import static org.testng.AssertJUnit.assertTrue;
import jalview.analysis.AlignmentGenerator;
-import jalview.gui.JvOptionPane;
import java.util.Arrays;
import java.util.BitSet;
-import java.util.List;
-import java.util.Random;
+import java.util.Iterator;
-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
- int pos = cs.subtractVisibleColumns(3, 10);
- assertEquals(7, pos);
-
- // 0 returns same position
- pos = cs.subtractVisibleColumns(0, 10);
- assertEquals(10, pos);
-
- // overflow to left returns negative number
- pos = cs.subtractVisibleColumns(3, 0);
- assertEquals(-3, pos);
-
- // test that with hidden columns to left of result column
- // behaviour is the same as above
- cs.hideColumns(1, 3);
-
- // position n to left of provided position
- pos = cs.subtractVisibleColumns(3, 10);
- assertEquals(7, pos);
-
- // 0 returns same position
- pos = cs.subtractVisibleColumns(0, 10);
- assertEquals(10, pos);
-
- // test with one set of hidden columns between start and required position
- cs.hideColumns(12, 15);
- pos = cs.subtractVisibleColumns(8, 17);
- assertEquals(5, pos);
-
- // test with two sets of hidden columns between start and required position
- cs.hideColumns(20, 21);
- pos = cs.subtractVisibleColumns(8, 23);
- assertEquals(9, pos);
-
- // repeat last 2 tests with no hidden columns to left of required position
- ColumnSelection colsel = new ColumnSelection();
- cs.revealAllHiddenColumns(colsel);
-
- // test with one set of hidden columns between start and required position
- cs.hideColumns(12, 15);
- pos = cs.subtractVisibleColumns(8, 17);
- assertEquals(5, pos);
-
- // test with two sets of hidden columns between start and required position
- cs.hideColumns(20, 21);
- pos = cs.subtractVisibleColumns(8, 23);
- assertEquals(9, pos);
-
- }
+ Iterator<int[]> visible = cs.getVisContigsIterator(3, 10, false);
+ int[] region = visible.next();
+ assertEquals("[3, 9]", Arrays.toString(region));
+ assertFalse(visible.hasNext());
- @Test(groups = { "Functional" })
- public void testGetVisibleContigs()
- {
- HiddenColumns cs = new HiddenColumns();
cs.hideColumns(3, 6);
cs.hideColumns(8, 9);
cs.hideColumns(12, 12);
- // start position is inclusive, end position exclusive:
- int[] visible = cs.getVisibleContigs(1, 13);
- assertEquals("[1, 2, 7, 7, 10, 11]", Arrays.toString(visible));
-
- visible = cs.getVisibleContigs(4, 14);
- assertEquals("[7, 7, 10, 11, 13, 13]", Arrays.toString(visible));
-
- visible = cs.getVisibleContigs(3, 10);
- assertEquals("[7, 7]", Arrays.toString(visible));
-
- visible = cs.getVisibleContigs(4, 6);
- assertEquals("[]", Arrays.toString(visible));
+ // Test 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" })
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")
HiddenColumns cs = new HiddenColumns();
cs.hideColumns(10, 11);
cs.hideColumns(5, 7);
+ Iterator<int[]> regions = cs.iterator();
assertEquals("[5, 7]",
- Arrays.toString(cs.getHiddenColumnsCopy().get(0)));
+ Arrays.toString(regions.next()));
HiddenColumns cs2 = new HiddenColumns(cs);
+ regions = cs2.iterator();
assertTrue(cs2.hasHiddenColumns());
- assertEquals(2, cs2.getHiddenColumnsCopy().size());
+ assertEquals(2, cs2.getNumberOfRegions());
// hidden columns are held in column order
assertEquals("[5, 7]",
- Arrays.toString(cs2.getHiddenColumnsCopy().get(0)));
+ Arrays.toString(regions.next()));
assertEquals("[10, 11]",
- Arrays.toString(cs2.getHiddenColumnsCopy().get(1)));
+ Arrays.toString(regions.next()));
}
- /**
- * Test the code used to locate the reference sequence ruler origin
- */
- @Test(groups = { "Functional" })
- public void testLocateVisibleBoundsofSequence()
+ @Test(groups = "Functional")
+ public void testCopyConstructor2()
{
- // create random alignment
- AlignmentGenerator gen = new AlignmentGenerator(false);
- AlignmentI al = gen.generate(50, 20, 123, 5, 5);
+ HiddenColumns cs = new HiddenColumns();
+ cs.hideColumns(10, 11);
+ cs.hideColumns(5, 7);
- HiddenColumns cs = al.getHiddenColumns();
- ColumnSelection colsel = new ColumnSelection();
+ HiddenColumns cs2 = new HiddenColumns(cs, 3, 9, 1);
+ assertTrue(cs2.hasHiddenColumns());
+ Iterator<int[]> regions = cs2.iterator();
- SequenceI seq = new Sequence("RefSeq", "-A-SD-ASD--E---");
- assertEquals(2, seq.findIndex(seq.getStart()));
-
- // no hidden columns
