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.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
*/
public void testFindColumnPosition()
{
HiddenColumns cs = new HiddenColumns();
- assertEquals(5, cs.findColumnPosition(5));
+ assertEquals(5, cs.absoluteToVisibleColumn(5));
// hiding column 6 makes no difference
cs.hideColumns(6, 6);
- assertEquals(5, cs.findColumnPosition(5));
+ assertEquals(5, cs.absoluteToVisibleColumn(5));
// hiding column 4 moves column 5 to column 4
cs.hideColumns(4, 4);
- assertEquals(4, cs.findColumnPosition(5));
+ assertEquals(4, cs.absoluteToVisibleColumn(5));
// hiding column 4 moves column 4 to position 3
- assertEquals(3, cs.findColumnPosition(4));
+ assertEquals(3, cs.absoluteToVisibleColumn(4));
// hiding columns 1 and 2 moves column 5 to column 2
cs.hideColumns(1, 2);
- assertEquals(2, cs.findColumnPosition(5));
+ assertEquals(2, cs.absoluteToVisibleColumn(5));
// check with > 1 hidden column regions
// where some columns are in the hidden regions
cs2.hideColumns(40, 44);
// hiding columns 5-10 and 20-27 moves column 8 to column 4
- assertEquals(4, cs2.findColumnPosition(8));
+ assertEquals(4, cs2.absoluteToVisibleColumn(8));
// and moves column 24 to 13
- assertEquals(13, cs2.findColumnPosition(24));
+ assertEquals(13, cs2.absoluteToVisibleColumn(24));
// and moves column 28 to 14
- assertEquals(14, cs2.findColumnPosition(28));
+ assertEquals(14, cs2.absoluteToVisibleColumn(28));
// and moves column 40 to 25
- assertEquals(25, cs2.findColumnPosition(40));
+ 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.findColumnPosition(2));
+ assertEquals(0, cs3.absoluteToVisibleColumn(2));
+ // check that column after the last hidden region doesn't crash
+ assertEquals(46, cs2.absoluteToVisibleColumn(65));
}
- /**
- * Test the method that finds the visible column position a given distance
- * before another column
- */
@Test(groups = { "Functional" })
- public void testFindColumnNToLeft()
+ public void testVisibleContigsIterator()
{
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();
-
- List<int[]> visible = cs.getVisibleContigs(3, 10);
- assertEquals("[3, 9]", Arrays.toString(visible.get(0)));
+ Iterator<int[]> 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);
// Test both ends visible region
// start position is inclusive, end position exclusive
- visible = cs.getVisibleContigs(1, 13);
- assertEquals("[1, 2]", Arrays.toString(visible.get(0)));
- assertEquals("[7, 7]", Arrays.toString(visible.get(1)));
- assertEquals("[10, 11]", Arrays.toString(visible.get(2)));
+ 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.getVisibleContigs(4, 14);
- assertEquals("[7, 7]", Arrays.toString(visible.get(0)));
- assertEquals("[10, 11]", Arrays.toString(visible.get(1)));
- assertEquals("[13, 13]", Arrays.toString(visible.get(2)));
+ 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.getVisibleContigs(3, 10);
- assertEquals("[7, 7]", Arrays.toString(visible.get(0)));
+ 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.getVisibleContigs(0, 13);
- assertEquals("[0, 2]", Arrays.toString(visible.get(0)));
- assertEquals("[7, 7]", Arrays.toString(visible.get(1)));
- assertEquals("[10, 11]", Arrays.toString(visible.get(2)));
+ 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.getVisibleContigs(4, 6);
- assertEquals(0, visible.size());
+ visible = cs.getVisContigsIterator(4, 6, false);
+ assertFalse(visible.hasNext());
}
@Test(groups = { "Functional" })
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")
* Test the code used to locate the reference sequence ruler origin
*/
@Test(groups = { "Functional" })
- public void testLocateVisibleBoundsofSequence()
+ public void testLocateVisibleStartofSequence()
{
// create random alignment
AlignmentGenerator gen = new AlignmentGenerator(false);
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)));
