq() - av.getStartSeq();
        viewWidth = av.getEndRes() - av.getStartRes();
      } catch (InterruptedException e)
      {

      }
    }

    // calculate before hidden columns so we get absolute values
    alheight = av.getAlignment().getHeight();
    alwidth = av.getAlignment().getWidth();

    boxWidth = Math.round((float) (av.getEndRes() - av.getStartRes() + 1)
            / alwidth * od.getWidth());
    boxHeight = Math.round((float) (av.getEndSeq() - av.getStartSeq())
            / alheight * od.getHeight());
    System.out.println(boxHeight);

  }

  @AfterMethod(alwaysRun = true)
  public void tearDown()
  {
    Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
            Boolean.toString(showConservationSetting));
    Desktop.instance.closeAll_actionPerformed(null);
  }

  /**
   * Test that the OverviewDimensions constructor sets width and height
   * correctly
   */
  @Test(groups = { "Functional" })
  public void testConstructor()
  {
    SequenceI seqa = new Sequence("Seq1", "ABC");
    SequenceI seqb = new Sequence("Seq2", "ABC");
    SequenceI seqc = new Sequence("Seq3", "ABC");
    SequenceI seqd = new Sequence("Seq4", "ABC");
    SequenceI seqe = new Sequence("Seq5",
            "ABCABCABCABCABCABCABCABCBACBACBACBAC");

    int defaultGraphHeight = 20;
    int maxWidth = 400;
    int minWidth = 120;
    int maxSeqHeight = 300;
    int minSeqHeight = 40;

    Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
            Boolean.toString(true));

    // test for alignment with width > height
    SequenceI[] seqs1 = new SequenceI[] { seqa, seqb };
    Alignment al1 = new Alignment(seqs1);
    al1.setDataset(null);
    AlignViewport av1 = new AlignViewport(al1);

    OverviewDimensions od = new OverviewDimensions(av1);
    int scaledHeight = 266;
    assertEquals(od.getGraphHeight(), defaultGraphHeight);
    assertEquals(od.getSequencesHeight(), scaledHeight);
    assertEquals(od.getWidth(), maxWidth);
    assertEquals(od.getHeight(), scaledHeight + defaultGraphHeight);

    // test for alignment with width < height
    SequenceI[] seqs2 = new SequenceI[] { seqa, seqb, seqc, seqd };
    Alignment al2 = new Alignment(seqs2);
    al2.setDataset(null);
    AlignViewport av2 = new AlignViewport(al2);

    od = new OverviewDimensions(av2);
    int scaledWidth = 300;
    assertEquals(od.getGraphHeight(), defaultGraphHeight);
    assertEquals(od.getSequencesHeight(), maxSeqHeight);
    assertEquals(od.getWidth(), scaledWidth);
    assertEquals(od.getHeight(), scaledWidth + defaultGraphHeight);

    // test for alignment with width > height and sequence height scaled below
    // min value
    SequenceI[] seqs3 = new SequenceI[] { seqe };
    Alignment al3 = new Alignment(seqs3);
    al3.setDataset(null);
    AlignViewport av3 = new AlignViewport(al3);

    od = new OverviewDimensions(av3);
    assertEquals(od.getGraphHeight(), defaultGraphHeight);
    assertEquals(od.getSequencesHeight(), minSeqHeight);
    assertEquals(od.getWidth(), maxWidth);
    assertEquals(od.getHeight(), minSeqHeight + defaultGraphHeight);

    // test for alignment with width < height and width scaled below min value
    SequenceI[] seqs4 = new SequenceI[] { seqa, seqb, seqc, seqd, seqa,
        seqb, seqc, seqd, seqa, seqb, seqc, seqd, seqa, seqb, seqc, seqd };
    Alignment al4 = new Alignment(seqs4);
    al4.setDataset(null);
    AlignViewport av4 = new AlignViewport(al4);

    od = new OverviewDimensions(av4);
    assertEquals(od.getGraphHeight(), defaultGraphHeight);
    assertEquals(od.getSequencesHeight(), maxSeqHeight);
    assertEquals(od.getWidth(), minWidth);
    assertEquals(od.getHeight(), maxSeqHeight + defaultGraphHeight);

    // test for alignment where no conservation annotation is shown
    Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
            Boolean.toString(false));

    Alignment al5 = new Alignment(seqs4);
    al5.setDataset(null);
    AlignViewport av5 = new AlignViewport(al5);

    od = new OverviewDimensions(av5);
    assertEquals(od.getGraphHeight(), 0);
    assertEquals(od.getSequencesHeight(), maxSeqHeight);
    assertEquals(od.getWidth(), minWidth);
    assertEquals(od.getHeight(), maxSeqHeight);
  }