- assertEquals(
- Arrays.toString(new int[] { seq.findIndex(seq.getStart()) - 1,
- seq.findIndex(seq.getEnd()) - 1, seq.getStart(),
- seq.getEnd(), seq.findIndex(seq.getStart()) - 1,
- seq.findIndex(seq.getEnd()) - 1 }),
- Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));
-
- // hidden column on gap after end of sequence - should not affect bounds
- colsel.hideSelectedColumns(13, al.getHiddenColumns());
- assertEquals(
- Arrays.toString(new int[] { seq.findIndex(seq.getStart()) - 1,
- seq.findIndex(seq.getEnd()) - 1, seq.getStart(),
- seq.getEnd(), seq.findIndex(seq.getStart()) - 1,
- seq.findIndex(seq.getEnd()) - 1 }),
- Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));
+ // only [5,7] returned, offset by 1
+ assertEquals("[4, 6]",
+ Arrays.toString(regions.next()));
+ assertEquals(3, cs2.getSize());
- cs.revealAllHiddenColumns(colsel);
- // hidden column on gap before beginning of sequence - should vis bounds by
- // one
- colsel.hideSelectedColumns(0, al.getHiddenColumns());
- assertEquals(
- Arrays.toString(new int[] { seq.findIndex(seq.getStart()) - 2,
- seq.findIndex(seq.getEnd()) - 2, seq.getStart(),
- seq.getEnd(), seq.findIndex(seq.getStart()) - 1,
- seq.findIndex(seq.getEnd()) - 1 }),
- Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));
-
- cs.revealAllHiddenColumns(colsel);
- // hide columns around most of sequence - leave one residue remaining
- cs.hideColumns(1, 3);
- cs.hideColumns(6, 11);
- assertEquals("-D",
- cs.getVisibleSequenceStrings(0, 5, new SequenceI[] { seq })[0]);
- assertEquals(
- Arrays.toString(new int[] { 1, 1, 3, 3,
- seq.findIndex(seq.getStart()) - 1,
- seq.findIndex(seq.getEnd()) - 1 }),
- Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));
- cs.revealAllHiddenColumns(colsel);
+ cs2 = new HiddenColumns(cs, 8, 15, 4);
+ regions = cs2.iterator();
+ assertTrue(cs2.hasHiddenColumns());
- // hide whole sequence - should just get location of hidden region
- // containing sequence
- cs.hideColumns(1, 11);
- assertEquals(
- Arrays.toString(new int[] { 0, 1, 0, 0,
- seq.findIndex(seq.getStart()) - 1,
- seq.findIndex(seq.getEnd()) - 1 }),
- Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));
+ // 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 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()
ColumnSelection colsel = new ColumnSelection();
HiddenColumns cs = al.getHiddenColumns();
colsel.hideSelectedColumns(5, al.getHiddenColumns());
- List<int[]> hidden = cs.getHiddenColumnsCopy();
- assertEquals(1, hidden.size());
- assertEquals("[5, 5]", Arrays.toString(hidden.get(0)));
+ Iterator<int[]> regions = cs.iterator();
+ assertEquals(1, cs.getNumberOfRegions());
+ assertEquals("[5, 5]", Arrays.toString(regions.next()));
+ assertEquals(cs.getSize(), 1);
colsel.hideSelectedColumns(3, al.getHiddenColumns());
- hidden = cs.getHiddenColumnsCopy();
- assertEquals(2, hidden.size());
+ regions = cs.iterator();
+ assertEquals(2, cs.getNumberOfRegions());
// 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)));
+ 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());
- hidden = cs.getHiddenColumnsCopy();
- assertEquals(1, hidden.size());
- assertEquals("[3, 5]", Arrays.toString(hidden.get(0)));
+ 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
- assertTrue(cs.getHiddenColumnsCopy().isEmpty());
+ assertEquals(0, cs.getNumberOfRegions());
+ assertEquals(cs.getSize(), 0);
cs.hideColumns(3, 6);
- hidden = cs.getHiddenColumnsCopy();
- int[] firstHiddenRange = hidden.get(0);
+ 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);
- hidden = cs.getHiddenColumnsCopy();
- assertEquals(1, hidden.size());
+ regions = cs.iterator();
+ assertEquals(1, cs.getNumberOfRegions());
assertEquals("[3, 6]",
- Arrays.toString(cs.getHiddenColumnsCopy().get(0)));
+ Arrays.toString(regions.next()));
+ assertEquals(cs.getSize(), 4);
cs.hideColumns(3, 5);
- hidden = cs.getHiddenColumnsCopy();
- assertEquals(1, hidden.size());
+ regions = cs.iterator();
+ assertEquals(1, cs.getNumberOfRegions());
assertEquals("[3, 6]",
- Arrays.toString(cs.getHiddenColumnsCopy().get(0)));
+ Arrays.toString(regions.next()));
+ assertEquals(cs.getSize(), 4);
cs.hideColumns(4, 6);
- hidden = cs.getHiddenColumnsCopy();
- assertEquals(1, hidden.size());
+ regions = cs.iterator();
