/*
 * 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.datamodel;

import static org.testng.Assert.assertNull;
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertTrue;

import jalview.analysis.AlignmentGenerator;
import jalview.gui.JvOptionPane;
import jalview.util.Comparison;

import java.util.Arrays;
import java.util.BitSet;
import java.util.Iterator;
import java.util.Random;

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

public class HiddenColumnsTest
{

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

  /**
   * Test the method which counts the number of hidden columns
   */
  @Test(groups = { "Functional" })
  public void testGetSize()
  {
    HiddenColumns hidden = new HiddenColumns();
    assertEquals(0, hidden.getSize());

    hidden.hideColumns(3, 5);
    assertEquals(3, hidden.getSize());

    hidden.hideColumns(8, 8);
    assertEquals(4, hidden.getSize());

    hidden.hideColumns(9, 14);
    assertEquals(10, hidden.getSize());

    ColumnSelection cs = new ColumnSelection();
    hidden.revealAllHiddenColumns(cs);
    assertEquals(0, hidden.getSize());
  }

  /**
   * Test the method that finds the visible column position of an alignment
   * column, allowing for hidden columns.
   */
  @Test(groups = { "Functional" })
  public void testFindColumnPosition()
  {
    HiddenColumns cs = new HiddenColumns();
    assertEquals(5, cs.findColumnPosition(5));

    // hiding column 6 makes no difference
    cs.hideColumns(6, 6);
    assertEquals(5, cs.findColumnPosition(5));

    // hiding column 4 moves column 5 to column 4
    cs.hideColumns(4, 4);
    assertEquals(4, cs.findColumnPosition(5));

    // hiding column 4 moves column 4 to position 3
    assertEquals(3, cs.findColumnPosition(4));

    // hiding columns 1 and 2 moves column 5 to column 2
    cs.hideColumns(1, 2);
    assertEquals(2, cs.findColumnPosition(5));

    // check with > 1 hidden column regions
    // where some columns are in the hidden regions
    HiddenColumns cs2 = new HiddenColumns();
    cs2.hideColumns(5, 10);
    cs2.hideColumns(20, 27);
    cs2.hideColumns(40, 44);

    // hiding columns 5-10 and 20-27 moves column 8 to column 4
    assertEquals(4, cs2.findColumnPosition(8));

    // and moves column 24 to 13
    assertEquals(13, cs2.findColumnPosition(24));

    // and moves column 28 to 14
    assertEquals(14, cs2.findColumnPosition(28));

    // and moves column 40 to 25
    assertEquals(25, cs2.findColumnPosition(40));

    // check when hidden columns start at 0 that the visible column
    // is returned as 0
    HiddenColumns cs3 = new HiddenColumns();
    cs3.hideColumns(0, 4);
    assertEquals(0, cs3.findColumnPosition(2));

  }

  /**
   * Test the method that finds the visible column position a given distance
   * before another column
   */
  @Test(groups = { "Functional" })
  public void testFindColumnNToLeft()
  {
    HiddenColumns cs = new HiddenColumns();

    // test that without hidden columns, findColumnNToLeft returns
    // position n to left of provided position
    long pos = cs.subtractVisibleColumns(3, 10);
    assertEquals(7, pos);

    // 0 returns same position
    pos = cs.subtractVisibleColumns(0, 10);
    assertEquals(10, pos);

    // overflow to left returns negative number
    pos = cs.subtractVisibleColumns(3, 0);
    assertEquals(-3, pos);

    // test that with hidden columns to left of result column
    // behaviour is the same as above
    cs.hideColumns(1, 3);

    // position n to left of provided position
    pos = cs.subtractVisibleColumns(3, 10);
    assertEquals(7, pos);

    // 0 returns same position
    pos = cs.subtractVisibleColumns(0, 10);
    assertEquals(10, pos);

    // test with one set of hidden columns between start and required position
    cs.hideColumns(12, 15);
    pos = cs.subtractVisibleColumns(8, 17);
    assertEquals(5, pos);

    // test with two sets of hidden columns between start and required position
    cs.hideColumns(20, 21);
    pos = cs.subtractVisibleColumns(8, 23);
    assertEquals(9, pos);

    // repeat last 2 tests with no hidden columns to left of required position
    ColumnSelection colsel = new ColumnSelection();
    cs.revealAllHiddenColumns(colsel);

    // test with one set of hidden columns between start and required position
    cs.hideColumns(12, 15);
    pos = cs.subtractVisibleColumns(8, 17);
    assertEquals(5, pos);

    // test with two sets of hidden columns between start and required position
    cs.hideColumns(20, 21);
    pos = cs.subtractVisibleColumns(8, 23);
    assertEquals(9, pos);

  }

  @Test(groups = { "Functional" })
  public void testVisibleContigsIterator()
  {
    HiddenColumns cs = new HiddenColumns();

    Iterator<int[]> visible = cs.getVisContigsIterator(3, 10);
    int[] region = visible.next();
    assertEquals("[3, 9]", Arrays.toString(region));
    assertFalse(visible.hasNext());

    cs.hideColumns(3, 6);
    cs.hideColumns(8, 9);
    cs.hideColumns(12, 12);

    // Test both ends visible region

    // start position is inclusive, end position exclusive
    visible = cs.getVisContigsIterator(1, 13);
    region = visible.next();
    assertEquals("[1, 2]", Arrays.toString(region));
    region = visible.next();
    assertEquals("[7, 7]", Arrays.toString(region));
    region = visible.next();
    assertEquals("[10, 11]", Arrays.toString(region));
    assertFalse(visible.hasNext());

    // Test start hidden, end visible
    visible = cs.getVisContigsIterator(4, 14);
    region = visible.next();
    assertEquals("[7, 7]", Arrays.toString(region));
    region = visible.next();
    assertEquals("[10, 11]", Arrays.toString(region));
    region = visible.next();
    assertEquals("[13, 13]", Arrays.toString(region));
    assertFalse(visible.hasNext());

    // Test start hidden, end hidden
    visible = cs.getVisContigsIterator(3, 10);
    region = visible.next();
    assertEquals("[7, 7]", Arrays.toString(region));
    assertFalse(visible.hasNext());