+ assertEquals(seq.findIndex(seq.getStart()) - 1, cs.locateVisibleStartOfSequence(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)));
+ assertEquals(seq.findIndex(seq.getStart()) - 1,cs.locateVisibleStartOfSequence(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)));
+ assertEquals(seq.findIndex(seq.getStart()) - 2,cs.locateVisibleStartOfSequence(seq));
cs.revealAllHiddenColumns(colsel);
// hide columns around most of sequence - leave one residue remaining
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)));
+ assertEquals(1, cs.locateVisibleStartOfSequence(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)));
+ assertEquals(0,cs.locateVisibleStartOfSequence(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)));
+ assertEquals(0,cs.locateVisibleStartOfSequence(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)));
+ assertEquals(0,cs.locateVisibleStartOfSequence(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)));
+ assertEquals(0,cs.locateVisibleStartOfSequence(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)));
+ assertEquals(0,cs.locateVisibleStartOfSequence(seq2));
cs.revealAllHiddenColumns(colsel);
cs.hideColumns(0, 0);
- int[] test = cs.locateVisibleBoundsOfSequence(seq);
- assertEquals(Arrays.toString(new int[] { 0, 1, 11 }),
- Arrays.toString(test));
+ assertEquals(0,cs.locateVisibleStartOfSequence(seq));
cs.revealAllHiddenColumns(colsel);
cs.hideColumns(0, 1);
- test = cs.locateVisibleBoundsOfSequence(seq);
- assertEquals(Arrays.toString(new int[] { 1, 1, 11 }),
- Arrays.toString(test));
+ assertEquals(1,cs.locateVisibleStartOfSequence(seq));
cs.revealAllHiddenColumns(colsel);
cs.hideColumns(0, 2);
- test = cs.locateVisibleBoundsOfSequence(seq);
- assertEquals(Arrays.toString(new int[] { 0, 1, 11 }),
- Arrays.toString(test));
+ assertEquals(0,cs.locateVisibleStartOfSequence(seq));
cs.revealAllHiddenColumns(colsel);
cs.hideColumns(1, 1);
- test = cs.locateVisibleBoundsOfSequence(seq);
- assertEquals(Arrays.toString(new int[] { 2, 1, 11 }),
- Arrays.toString(test));
+ assertEquals(2,cs.locateVisibleStartOfSequence(seq));
cs.revealAllHiddenColumns(colsel);
cs.hideColumns(1, 2);
- test = cs.locateVisibleBoundsOfSequence(seq);
- assertEquals(Arrays.toString(new int[] { 1, 1, 11 }),
- Arrays.toString(test));
+ assertEquals(1,cs.locateVisibleStartOfSequence(seq));
cs.revealAllHiddenColumns(colsel);
cs.hideColumns(1, 3);
- test = cs.locateVisibleBoundsOfSequence(seq);
- assertEquals(Arrays.toString(new int[] { 1, 1, 11 }),
- Arrays.toString(test));
+ assertEquals(1,cs.locateVisibleStartOfSequence(seq));
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));
+ assertEquals(0,cs.locateVisibleStartOfSequence(seq));
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));
+ assertEquals(0,cs.locateVisibleStartOfSequence(seq));
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));
+ assertEquals(0,cs.locateVisibleStartOfSequence(seq));
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));
+ assertEquals(1,cs.locateVisibleStartOfSequence(seq));
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));
+ assertEquals(1,cs.locateVisibleStartOfSequence(seq));
cs.revealAllHiddenColumns(colsel);
cs.hideColumns(1, 11);
- test = cs.locateVisibleBoundsOfSequence(seq);
- assertEquals(Arrays.toString(new int[] { 0, 1, 11 }),
- Arrays.toString(test));
+ assertEquals(0,cs.locateVisibleStartOfSequence(seq));
cs.revealAllHiddenColumns(colsel);
cs.hideColumns(0, 12);
- test = cs.locateVisibleBoundsOfSequence(seq);
- assertEquals(Arrays.toString(new int[] { 0, 1, 11 }),
- Arrays.toString(test));
+ assertEquals(0,cs.locateVisibleStartOfSequence(seq));
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));
+ assertEquals(0,cs.locateVisibleStartOfSequence(seq));
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));
+ assertEquals(0,cs.locateVisibleStartOfSequence(seq));
- // 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)));