  /**
   * Test that validation after mouse adjustments to boxX and boxY sets box
   * dimensions and scroll values correctly, when there are no hidden rows or
   * columns.
   * 
   * The current implementation uses multiple transformations between coordinate
   * systems which often involve casting to int, which causes values to be
   * truncated. As a result we can lose accuracy. The tests below use
   * approximate test values where appropriate.
   */
  @Test(groups = { "Functional" })
  public void testSetBoxFromMouseClick()
  {
    od.setBoxPositionByMouse(0, 0);
    assertEquals(od.getBoxX(), 0);
    assertEquals(od.getBoxY(), 0);
    assertEquals(od.getBoxWidth(), boxWidth);
    assertEquals(od.getScrollCol(), 0);
    assertEquals(od.getScrollRow(), 0);

    // negative boxX value reset to 0
    mouseClick(od, -5, 10);
    assertEquals(od.getBoxX(), 0);
    assertEquals(od.getBoxWidth(), boxWidth);
    assertEquals(od.getBoxHeight(), boxHeight);
    assertEquals(od.getScrollRow(),
            Math.round((float) 10 * alheight / od.getSequencesHeight()));
    assertEquals(od.getScrollCol(), 0);

    // negative boxY value reset to 0
    mouseClick(od, 6, -2);
    assertEquals(od.getBoxY(), 0);
    assertEquals(od.getBoxWidth(), boxWidth);
    assertEquals(od.getBoxHeight(), boxHeight);
    assertEquals(od.getScrollCol(),
            Math.round((float) 6 * alwidth / od.getWidth()));
    assertEquals(od.getScrollRow(), 0);

    // overly large boxX value reset to width-boxWidth
    mouseClick(od, 100, 6);
    assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth());
    assertEquals(od.getBoxY(), 6);
    assertEquals(od.getBoxWidth(), boxWidth);
    assertEquals(od.getBoxHeight(), boxHeight);
    assertEquals(od.getScrollCol(),
            Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
    assertEquals(od.getScrollRow(),
            Math.round((float) od.getBoxY() * alheight
                    / od.getSequencesHeight()));

    // overly large boxY value reset to sequenceHeight - boxHeight
    mouseClick(od, 10, 520);
    assertEquals(od.getBoxX(), 10);
    assertEquals(od.getBoxY(), od.getSequencesHeight() - od.getBoxHeight());
    assertEquals(od.getBoxWidth(), boxWidth);
    assertEquals(od.getBoxHeight(), boxHeight);
    assertEquals(od.getScrollCol(),
            Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
    assertEquals(od.getScrollRow(),
            Math.round((float) od.getBoxY() * alheight
                    / od.getSequencesHeight()));

    // click past end of alignment, as above
    mouseClick(od, 3000, 5);
    assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth());
    assertEquals(od.getBoxWidth(), boxWidth);
    assertEquals(od.getBoxHeight(), boxHeight);
    assertEquals(od.getScrollCol(),
            Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
    assertEquals(od.getScrollRow(),
            Math.round((float) od.getBoxY() * alheight
                    / od.getSequencesHeight()));

    // move viewport so startRes non-zero and then mouseclick
    moveViewportH(50);

    // click at viewport position
    int oldboxx = od.getBoxX();
    int oldboxy = od.getBoxY();
    mouseClick(od, od.getBoxX() + 5, od.getBoxY() + 2);
    assertEquals(od.getBoxX(), oldboxx + 5);
    assertEquals(od.getBoxWidth(), boxWidth);
    assertEquals(od.getBoxHeight(), boxHeight);
    assertEquals(od.getScrollCol(),
            Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
    assertEquals(od.getBoxY(), oldboxy + 2);
    assertEquals(od.getScrollRow(),
            Math.round((float) od.getBoxY() * alheight
                    / od.getSequencesHeight()));

    // click at top corner
    mouseClick(od, 0, 0);
    assertEquals(od.getBoxX(), 0);
    assertEquals(od.getScrollCol(), 0);
    assertEquals(od.getBoxY(), 0);
    assertEquals(od.getScrollRow(), 0);
    assertEquals(od.getBoxWidth(), boxWidth);
    assertEquals(od.getBoxHeight(), boxHeight);
  }

  /**
   * Test setting of the box position, when there are hidden cols at the start
   * of the alignment
   */
  @Test(groups = { "Functional" })
  public void testFromMouseWithHiddenColsAtStart()
  {
    od.setBoxPositionByMouse(0, 0);
    assertEquals(od.getBoxX(), 0);
    assertEquals(od.getBoxY(), 0);
    assertEquals(od.getBoxWidth(), boxWidth);
    assertEquals(od.getScrollCol(), 0);
    assertEquals(od.getScrollRow(), 0);

    // hide cols at start and check updated box position is correct
    // changes boxX but not boxwidth
    int lastHiddenCol = 30;
    hideColumns(0, lastHiddenCol);

    od.setBoxPosition();
    assertEquals(od.getBoxX(),
            Math.round((float) (lastHiddenCol + 1) * od.getWidth()
                    / alwidth));
    assertEquals(od.getBoxWidth(), boxWidth);
    assertEquals(od.getBoxHeight(), boxHeight);