    // Test start visible, end hidden
    visible = cs.getVisContigsIterator(0, 13);
    region = visible.next();
    assertEquals("[0, 2]", Arrays.toString(region));
    region = visible.next();
    assertEquals("[7, 7]", Arrays.toString(region));
    region = visible.next();
    assertEquals("[10, 11]", Arrays.toString(region));
    assertFalse(visible.hasNext());

    // Test empty result
    visible = cs.getVisContigsIterator(4, 6);
    assertFalse(visible.hasNext());
  }

  @Test(groups = { "Functional" })
  public void testEquals()
  {
    HiddenColumns cs = new HiddenColumns();
    cs.hideColumns(5, 9);

    // a different set of hidden columns
    HiddenColumns cs2 = new HiddenColumns();

    // with no hidden columns
    assertFalse(cs.equals(cs2));
    assertFalse(cs2.equals(cs));

    // with hidden columns added in a different order
    cs2.hideColumns(6, 9);
    cs2.hideColumns(5, 8);

    assertTrue(cs.equals(cs2));
    assertTrue(cs.equals(cs));
    assertTrue(cs2.equals(cs));
    assertTrue(cs2.equals(cs2));
  }

  @Test(groups = "Functional")
  public void testCopyConstructor()
  {
    HiddenColumns cs = new HiddenColumns();
    cs.hideColumns(10, 11);
    cs.hideColumns(5, 7);
    Iterator<int[]> regions = cs.iterator();
    assertEquals("[5, 7]",
            Arrays.toString(regions.next()));

    HiddenColumns cs2 = new HiddenColumns(cs);
    regions = cs2.iterator();
    assertTrue(cs2.hasHiddenColumns());
    assertEquals(2, cs2.getNumberOfRegions());
    // hidden columns are held in column order
    assertEquals("[5, 7]",
            Arrays.toString(regions.next()));
    assertEquals("[10, 11]",
            Arrays.toString(regions.next()));
  }

  @Test(groups = "Functional")
  public void testCopyConstructor2()
  {
    HiddenColumns cs = new HiddenColumns();
    cs.hideColumns(10, 11);
    cs.hideColumns(5, 7);

    HiddenColumns cs2 = new HiddenColumns(cs, 3, 9, 1);
    assertTrue(cs2.hasHiddenColumns());
    Iterator<int[]> regions = cs2.iterator();

    // only [5,7] returned, offset by 1
    assertEquals("[4, 6]",
            Arrays.toString(regions.next()));
    assertEquals(3, cs2.getSize());

    cs2 = new HiddenColumns(cs, 8, 15, 4);
    regions = cs2.iterator();
    assertTrue(cs2.hasHiddenColumns());

    // only [10,11] returned, offset by 4
    assertEquals("[6, 7]",
            Arrays.toString(regions.next()));
    assertEquals(2, cs2.getSize());

    cs2 = new HiddenColumns(cs, 6, 10, 4);
    assertFalse(cs2.hasHiddenColumns());
  }

  /**
   * Test the code used to locate the reference sequence ruler origin
   */
  @Test(groups = { "Functional" })
  public void testLocateVisibleBoundsofSequence()
  {
    // create random alignment
    AlignmentGenerator gen = new AlignmentGenerator(false);
    AlignmentI al = gen.generate(50, 20, 123, 5, 5);

    HiddenColumns cs = al.getHiddenColumns();
    ColumnSelection colsel = new ColumnSelection();

    SequenceI seq = new Sequence("RefSeq", "-A-SD-ASD--E---");
    assertEquals(2, seq.findIndex(seq.getStart()));

    // no hidden columns
    assertEquals(
            Arrays.toString(new int[]
    { seq.findIndex(seq.getStart()) - 1, seq.findIndex(seq.getStart()) - 1,
        seq.findIndex(seq.getEnd()) - 1 }),
            Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));

    // hidden column on gap after end of sequence - should not affect bounds
    colsel.hideSelectedColumns(13, al.getHiddenColumns());
    assertEquals(
            Arrays.toString(new int[]
    { seq.findIndex(seq.getStart()) - 1, seq.findIndex(seq.getStart()) - 1,
        seq.findIndex(seq.getEnd()) - 1 }),
            Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));

    cs.revealAllHiddenColumns(colsel);
    // hidden column on gap before beginning of sequence - should vis bounds by
    // one
    colsel.hideSelectedColumns(0, al.getHiddenColumns());
    assertEquals(
            Arrays.toString(new int[]
    { seq.findIndex(seq.getStart()) - 2, seq.findIndex(seq.getStart()) - 1,
        seq.findIndex(seq.getEnd()) - 1 }),
            Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));

    cs.revealAllHiddenColumns(colsel);
    // hide columns around most of sequence - leave one residue remaining
    cs.hideColumns(1, 3);
    cs.hideColumns(6, 11);
    assertEquals("-D",
            cs.getVisibleSequenceStrings(0, 5, new SequenceI[]
    { seq })[0]);

    assertEquals(
            Arrays.toString(
                    new int[]
            { 1, seq.findIndex(seq.getStart()) - 1,
        seq.findIndex(seq.getEnd()) - 1 }),
            Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));
    cs.revealAllHiddenColumns(colsel);

    // hide whole sequence - should just get location of hidden region
    // containing sequence
    cs.hideColumns(1, 11);
    assertEquals(
            Arrays.toString(
                    new int[]
            { 0, seq.findIndex(seq.getStart()) - 1,
        seq.findIndex(seq.getEnd()) - 1 }),
            Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));

    cs.revealAllHiddenColumns(colsel);
    cs.hideColumns(0, 15);
    assertEquals(Arrays
            .toString(new int[]
    { 0, seq.findIndex(seq.getStart()) - 1,
        seq.findIndex(seq.getEnd()) - 1 }),
            Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));