+ assertEquals(3,cs.locateVisibleStartOfSequence(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)));
+ assertEquals(9,cs.locateVisibleStartOfSequence(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));
+ assertEquals(6, cs.locateVisibleStartOfSequence(seq));
}
@Test(groups = { "Functional" })
- public void testLocateVisibleBoundsPathologicals()
+ public void testLocateVisibleStartPathologicals()
{
// 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));
+ cs.hideInsertionsFor(al.getSequenceAt(0).getInsertions());
assertEquals("G", ""
- + al.getSequenceAt(0).getCharAt(cs.adjustForHiddenColumns(9)));
+ + al.getSequenceAt(0).getCharAt(cs.visibleToAbsoluteColumn(9)));
+ // KM: no idea what this is meant to be testing... seems to be an unfinished
+ // test
}
@Test(groups = { "Functional" })
regions = cs.iterator();
assertEquals(1, cs.getNumberOfRegions());
assertEquals("[1, 7]", Arrays.toString(regions.next()));
+
+ 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()));
}
/**
{
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);
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" })
{
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);
assertTrue(cs.isVisible(5));
assertFalse(cs.isVisible(6));
assertFalse(cs.isVisible(7));
+ assertTrue(cs.isVisible(8));
}
/**
// one hidden range
one.set(1);
cs = new HiddenColumns();
- cs.hideMarkedBits(one);
+ cs.hideColumns(one);
assertEquals(1, cs.getNumberOfRegions());
one.set(2);
cs = new HiddenColumns();
- cs.hideMarkedBits(one);
+ cs.hideColumns(one);
assertEquals(1, cs.getNumberOfRegions());
one.set(3);
cs = new HiddenColumns();
- cs.hideMarkedBits(one);
+ cs.hideColumns(one);
assertEquals(1, cs.getNumberOfRegions());
// split
one.clear(2);
cs = new HiddenColumns();
- cs.hideMarkedBits(one);
+ cs.hideColumns(one);
assertEquals(2, cs.getNumberOfRegions());
- assertEquals(0, cs.adjustForHiddenColumns(0));
- assertEquals(2, cs.adjustForHiddenColumns(1));
- assertEquals(4, cs.adjustForHiddenColumns(2));
+ assertEquals(0, cs.visibleToAbsoluteColumn(0));
+ assertEquals(2, cs.visibleToAbsoluteColumn(1));
+ assertEquals(4, cs.visibleToAbsoluteColumn(2));
// one again
one.clear(1);
cs = new HiddenColumns();
- cs.hideMarkedBits(one);
+ cs.hideColumns(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));
+ assertEquals(0, cs.visibleToAbsoluteColumn(0));
+ assertEquals(1, cs.visibleToAbsoluteColumn(1));
+ assertEquals(2, cs.visibleToAbsoluteColumn(2));
+ assertEquals(4, cs.visibleToAbsoluteColumn(3));
}
@Test(groups = { "Functional" })
{ number.nextLong(), number.nextLong(), number.nextLong() });
toMark.set(n * number.nextInt(10), n * (25 + number.nextInt(25)));
HiddenColumns hc = new HiddenColumns();
- hc.hideMarkedBits(toMark);
+
+ if (n == 0)
+ {
+ hc.markHiddenRegions(fromMark = new BitSet());
+ assertTrue(fromMark.isEmpty());
+ }
+
+ hc.hideColumns(toMark);
// see if we can recover bitfield
hc.markHiddenRegions(fromMark = new BitSet());
}
@Test(groups = { "Functional" })
- public void testFindHiddenRegionPositions()
- {
- HiddenColumns hc = new HiddenColumns();
-
- List<Integer> positions = hc.findHiddenRegionPositions(0, 20);
- assertTrue(positions.isEmpty());
-
- hc.hideColumns(3, 7);
- hc.hideColumns(10, 10);
- hc.hideColumns(14, 15);
-
- positions = hc.findHiddenRegionPositions(0, 20);
- assertEquals(3, positions.size());
- assertEquals(3, positions.get(0).intValue());
- assertEquals(5, positions.get(1).intValue());
- assertEquals(8, positions.get(2).intValue());
-
- positions = hc.findHiddenRegionPositions(7, 20);
- assertEquals(2, positions.size());
- assertEquals(5, positions.get(0).intValue());
- assertEquals(8, positions.get(1).intValue());
-
- positions = hc.findHiddenRegionPositions(11, 13);
- assertEquals(0, positions.size());
-
- positions = hc.findHiddenRegionPositions(7, 20);
- assertEquals(2, positions.size());
- assertEquals(5, positions.get(0).intValue());
