/*
* 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 java.util.Arrays;
import java.util.BitSet;
import java.util.Iterator;
import org.testng.annotations.Test;
public class HiddenColumnsTest
{
/**
* 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.absoluteToVisibleColumn(5));
// hiding column 6 makes no difference
cs.hideColumns(6, 6);
assertEquals(5, cs.absoluteToVisibleColumn(5));
// hiding column 4 moves column 5 to column 4
cs.hideColumns(4, 4);
assertEquals(4, cs.absoluteToVisibleColumn(5));
// hiding column 4 moves column 4 to position 3
assertEquals(3, cs.absoluteToVisibleColumn(4));
// hiding columns 1 and 2 moves column 5 to column 2
cs.hideColumns(1, 2);
assertEquals(2, cs.absoluteToVisibleColumn(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.absoluteToVisibleColumn(8));
// and moves column 24 to 13
assertEquals(13, cs2.absoluteToVisibleColumn(24));
// and moves column 28 to 14
assertEquals(14, cs2.absoluteToVisibleColumn(28));
// and moves column 40 to 25
assertEquals(25, cs2.absoluteToVisibleColumn(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.absoluteToVisibleColumn(2));
// check that column after the last hidden region doesn't crash
assertEquals(46, cs2.absoluteToVisibleColumn(65));
}
@Test(groups = { "Functional" })
public void testVisibleContigsIterator()
{
HiddenColumns cs = new HiddenColumns();
Iterator visible = cs.getVisContigsIterator(3, 10, false);
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, false);
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, false);
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, false);
region = visible.next();
assertEquals("[7, 7]", Arrays.toString(region));
assertFalse(visible.hasNext());
// Test start visible, end hidden
visible = cs.getVisContigsIterator(0, 13, false);
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, false);
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 the wrong kind of object
assertFalse(cs.equals(new HiddenColumnsCursor()));
// with a different hiddenColumns object - by size
HiddenColumns cs3 = new HiddenColumns();
cs3.hideColumns(2, 3);
assertFalse(cs.equals(cs3));
// with hidden columns added in a different order
cs2.hideColumns(6, 9);
assertFalse(cs.equals(cs2));
assertFalse(cs2.equals(cs));
cs2.hideColumns(5, 8);
assertTrue(cs.equals(cs2));
assertTrue(cs.equals(cs));
assertTrue(cs2.equals(cs));
assertTrue(cs2.equals(cs2));
// different ranges, same size
cs.hideColumns(10, 12);
cs2.hideColumns(10, 15);
assertFalse(cs.equals(cs2));
}
@Test(groups = "Functional")
public void testCopyConstructor()
{
HiddenColumns cs = new HiddenColumns();
cs.hideColumns(10, 11);
cs.hideColumns(5, 7);
Iterator 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 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(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 regions = cs.iterator();
assertEquals(1, cs.getNumberOfRegions());
assertEquals("[5, 5]", Arrays.toString(regions.next()));
assertEquals(cs.getSize(), 1);
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()));
assertEquals(cs.getSize(), 2);
// 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()));
assertEquals(cs.getSize(), 3);
// 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());
assertEquals(cs.getSize(), 0);
cs.hideColumns(3, 6);
regions = cs.iterator();
int[] firstHiddenRange = regions.next();
assertEquals("[3, 6]", Arrays.toString(firstHiddenRange));
assertEquals(cs.getSize(), 4);
// 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()));
assertEquals(cs.getSize(), 4);
cs.hideColumns(3, 5);
regions = cs.iterator();