    SequenceI seq2 = new Sequence("RefSeq2", "-------A-SD-ASD--E---");

    cs.revealAllHiddenColumns(colsel);
    cs.hideColumns(7, 17);
    assertEquals(
            Arrays.toString(
                    new int[]
            { 0, seq2.findIndex(seq2.getStart()) - 1,
        seq2.findIndex(seq2.getEnd()) - 1 }),
            Arrays.toString(cs.locateVisibleBoundsOfSequence(seq2)));

    cs.revealAllHiddenColumns(colsel);
    cs.hideColumns(3, 17);
    assertEquals(
            Arrays.toString(
                    new int[]
            { 0, seq2.findIndex(seq2.getStart()) - 1,
        seq2.findIndex(seq2.getEnd()) - 1 }),
            Arrays.toString(cs.locateVisibleBoundsOfSequence(seq2)));

    cs.revealAllHiddenColumns(colsel);
    cs.hideColumns(3, 19);
    assertEquals(
            Arrays.toString(
                    new int[]
            { 0, seq2.findIndex(seq2.getStart()) - 1,
        seq2.findIndex(seq2.getEnd()) - 1 }),
            Arrays.toString(cs.locateVisibleBoundsOfSequence(seq2)));

    cs.revealAllHiddenColumns(colsel);
    cs.hideColumns(0, 0);
    int[] test = cs.locateVisibleBoundsOfSequence(seq);
    assertEquals(Arrays.toString(new int[] { 0, 1, 11 }),
            Arrays.toString(test));

    cs.revealAllHiddenColumns(colsel);
    cs.hideColumns(0, 1);
    test = cs.locateVisibleBoundsOfSequence(seq);
    assertEquals(Arrays.toString(new int[] { 1, 1, 11 }),
            Arrays.toString(test));

    cs.revealAllHiddenColumns(colsel);
    cs.hideColumns(0, 2);
    test = cs.locateVisibleBoundsOfSequence(seq);
    assertEquals(Arrays.toString(new int[] { 0, 1, 11 }),
            Arrays.toString(test));

    cs.revealAllHiddenColumns(colsel);
    cs.hideColumns(1, 1);
    test = cs.locateVisibleBoundsOfSequence(seq);
    assertEquals(Arrays.toString(new int[] { 2, 1, 11 }),
            Arrays.toString(test));

    cs.revealAllHiddenColumns(colsel);
    cs.hideColumns(1, 2);
    test = cs.locateVisibleBoundsOfSequence(seq);
    assertEquals(Arrays.toString(new int[] { 1, 1, 11 }),
            Arrays.toString(test));

    cs.revealAllHiddenColumns(colsel);
    cs.hideColumns(1, 3);
    test = cs.locateVisibleBoundsOfSequence(seq);
    assertEquals(Arrays.toString(new int[] { 1, 1, 11 }),
            Arrays.toString(test));

    cs.revealAllHiddenColumns(colsel);
    cs.hideColumns(0, 2);
    cs.hideColumns(5, 6);
    test = cs.locateVisibleBoundsOfSequence(seq);
    assertEquals(Arrays.toString(new int[] { 0, 1, 11 }),
            Arrays.toString(test));

    cs.revealAllHiddenColumns(colsel);
    cs.hideColumns(0, 2);
    cs.hideColumns(5, 6);
    cs.hideColumns(9, 10);
    test = cs.locateVisibleBoundsOfSequence(seq);
    assertEquals(Arrays.toString(new int[] { 0, 1, 11 }),
            Arrays.toString(test));

    cs.revealAllHiddenColumns(colsel);
    cs.hideColumns(0, 2);
    cs.hideColumns(7, 11);
    test = cs.locateVisibleBoundsOfSequence(seq);
    assertEquals(Arrays.toString(new int[] { 0, 1, 11 }),
            Arrays.toString(test));

    cs.revealAllHiddenColumns(colsel);
    cs.hideColumns(2, 4);
    cs.hideColumns(7, 11);
    test = cs.locateVisibleBoundsOfSequence(seq);
    assertEquals(Arrays.toString(new int[] { 1, 1, 11 }),
            Arrays.toString(test));

    cs.revealAllHiddenColumns(colsel);
    cs.hideColumns(2, 4);
    cs.hideColumns(7, 12);
    test = cs.locateVisibleBoundsOfSequence(seq);
    assertEquals(Arrays.toString(new int[] { 1, 1, 11 }),
            Arrays.toString(test));

    cs.revealAllHiddenColumns(colsel);
    cs.hideColumns(1, 11);
    test = cs.locateVisibleBoundsOfSequence(seq);
    assertEquals(Arrays.toString(new int[] { 0, 1, 11 }),
            Arrays.toString(test));

    cs.revealAllHiddenColumns(colsel);
    cs.hideColumns(0, 12);
    test = cs.locateVisibleBoundsOfSequence(seq);
    assertEquals(Arrays.toString(new int[] { 0, 1, 11 }),
            Arrays.toString(test));

    cs.revealAllHiddenColumns(colsel);
    cs.hideColumns(0, 4);
    cs.hideColumns(6, 12);
    test = cs.locateVisibleBoundsOfSequence(seq);
    assertEquals(Arrays.toString(new int[] { 0, 1, 11 }),
            Arrays.toString(test));

    cs.revealAllHiddenColumns(colsel);
    cs.hideColumns(0, 1);
    cs.hideColumns(3, 12);
    test = cs.locateVisibleBoundsOfSequence(seq);
    assertEquals(Arrays.toString(new int[] { 0, 1, 11 }),
            Arrays.toString(test));

    // These tests cover different behaviour to original
    // locateVisibleBoundsOfSequence
    // Previously first values of each were 3,9 and 6 respectively.
    cs.revealAllHiddenColumns(colsel);
    cs.hideColumns(3, 14);
    cs.hideColumns(17, 19);
    assertEquals(
            Arrays.toString(
                    new int[]
            { 3, seq2.findIndex(seq2.getStart()) - 1,
        seq2.findIndex(seq2.getEnd()) - 1 }),
            Arrays.toString(cs.locateVisibleBoundsOfSequence(seq2)));

    cs.revealAllHiddenColumns(colsel);
    cs.hideColumns(3, 7);
    cs.hideColumns(9, 14);
    cs.hideColumns(17, 19);
    assertEquals(
            Arrays.toString(
                    new int[]
            { 9, seq2.findIndex(seq2.getStart()) - 1,
        seq2.findIndex(seq2.getEnd()) - 1 }),
            Arrays.toString(cs.locateVisibleBoundsOfSequence(seq2)));

    cs.revealAllHiddenColumns(colsel);
    cs.hideColumns(0, 1);
    cs.hideColumns(3, 4);
    cs.hideColumns(6, 8);
    cs.hideColumns(10, 12);
    test = cs.locateVisibleBoundsOfSequence(seq);
    assertEquals(Arrays.toString(new int[] { 6, 1, 11 }),
            Arrays.toString(test));