- assertEquals(8, positions.get(1).intValue());
-
- positions = hc.findHiddenRegionPositions(0, 1);
- assertEquals(0, positions.size());
-
- positions = hc.findHiddenRegionPositions(17, 20);
- assertEquals(0, positions.size());
-
- positions = hc.findHiddenRegionPositions(10, 15);
- assertEquals(2, positions.size());
- assertEquals(5, positions.get(0).intValue());
- assertEquals(8, positions.get(1).intValue());
- }
-
- @Test(groups = { "Functional" })
public void testRegionsToString()
{
HiddenColumns hc = new HiddenColumns();
}
@Test(groups = "Functional")
- public void testGetVisibleStartAndEndIndexTest()
+ public void testGetVisibleStartAndEndIndex()
{
Sequence seq = new Sequence("testSeq", "ABCDEFGHIJKLMNOPQRSTUVWXYZ");
AlignmentI align = new Alignment(new SequenceI[] { seq });
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")
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(8);
assertEquals(14, result[0]);
assertEquals(15, result[1]);
+
+ result = hc.getRegionWithEdgeAtRes(16);
+ assertNull(result);
}
@Test(groups = "Functional")
gappedseq.insertCharAt(7, al.getGapCharacter());
gappedseq.insertCharAt(8, al.getGapCharacter());
+ // force different kinds of padding
+ al.getSequenceAt(3).deleteChars(2, 23);
+ al.getSequenceAt(4).deleteChars(2, 27);
+ al.getSequenceAt(5).deleteChars(10, 27);
+
// create an alignment view with the gapped sequence
SequenceI[] seqs = new SequenceI[1];
seqs[0] = gappedseq;
false);
// confirm that original contigs are as expected
- List<int[]> visible = hidden.getVisibleContigs(0, 25);
- assertEquals("[0, 14]", Arrays.toString(visible.get(0)));
- assertEquals("[18, 24]", Arrays.toString(visible.get(1)));
+ Iterator<int[]> visible = hidden.getVisContigsIterator(0, 25, false);
+ 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.getVisibleContigs(0, 25);
- assertEquals("[0, 10]", Arrays.toString(visible.get(0)));
- assertEquals("[14, 24]", Arrays.toString(visible.get(1)));
+ visible = result.getVisContigsIterator(0, 25, false);
+ 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
false);
// confirm that original contigs are as expected
- List<int[]> visible = hidden.getVisibleContigs(0, 20);
- assertEquals("[0, 6]", Arrays.toString(visible.get(0)));
- assertEquals("[11, 19]", Arrays.toString(visible.get(1)));
+ Iterator<int[]> visible = hidden.getVisContigsIterator(0, 20, false);
+ 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.getVisibleContigs(0, 20);
- assertEquals("[0, 4]", Arrays.toString(visible.get(0)));
- assertEquals("[7, 19]", Arrays.toString(visible.get(1)));
+ visible = result.getVisContigsIterator(0, 20, false);
+ 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
{
HiddenColumns h = new HiddenColumns();
- // new HiddenColumns2 has no hidden cols
- assertFalse(h.hasManyHiddenColumns());
+ // h has no hidden cols
+ assertFalse(h.hasMultiHiddenColumnRegions());
// one set of columns hidden, returns false
h.hideColumns(5, 10);
- assertFalse(h.hasManyHiddenColumns());
+ assertFalse(h.hasMultiHiddenColumnRegions());
// two sets hidden, returns true
h.hideColumns(15, 17);
- assertTrue(h.hasManyHiddenColumns());
+ assertTrue(h.hasMultiHiddenColumnRegions());
// back to one block, asserts false
h.hideColumns(11, 14);
- assertFalse(h.hasManyHiddenColumns());
+ assertFalse(h.hasMultiHiddenColumnRegions());
}
@Test(groups = "Functional")
{
HiddenColumns h = new HiddenColumns();
// returns input value when there are no hidden columns
- assertEquals(10, h.adjustForHiddenColumns(10));
+ assertEquals(10, h.visibleToAbsoluteColumn(10));
h.hideColumns(20, 30);
- assertEquals(10, h.adjustForHiddenColumns(10));
- assertEquals(20 + 11, h.adjustForHiddenColumns(20));
- assertEquals(35 + 11, h.adjustForHiddenColumns(35));
+ 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.adjustForHiddenColumns(10));
- assertEquals(20 + 14, h.adjustForHiddenColumns(20));
- assertEquals(35 + 14, h.adjustForHiddenColumns(35));