    // try to click in hidden cols, check box does not move
    // this test currently fails as the overview box does not behave like this!
    /*    int xpos = 10;
        mouseClick(od, xpos, 0);
        assertEquals(od.getBoxX(),
                Math.round ((lastHiddenCol + 1) * od.getWidth() / alwidth));
        assertEquals(od.getBoxY(), 0);
        assertEquals(od.getBoxWidth(), boxWidth);
        assertEquals(od.getBoxHeight(), boxHeight);
        assertEquals(od.getScrollRow(), 0);
        assertEquals(od.getScrollCol(),
                Math.round (xpos * alwidth / od.getWidth()));
    */
    // click to right of hidden columns, box moves to click point
    testBoxIsAtClickPoint(40, 0);
    assertEquals(od.getScrollRow(), 0);
    assertEquals(od.getScrollCol(),
            Math.round((float) 40 * alwidth / od.getWidth())
                    - (lastHiddenCol + 1));

    // click to right of hidden columns such that box runs over right hand side
    // of alignment
    // box position is adjusted away from the edge
    // overly large boxX value reset to width-boxWidth
    int xpos = 100;
    mouseClick(od, xpos, 5);
    assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth());
    assertEquals(od.getBoxY(), 5);
    assertEquals(od.getBoxWidth(), boxWidth);
    assertEquals(od.getBoxHeight(), boxHeight);
    assertEquals(od.getScrollCol(),
            Math.round((float) od.getBoxX() * alwidth / od.getWidth())
                    - (lastHiddenCol + 1));
    assertEquals(od.getScrollRow(),
            Math.round((float) od.getBoxY() * alheight
                    / od.getSequencesHeight()));
  }

  /**
   * Test setting of the box position, when there are hidden cols in the middle
   * of the alignment
   */
  @Test(groups = { "Functional" })
  public void testFromMouseWithHiddenColsInMiddle()
  {
    od.setBoxPositionByMouse(0, 0);
    assertEquals(od.getBoxX(), 0);
    assertEquals(od.getBoxY(), 0);
    assertEquals(od.getBoxWidth(), boxWidth);
    assertEquals(od.getScrollCol(), 0);
    assertEquals(od.getScrollRow(), 0);
    
    // hide columns 60-68, no change to box position or dimensions
    int firstHidden = 60;
    int lastHidden = 68;
    hideColumns(firstHidden, lastHidden);

    od.setBoxPosition();
    assertEquals(od.getBoxX(), 0);
    assertEquals(od.getBoxY(), 0);
    assertEquals(od.getBoxWidth(), boxWidth);
    assertEquals(od.getScrollCol(), 0);
    assertEquals(od.getScrollRow(), 0);

    // move box so that it overlaps with hidden cols on one side
    // box width changes, boxX and scrollCol as for unhidden case
    int xpos = 50 - boxWidth; // 50 is position in overview halfway between cols
                              // 60 and 70
    mouseClick(od, xpos, 0);
    assertEquals(od.getBoxX(), xpos);
    assertEquals(od.getBoxY(), 0);
    assertEquals(
            od.getBoxWidth(),
            Math.round(boxWidth + (float) (lastHidden - firstHidden + 1)
                    * od.getWidth() / alwidth));
    assertEquals(od.getBoxHeight(), boxHeight);
    assertEquals(od.getScrollCol(),
            Math.round(xpos * alwidth / od.getWidth()));
    assertEquals(od.getScrollRow(), 0);

    // move box so that it completely covers hidden cols
    // box width changes, boxX and scrollCol as for hidden case
    xpos = 30;
    mouseClick(od, xpos, 0);
    assertEquals(od.getBoxX(), xpos);
    assertEquals(od.getBoxY(), 0);
    assertEquals(
            od.getBoxWidth(),
            Math.round(boxWidth + (float) (lastHidden - firstHidden + 1)
                    * od.getWidth() / alwidth));
    assertEquals(od.getBoxHeight(), boxHeight);
    assertEquals(od.getScrollCol(),
            Math.round(xpos * alwidth / od.getWidth()));
    assertEquals(od.getScrollRow(), 0);

    // move box so boxX is in hidden cols, box overhangs at right
    // box width back to normal, boxX and scrollCol move to right of hidden area
    // TODO currently this test fails in the Jalview GUI, there is a gap between
    // the rhs of the hidden area and the box
    /*    xpos = 50;
        mouseClick(od, xpos, 0);
        assertEquals(od.getBoxX(),
                (lastHidden + 1) * scalew * av.getCharWidth());
        assertEquals(od.getBoxY(), 0);
        assertEquals(od.getBoxWidth(), boxWidth);
        assertEquals(od.getBoxHeight(), boxHeight);
        assertEquals(od.getScrollCol(),
                Math.round(xpos * alwidth / od.getWidth()));
        assertEquals(od.getScrollRow(), 0);*/