  }

  @Test(groups = { "Functional" })
  public void testLocateVisibleBoundsPathologicals()
  {
    // test some pathological cases we missed
    AlignmentI al = new Alignment(
            new SequenceI[]
    { new Sequence("refseqGaptest", "KTDVTI----------NFI-----G----L") });
    HiddenColumns cs = new HiddenColumns();
    cs.hideInsertionsFor(al.getSequenceAt(0));
    assertEquals("G", ""
            + al.getSequenceAt(0).getCharAt(cs.adjustForHiddenColumns(9)));

  }

  @Test(groups = { "Functional" })
  public void testHideColumns()
  {
    // create random alignment
    AlignmentGenerator gen = new AlignmentGenerator(false);
    AlignmentI al = gen.generate(50, 20, 123, 5, 5);

    ColumnSelection colsel = new ColumnSelection();
    HiddenColumns cs = al.getHiddenColumns();
    colsel.hideSelectedColumns(5, al.getHiddenColumns());
    Iterator<int[]> regions = cs.iterator();
    assertEquals(1, cs.getNumberOfRegions());
    assertEquals("[5, 5]", Arrays.toString(regions.next()));

    colsel.hideSelectedColumns(3, al.getHiddenColumns());
    regions = cs.iterator();
    assertEquals(2, cs.getNumberOfRegions());
    // two hidden ranges, in order:
    assertEquals("[3, 3]", Arrays.toString(regions.next()));
    assertEquals("[5, 5]", Arrays.toString(regions.next()));

    // hiding column 4 expands [3, 3] to [3, 4]
    // and merges to [5, 5] to make [3, 5]
    colsel.hideSelectedColumns(4, al.getHiddenColumns());
    regions = cs.iterator();
    assertEquals(1, cs.getNumberOfRegions());
    assertEquals("[3, 5]", Arrays.toString(regions.next()));

    // clear hidden columns (note they are added to selected)
    cs.revealAllHiddenColumns(colsel);
    // it is now actually null but getter returns an empty list
    assertEquals(0, cs.getNumberOfRegions());

    cs.hideColumns(3, 6);
    regions = cs.iterator();
    int[] firstHiddenRange = regions.next();
    assertEquals("[3, 6]", Arrays.toString(firstHiddenRange));

    // adding a subrange of already hidden should do nothing
    cs.hideColumns(4, 5);
    regions = cs.iterator();
    assertEquals(1, cs.getNumberOfRegions());
    assertEquals("[3, 6]",
            Arrays.toString(regions.next()));
    cs.hideColumns(3, 5);
    regions = cs.iterator();
    assertEquals(1, cs.getNumberOfRegions());
    assertEquals("[3, 6]",
            Arrays.toString(regions.next()));
    cs.hideColumns(4, 6);
    regions = cs.iterator();
    assertEquals(1, cs.getNumberOfRegions());
    assertEquals("[3, 6]",
            Arrays.toString(regions.next()));
    cs.hideColumns(3, 6);
    regions = cs.iterator();
    assertEquals(1, cs.getNumberOfRegions());
    assertEquals("[3, 6]",
            Arrays.toString(regions.next()));

    cs.revealAllHiddenColumns(colsel);
    cs.hideColumns(2, 4);
    regions = cs.iterator();
    assertEquals(1, cs.getNumberOfRegions());
    assertEquals("[2, 4]", Arrays.toString(regions.next()));

    // extend contiguous with 2 positions overlap
    cs.hideColumns(3, 5);
    regions = cs.iterator();
    assertEquals(1, cs.getNumberOfRegions());
    assertEquals("[2, 5]", Arrays.toString(regions.next()));

    // extend contiguous with 1 position overlap
    cs.hideColumns(5, 6);
    regions = cs.iterator();
    assertEquals(1, cs.getNumberOfRegions());
    assertEquals("[2, 6]", Arrays.toString(regions.next()));

    // extend contiguous with overlap both ends:
    cs.hideColumns(1, 7);
    regions = cs.iterator();
    assertEquals(1, cs.getNumberOfRegions());
    assertEquals("[1, 7]", Arrays.toString(regions.next()));
  }

  /**
   * Test the method that reveals a range of hidden columns given the start
   * column of the range
   */
  @Test(groups = { "Functional" })
  public void testRevealHiddenColumns()
  {
    ColumnSelection colsel = new ColumnSelection();
    HiddenColumns cs = new HiddenColumns();
    cs.hideColumns(5, 8);
    colsel.addElement(10);
    cs.revealHiddenColumns(5, colsel);

    // hiddenColumns now empty
    assertEquals(0, cs.getSize());

    // revealed columns are marked as selected (added to selection):
    assertEquals("[10, 5, 6, 7, 8]", colsel.getSelected().toString());

    // calling with a column other than the range start does nothing:
    colsel = new ColumnSelection();
    cs = new HiddenColumns();
    cs.hideColumns(5, 8);

    int prevSize = cs.getSize();
    cs.revealHiddenColumns(6, colsel);
    assertEquals(prevSize, cs.getSize());
    assertTrue(colsel.getSelected().isEmpty());
  }

  @Test(groups = { "Functional" })
  public void testRevealAllHiddenColumns()
  {
    HiddenColumns hidden = new HiddenColumns();
    ColumnSelection colsel = new ColumnSelection();
    hidden.hideColumns(5, 8);
    hidden.hideColumns(2, 3);
    colsel.addElement(11);
    colsel.addElement(1);
    hidden.revealAllHiddenColumns(colsel);

    /*
     * revealing hidden columns adds them (in order) to the (unordered)
     * selection list
     */

    // hiddenColumns now empty
    assertEquals(0, hidden.getSize());

    assertEquals("[11, 1, 2, 3, 5, 6, 7, 8]",
            colsel.getSelected().toString());
  }