+ 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.adjustForHiddenColumns(2));
+ assertEquals(4, h.visibleToAbsoluteColumn(2));
}
@Test(groups = "Functional")
h.hideColumns(15, 20);
assertEquals(15, h.getHiddenBoundaryRight(7));
assertEquals(15, h.getHiddenBoundaryRight(14));
+
+ // returns same value if there is no next hidden column
+ assertEquals(22, h.getHiddenBoundaryRight(22));
}
@Test(groups = "Functional")
SequenceI seq1 = new Sequence("TEST1", "GAL---MFW-KQESPVICY--HRNDT");
SequenceI seq2 = new Sequence("TEST1", "GALMFWKQESPVICYHRNDT");
- h.hideInsertionsFor(seq2);
+ h.hideInsertionsFor(seq2.getInsertions());
assertTrue(h.equals(h2));
- h.hideInsertionsFor(seq1);
+ h.hideInsertionsFor(seq1.getInsertions());
h2.hideColumns(3, 5);
h2.hideColumns(9, 9);
h2.hideColumns(19, 20);
HiddenColumns h2 = new HiddenColumns();
BitSet tohide = new BitSet(21);
- h.hideMarkedBits(tohide);
+ h.hideColumns(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);
+ h.hideColumns(tohide);
h2.hideColumns(3, 5);
h2.hideColumns(9, 9);
AlignmentAnnotation ann = new AlignmentAnnotation("an", "some an",
anns);
+ // null annotation
+ AlignmentAnnotation nullann = null;
+ h.makeVisibleAnnotation(nullann);
+ assertNull(nullann);
+
+ h.makeVisibleAnnotation(1, 2, nullann);
+ assertNull(nullann);
+
+ // null annotations
+ AlignmentAnnotation emptyann = new AlignmentAnnotation("an", "some ann", null);
+ h.makeVisibleAnnotation(emptyann);
+ assertNull(emptyann.annotations);
+
+ h.makeVisibleAnnotation(3, 4, emptyann);
+ assertNull(emptyann.annotations);
+
+ // without bounds, does everything
+ h.makeVisibleAnnotation(ann);
+ assertEquals(12, ann.annotations.length);
+ assertNull(ann.annotations[0]);
+ assertNull(ann.annotations[1]);
+ assertEquals(1.0f, ann.annotations[2].value);
+ assertEquals(2.0f, ann.annotations[3].value);
+ assertEquals(3.0f, ann.annotations[4].value);
+ assertNull(ann.annotations[5]);
+ assertNull(ann.annotations[6]);
+ assertEquals(4.0f, ann.annotations[7].value);
+ assertEquals(5.0f, ann.annotations[8].value);
+ assertEquals(6.0f, ann.annotations[9].value);
+ assertEquals(7.0f, ann.annotations[10].value);
+ assertEquals(8.0f, ann.annotations[11].value);
+
// without hidden cols, just truncates
h.makeVisibleAnnotation(3, 5, 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);
+
+ 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), new Annotation(9), new Annotation(10),
+ new Annotation(11), new Annotation(12), new Annotation(13),
+ new Annotation(14), new Annotation(15) };
+ ann = new AlignmentAnnotation("an", "some an", anns);
+ h = new HiddenColumns();
+ h.hideColumns(5, 18);
+ h.hideColumns(20, 21);
+ h.makeVisibleAnnotation(1, 21, ann);
+ assertEquals(5, ann.annotations.length);
+ assertEquals(1.0f, ann.annotations[1].value);
+ assertEquals(2.0f, ann.annotations[2].value);
+ assertEquals(3.0f, ann.annotations[3].value);
+ assertNull(ann.annotations[0]);
+ assertNull(ann.annotations[4]);
}
@Test(groups = "Functional")
h.hideColumns(0, 30);
result = h.subtractVisibleColumns(31, 0);
assertEquals(-31, result);
+
+ 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 testBoundedIterator()
{
HiddenColumns h = new HiddenColumns();
- Iterator<int[]> it = h.getBoundedIterator(0, 10, false);
+ Iterator<int[]> it = h.getBoundedIterator(0, 10);
// no hidden columns = nothing to iterate over
assertFalse(it.hasNext());
// all regions are returned
h.hideColumns(3, 10);
h.hideColumns(14, 16);
- it = h.getBoundedIterator(0, 20, false);
+ it = h.getBoundedIterator(0, 20);
assertTrue(it.hasNext());
int[] next = it.next();
assertEquals(3, next[0]);
// [start,end] overlaps a region
// 1 region returned
- it = h.getBoundedIterator(5, 7, false);
+ it = h.getBoundedIterator(5, 7);
assertTrue(it.hasNext());
next = it.next();
assertEquals(3, next[0]);
// [start,end] fully contains 1 region and start of last
// - 2 regions returned
