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

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

import java.util.Arrays;
import java.util.BitSet;
import java.util.List;
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
    int 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 testGetVisibleContigs()
  {
    HiddenColumns cs = new HiddenColumns();
    cs.hideColumns(3, 6);
    cs.hideColumns(8, 9);
    cs.hideColumns(12, 12);

    // start position is inclusive, end position exclusive:
    int[] visible = cs.getVisibleContigs(1, 13);
    assertEquals("[1, 2, 7, 7, 10, 11]", Arrays.toString(visible));

    visible = cs.getVisibleContigs(4, 14);
    assertEquals("[7, 7, 10, 11, 13, 13]", Arrays.toString(visible));

    visible = cs.getVisibleContigs(3, 10);
    assertEquals("[7, 7]", Arrays.toString(visible));

    visible = cs.getVisibleContigs(4, 6);
    assertEquals("[]", Arrays.toString(visible));
  }

  @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);
    assertEquals("[5, 7]", Arrays.toString(cs.getHiddenRegions().get(0)));

    HiddenColumns cs2 = new HiddenColumns(cs);
    assertTrue(cs2.hasHiddenColumns());
    assertEquals(2, cs2.getHiddenRegions().size());
    // hidden columns are held in column order
    assertEquals("[5, 7]", Arrays.toString(cs2.getHiddenRegions().get(0)));
    assertEquals("[10, 11]", Arrays.toString(cs2.getHiddenRegions().get(1)));
  }

  /**
   * 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.getEnd()) - 1, seq.getStart(),
                seq.getEnd(), 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.getEnd()) - 1, seq.getStart(),
                seq.getEnd(), 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.getEnd()) - 2, seq.getStart(),
                seq.getEnd(), 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, 1, 3, 3,
                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, 1, 0, 0,
                seq.findIndex(seq.getStart()) - 1,
                seq.findIndex(seq.getEnd()) - 1 }),
            Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));

  }

  @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());
    List<int[]> hidden = cs.getHiddenRegions();
    assertEquals(1, hidden.size());
    assertEquals("[5, 5]", Arrays.toString(hidden.get(0)));

    colsel.hideSelectedColumns(3, al.getHiddenColumns());
    assertEquals(2, hidden.size());
    // two hidden ranges, in order:
    assertSame(hidden, cs.getHiddenRegions());
    assertEquals("[3, 3]", Arrays.toString(hidden.get(0)));
    assertEquals("[5, 5]", Arrays.toString(hidden.get(1)));

    // hiding column 4 expands [3, 3] to [3, 4]
    // and merges to [5, 5] to make [3, 5]
    colsel.hideSelectedColumns(4, al.getHiddenColumns());
    hidden = cs.getHiddenRegions();
    assertEquals(1, hidden.size());
    assertEquals("[3, 5]", Arrays.toString(hidden.get(0)));

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

    cs.hideColumns(3, 6);
    hidden = cs.getHiddenRegions();
    int[] firstHiddenRange = hidden.get(0);
    assertEquals("[3, 6]", Arrays.toString(firstHiddenRange));

    // adding a subrange of already hidden should do nothing
    cs.hideColumns(4, 5);
    assertEquals(1, hidden.size());
    assertSame(firstHiddenRange, cs.getHiddenRegions().get(0));
    cs.hideColumns(3, 5);
    assertEquals(1, hidden.size());
    assertSame(firstHiddenRange, cs.getHiddenRegions().get(0));
    cs.hideColumns(4, 6);
    assertEquals(1, hidden.size());
    assertSame(firstHiddenRange, cs.getHiddenRegions().get(0));
    cs.hideColumns(3, 6);
    assertEquals(1, hidden.size());
    assertSame(firstHiddenRange, cs.getHiddenRegions().get(0));

    cs.revealAllHiddenColumns(colsel);
    cs.hideColumns(2, 4);
    hidden = cs.getHiddenRegions();
    assertEquals(1, hidden.size());
    assertEquals("[2, 4]", Arrays.toString(hidden.get(0)));

    // extend contiguous with 2 positions overlap
    cs.hideColumns(3, 5);
    assertEquals(1, hidden.size());
    assertEquals("[2, 5]", Arrays.toString(hidden.get(0)));

    // extend contiguous with 1 position overlap
    cs.hideColumns(5, 6);
    assertEquals(1, hidden.size());
    assertEquals("[2, 6]", Arrays.toString(hidden.get(0)));

    // extend contiguous with overlap both ends:
    cs.hideColumns(1, 7);
    assertEquals(1, hidden.size());
    assertEquals("[1, 7]", Arrays.toString(hidden.get(0)));
  }

  /**
   * 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);
    // hidden columns list now null but getter returns empty list:
    assertTrue(cs.getHiddenRegions().isEmpty());
    // 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);
    List<int[]> hidden = cs.getHiddenRegions();
    cs.revealHiddenColumns(6, colsel);
    assertSame(hidden, cs.getHiddenRegions());
    assertTrue(colsel.getSelected().isEmpty());
  }

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

    /*
     * revealing hidden columns adds them (in order) to the (unordered)
     * selection list
     */
    assertTrue(cs.getHiddenRegions().isEmpty());
    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);
    List<int[]> hidden = cs.getHiddenRegions();
    assertEquals(2, hidden.size());
    assertEquals("[49, 59]", Arrays.toString(hidden.get(0)));
    assertEquals("[69, 79]", Arrays.toString(hidden.get(1)));

    cs.hideColumns(48, 80);
    hidden = cs.getHiddenRegions();
    assertEquals(1, hidden.size());
    assertEquals("[48, 80]", Arrays.toString(hidden.get(0)));

    /*
     * 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);
    hidden = cs.getHiddenRegions();
    assertEquals(1, hidden.size());
    assertEquals("[10, 60]", Arrays.toString(hidden.get(0)));

    /*
     * 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);
    hidden = cs.getHiddenRegions();
    assertEquals(2, hidden.size());
    assertEquals("[10, 50]", Arrays.toString(hidden.get(0)));
    assertEquals("[60, 70]", Arrays.toString(hidden.get(1)));
  }

  @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.getHiddenRegions().size());

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

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

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

    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.getHiddenRegions().size());

    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 testGetBitset()
  {
    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);
    }
  }
}