  @Test(groups = { "Functional" })
  public void testIsVisible()
  {
    HiddenColumns cs = new HiddenColumns();
    cs.hideColumns(2, 4);
    cs.hideColumns(6, 7);
    assertTrue(cs.isVisible(0));
    assertTrue(cs.isVisible(-99));
    assertTrue(cs.isVisible(1));
    assertFalse(cs.isVisible(2));
    assertFalse(cs.isVisible(3));
    assertFalse(cs.isVisible(4));
    assertTrue(cs.isVisible(5));
    assertFalse(cs.isVisible(6));
    assertFalse(cs.isVisible(7));
  }

  /**
   * Test for the case when a hidden range encloses more one already hidden
   * range
   */
  @Test(groups = { "Functional" })
  public void testHideColumns_subsumingHidden()
  {
    /*
     * JAL-2370 bug scenario:
     * two hidden ranges subsumed by a third
     */
    HiddenColumns cs = new HiddenColumns();
    cs.hideColumns(49, 59);
    cs.hideColumns(69, 79);
    Iterator<int[]> regions = cs.iterator();
    assertEquals(2, cs.getNumberOfRegions());
    assertEquals("[49, 59]", Arrays.toString(regions.next()));
    assertEquals("[69, 79]", Arrays.toString(regions.next()));

    cs.hideColumns(48, 80);
    regions = cs.iterator();
    assertEquals(1, cs.getNumberOfRegions());
    assertEquals("[48, 80]", Arrays.toString(regions.next()));

    /*
     * another...joining hidden ranges
     */
    cs = new HiddenColumns();
    cs.hideColumns(10, 20);
    cs.hideColumns(30, 40);
    cs.hideColumns(50, 60);
    // hiding 21-49 should merge to one range
    cs.hideColumns(21, 49);
    regions = cs.iterator();
    assertEquals(1, cs.getNumberOfRegions());
    assertEquals("[10, 60]", Arrays.toString(regions.next()));

    /*
     * another...left overlap, subsumption, right overlap,
     * no overlap of existing hidden ranges
     */
    cs = new HiddenColumns();
    cs.hideColumns(10, 20);
    cs.hideColumns(10, 20);
    cs.hideColumns(30, 35);
    cs.hideColumns(40, 50);
    cs.hideColumns(60, 70);

    cs.hideColumns(15, 45);
    regions = cs.iterator();
    assertEquals(2, cs.getNumberOfRegions());
    assertEquals("[10, 50]", Arrays.toString(regions.next()));
    assertEquals("[60, 70]", Arrays.toString(regions.next()));
  }

  @Test(groups = { "Functional" })
  public void testHideBitset()
  {
    HiddenColumns cs;

    BitSet one = new BitSet();

    // one hidden range
    one.set(1);
    cs = new HiddenColumns();
    cs.hideMarkedBits(one);
    assertEquals(1, cs.getNumberOfRegions());

    one.set(2);
    cs = new HiddenColumns();
    cs.hideMarkedBits(one);
    assertEquals(1, cs.getNumberOfRegions());

    one.set(3);
    cs = new HiddenColumns();
    cs.hideMarkedBits(one);
    assertEquals(1, cs.getNumberOfRegions());

    // split
    one.clear(2);
    cs = new HiddenColumns();
    cs.hideMarkedBits(one);
    assertEquals(2, cs.getNumberOfRegions());

    assertEquals(0, cs.adjustForHiddenColumns(0));
    assertEquals(2, cs.adjustForHiddenColumns(1));
    assertEquals(4, cs.adjustForHiddenColumns(2));

    // one again
    one.clear(1);
    cs = new HiddenColumns();
    cs.hideMarkedBits(one);

    assertEquals(1, cs.getNumberOfRegions());

    assertEquals(0, cs.adjustForHiddenColumns(0));
    assertEquals(1, cs.adjustForHiddenColumns(1));
    assertEquals(2, cs.adjustForHiddenColumns(2));
    assertEquals(4, cs.adjustForHiddenColumns(3));
  }

  @Test(groups = { "Functional" })
  public void testMarkHiddenRegions()
  {
    BitSet toMark, fromMark;
    long seed = -3241532;
    Random number = new Random(seed);
    for (int n = 0; n < 1000; n++)
    {
      // create a random bitfield
      toMark = BitSet
              .valueOf(new long[]
      { number.nextLong(), number.nextLong(), number.nextLong() });
      toMark.set(n * number.nextInt(10), n * (25 + number.nextInt(25)));
      HiddenColumns hc = new HiddenColumns();
      hc.hideMarkedBits(toMark);

      // see if we can recover bitfield
      hc.markHiddenRegions(fromMark = new BitSet());
      assertEquals(toMark, fromMark);
    }
  }

  @Test(groups = { "Functional" })
  public void testRegionsToString()
  {
    HiddenColumns hc = new HiddenColumns();

    String result = hc.regionsToString(",", "--");
    assertEquals("", result);

    hc.hideColumns(3, 7);
    hc.hideColumns(10, 10);
    hc.hideColumns(14, 15);

    result = hc.regionsToString(",", "--");
    assertEquals("3--7,10--10,14--15", result);
  }

  @Test(groups = "Functional")
  public void testGetVisibleStartAndEndIndexTest()
  {
    Sequence seq = new Sequence("testSeq", "ABCDEFGHIJKLMNOPQRSTUVWXYZ");
    AlignmentI align = new Alignment(new SequenceI[] { seq });
    HiddenColumns hc = new HiddenColumns();

    int[] startEnd = hc.getVisibleStartAndEndIndex(align.getWidth());
    assertEquals(0, startEnd[0]);
    assertEquals(25, startEnd[1]);

    hc.hideColumns(0, 0);
    startEnd = hc.getVisibleStartAndEndIndex(align.getWidth());
    assertEquals(1, startEnd[0]);
    assertEquals(25, startEnd[1]);

    hc.hideColumns(6, 9);
    hc.hideColumns(11, 12);
    startEnd = hc.getVisibleStartAndEndIndex(align.getWidth());
    assertEquals(1, startEnd[0]);
    assertEquals(25, startEnd[1]);

    hc.hideColumns(24, 25);
    startEnd = hc.getVisibleStartAndEndIndex(align.getWidth());
    System.out.println(startEnd[0] + " : " + startEnd[1]);
    assertEquals(1, startEnd[0]);
    assertEquals(23, startEnd[1]);
  }

