/*
 * 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.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.AlignViewport;
import jalview.io.DataSourceType;
import jalview.io.FileLoader;

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

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");

  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"
                  + "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC"
                  + "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC"
                  + "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC"
                  + "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");

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

  AlignFrame af;
  AlignViewport av;
  OverviewDimensions od;

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

  @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 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);

    // Initial box sizing - default path through code
    od.setBoxPosition();
    scalew = (float) od.getWidth()
            / (av.getAlignment().getWidth() * av.getCharWidth());
    scaleh = (float) od.getSequencesHeight()
            / (av.getAlignment().getHeight() * av.getCharHeight());
    boxWidth = (int) ((av.getEndRes() - av.getStartRes() + 1)
            * av.getCharWidth() * scalew);
    boxHeight = (int) ((av.getEndSeq() - av.getStartSeq())
            * av.getCharHeight() * scaleh);
  }


  @AfterClass(alwaysRun = true)
  public void tearDown()
  {
    Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
            Boolean.toString(showConservationSetting));
  }

  /**
   * 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.checkValid();
    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(),
            (int) (10 / scaleh / av.getCharHeight()));
    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(), (int) (6 / scalew / av.getCharWidth()));
    assertEquals(od.getScrollRow(), 0);

    // overly large boxX value reset to width-boxWidth
    mouseClick(od, 100, 6);
    assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth(), 1.5);
    assertEquals(od.getBoxY(), 6, 1.5);
    assertEquals(od.getBoxWidth(), boxWidth);
    assertEquals(od.getBoxHeight(), boxHeight);
    assertEquals(od.getScrollCol(),
            (od.getBoxX() / scalew / av.getCharWidth()), 1.5);
    assertEquals(od.getScrollRow(),
            (od.getBoxY() / scaleh / av.getCharHeight()), 1.5);

    // overly large boxY value reset to sequenceHeight - boxHeight
    mouseClick(od, 10, 520);
    assertEquals(od.getBoxX(), 10, 1.5);
    assertEquals(od.getBoxY(), od.getSequencesHeight() - od.getBoxHeight(),
            1.5);
    assertEquals(od.getBoxWidth(), boxWidth);
    assertEquals(od.getBoxHeight(), boxHeight, 1.5);
    assertEquals(od.getScrollCol(),
            (od.getBoxX() / scalew / av.getCharWidth()), 1.5);
    assertEquals(od.getScrollRow(),
            (od.getBoxY() / scaleh / av.getCharHeight()), 1.5);

    // click past end of alignment, as above
    mouseClick(od, 3000, 5);
    assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth(), 1.5);
    assertEquals(od.getBoxWidth(), boxWidth);
    assertEquals(od.getBoxHeight(), boxHeight, 1.5);
    assertEquals(od.getScrollCol(),
            (od.getBoxX() / scalew / av.getCharWidth()), 1.5);
    assertEquals(od.getScrollRow(),
            (od.getBoxY() / scaleh / av.getCharHeight()), 1.5);

    // move viewport so startRes non-zero and then mouseclick
    moveViewportH(av, od, 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, 1.5);
    assertEquals(od.getBoxWidth(), boxWidth);
    assertEquals(od.getBoxHeight(), boxHeight, 1.5);
    assertEquals(od.getScrollCol(),
            (od.getBoxX() / scalew / av.getCharWidth()), 1.5);
    assertEquals(od.getBoxY(), oldboxy + 2, 1.5);
    assertEquals(od.getScrollRow(),
            (od.getBoxY() / scaleh / av.getCharHeight()), 1.5);

    // 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, 1.5);
  }

  /**
   * Test setting of the box position, when there are hidden cols at the start
   * of the alignment
   */
  @Test(groups = { "Functional" })
  public void testFromMouseWithHiddenColsAtStart()
  {
    od.checkValid();
    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;
    av.hideColumns(0, lastHiddenCol);
    od.setBoxPosition();
    assertEquals(od.getBoxX(),
            (int) ((lastHiddenCol + 1) * scalew * av.getCharWidth()));
    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(),
                (int) ((lastHiddenCol + 1) * scalew * av.getCharWidth()));
        assertEquals(od.getBoxY(), 0);
        assertEquals(od.getBoxWidth(), boxWidth);
        assertEquals(od.getBoxHeight(), boxHeight);
        assertEquals(od.getScrollRow(), 0);
        assertEquals(od.getScrollCol(),
                (int) (xpos / scalew / av.getCharWidth()));
    */
    // click to right of hidden columns, box moves to click point
    testBoxIsAtClickPoint(40, 0);
    assertEquals(od.getScrollRow(), 0);
    assertEquals(od.getScrollCol(),
 (int) (40 / scalew / av.getCharWidth())
            - lastHiddenCol, 1.5);

    // 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(), 1.5);
    assertEquals(od.getBoxY(), 5, 1.5);
    assertEquals(od.getBoxWidth(), boxWidth);
    assertEquals(od.getBoxHeight(), boxHeight);
    assertEquals(od.getScrollCol(),
            (int) (od.getBoxX() / scalew / av.getCharWidth())
                    - lastHiddenCol, 1.5);
    assertEquals(od.getScrollRow(),
            (int) (od.getBoxY() / scaleh / av.getCharHeight()), 1.5);