    // move box so boxX is to right of hidden cols, but does not go beyond full
    // width of alignment
    // box width, boxX and scrollCol all as for non-hidden case
    // TODO currently this test fails in the Jalview GUI because boxX is
    // calculated
    // based on the current boxWidth, which includes hidden columns, thereby
    // pushing
    // the box off the end of the alignment. So boxX is adjusted backwards
    // unnecessarily.
    /*   xpos = 72;
       testBoxIsAtClickPoint(xpos, 0);
       assertEquals(od.getScrollRow(), 0);
       assertEquals(od.getScrollCol(),
               Math.round(xpos * alwidth / od.getWidth())
               - lastHidden);*/
    
    // move box so it goes beyond full width of alignment
    // boxX, scrollCol adjusted back, box width normal
    xpos = 3000;
    mouseClick(od, xpos, 5);
    assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth());
    assertEquals(od.getBoxY(), 5);
    assertEquals(od.getBoxWidth(), boxWidth);
    assertEquals(od.getBoxHeight(), boxHeight);
    assertEquals(od.getScrollCol(),
            Math.round(((float) od.getBoxX() * alwidth / od.getWidth())
                    - (lastHidden - firstHidden + 1)));
    assertEquals(od.getScrollRow(),
            Math.round((float) od.getBoxY() * alheight
                    / od.getSequencesHeight()));

  }

  /**
   * Test setting of the box position, when there are hidden cols at the end of
   * the alignment
   */
  @Test(groups = { "Functional" })
  public void testFromMouseWithHiddenColsAtEnd()
  {
    od.setBoxPositionByMouse(0, 0);
    assertEquals(od.getBoxX(), 0);
    assertEquals(od.getBoxY(), 0);
    assertEquals(od.getBoxWidth(), boxWidth);
    assertEquals(od.getScrollCol(), 0);
    assertEquals(od.getScrollRow(), 0);

    // hide columns 140-157, no change to box position or dimensions
    int firstHidden = 140;
    int lastHidden = 157;
    hideColumns(firstHidden, lastHidden);
    od.setBoxPosition();
    assertEquals(od.getBoxX(), 0);
    assertEquals(od.getBoxY(), 0);
    assertEquals(od.getBoxWidth(), boxWidth);
    assertEquals(od.getScrollCol(), 0);
    assertEquals(od.getScrollRow(), 0);

    // click to left of hidden cols, without overlapping
    // boxX, scrollCol and width as normal
    int xpos = 5;
    testBoxIsAtClickPoint(xpos, 0);
    assertEquals(od.getScrollRow(), 0);
    assertEquals(od.getScrollCol(),
            Math.round((float) xpos * alwidth / od.getWidth()));

    // click to left of hidden cols, with overlap
    // boxX and scrollCol adjusted for hidden cols, width normal
    // TODO this fails because setBoxPosition screws up the hidden cols calc
    // only works in GUI because of AlignmentPanel::setScrollValues
    /*xpos = 115 - boxWidth;
    mouseClick(od, xpos, 0);
    assertEquals(
            od.getBoxX(),
            Math.round((firstHidden - 1) * scalew * av.getCharWidth())
                    - od.getBoxWidth());
    assertEquals(od.getBoxY(), 0);
    assertEquals(od.getBoxWidth(), boxWidth);
    assertEquals(od.getBoxHeight(), boxHeight);
    assertEquals(od.getScrollCol(),
            Math.round(od.getBoxX() * alwidth / od.getWidth()));
    assertEquals(od.getScrollRow(), 0);*/

    // click in hidden cols
    // boxX and scrollCol adjusted for hidden cols, width normal
    // TODO breaks as above test
    /*xpos = 115;
    assertEquals(
            od.getBoxX(),
            Math.round((firstHidden - 1) * scalew * av.getCharWidth())
                    - od.getBoxWidth());
    assertEquals(od.getBoxY(), 0);
    assertEquals(od.getBoxWidth(), boxWidth);
    assertEquals(od.getBoxHeight(), boxHeight);
    assertEquals(od.getScrollCol(),
            Math.round(od.getBoxX() * alwidth / od.getWidth()));
    assertEquals(od.getScrollRow(), 0);*/

    // click off end of alignment
    // boxX and scrollCol adjusted for hidden cols, width normal
    // TODO breaks as above test
    /*    xpos = 3000;
        assertEquals(
                od.getBoxX(),
                Math.round((firstHidden - 1) * scalew * av.getCharWidth())
                        - od.getBoxWidth());
        assertEquals(od.getBoxY(), 0);
        assertEquals(od.getBoxWidth(), boxWidth);
        assertEquals(od.getBoxHeight(), boxHeight);
        assertEquals(od.getScrollCol(),
                Math.round(od.getBoxX() * alwidth / od.getWidth()));
        assertEquals(od.getScrollRow(), 0);*/
  }

  /**
   * Test that the box position is set correctly when set from the viewport,
   * with no hidden rows or columns
   */
  @Test(groups = { "Functional" })
  public void testSetBoxFromViewport()
  {
    // move viewport to start of alignment
    moveViewport(0, 0);
    assertEquals(od.getBoxX(), 0);
    assertEquals(od.getBoxY(), 0);
    assertEquals(od.getBoxWidth(), boxWidth);
    assertEquals(od.getBoxHeight(), boxHeight);