  @Test(groups = "Functional")
  public void testGetRegionWithEdgeAtRes()
  {
    HiddenColumns hc = new HiddenColumns();

    int[] result = hc.getRegionWithEdgeAtRes(5);
    assertNull(result);

    hc.hideColumns(3, 7);
    hc.hideColumns(10, 10);
    hc.hideColumns(14, 15);

    result = hc.getRegionWithEdgeAtRes(2);
    assertEquals(3, result[0]);
    assertEquals(7, result[1]);

    result = hc.getRegionWithEdgeAtRes(5);
    assertEquals(10, result[0]);
    assertEquals(10, result[1]);

    result = hc.getRegionWithEdgeAtRes(6);
    assertNull(result);

    result = hc.getRegionWithEdgeAtRes(0);
    assertNull(result);

    result = hc.getRegionWithEdgeAtRes(7);
    assertEquals(14, result[0]);
    assertEquals(15, result[1]);

    result = hc.getRegionWithEdgeAtRes(8);
    assertEquals(14, result[0]);
    assertEquals(15, result[1]);
  }

  @Test(groups = "Functional")
  public void testPropagateInsertions()
  {
    // create an alignment with no gaps - this will be the profile seq and other
    // JPRED seqs
    AlignmentGenerator gen = new AlignmentGenerator(false);
    AlignmentI al = gen.generate(25, 10, 1234, 0, 0);

    // get the profileseq
    SequenceI profileseq = al.getSequenceAt(0);
    SequenceI gappedseq = new Sequence(profileseq);
    gappedseq.insertCharAt(5, al.getGapCharacter());
    gappedseq.insertCharAt(6, al.getGapCharacter());
    gappedseq.insertCharAt(7, al.getGapCharacter());
    gappedseq.insertCharAt(8, al.getGapCharacter());

    // create an alignment view with the gapped sequence
    SequenceI[] seqs = new SequenceI[1];
    seqs[0] = gappedseq;
    AlignmentI newal = new Alignment(seqs);
    HiddenColumns hidden = new HiddenColumns();
    hidden.hideColumns(15, 17);

    AlignmentView view = new AlignmentView(newal, hidden, null, true, false,
            false);

    // confirm that original contigs are as expected
    Iterator<int[]> visible = hidden.getVisContigsIterator(0, 25);
    int[] region = visible.next();
    assertEquals("[0, 14]", Arrays.toString(region));
    region = visible.next();
    assertEquals("[18, 24]", Arrays.toString(region));

    // propagate insertions
    HiddenColumns result = HiddenColumns.propagateInsertions(profileseq, al,
            view);

    // confirm that the contigs have changed to account for the gaps
    visible = result.getVisContigsIterator(0, 25);
    region = visible.next();
    assertEquals("[0, 10]", Arrays.toString(region));
    region = visible.next();
    assertEquals("[14, 24]", Arrays.toString(region));

    // confirm the alignment has been changed so that the other sequences have
    // gaps inserted where the columns are hidden
    assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[10]));
    assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[11]));
    assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[12]));
    assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[13]));
    assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[14]));

  }

  @Test(groups = "Functional")
  public void testPropagateInsertionsOverlap()
  {
    // test propagateInsertions where gaps and hiddenColumns overlap

    // create an alignment with no gaps - this will be the profile seq and other
    // JPRED seqs
    AlignmentGenerator gen = new AlignmentGenerator(false);
    AlignmentI al = gen.generate(20, 10, 1234, 0, 0);

    // get the profileseq
    SequenceI profileseq = al.getSequenceAt(0);
    SequenceI gappedseq = new Sequence(profileseq);
    gappedseq.insertCharAt(5, al.getGapCharacter());
    gappedseq.insertCharAt(6, al.getGapCharacter());
    gappedseq.insertCharAt(7, al.getGapCharacter());
    gappedseq.insertCharAt(8, al.getGapCharacter());

    // create an alignment view with the gapped sequence
    SequenceI[] seqs = new SequenceI[1];
    seqs[0] = gappedseq;
    AlignmentI newal = new Alignment(seqs);

    // hide columns so that some overlap with the gaps
    HiddenColumns hidden = new HiddenColumns();
    hidden.hideColumns(7, 10);

    AlignmentView view = new AlignmentView(newal, hidden, null, true, false,
            false);

    // confirm that original contigs are as expected
    Iterator<int[]> visible = hidden.getVisContigsIterator(0, 20);
    int[] region = visible.next();
    assertEquals("[0, 6]", Arrays.toString(region));
    region = visible.next();
    assertEquals("[11, 19]", Arrays.toString(region));
    assertFalse(visible.hasNext());

    // propagate insertions
    HiddenColumns result = HiddenColumns.propagateInsertions(profileseq, al,
            view);

    // confirm that the contigs have changed to account for the gaps
    visible = result.getVisContigsIterator(0, 20);
    region = visible.next();
    assertEquals("[0, 4]", Arrays.toString(region));
    region = visible.next();
    assertEquals("[7, 19]", Arrays.toString(region));
    assertFalse(visible.hasNext());

    // confirm the alignment has been changed so that the other sequences have
    // gaps inserted where the columns are hidden
    assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[4]));
    assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[5]));
    assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[6]));
    assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[7]));
  }

  @Test(groups = "Functional")
  public void testHasHiddenColumns()
  {
    HiddenColumns h = new HiddenColumns();

    // new HiddenColumns2 has no hidden cols
    assertFalse(h.hasHiddenColumns());

    // some columns hidden, returns true
    h.hideColumns(5, 10);
    assertTrue(h.hasHiddenColumns());

    // reveal columns, no hidden cols again
    ColumnSelection sel = new ColumnSelection();
    h.revealAllHiddenColumns(sel);
    assertFalse(h.hasHiddenColumns());
  }

  @Test(groups = "Functional")
  public void testHasManyHiddenColumns()
  {
    HiddenColumns h = new HiddenColumns();

    // new HiddenColumns2 has no hidden cols
    assertFalse(h.hasManyHiddenColumns());

    // one set of columns hidden, returns false
    h.hideColumns(5, 10);
    assertFalse(h.hasManyHiddenColumns());

    // two sets hidden, returns true
    h.hideColumns(15, 17);
    assertTrue(h.hasManyHiddenColumns());