assertEquals(1, cs.getNumberOfRegions());
assertEquals("[3, 6]", Arrays.toString(regions.next()));
assertEquals(cs.getSize(), 4);
cs.hideColumns(4, 6);
regions = cs.iterator();
assertEquals(1, cs.getNumberOfRegions());
assertEquals("[3, 6]", Arrays.toString(regions.next()));
assertEquals(cs.getSize(), 4);
cs.hideColumns(3, 6);
regions = cs.iterator();
assertEquals(1, cs.getNumberOfRegions());
assertEquals("[3, 6]", Arrays.toString(regions.next()));
assertEquals(cs.getSize(), 4);
cs.revealAllHiddenColumns(colsel);
cs.hideColumns(2, 4);
regions = cs.iterator();
assertEquals(1, cs.getNumberOfRegions());
assertEquals("[2, 4]", Arrays.toString(regions.next()));
assertEquals(cs.getSize(), 3);
// extend contiguous with 2 positions overlap
cs.hideColumns(3, 5);
regions = cs.iterator();
assertEquals(1, cs.getNumberOfRegions());
assertEquals("[2, 5]", Arrays.toString(regions.next()));
assertEquals(cs.getSize(), 4);
// extend contiguous with 1 position overlap
cs.hideColumns(5, 6);
regions = cs.iterator();
assertEquals(1, cs.getNumberOfRegions());
assertEquals("[2, 6]", Arrays.toString(regions.next()));
assertEquals(cs.getSize(), 5);
// extend contiguous with overlap both ends:
cs.hideColumns(1, 7);
regions = cs.iterator();
assertEquals(1, cs.getNumberOfRegions());
assertEquals("[1, 7]", Arrays.toString(regions.next()));
assertEquals(cs.getSize(), 7);
cs.revealAllHiddenColumns(colsel);
cs.hideColumns(15, 18);
cs.hideColumns(2, 4);
cs.hideColumns(7, 9);
regions = cs.iterator();
assertEquals(3, cs.getNumberOfRegions());
assertEquals("[2, 4]", Arrays.toString(regions.next()));
assertEquals("[7, 9]", Arrays.toString(regions.next()));
assertEquals("[15, 18]", Arrays.toString(regions.next()));
assertEquals(cs.getSize(), 10);
}
/**
* 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();
// test with null hidden columns
cs.revealHiddenColumns(5, colsel);
assertTrue(colsel.getSelected().isEmpty());
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());
// reveal hidden columns when there is more than one region
cs.hideColumns(20, 23);
// now there are 2 hidden regions
assertEquals(2, cs.getNumberOfRegions());
cs.revealHiddenColumns(20, colsel);
// hiddenColumns now has one region
assertEquals(1, cs.getNumberOfRegions());
// revealed columns are marked as selected (added to selection):
assertEquals("[20, 21, 22, 23]", colsel.getSelected().toString());
// call with a column past the end of the hidden column ranges
colsel.clear();
cs.revealHiddenColumns(20, colsel);
// hiddenColumns still has 1 region
assertEquals(1, cs.getNumberOfRegions());
assertTrue(colsel.getSelected().isEmpty());
}
@Test(groups = { "Functional" })
public void testRevealAllHiddenColumns()
{
HiddenColumns hidden = new HiddenColumns();
ColumnSelection colsel = new ColumnSelection();
// test with null hidden columns
hidden.revealAllHiddenColumns(colsel);
assertTrue(colsel.getSelected().isEmpty());
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();
assertTrue(cs.isVisible(5));
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));
assertTrue(cs.isVisible(8));
}
/**
* 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 regions = cs.iterator();
assertEquals(2, cs.getNumberOfRegions());
assertEquals("[49, 59]", Arrays.toString(regions.next()));
assertEquals("[69, 79]", Arrays.toString(regions.next()));
assertEquals(22, cs.getSize());
cs.hideColumns(48, 80);
regions = cs.iterator();
assertEquals(1, cs.getNumberOfRegions());
assertEquals("[48, 80]", Arrays.toString(regions.next()));
assertEquals(33, cs.getSize());
/*
* 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()));