    // move viewport to right
    moveViewportH(70);
    assertEquals(od.getBoxX(),
            Math.round((float) 70 * od.getWidth() / alwidth));
    assertEquals(od.getBoxY(), 0);
    assertEquals(od.getBoxWidth(), boxWidth);
    assertEquals(od.getBoxHeight(), boxHeight);

    // move viewport down
    moveViewportV(100);
    assertEquals(od.getBoxX(),
            Math.round((float) 70 * od.getWidth() / alwidth));
    assertEquals(od.getBoxY(),
            Math.round(100 * od.getSequencesHeight() / alheight));
    assertEquals(od.getBoxWidth(), boxWidth);
    assertEquals(od.getBoxHeight(), boxHeight);

    // move viewport to bottom right
    moveViewport(98, 508);
    assertEquals(od.getBoxX(),
            Math.round((float) 98 * od.getWidth() / alwidth));
    assertEquals(od.getBoxY(),
            Math.round((float) 508 * od.getSequencesHeight() / alheight));
    assertEquals(od.getBoxWidth(), boxWidth);
    assertEquals(od.getBoxHeight(), boxHeight);
  }

  /**
   * Test that the box position is set correctly when there are hidden columns
   * at the start
   */
  @Test(groups = { "Functional" })
  public void testSetBoxFromViewportHiddenColsAtStart()
  {
    int firstHidden = 0;
    int lastHidden = 20;
    hideColumns(firstHidden, lastHidden);

    // move viewport to start of alignment
    moveViewport(0, 0);
    assertEquals(od.getBoxX(),
            Math.round((float) (lastHidden + 1) * od.getWidth() / alwidth));
    assertEquals(od.getBoxY(), 0);
    assertEquals(od.getBoxWidth(), boxWidth);
    assertEquals(od.getBoxHeight(), boxHeight);

    // move viewport to end of alignment - need to make startRes by removing
    // hidden cols because of how viewport/overview are implemented
    moveViewport(98 - lastHidden - 1, 0);
    assertEquals(od.getBoxX(),
            Math.round((float) 98 * od.getWidth() / alwidth));
    assertEquals(od.getBoxY(), 0);
    assertEquals(od.getBoxWidth(), boxWidth);
    assertEquals(od.getBoxHeight(), boxHeight);
  }

  /**
   * Test that the box position is set correctly when there are hidden columns
   * in the middle
   */
  @Test(groups = { "Functional" })
  public void testSetBoxFromViewportHiddenColsInMiddle()
  {
    int firstHidden = 65;
    int lastHidden = 75;
    hideColumns(firstHidden, lastHidden);

    // move viewport before hidden columns
    moveViewport(3, 0);

    assertEquals(od.getBoxX(),
            Math.round((float) 3 * od.getWidth() / alwidth));
    assertEquals(od.getBoxY(), 0);
    System.out.println(od.getBoxWidth());
    assertEquals(od.getBoxWidth(), boxWidth);
    System.out.println(od.getBoxWidth());
    assertEquals(od.getBoxHeight(), boxHeight);

    // move viewport to left of hidden columns with overlap
    moveViewport(10, 0);
    assertEquals(od.getBoxX(),
            Math.round((float) 10 * od.getWidth() / alwidth));
    assertEquals(od.getBoxY(), 0);
    assertEquals(
            od.getBoxWidth(),
            boxWidth
                    + Math.round((float) (lastHidden - firstHidden + 1)
                            * od.getWidth() / alwidth));
    assertEquals(od.getBoxHeight(), boxHeight);

    // move viewport to straddle hidden columns
    moveViewport(60, 0);
    assertEquals(od.getBoxX(),
            Math.round((float) 60 * od.getWidth() / alwidth));
    assertEquals(od.getBoxY(), 0);
    assertEquals(
            od.getBoxWidth(),
            boxWidth
                    + Math.round((lastHidden - firstHidden + 1)
                            * od.getWidth() / alwidth));
    assertEquals(od.getBoxHeight(), boxHeight);

    // move viewport to right of hidden columns, no overlap
    moveViewport(80 - (lastHidden - firstHidden + 1), 0);
    assertEquals(od.getBoxX(),
            Math.round((float) 80 * od.getWidth() / alwidth));
    assertEquals(od.getBoxY(), 0);
    assertEquals(od.getBoxWidth(), boxWidth);
    assertEquals(od.getBoxHeight(), boxHeight);

  }

  /**
   * Test that the box position is set correctly when there are hidden columns
   * at the end
   */
  @Test(groups = { "Functional" })
  public void testSetBoxFromViewportHiddenColsAtEnd()
  {
    int firstHidden = 145;
    int lastHidden = 157;
    hideColumns(firstHidden, lastHidden);

    // move viewport before hidden columns
    moveViewport(3, 0);
    assertEquals(od.getBoxX(),
            Math.round((float) 3 * od.getWidth() / alwidth));
    assertEquals(od.getBoxY(), 0);
    assertEquals(od.getBoxWidth(), boxWidth);
    assertEquals(od.getBoxHeight(), boxHeight);