    // back to one block, asserts false
    h.hideColumns(11, 14);
    assertFalse(h.hasManyHiddenColumns());
  }

  @Test(groups = "Functional")
  public void testAdjustForHiddenColumns()
  {
    HiddenColumns h = new HiddenColumns();
    // returns input value when there are no hidden columns
    assertEquals(10, h.adjustForHiddenColumns(10));

    h.hideColumns(20, 30);
    assertEquals(10, h.adjustForHiddenColumns(10));
    assertEquals(20 + 11, h.adjustForHiddenColumns(20));
    assertEquals(35 + 11, h.adjustForHiddenColumns(35));

    h.hideColumns(5, 7);
    assertEquals(10 + 3, h.adjustForHiddenColumns(10));
    assertEquals(20 + 14, h.adjustForHiddenColumns(20));
    assertEquals(35 + 14, h.adjustForHiddenColumns(35));

    ColumnSelection sel = new ColumnSelection();
    h.revealAllHiddenColumns(sel);
    h.hideColumns(0, 1);
    assertEquals(4, h.adjustForHiddenColumns(2));
  }

  @Test(groups = "Functional")
  public void testGetHiddenBoundaryLeft()
  {
    HiddenColumns h = new HiddenColumns();

    // returns same value if no hidden cols
    assertEquals(3, h.getHiddenBoundaryLeft(3));

    h.hideColumns(5, 10);
    assertEquals(10, h.getHiddenBoundaryLeft(15));
    assertEquals(3, h.getHiddenBoundaryLeft(3));
    assertEquals(7, h.getHiddenBoundaryLeft(7));

    h.hideColumns(15, 20);
    assertEquals(10, h.getHiddenBoundaryLeft(15));
    assertEquals(20, h.getHiddenBoundaryLeft(21));
  }

  @Test(groups = "Functional")
  public void testGetHiddenBoundaryRight()
  {
    HiddenColumns h = new HiddenColumns();

    // returns same value if no hidden cols
    assertEquals(3, h.getHiddenBoundaryRight(3));

    h.hideColumns(5, 10);
    assertEquals(5, h.getHiddenBoundaryRight(3));
    assertEquals(15, h.getHiddenBoundaryRight(15));
    assertEquals(7, h.getHiddenBoundaryRight(7));

    h.hideColumns(15, 20);
    assertEquals(15, h.getHiddenBoundaryRight(7));
    assertEquals(15, h.getHiddenBoundaryRight(14));
  }

  @Test(groups = "Functional")
  public void testIterator()
  {
    HiddenColumns h = new HiddenColumns();
    Iterator<int[]> result = h.iterator();
    assertFalse(result.hasNext());

    h.hideColumns(5, 10);
    result = h.iterator();
    int[] next = result.next();
    assertEquals(5, next[0]);
    assertEquals(10, next[1]);
    assertFalse(result.hasNext());

    h.hideColumns(22, 23);
    result = h.iterator();
    next = result.next();
    assertEquals(5, next[0]);
    assertEquals(10, next[1]);
    next = result.next();
    assertEquals(22, next[0]);
    assertEquals(23, next[1]);
    assertFalse(result.hasNext());

    // test for only one hidden region at start of alignment
    ColumnSelection sel = new ColumnSelection();
    h.revealAllHiddenColumns(sel);
    h.hideColumns(0, 1);
    result = h.iterator();
    next = result.next();
    assertEquals(0, next[0]);
    assertEquals(1, next[1]);
    assertFalse(result.hasNext());
  }

  @Test(groups = "Functional")
  public void testGetVisibleSequenceStrings()
  {
    HiddenColumns h = new HiddenColumns();
    SequenceI seq1 = new Sequence("TEST1", "GALMFWKQESPVICYHRNDT");
    SequenceI seq2 = new Sequence("TEST2", "VICYHRNDTGA");
    SequenceI[] seqs = new SequenceI[2];
    seqs[0] = seq1;
    seqs[1] = seq2;
    String[] result = h.getVisibleSequenceStrings(5, 10, seqs);
    assertEquals(2, result.length);
    assertEquals("WKQES", result[0]);
    assertEquals("RNDTG", result[1]);

    h.hideColumns(6, 8);
    result = h.getVisibleSequenceStrings(5, 10, seqs);
    assertEquals(2, result.length);
    assertEquals("WS", result[0]);
    assertEquals("RG", result[1]);

    SequenceI seq = new Sequence("RefSeq", "-A-SD-ASD--E---");
    ColumnSelection sel = new ColumnSelection();
    h.revealAllHiddenColumns(sel);
    h.hideColumns(1, 3);
    h.hideColumns(6, 11);
    assertEquals("-D",
            h.getVisibleSequenceStrings(0, 5, new SequenceI[]
    { seq })[0]);
  }

  @Test(groups = "Functional")
  public void testHideInsertionsFor()
  {
    HiddenColumns h = new HiddenColumns();
    HiddenColumns h2 = new HiddenColumns();
    SequenceI seq1 = new Sequence("TEST1", "GAL---MFW-KQESPVICY--HRNDT");
    SequenceI seq2 = new Sequence("TEST1", "GALMFWKQESPVICYHRNDT");

    h.hideInsertionsFor(seq2);
    assertTrue(h.equals(h2));

    h.hideInsertionsFor(seq1);
    h2.hideColumns(3, 5);
    h2.hideColumns(9, 9);
    h2.hideColumns(19, 20);
    assertTrue(h.equals(h2));
  }

  @Test(groups = "Functional")
  public void testHideMarkedBits()
  {
    HiddenColumns h = new HiddenColumns();
    HiddenColumns h2 = new HiddenColumns();

    BitSet tohide = new BitSet(21);
    h.hideMarkedBits(tohide);
    assertTrue(h.equals(h2));

    // NB in hideMarkedBits, the last bit is not set to hidden
    tohide.set(3, 6);
    tohide.set(9);
    tohide.set(19, 21);
    h.hideMarkedBits(tohide);

    h2.hideColumns(3, 5);
    h2.hideColumns(9, 9);
    h2.hideColumns(19, 20);
    assertTrue(h.equals(h2));
  }