assertEquals(51, cs.getSize());
/*
* 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()));
assertEquals(52, cs.getSize());
}
@Test(groups = { "Functional" })
public void testHideColumns_BitSet()
{
HiddenColumns cs;
BitSet one = new BitSet();
// one hidden range
one.set(1);
cs = new HiddenColumns();
cs.hideColumns(one);
assertEquals(1, cs.getNumberOfRegions());
assertEquals(1, cs.getSize());
one.set(2);
cs = new HiddenColumns();
cs.hideColumns(one);
assertEquals(1, cs.getNumberOfRegions());
assertEquals(2, cs.getSize());
one.set(3);
cs = new HiddenColumns();
cs.hideColumns(one);
assertEquals(1, cs.getNumberOfRegions());
assertEquals(3, cs.getSize());
// split
one.clear(2);
cs = new HiddenColumns();
cs.hideColumns(one);
assertEquals(2, cs.getNumberOfRegions());
assertEquals(2, cs.getSize());
assertEquals(0, cs.visibleToAbsoluteColumn(0));
assertEquals(2, cs.visibleToAbsoluteColumn(1));
assertEquals(4, cs.visibleToAbsoluteColumn(2));
// one again
one.clear(1);
cs = new HiddenColumns();
cs.hideColumns(one);
assertEquals(1, cs.getSize());
assertEquals(1, cs.getNumberOfRegions());
assertEquals(0, cs.visibleToAbsoluteColumn(0));
assertEquals(1, cs.visibleToAbsoluteColumn(1));
assertEquals(2, cs.visibleToAbsoluteColumn(2));
assertEquals(4, cs.visibleToAbsoluteColumn(3));
}
@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 testGetVisibleStartAndEndIndex()
{
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]);
// force lowest range to start of alignment
hc = new HiddenColumns();
hc.hideColumns(3, 4);
startEnd = hc.getVisibleStartAndEndIndex(align.getWidth());
assertEquals(0, startEnd[0]);
assertEquals(25, 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(4);
assertEquals(10, result[0]);
assertEquals(10, 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]);
result = hc.getRegionWithEdgeAtRes(16);
assertNull(result);
}
@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();
// h has no hidden cols
assertFalse(h.hasMultiHiddenColumnRegions());
// one set of columns hidden, returns false
h.hideColumns(5, 10);
assertFalse(h.hasMultiHiddenColumnRegions());
// two sets hidden, returns true
h.hideColumns(15, 17);
assertTrue(h.hasMultiHiddenColumnRegions());
// back to one block, asserts false
h.hideColumns(11, 14);
assertFalse(h.hasMultiHiddenColumnRegions());
}
@Test(groups = "Functional")
public void testAdjustForHiddenColumns()
{
HiddenColumns h = new HiddenColumns();
// returns input value when there are no hidden columns
assertEquals(10, h.visibleToAbsoluteColumn(10));
h.hideColumns(20, 30);
assertEquals(10, h.visibleToAbsoluteColumn(10));
assertEquals(20 + 11, h.visibleToAbsoluteColumn(20));
assertEquals(35 + 11, h.visibleToAbsoluteColumn(35));
h.hideColumns(5, 7);
assertEquals(10 + 3, h.visibleToAbsoluteColumn(10));
assertEquals(20 + 14, h.visibleToAbsoluteColumn(20));
assertEquals(35 + 14, h.visibleToAbsoluteColumn(35));
ColumnSelection sel = new ColumnSelection();
h.revealAllHiddenColumns(sel);
h.hideColumns(0, 1);
assertEquals(4, h.visibleToAbsoluteColumn(2));
}
@Test(groups = "Functional")
public void testGetNextHiddenBoundary_Left()
{
HiddenColumns h = new HiddenColumns();
// returns same value if no hidden cols
assertEquals(3, h.getNextHiddenBoundary(true, 3));
h.hideColumns(5, 10);
assertEquals(10, h.getNextHiddenBoundary(true, 15));
assertEquals(3, h.getNextHiddenBoundary(true, 3));
assertEquals(7, h.getNextHiddenBoundary(true, 7));
h.hideColumns(15, 20);
assertEquals(10, h.getNextHiddenBoundary(true, 15));
assertEquals(20, h.getNextHiddenBoundary(true, 21));
}