    // move viewport to hidden columns
    // TODO boxwidth includes hidden in overview panel (why?)
    moveViewport(98, 0);
    assertEquals(od.getBoxX(),
            Math.round((float) 98 * od.getWidth() / alwidth));
    assertEquals(od.getBoxY(), 0);
    assertEquals(
            od.getBoxWidth(),
            boxWidth
                    + Math.round((float) (lastHidden - firstHidden + 1)
                            * od.getWidth() / alwidth));
    assertEquals(od.getBoxHeight(), boxHeight);
  }

  /**
   * Test that the box position is set correctly when there are hidden rows at
   * the start
   */
  @Test(groups = { "Functional" })
  public void testSetBoxFromViewportHiddenRowsAtStart()
  {
    int firstHidden = 0;
    int lastHidden = 20;
    hideSequences(firstHidden, lastHidden + 1, lastHidden + 1);

    // move viewport to start of alignment:
    // box moves to below hidden rows, height remains same
    moveViewport(0, 0);
    assertEquals(od.getBoxX(), 0);
    assertEquals(od.getBoxY(),
            Math.round((float) (lastHidden + 1) * od.getSequencesHeight()
                    / alheight));
    assertEquals(od.getBoxWidth(), boxWidth);
    assertEquals(od.getBoxHeight(), boxHeight);

    // move viewport to end of alignment, need to account for hidden rows
    // because of how alignment panel/overview panel are implemented

    // AlignViewport adjusts endSeq using Alignment height which excludes hidden
    // rows if we happen to be at the bottom of the alignment
    // od.setBoxPosition adjusts endSeq to include hidden rows
    // od.checkValid adjusts scroll position to exclude hidden rows
    // TODO this test fails because of the above!

    /*    moveViewport(0, 525 - viewHeight - lastHidden - 1);
        assertEquals(od.getBoxX(), 0);
        assertEquals(od.getBoxY(),
                (525 - viewHeight) * scaleh
                * av.getCharHeight());
        assertEquals(od.getBoxWidth(), boxWidth);
        assertEquals(od.getBoxHeight(), boxHeight);*/
  }

  /**
   * Test that the box position is set correctly when there are hidden rows in
   * the middle
   */
  @Test(groups = { "Functional" })
  public void testSetBoxFromViewportHiddenRowsInMiddle()
  {
    int firstHidden = 200;
    int lastHidden = 210;
    hideSequences(firstHidden, lastHidden + 1, lastHidden + 1);

    // move viewport to start of alignment:
    // box, height etc as in non-hidden case
    // TODO fails with boxy=12 because that's what setBoxPosition sets it to!
    /*moveViewport(0, 0);
    assertEquals(od.getBoxX(), 0);
    assertEquals(od.getBoxY(), 0);
    assertEquals(od.getBoxWidth(), boxWidth);
    assertEquals(od.getBoxHeight(), boxHeight);*/

    // move viewport to straddle hidden rows
    // TODO also fails with boxY out by 12
    /*moveViewport(0, 198);
    assertEquals(od.getBoxX(), 0);
    assertEquals(od.getBoxY(), Math.round (198 * scaleh * av.getCharHeight()),
            1.5);
    assertEquals(od.getBoxWidth(), boxWidth);
    assertEquals(od.getBoxHeight(), boxHeight
            + ((lastHidden - firstHidden) * scaleh * av.getCharHeight()),
            1.5);*/
  }

  /**
   * Test that the box position is set correctly when there are hidden rows at
   * the bottom
   */
  @Test(groups = { "Functional" })
  public void testSetBoxFromViewportHiddenRowsAtEnd()
  {
    int firstHidden = 500;
    int lastHidden = 524;
    hideSequences(firstHidden - 1, lastHidden, firstHidden - 1);

    // move viewport to start of alignment:
    // box, height etc as in non-hidden case
    moveViewport(0, 0);
    assertEquals(od.getBoxX(), 0);
    assertEquals(od.getBoxY(), 0);
    assertEquals(od.getBoxWidth(), boxWidth);
    assertEquals(od.getBoxHeight(), boxHeight);

    // move viewport to end of alignment
    // TODO fails with wrong boxHeight who knows why
    /*moveViewport(0, firstHidden - viewHeight - 1);
        assertEquals(od.getBoxX(), 0);
        assertEquals(od.getBoxY(),
     Math.round ((firstHidden - viewHeight - 1)
                * scaleh * av.getCharHeight()));
        assertEquals(od.getBoxWidth(), boxWidth);
        assertEquals(
                od.getBoxHeight(),
                boxHeight
                        + Math.round ((lastHidden - firstHidden + 1) * scaleh * av
                                .getCharHeight()));*/

