/*
* 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 .
* 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.ArrayList;
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
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 testGetVisibleContigs()
{
HiddenColumns cs = new HiddenColumns();
int[] visible = cs.getVisibleContigs(3, 10);
assertEquals("[3, 9]", Arrays.toString(visible));
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.getVisibleContigs(1, 13);
assertEquals("[1, 2, 7, 7, 10, 11]", Arrays.toString(visible));
// Test start hidden, end visible
visible = cs.getVisibleContigs(4, 14);
assertEquals("[7, 7, 10, 11, 13, 13]", Arrays.toString(visible));
// Test start hidden, end hidden
visible = cs.getVisibleContigs(3, 10);
assertEquals("[7, 7]", Arrays.toString(visible));
// Test start visible, end hidden
visible = cs.getVisibleContigs(0, 13);
assertEquals("[0, 2, 7, 7, 10, 11]", Arrays.toString(visible));
// Test empty result
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.getHiddenColumnsCopy().get(0)));
HiddenColumns cs2 = new HiddenColumns(cs);
assertTrue(cs2.hasHiddenColumns());
assertEquals(2, cs2.getHiddenColumnsCopy().size());
// hidden columns are held in column order
assertEquals("[5, 7]",
Arrays.toString(cs2.getHiddenColumnsCopy().get(0)));
assertEquals("[10, 11]",
Arrays.toString(cs2.getHiddenColumnsCopy().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.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());
List hidden = cs.getHiddenColumnsCopy();
assertEquals(1, hidden.size());
assertEquals("[5, 5]", Arrays.toString(hidden.get(0)));
colsel.hideSelectedColumns(3, al.getHiddenColumns());
hidden = cs.getHiddenColumnsCopy();
assertEquals(2, hidden.size());
// two hidden ranges, in order:
assertEquals(hidden.size(), cs.getHiddenColumnsCopy().size());
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.getHiddenColumnsCopy();
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.getHiddenColumnsCopy().isEmpty());
cs.hideColumns(3, 6);
hidden = cs.getHiddenColumnsCopy();
int[] firstHiddenRange = hidden.get(0);
assertEquals("[3, 6]", Arrays.toString(firstHiddenRange));
// adding a subrange of already hidden should do nothing
cs.hideColumns(4, 5);
hidden = cs.getHiddenColumnsCopy();
assertEquals(1, hidden.size());
assertEquals("[3, 6]",
Arrays.toString(cs.getHiddenColumnsCopy().get(0)));
cs.hideColumns(3, 5);
hidden = cs.getHiddenColumnsCopy();
assertEquals(1, hidden.size());
assertEquals("[3, 6]",
Arrays.toString(cs.getHiddenColumnsCopy().get(0)));
cs.hideColumns(4, 6);
hidden = cs.getHiddenColumnsCopy();
assertEquals(1, hidden.size());
assertEquals("[3, 6]",
Arrays.toString(cs.getHiddenColumnsCopy().get(0)));
cs.hideColumns(3, 6);
hidden = cs.getHiddenColumnsCopy();
assertEquals(1, hidden.size());
assertEquals("[3, 6]",
Arrays.toString(cs.getHiddenColumnsCopy().get(0)));
cs.revealAllHiddenColumns(colsel);
cs.hideColumns(2, 4);
hidden = cs.getHiddenColumnsCopy();
assertEquals(1, hidden.size());
assertEquals("[2, 4]", Arrays.toString(hidden.get(0)));
// extend contiguous with 2 positions overlap
cs.hideColumns(3, 5);
hidden = cs.getHiddenColumnsCopy();
assertEquals(1, hidden.size());
assertEquals("[2, 5]", Arrays.toString(hidden.get(0)));
// extend contiguous with 1 position overlap
cs.hideColumns(5, 6);
hidden = cs.getHiddenColumnsCopy();
assertEquals(1, hidden.size());
assertEquals("[2, 6]", Arrays.toString(hidden.get(0)));
// extend contiguous with overlap both ends:
cs.hideColumns(1, 7);
hidden = cs.getHiddenColumnsCopy();
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);
// 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);
List hidden = cs.getHiddenColumnsCopy();
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.getHiddenColumnsCopy();
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.getHiddenColumnsCopy();
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.getHiddenColumnsCopy();
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.getHiddenColumnsCopy().size());
one.set(2);
cs = new HiddenColumns();
cs.hideMarkedBits(one);
assertEquals(1, cs.getHiddenColumnsCopy().size());
one.set(3);
cs = new HiddenColumns();
cs.hideMarkedBits(one);
assertEquals(1, cs.getHiddenColumnsCopy().size());
// split
one.clear(2);
cs = new HiddenColumns();
cs.hideMarkedBits(one);
assertEquals(2, cs.getHiddenColumnsCopy().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.getHiddenColumnsCopy().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 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 testFindHiddenRegionPositions()
{
HiddenColumns hc = new HiddenColumns();
List positions = hc.findHiddenRegionPositions();
assertTrue(positions.isEmpty());
hc.hideColumns(3, 7);
hc.hideColumns(10, 10);
hc.hideColumns(14, 15);
positions = hc.findHiddenRegionPositions();
assertEquals(3, positions.size());
assertEquals(3, positions.get(0).intValue());
assertEquals(5, positions.get(1).intValue());
assertEquals(8, positions.get(2).intValue());
}
@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
int[] oldcontigs = hidden.getVisibleContigs(0, 25);
int[] testcontigs = { 0, 14, 18, 24 };
assertTrue(Arrays.equals(oldcontigs, testcontigs));
// propagate insertions
HiddenColumns result = HiddenColumns.propagateInsertions(profileseq, al,
view);
// confirm that the contigs have changed to account for the gaps
int[] newcontigs = result.getVisibleContigs(0, 25);
testcontigs[1] = 10;
testcontigs[2] = 14;
assertTrue(Arrays.equals(newcontigs, testcontigs));
// 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
int[] oldcontigs = hidden.getVisibleContigs(0, 20);
int[] testcontigs = { 0, 6, 11, 19 };
assertTrue(Arrays.equals(oldcontigs, testcontigs));
// propagate insertions
HiddenColumns result = HiddenColumns.propagateInsertions(profileseq, al,
view);
// confirm that the contigs have changed to account for the gaps
int[] newcontigs = result.getVisibleContigs(0, 20);
testcontigs[1] = 4;
testcontigs[2] = 7;
assertTrue(Arrays.equals(newcontigs, testcontigs));
// 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 testGetHiddenColumnsCopy()
{
HiddenColumns h = new HiddenColumns();
ArrayList result = h.getHiddenColumnsCopy();
assertTrue(result.isEmpty());
h.hideColumns(5, 10);
result = h.getHiddenColumnsCopy();
assertEquals(1, result.size());
assertEquals(5, result.get(0)[0]);
assertEquals(10, result.get(0)[1]);
h.hideColumns(22, 23);
result = h.getHiddenColumnsCopy();
assertEquals(2, result.size());
assertEquals(5, result.get(0)[0]);
assertEquals(10, result.get(0)[1]);
assertEquals(22, result.get(1)[0]);
assertEquals(23, result.get(1)[1]);
// test for only one hidden region at start of alignment
ColumnSelection sel = new ColumnSelection();
h.revealAllHiddenColumns(sel);
h.hideColumns(0, 1);
result = h.getHiddenColumnsCopy();
assertEquals(1, result.size());
assertEquals(0, result.get(0)[0]);
assertEquals(1, result.get(0)[1]);
}
@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);
}
}