  }

  /**
   * Test setting of the box position, when there are hidden cols in the middle
   * of the alignment
   */
  @Test(groups = { "Functional" })
  public void testFromMouseWithHiddenColsInMiddle()
  {
    od.checkValid();
    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;
    av.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, 1.5);
    assertEquals(od.getBoxY(), 0);
    assertEquals(od.getBoxWidth(), boxWidth
            + (lastHidden - firstHidden + 1) * scalew * av.getCharWidth(),
            1.5);
    assertEquals(od.getBoxHeight(), boxHeight);
    assertEquals(od.getScrollCol(), (int) (xpos / scalew / av.getCharWidth()), 1.5);
    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, 1.5);
    assertEquals(od.getBoxY(), 0);
    assertEquals(od.getBoxWidth(), boxWidth
            + (lastHidden - firstHidden + 1) * scalew * av.getCharWidth(),
            1.5);
    assertEquals(od.getBoxHeight(), boxHeight);
    assertEquals(od.getScrollCol(),
            (int) (xpos / scalew / av.getCharWidth()), 1.5);
    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(), 1.5);
        assertEquals(od.getBoxY(), 0);
        assertEquals(od.getBoxWidth(), boxWidth, 1.5);
        assertEquals(od.getBoxHeight(), boxHeight);
        assertEquals(od.getScrollCol(),
                (int) (xpos / scalew / av.getCharWidth()), 1.5);
        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(),
               (int) (xpos / scalew / av.getCharWidth())
               - lastHidden, 1.5);*/
    
    // 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(), 1.5);
    assertEquals(od.getBoxY(), 5, 1.5);
    assertEquals(od.getBoxWidth(), boxWidth);
    assertEquals(od.getBoxHeight(), boxHeight);
    assertEquals(od.getScrollCol(),
            (od.getBoxX() / scalew / av.getCharWidth())
                    - (lastHidden - firstHidden + 1),
            1.5);
    assertEquals(od.getScrollRow(),
            (int) (od.getBoxY() / scaleh / av.getCharHeight()), 1.5);

  }

  /**
   * Test setting of the box position, when there are hidden cols at the end of
   * the alignment
   */
  @Test(groups = { "Functional" })
  public void testFromMouseWithHiddenColsAtEnd()
  {
    od.checkValid();
    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;
    av.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(),
            (int) (xpos / scalew / av.getCharWidth()), 1.5);

    // 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(),
            (int) ((firstHidden - 1) * scalew * av.getCharWidth())
                    - od.getBoxWidth(), 1.5);
    assertEquals(od.getBoxY(), 0);
    assertEquals(od.getBoxWidth(), boxWidth, 1.5);
    assertEquals(od.getBoxHeight(), boxHeight);
    assertEquals(od.getScrollCol(),
            (int) (od.getBoxX() / scalew / av.getCharWidth()), 1.5);
    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(),
            (int) ((firstHidden - 1) * scalew * av.getCharWidth())
                    - od.getBoxWidth(), 1.5);
    assertEquals(od.getBoxY(), 0);
    assertEquals(od.getBoxWidth(), boxWidth, 1.5);
    assertEquals(od.getBoxHeight(), boxHeight);
    assertEquals(od.getScrollCol(),
            (int) (od.getBoxX() / scalew / av.getCharWidth()), 1.5);
    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(),
                (int) ((firstHidden - 1) * scalew * av.getCharWidth())
                        - od.getBoxWidth(), 1.5);
        assertEquals(od.getBoxY(), 0);
        assertEquals(od.getBoxWidth(), boxWidth, 1.5);
        assertEquals(od.getBoxHeight(), boxHeight);
        assertEquals(od.getScrollCol(),
                (int) (od.getBoxX() / scalew / av.getCharWidth()), 1.5);
        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(av, od, 0, 0);
    assertEquals(od.getBoxX(), 0);
    assertEquals(od.getBoxY(), 0);
    assertEquals(od.getBoxWidth(), boxWidth);
    assertEquals(od.getBoxHeight(), boxHeight);

    // move viewport to right
    moveViewportH(av, od, 70);
    assertEquals(od.getBoxX(), (int) (70 * scalew * av.getCharWidth()));
    assertEquals(od.getBoxY(), 0);
    assertEquals(od.getBoxWidth(), boxWidth);
    assertEquals(od.getBoxHeight(), boxHeight);

    // move viewport down
    moveViewportV(av, od, 100);
    assertEquals(od.getBoxX(), (int) (70 * scalew * av.getCharWidth()));
    assertEquals(od.getBoxY(), (int) (100 * scaleh * av.getCharHeight()));
    assertEquals(od.getBoxWidth(), boxWidth);
    assertEquals(od.getBoxHeight(), boxHeight);