@Test(groups = "Functional")
public void testGetNextHiddenBoundary_Right()
{
HiddenColumns h = new HiddenColumns();
// returns same value if no hidden cols
assertEquals(3, h.getNextHiddenBoundary(false, 3));
h.hideColumns(5, 10);
assertEquals(5, h.getNextHiddenBoundary(false, 3));
assertEquals(15, h.getNextHiddenBoundary(false, 15));
assertEquals(7, h.getNextHiddenBoundary(false, 7));
h.hideColumns(15, 20);
assertEquals(15, h.getNextHiddenBoundary(false, 7));
assertEquals(15, h.getNextHiddenBoundary(false, 14));
// returns same value if there is no next hidden column
assertEquals(22, h.getNextHiddenBoundary(false, 22));
}
@Test(groups = "Functional")
public void testIterator()
{
HiddenColumns h = new HiddenColumns();
Iterator 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.hideList(seq2.getInsertions());
assertTrue(h.equals(h2));
assertEquals(0, h.getSize());
h.hideList(seq1.getInsertions());
h2.hideColumns(3, 5);
h2.hideColumns(9, 9);
h2.hideColumns(19, 20);
assertTrue(h.equals(h2));
assertEquals(6, h.getSize());
}
@Test(groups = "Functional")
public void testHideColumns_BitSet_range()
{
HiddenColumns h = new HiddenColumns();
HiddenColumns h2 = new HiddenColumns();
BitSet tohide = new BitSet(25);
h.hideColumns(tohide);
assertTrue(h.equals(h2));
// when setting bitset, first param is inclusive, second exclusive
tohide.set(3, 6);
tohide.set(9);
tohide.set(15, 21);
h.clearAndHideColumns(tohide, 5, 23);
h2.hideColumns(5, 5);
h2.hideColumns(9, 9);
h2.hideColumns(15, 20);
assertTrue(h.equals(h2));
assertEquals(h.getSize(), h2.getSize());
tohide.clear();
tohide.set(41);
h.clearAndHideColumns(tohide, 23, 30);
assertTrue(h.equals(h2));
assertEquals(h.getSize(), h2.getSize());
tohide.set(41);
h.clearAndHideColumns(tohide, 30, 45);
h2.hideColumns(41, 41);
assertTrue(h.equals(h2));
assertEquals(h.getSize(), h2.getSize());
tohide.clear();
tohide.set(25, 28);
h.clearAndHideColumns(tohide, 17, 50);
h2 = new HiddenColumns();
h2.hideColumns(5, 5);
h2.hideColumns(9, 9);
h2.hideColumns(15, 16);
h2.hideColumns(25, 27);
assertTrue(h.equals(h2));
assertEquals(h.getSize(), h2.getSize());
HiddenColumns hc = new HiddenColumns();
hc.hideColumns(3, 5);
hc.hideColumns(15, 20);
hc.hideColumns(45, 60);
tohide = new BitSet();
// all unhidden if tohide is empty and range covers hidden
hc.clearAndHideColumns(tohide, 1, 70);
assertTrue(!hc.hasHiddenColumns());
assertEquals(0, hc.getSize());
hc.hideColumns(3, 5);
hc.hideColumns(15, 20);
hc.hideColumns(45, 60);
assertEquals(25, hc.getSize());
// but not if range does not cover hidden
hc.clearAndHideColumns(tohide, 23, 40);
assertTrue(hc.hasHiddenColumns());
assertEquals(25, hc.getSize());
// and partial unhide if range partially covers
hc.clearAndHideColumns(tohide, 1, 17);
Iterator it = hc.iterator();
assertTrue(it.hasNext());
int[] region = it.next();
assertEquals(18, region[0]);
assertEquals(20, region[1]);
assertTrue(it.hasNext());
region = it.next();
assertEquals(45, region[0]);
assertEquals(60, region[1]);
assertFalse(it.hasNext());
assertEquals(19, hc.getSize());
}
@Test(groups = "Functional")
public void testOffsetByVisibleColumns()
{
HiddenColumns h = new HiddenColumns();
int result = h.offsetByVisibleColumns(-1, 10);
assertEquals(9, result);
h.hideColumns(7, 9);
result = h.offsetByVisibleColumns(-4, 10);
assertEquals(3, result);
h.hideColumns(14, 15);
result = h.offsetByVisibleColumns(-4, 10);
assertEquals(3, result);
result = h.offsetByVisibleColumns(-10, 17);
assertEquals(2, result);
result = h.offsetByVisibleColumns(-1, 7);
assertEquals(5, result);
result = h.offsetByVisibleColumns(-1, 8);