- it = h.getBoundedIterator(3, 15, false);
+ it = h.getBoundedIterator(3, 15);
assertTrue(it.hasNext());
next = it.next();
assertEquals(3, next[0]);
// [start,end] contains end of first region and whole of last region
// - 2 regions returned
- it = h.getBoundedIterator(4, 20, false);
+ it = h.getBoundedIterator(4, 20);
assertTrue(it.hasNext());
next = it.next();
assertEquals(3, next[0]);
public void testBoundedStartIterator()
{
HiddenColumns h = new HiddenColumns();
- Iterator<Integer> it = h.getBoundedStartIterator(0, 10, false);
+ Iterator<Integer> it = h.getBoundedStartIterator(0, 10);
// no hidden columns = nothing to iterate over
assertFalse(it.hasNext());
// all regions are returned
h.hideColumns(3, 10);
h.hideColumns(14, 16);
- it = h.getBoundedStartIterator(0, 20, false);
+ it = h.getBoundedStartIterator(0, 20);
assertTrue(it.hasNext());
int next = it.next();
assertEquals(3, next);
// [start,end] does not contain a start of a region
// no regions to iterate over
- it = h.getBoundedStartIterator(4, 5, false);
+ 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, false);
+ it = h.getBoundedStartIterator(3, 7);
assertTrue(it.hasNext());
next = it.next();
assertEquals(3, next);
// [start,end] contains whole of last region
// - 1 region returned
- it = h.getBoundedStartIterator(4, 20, false);
+ it = h.getBoundedStartIterator(4, 20);
assertTrue(it.hasNext());
next = it.next();
assertEquals(6, next);
}
@Test(groups = "Functional")
- public void testVisRegionsIterator()
+ public void testVisibleBlocksVisBoundsIterator()
{
HiddenColumns h = new HiddenColumns();
- Iterator<int[]> it = h.getBoundedVisRegionIterator(0, 15);
-
- // no hidden columns = single visible contig
- assertTrue(it.hasNext());
- assertEquals("[0, 15]", Arrays.toString(it.next()));
-
- // hidden column region at start
+ Iterator<int[]> 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);
- it = h.getBoundedVisRegionIterator(0, 15);
- assertTrue(it.hasNext());
- assertEquals("[6, 15]", Arrays.toString(it.next()));
+ regions = h.getVisContigsIterator(0, 31, true);
- // hidden column region at end
- h = new HiddenColumns();
- h.hideColumns(8, 15);
- it = h.getBoundedVisRegionIterator(0, 15);
- assertTrue(it.hasNext());
- assertEquals("[0, 7]", Arrays.toString(it.next()));
+ assertTrue(regions.hasNext());
+ region = regions.next();
+ assertEquals(6, region[0]);
+ assertEquals(36, region[1]);
+ assertFalse(regions.hasNext());
- // hidden column region across whole region
+ // single hidden region at right
h = new HiddenColumns();
- h.hideColumns(0, 20);
- it = h.getBoundedVisRegionIterator(0, 15);
- assertFalse(it.hasNext());
-
- // hidden column region in middle
+ 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(1, 14);
- it = h.getBoundedVisRegionIterator(0, 15);
- assertTrue(it.hasNext());
- assertEquals("[0, 0]", Arrays.toString(it.next()));
- assertTrue(it.hasNext());
- assertEquals("[15, 15]", Arrays.toString(it.next()));
-
- // hidden column region just off either end
+ 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(3, 14);
- it = h.getBoundedVisRegionIterator(4, 13);
- assertFalse(it.hasNext());
-
- // multiple regions
+ 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(7, 11);
- h.hideColumns(14, 19);
- h.hideColumns(24, 25);
- h.hideColumns(35, 39);
- it = h.getBoundedVisRegionIterator(8, 26);
- assertTrue(it.hasNext());
- assertEquals("[12, 13]", Arrays.toString(it.next()));
- assertTrue(it.hasNext());
- assertEquals("[20, 23]", Arrays.toString(it.next()));
- assertTrue(it.hasNext());
- assertEquals("[26, 26]", Arrays.toString(it.next()));
- assertFalse(it.hasNext());
+ 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<Integer> it = h.getVisibleColsIterator(0, 10);
+
+ assertTrue(it instanceof VisibleColsIterator);
+ }
+
+ @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());
}
}
git://source.jalview.org / jalview.git / blobdiff