    // move viewport to bottom right
    moveViewport(av, od, 98, 508);
    assertEquals(od.getBoxX(), (int) (98 * scalew * av.getCharWidth()));
    assertEquals(od.getBoxY(), (int) (508 * scaleh * av.getCharHeight()));
    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;
    av.hideColumns(firstHidden, lastHidden);

    // move viewport to start of alignment
    moveViewport(av, od, 0, 0);
    assertEquals(od.getBoxX(),
            (int) ((lastHidden + 1) * scalew * av.getCharWidth()));
    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(av, od, 98 - lastHidden - 1, 0);
    assertEquals(od.getBoxX(), 98 * scalew * av.getCharWidth(), 1.5);
    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;
    av.hideColumns(firstHidden, lastHidden);

    // move viewport before hidden columns
    moveViewport(av, od, 3, 0);
    assertEquals(od.getBoxX(), (int) (3 * scalew * av.getCharWidth()));
    assertEquals(od.getBoxY(), 0);
    assertEquals(od.getBoxWidth(), boxWidth);
    assertEquals(od.getBoxHeight(), boxHeight);

    // move viewport to left of hidden columns with overlap
    moveViewport(av, od, 10, 0);
    assertEquals(od.getBoxX(), (int) (10 * scalew * av.getCharWidth()));
    assertEquals(od.getBoxY(), 0);
    assertEquals(
            od.getBoxWidth(),
            boxWidth
                    + (int) ((lastHidden - firstHidden + 1) * scalew * av
                            .getCharWidth()), 1.5);
    assertEquals(od.getBoxHeight(), boxHeight);

    // move viewport to straddle hidden columns
    moveViewport(av, od, 60, 0);
    assertEquals(od.getBoxX(), (int) (60 * scalew * av.getCharWidth()));
    assertEquals(od.getBoxY(), 0);
    assertEquals(
            od.getBoxWidth(),
            boxWidth
                    + (int) ((lastHidden - firstHidden + 1) * scalew * av
                            .getCharWidth()), 1.5);
    assertEquals(od.getBoxHeight(), boxHeight);

    // move viewport to right of hidden columns, no overlap
    moveViewport(av, od, 80 - (lastHidden - firstHidden + 1), 0);
    assertEquals(od.getBoxX(), (int) (80 * scalew * av.getCharWidth()), 1.5);
    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;
    av.hideColumns(firstHidden, lastHidden);

    // move viewport before hidden columns
    moveViewport(av, od, 3, 0);
    assertEquals(od.getBoxX(), (int) (3 * scalew * av.getCharWidth()), 1.5);
    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(av, od, 98, 0);
    assertEquals(od.getBoxX(), (int) (98 * scalew * av.getCharWidth()), 1.5);
    assertEquals(od.getBoxY(), 0);
    assertEquals(
            od.getBoxWidth(),
            boxWidth
                    + (int) ((lastHidden - firstHidden + 1) * scalew * av
                            .getCharWidth()), 1.5);
    assertEquals(od.getBoxHeight(), boxHeight);
  }

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

  /*
   * Move viewport vertically: startSeq and endSeq give new vertical extent. Horizontal extent stays the same.
   */
  private void moveViewportV(AlignViewport av, OverviewDimensions od,
          int startSeq)
  {
    int height = av.getEndSeq() - av.getStartSeq();
    av.setStartSeq(startSeq);
    av.setEndSeq(startSeq + height);
    od.setBoxPosition();
  }

  /*
   * Move viewport horizontally and vertically.
   */
  private void moveViewport(AlignViewport av, OverviewDimensions od,
          int startRes, int startSeq)
  {
    int width = av.getEndRes() - av.getStartRes();
    int height = av.getEndSeq() - av.getStartSeq();
    av.setStartRes(startRes);
    av.setEndRes(startRes + width);
    av.setStartSeq(startSeq);
    av.setEndSeq(startSeq + height);
    od.setBoxPosition();
  }

  /*
   * Mouse click as position x,y in overview window
   */
  private void mouseClick(OverviewDimensions od, int x, int y)
  {
    od.setBoxX(x);
    od.setBoxY(y);
    od.checkValid();
    // updates require an OverviewPanel to exist which it doesn't here
    // so call setBoxPosition() as it would be called by the AlignmentPanel
    // normally
    AlignViewport av = af.getViewport();
    int width = av.getEndRes() - av.getStartRes();
    int height = av.getEndSeq() - av.getStartSeq();
    av.setStartRes(od.getScrollCol());
    av.setEndRes(od.getScrollCol() + width);
    av.setStartSeq(od.getScrollRow());
    av.setEndSeq(od.getScrollRow() + height);
    od.setBoxPosition();
  }
  
  private void testBoxIsAtClickPoint(int xpos, int ypos)
  {
    mouseClick(od, xpos, ypos);
    assertEquals(od.getBoxX(), xpos, 1.5);
    assertEquals(od.getBoxY(), ypos, 1.5);
    assertEquals(od.getBoxWidth(), boxWidth);
    assertEquals(od.getBoxHeight(), boxHeight);

  }
}