assertEquals(5, result);
result = h.offsetByVisibleColumns(-3, 15);
assertEquals(10, result);
ColumnSelection sel = new ColumnSelection();
h.revealAllHiddenColumns(sel);
h.hideColumns(0, 30);
result = h.offsetByVisibleColumns(-31, 0);
assertEquals(-31, result);
HiddenColumns cs = new HiddenColumns();
// test that without hidden columns, offsetByVisibleColumns returns
// position n to left of provided position
long pos = cs.offsetByVisibleColumns(-3, 10);
assertEquals(7, pos);
// 0 returns same position
pos = cs.offsetByVisibleColumns(0, 10);
assertEquals(10, pos);
// overflow to left returns negative number
pos = cs.offsetByVisibleColumns(-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.offsetByVisibleColumns(-3, 10);
assertEquals(7, pos);
// 0 returns same position
pos = cs.offsetByVisibleColumns(0, 10);
assertEquals(10, pos);
// test with one set of hidden columns between start and required position
cs.hideColumns(12, 15);
pos = cs.offsetByVisibleColumns(-8, 17);
assertEquals(5, pos);
// test with two sets of hidden columns between start and required position
cs.hideColumns(20, 21);
pos = cs.offsetByVisibleColumns(-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.offsetByVisibleColumns(-8, 17);
assertEquals(5, pos);
// test with two sets of hidden columns between start and required position
cs.hideColumns(20, 21);
pos = cs.offsetByVisibleColumns(-8, 23);
assertEquals(9, pos);
// test with right (positive) offsets
// test that without hidden columns, offsetByVisibleColumns returns
// position n to right of provided position
pos = cs.offsetByVisibleColumns(3, 7);
assertEquals(10, pos);
// test that with hidden columns to left of result column
// behaviour is the same as above
cs.hideColumns(1, 3);
// test with one set of hidden columns between start and required position
cs.hideColumns(12, 15);
pos = cs.offsetByVisibleColumns(8, 5);
assertEquals(17, pos);
// test with two sets of hidden columns between start and required position
cs.hideColumns(20, 21);
pos = cs.offsetByVisibleColumns(8, 9);
assertEquals(23, pos);
// repeat last 2 tests with no hidden columns to left of required position
colsel = new ColumnSelection();
cs.revealAllHiddenColumns(colsel);
// test with one set of hidden columns between start and required position
cs.hideColumns(12, 15);
pos = cs.offsetByVisibleColumns(8, 5);
assertEquals(17, pos);
// test with two sets of hidden columns between start and required position
cs.hideColumns(20, 21);
pos = cs.offsetByVisibleColumns(8, 9);
assertEquals(23, pos);
}
@Test(groups = "Functional")
public void testBoundedIterator()
{
HiddenColumns h = new HiddenColumns();
Iterator 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 it = h.getStartRegionIterator(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.getStartRegionIterator(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.getStartRegionIterator(4, 5);
assertFalse(it.hasNext());
// [start,end] fully contains 1 region and start of last
// - 2 regions returned
it = h.getStartRegionIterator(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.getStartRegionIterator(4, 20);
assertTrue(it.hasNext());
next = it.next();
assertEquals(6, next);
assertFalse(it.hasNext());
}
@Test(groups = "Functional")
public void testVisibleBlocksVisBoundsIterator()
{
HiddenColumns h = new HiddenColumns();
Iterator regions = h.getVisContigsIterator(0, 31, true);
// only 1 visible region spanning 0-30 if nothing is hidden
assertTrue(regions.hasNext());
int[] region = regions.next();
assertEquals(0, region[0]);
assertEquals(30, region[1]);