  @Test(groups = "Functional")
  public void testMakeVisibleAnnotation()
  {
    HiddenColumns h = new HiddenColumns();
    Annotation[] anns = new Annotation[] { null, null, new Annotation(1),
        new Annotation(2), new Annotation(3), null, null, new Annotation(4),
        new Annotation(5), new Annotation(6), new Annotation(7),
        new Annotation(8) };
    AlignmentAnnotation ann = new AlignmentAnnotation("an", "some an",
            anns);

    // without hidden cols, just truncates
    h.makeVisibleAnnotation(3, 5, ann);
    assertEquals(3, ann.annotations.length);
    assertEquals(2.0f, ann.annotations[0].value);
    assertEquals(3.0f, ann.annotations[1].value);
    assertNull(ann.annotations[2]);

    anns = new Annotation[] { null, null, new Annotation(1),
        new Annotation(2), new Annotation(3), null, null, new Annotation(4),
        new Annotation(5), new Annotation(6), new Annotation(7),
        new Annotation(8) };
    ann = new AlignmentAnnotation("an", "some an", anns);
    h.hideColumns(4, 7);
    h.makeVisibleAnnotation(1, 9, ann);
    assertEquals(5, ann.annotations.length);
    assertNull(ann.annotations[0]);
    assertEquals(1.0f, ann.annotations[1].value);
    assertEquals(2.0f, ann.annotations[2].value);
    assertEquals(5.0f, ann.annotations[3].value);
    assertEquals(6.0f, ann.annotations[4].value);

    anns = new Annotation[] { null, null, new Annotation(1),
        new Annotation(2), new Annotation(3), null, null, new Annotation(4),
        new Annotation(5), new Annotation(6), new Annotation(7),
        new Annotation(8) };
    ann = new AlignmentAnnotation("an", "some an", anns);
    h.hideColumns(1, 2);
    h.makeVisibleAnnotation(1, 9, ann);
    assertEquals(3, ann.annotations.length);
    assertEquals(2.0f, ann.annotations[0].value);
    assertEquals(5.0f, ann.annotations[1].value);
    assertEquals(6.0f, ann.annotations[2].value);
  }

  @Test(groups = "Functional")
  public void testSubtractVisibleColumns()
  {
    HiddenColumns h = new HiddenColumns();
    int result = h.subtractVisibleColumns(1, 10);
    assertEquals(9, result);

    h.hideColumns(7, 9);
    result = h.subtractVisibleColumns(4, 10);
    assertEquals(3, result);

    h.hideColumns(14, 15);
    result = h.subtractVisibleColumns(4, 10);
    assertEquals(3, result);

    result = h.subtractVisibleColumns(10, 17);
    assertEquals(2, result);

    result = h.subtractVisibleColumns(1, 7);
    assertEquals(5, result);

    result = h.subtractVisibleColumns(1, 8);
    assertEquals(5, result);

    result = h.subtractVisibleColumns(3, 15);
    assertEquals(10, result);

    ColumnSelection sel = new ColumnSelection();
    h.revealAllHiddenColumns(sel);
    h.hideColumns(0, 30);
    result = h.subtractVisibleColumns(31, 0);
    assertEquals(-31, result);
  }

  @Test(groups = "Functional")
  public void testBoundedIterator()
  {
    HiddenColumns h = new HiddenColumns();
    Iterator<int[]> it = h.getBoundedIterator(0, 10);

    // no hidden columns = nothing to iterate over
    assertFalse(it.hasNext());

    // [start,end] contains all hidden columns
    // all regions are returned
    h.hideColumns(3, 10);
    h.hideColumns(14, 16);
    it = h.getBoundedIterator(0, 20);
    assertTrue(it.hasNext());
    int[] next = it.next();
    assertEquals(3, next[0]);
    assertEquals(10, next[1]);
    next = it.next();
    assertEquals(14, next[0]);
    assertEquals(16, next[1]);
    assertFalse(it.hasNext());

    // [start,end] overlaps a region
    // 1 region returned
    it = h.getBoundedIterator(5, 7);
    assertTrue(it.hasNext());
    next = it.next();
    assertEquals(3, next[0]);
    assertEquals(10, next[1]);
    assertFalse(it.hasNext());

    // [start,end] fully contains 1 region and start of last
    // - 2 regions returned
    it = h.getBoundedIterator(3, 15);
    assertTrue(it.hasNext());
    next = it.next();
    assertEquals(3, next[0]);
    assertEquals(10, next[1]);
    next = it.next();
    assertEquals(14, next[0]);
    assertEquals(16, next[1]);
    assertFalse(it.hasNext());

    // [start,end] contains end of first region and whole of last region
    // - 2 regions returned
    it = h.getBoundedIterator(4, 20);
    assertTrue(it.hasNext());
    next = it.next();
    assertEquals(3, next[0]);
    assertEquals(10, next[1]);
    next = it.next();
    assertEquals(14, next[0]);
    assertEquals(16, next[1]);
    assertFalse(it.hasNext());
  }

  @Test(groups = "Functional")
  public void testBoundedStartIterator()
  {
    HiddenColumns h = new HiddenColumns();
    Iterator<Integer> it = h.getBoundedStartIterator(0, 10);

    // no hidden columns = nothing to iterate over
    assertFalse(it.hasNext());

    // [start,end] contains all hidden columns
    // all regions are returned
    h.hideColumns(3, 10);
    h.hideColumns(14, 16);
    it = h.getBoundedStartIterator(0, 20);
    assertTrue(it.hasNext());
    int next = it.next();
    assertEquals(3, next);
    next = it.next();
    assertEquals(6, next);
    assertFalse(it.hasNext());

    // [start,end] does not contain a start of a region
    // no regions to iterate over
    it = h.getBoundedStartIterator(4, 5);
    assertFalse(it.hasNext());

    // [start,end] fully contains 1 region and start of last
    // - 2 regions returned
    it = h.getBoundedStartIterator(3, 7);
    assertTrue(it.hasNext());
    next = it.next();
    assertEquals(3, next);
    next = it.next();
    assertEquals(6, next);
    assertFalse(it.hasNext());

    // [start,end] contains whole of last region
    // - 1 region returned
    it = h.getBoundedStartIterator(4, 20);
    assertTrue(it.hasNext());
    next = it.next();
    assertEquals(6, next);
    assertFalse(it.hasNext());
  }
}