  }

  /**
   * Test setting of the box position, when there are hidden rows at the start
   * of the alignment
   */
  @Test(groups = { "Functional" })
  public void testFromMouseWithHiddenRowsAtStart()
  {
    od.setBoxPositionByMouse(0, 0);
    assertEquals(od.getBoxX(), 0);
    assertEquals(od.getBoxY(), 0);
    assertEquals(od.getBoxHeight(), boxHeight);
    assertEquals(od.getBoxWidth(), boxWidth);
    assertEquals(od.getScrollCol(), 0);
    assertEquals(od.getScrollRow(), 0);

    // hide rows at start and check updated box position is correct
    // changes boxY but not boxheight
    int lastHiddenRow = 30;
    hideSequences(0, lastHiddenRow + 1, lastHiddenRow + 1);

    od.setBoxPosition();
    assertEquals(od.getBoxX(), 0);
    assertEquals(od.getBoxY(),
            Math.round((float) (lastHiddenRow + 1)
                    * od.getSequencesHeight() / alheight));
    assertEquals(od.getBoxWidth(), boxWidth);
    assertEquals(od.getBoxHeight(), boxHeight);

    // click in hidden rows
    // TODO fails because boxHeight is 27 not 25 (possible rounding issue)
    /*    mouseClick(od, 0, 0);
        assertEquals(od.getBoxX(), 0);
        assertEquals(od.getBoxY(), 0);
        assertEquals(od.getBoxWidth(), boxWidth);
        assertEquals(od.getBoxHeight(), boxHeight
                + Math.round ((lastHiddenRow + 1) * scaleh * av.getCharHeight()),
                1.5);*/

    // click below hidden rows
    mouseClick(od, 0, 150);
    assertEquals(od.getBoxX(), 0);
    assertEquals(od.getBoxY(), 150);
    assertEquals(od.getBoxWidth(), boxWidth);
    assertEquals(od.getBoxHeight(), boxHeight);
  }

  /**
   * Test setting of the box position, when there are hidden rows at the middle
   * of the alignment
   */
  @Test(groups = { "Functional" })
  public void testFromMouseWithHiddenRowsInMiddle()
  {
    od.setBoxPositionByMouse(0, 0);

    assertEquals(od.getBoxX(), 0);
    assertEquals(od.getBoxY(), 0);
    assertEquals(od.getBoxWidth(), boxWidth);
    assertEquals(od.getBoxHeight(), boxHeight);
    assertEquals(od.getScrollCol(), 0);
    assertEquals(od.getScrollRow(), 0);

    // hide rows in middle and check updated box position is correct
    // no changes
    int firstHiddenRow = 50;
    int lastHiddenRow = 60;
    hideSequences(firstHiddenRow, lastHiddenRow + 1, lastHiddenRow + 1);

    od.setBoxPosition();

    assertEquals(od.getBoxX(), 0);
    assertEquals(od.getBoxY(), 0);
    assertEquals(od.getBoxWidth(), boxWidth);
    assertEquals(od.getBoxHeight(), boxHeight);

    // click above hidden rows, so that box overlaps
    int ypos = 40;
    // TODO test fails because box does not change height - dealt with by scroll
    // values
    /*    mouseClick(od, 0, Math.round (ypos * alheight / od.getSequencesHeight()));
        assertEquals(od.getBoxX(), 0);
        assertEquals(od.getBoxY(), Math.round (ypos * alheight / od.getSequencesHeight()),
                1.5);
        assertEquals(od.getBoxWidth(), boxWidth);
        assertEquals(
                od.getBoxHeight(),
                boxHeight
                        + Math.round ((lastHiddenRow - firstHiddenRow + 1) / scaleh / av
                                .getCharHeight()));
    */
    // click so that box straddles hidden rows
    ypos = 48;
    // TODO test fails because box does not change height - dealt with by scroll
    // values
    /*mouseClick(od, 0, Math.round (ypos * alheight / od.getSequencesHeight()));
    assertEquals(od.getBoxX(), 0);
    assertEquals(od.getBoxY(), Math.round (ypos * alheight / od.getSequencesHeight()),
            1.5);
    assertEquals(od.getBoxWidth(), boxWidth);
    assertEquals(
            od.getBoxHeight(),
            boxHeight
                    + Math.round ((lastHiddenRow - firstHiddenRow + 1) / scaleh / av
                            .getCharHeight()));*/
  }

  /**
   * Test setting of the box position, when there are hidden rows at the end of
   * the alignment
   */
  @Test(groups = { "Functional" })
  public void testFromMouseWithHiddenRowsAtEnd()
  {
    od.setBoxPositionByMouse(0, 0);
    assertEquals(od.getBoxX(), 0);
    assertEquals(od.getBoxY(), 0);
    assertEquals(od.getBoxWidth(), boxWidth);
    assertEquals(od.getBoxHeight(), boxHeight);
    assertEquals(od.getScrollCol(), 0);
    assertEquals(od.getScrollRow(), 0);

    // hide rows at end and check updated box position is correct
    // no changes
    int firstHidden = 500;
    int lastHidden = 524;
    hideSequences(firstHidden - 1, lastHidden, firstHidden - 1);

    od.setBoxPosition();
    assertEquals(od.getBoxX(), 0);
    assertEquals(od.getBoxY(), 0);
    assertEquals(od.getBoxWidth(), boxWidth);
    assertEquals(od.getBoxHeight(), boxHeight);