assertFalse(regions.hasNext());
// hide 1 region in middle
// 2 regions one on either side
// second region boundary accounts for hidden columns
h.hideColumns(10, 15);
regions = h.getVisContigsIterator(0, 31, true);
assertTrue(regions.hasNext());
region = regions.next();
assertEquals(0, region[0]);
assertEquals(9, region[1]);
region = regions.next();
assertEquals(16, region[0]);
assertEquals(36, region[1]);
assertFalse(regions.hasNext());
// single hidden region at left
h = new HiddenColumns();
h.hideColumns(0, 5);
regions = h.getVisContigsIterator(0, 31, true);
assertTrue(regions.hasNext());
region = regions.next();
assertEquals(6, region[0]);
assertEquals(36, region[1]);
assertFalse(regions.hasNext());
// single hidden region at right
h = new HiddenColumns();
h.hideColumns(27, 30);
regions = h.getVisContigsIterator(0, 31, true);
assertTrue(regions.hasNext());
region = regions.next();
assertEquals(0, region[0]);
assertEquals(26, region[1]);
region = regions.next();
assertEquals(31, region[0]);
assertEquals(34, region[1]);
assertFalse(regions.hasNext());
// hidden region at left + hidden region in middle
h = new HiddenColumns();
h.hideColumns(0, 5);
h.hideColumns(23, 25);
regions = h.getVisContigsIterator(0, 31, true);
assertTrue(regions.hasNext());
region = regions.next();
assertEquals(6, region[0]);
assertEquals(22, region[1]);
region = regions.next();
assertEquals(26, region[0]);
assertEquals(39, region[1]);
assertFalse(regions.hasNext());
// hidden region at right + hidden region in middle
h = new HiddenColumns();
h.hideColumns(27, 30);
h.hideColumns(11, 14);
regions = h.getVisContigsIterator(0, 31, true);
assertTrue(regions.hasNext());
region = regions.next();
assertEquals(0, region[0]);
assertEquals(10, region[1]);
region = regions.next();
assertEquals(15, region[0]);
assertEquals(26, region[1]);
region = regions.next();
assertEquals(31, region[0]);
assertEquals(38, region[1]);
assertFalse(regions.hasNext());
// hidden region at left and right
h = new HiddenColumns();
h.hideColumns(27, 35);
h.hideColumns(0, 4);
regions = h.getVisContigsIterator(0, 31, true);
assertTrue(regions.hasNext());
region = regions.next();
assertEquals(5, region[0]);
assertEquals(26, region[1]);
region = regions.next();
assertEquals(36, region[0]);
assertEquals(44, region[1]);
assertFalse(regions.hasNext());
// multiple hidden regions
h = new HiddenColumns();
h.hideColumns(1, 1);
h.hideColumns(3, 5);
h.hideColumns(9, 11);
h.hideColumns(22, 26);
regions = h.getVisContigsIterator(0, 31, true);
assertTrue(regions.hasNext());
region = regions.next();
assertEquals(0, region[0]);
assertEquals(0, region[1]);
region = regions.next();
assertEquals(2, region[0]);
assertEquals(2, region[1]);
region = regions.next();
assertEquals(6, region[0]);
assertEquals(8, region[1]);
region = regions.next();
assertEquals(12, region[0]);
assertEquals(21, region[1]);
region = regions.next();
assertEquals(27, region[0]);
assertEquals(42, region[1]);
assertFalse(regions.hasNext());
}
/*
* the VisibleColsIterator is tested elsewhere, this just tests that
* it can be retrieved from HiddenColumns
*/
@Test(groups = "Functional")
public void testGetVisibleColsIterator()
{
HiddenColumns h = new HiddenColumns();
Iterator it = h.getVisibleColsIterator(0, 10);
assertTrue(it instanceof RangeElementsIterator);
}
@Test(groups = "Functional")
public void testHashCode()
{
HiddenColumns h = new HiddenColumns();
h.hideColumns(0, 25);
int result = h.hashCode();
assertTrue(result > 0);
h.hideColumns(30, 50);
assertTrue(h.hashCode() > 0);
assertTrue(result != h.hashCode());
}
}