    // click above hidden rows
    int ypos = 40; // row 40
    mouseClick(od, 0,
            Math.round((float) ypos * od.getSequencesHeight() / alheight));
    assertEquals(od.getBoxX(), 0);
    assertEquals(od.getBoxY(),
            Math.round((float) ypos * od.getSequencesHeight() / alheight));
    assertEquals(od.getBoxWidth(), boxWidth);
    assertEquals(od.getBoxHeight(), boxHeight);

    // click above hidden rows so box overlaps
    // boxY moved upwards, boxHeight remains same
    // TODO fails with boxY located at row 497 - correction done by
    // setScrollValues
    /*   ypos = 497; // row 497
       mouseClick(od, 0, Math.round (ypos * scaleh * av.getCharHeight()));
       assertEquals(od.getBoxX(), 0);
       assertEquals(
               od.getBoxY(),
               Math.round ((firstHidden - viewHeight) * scaleh * av.getCharHeight()),
               1.5);
       assertEquals(od.getBoxWidth(), boxWidth);
       assertEquals(od.getBoxHeight(), boxHeight);*/

    // click within hidden rows
    ypos = 505;
    // TODO: fails with wrong boxHeight - correction done by setScrollValues(?)
    /*mouseClick(od, 0, Math.round (ypos * scaleh * av.getCharHeight()));
    assertEquals(od.getBoxX(), 0);
    assertEquals(
            od.getBoxY(),
            Math.round ((firstHidden - viewHeight) * scaleh * av.getCharHeight()),
            1.5);
    assertEquals(od.getBoxWidth(), boxWidth);
    assertEquals(od.getBoxHeight(), boxHeight);*/
  }

  /*
   * Move viewport horizontally: startRes + previous width gives new horizontal extent. Vertical extent stays the same.
   */
  private void moveViewportH(int startRes)
  {
    av.setStartRes(startRes);
    av.setEndRes(startRes + viewWidth);
    od.setBoxPosition();
  }

  /*
   * Move viewport vertically: startSeq and endSeq give new vertical extent. Horizontal extent stays the same.
   */
  private void moveViewportV(int startSeq)
  {
    av.setStartSeq(startSeq);
    av.setEndSeq(startSeq + viewHeight);
    od.setBoxPosition();
  }

  /*
   * Move viewport horizontally and vertically.
   */
  private void moveViewport(int startRes, int startSeq)
  {
    av.setStartRes(startRes);
    av.setEndRes(startRes + viewWidth);
    av.setStartSeq(startSeq);
    av.setEndSeq(startSeq + viewHeight);
    od.setBoxPosition();
  }

  /*
   * Mouse click as position x,y in overview window
   */
  private void mouseClick(OverviewDimensions od, int x, int y)
  {
    od.setBoxPositionByMouse(x, y);
    // updates require an OverviewPanel to exist which it doesn't here
    // so call setBoxPosition() as it would be called by the AlignmentPanel
    // normally
    // int width = av.getEndRes() - av.getStartRes();
    // int height = av.getEndSeq() - av.getStartSeq();
    av.setStartRes(od.getScrollCol());
    av.setEndRes(od.getScrollCol() + viewWidth);
    av.setStartSeq(od.getScrollRow());
    av.setEndSeq(od.getScrollRow() + viewHeight);
    od.setBoxPosition();
  }
  
  private void testBoxIsAtClickPoint(int xpos, int ypos)
  {
    mouseClick(od, xpos, ypos);
    assertEquals(od.getBoxX(), xpos);
    assertEquals(od.getBoxY(), ypos);
    assertEquals(od.getBoxWidth(), boxWidth);
    assertEquals(od.getBoxHeight(), boxHeight);

  }

  /*
   * Hide sequences between start and end, using hideseq to do the hiding
   * (start <= hideseq <= end. Sequence hideseq is not hidden but the others are
   */
  private void hideSequences(int start, int end, int hideseq)
  {
    SequenceGroup sg = new SequenceGroup();
    List<SequenceI> allseqs = av.getAlignment().getSequences();
    for (int i = start; i <= end; ++i)
    {
      sg.addSequence(allseqs.get(i), false);
    }
    av.setSelectionGroup(sg);

    /*
     * hide group
     */
    av.hideSequences(allseqs.get(hideseq), true);

    while (av.isCalcInProgress())
    {
      try
      {
        Thread.sleep(50);
      } catch (InterruptedException e)
      {
        System.out.println("Hiding seqs interruption");
      }
    }
  }

  private void hideColumns(int firstHidden, int lastHidden)
  {
    av.hideColumns(firstHidden, lastHidden);

    while (av.isCalcInProgress())
    {
      try
      {
        Thread.sleep(50);
      } catch (InterruptedException e)
      {
        System.out.println("Hiding cols interruption");
      }
    }
  }
}