+ assertEquals(1, cs.getNumberOfRegions());
assertEquals("[3, 6]",
- Arrays.toString(cs.getHiddenColumnsCopy().get(0)));
+ Arrays.toString(regions.next()));
+ assertEquals(cs.getSize(), 4);
cs.hideColumns(3, 6);
- hidden = cs.getHiddenColumnsCopy();
- assertEquals(1, hidden.size());
+ regions = cs.iterator();
+ assertEquals(1, cs.getNumberOfRegions());
assertEquals("[3, 6]",
- Arrays.toString(cs.getHiddenColumnsCopy().get(0)));
+ Arrays.toString(regions.next()));
+ assertEquals(cs.getSize(), 4);
cs.revealAllHiddenColumns(colsel);
cs.hideColumns(2, 4);
- hidden = cs.getHiddenColumnsCopy();
- assertEquals(1, hidden.size());
- assertEquals("[2, 4]", Arrays.toString(hidden.get(0)));
+ 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);
- hidden = cs.getHiddenColumnsCopy();
- assertEquals(1, hidden.size());
- assertEquals("[2, 5]", Arrays.toString(hidden.get(0)));
+ 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);
- hidden = cs.getHiddenColumnsCopy();
- assertEquals(1, hidden.size());
- assertEquals("[2, 6]", Arrays.toString(hidden.get(0)));
+ 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);
- hidden = cs.getHiddenColumnsCopy();
- assertEquals(1, hidden.size());
- assertEquals("[1, 7]", Arrays.toString(hidden.get(0)));
+ 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);
}
/**
{
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);
- // hidden columns list now null but getter returns empty list:
- assertTrue(cs.getHiddenColumnsCopy().isEmpty());
+
+ // 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());
colsel = new ColumnSelection();
cs = new HiddenColumns();
cs.hideColumns(5, 8);
- List<int[]> hidden = cs.getHiddenColumnsCopy();
+
+ int prevSize = cs.getSize();
cs.revealHiddenColumns(6, colsel);
- assertEquals(hidden.size(), cs.getHiddenColumnsCopy().size());
+ 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 cs = new HiddenColumns();
+ HiddenColumns hidden = new HiddenColumns();
ColumnSelection colsel = new ColumnSelection();
- cs.hideColumns(5, 8);
- cs.hideColumns(2, 3);
+
+ // 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);
- cs.revealAllHiddenColumns(colsel);
+ hidden.revealAllHiddenColumns(colsel);
/*
* revealing hidden columns adds them (in order) to the (unordered)
* selection list
*/
- assertTrue(cs.getHiddenColumnsCopy().isEmpty());
- assertEquals("[11, 1, 2, 3, 5, 6, 7, 8]", colsel.getSelected()
- .toString());
+
+ // 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(5));
assertFalse(cs.isVisible(6));
assertFalse(cs.isVisible(7));
+ assertTrue(cs.isVisible(8));
}
/**
HiddenColumns cs = new HiddenColumns();
cs.hideColumns(49, 59);
cs.hideColumns(69, 79);
- List<int[]> hidden = cs.getHiddenColumnsCopy();
- assertEquals(2, hidden.size());
- assertEquals("[49, 59]", Arrays.toString(hidden.get(0)));
- assertEquals("[69, 79]", Arrays.toString(hidden.get(1)));
+ Iterator<int[]> 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);
- hidden = cs.getHiddenColumnsCopy();
- assertEquals(1, hidden.size());
- assertEquals("[48, 80]", Arrays.toString(hidden.get(0)));
+ regions = cs.iterator();
+ assertEquals(1, cs.getNumberOfRegions());
+ assertEquals("[48, 80]", Arrays.toString(regions.next()));
+ assertEquals(33, cs.getSize());
/*
* another...joining hidden ranges
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)));
+ regions = cs.iterator();
+ assertEquals(1, cs.getNumberOfRegions());
+ assertEquals("[10, 60]", Arrays.toString(regions.next()));
+ assertEquals(51, cs.getSize());
/*
* another...left overlap, subsumption, right overlap,
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)));
+ 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 testHideBitset()
+ public void testHideColumns_BitSet()
{
HiddenColumns cs;
// one hidden range
one.set(1);
cs = new HiddenColumns();
- cs.hideMarkedBits(one);
- assertEquals(1, cs.getHiddenColumnsCopy().size());
+ cs.hideColumns(one);
+ assertEquals(1, cs.getNumberOfRegions());
+ assertEquals(1, cs.getSize());
one.set(2);
cs = new HiddenColumns();
- cs.hideMarkedBits(one);
- assertEquals(1, cs.getHiddenColumnsCopy().size());
+ cs.hideColumns(one);
+ assertEquals(1, cs.getNumberOfRegions());
+ assertEquals(2, cs.getSize());
one.set(3);
cs = new HiddenColumns();
- cs.hideMarkedBits(one);
- assertEquals(1, cs.getHiddenColumnsCopy().size());
+ cs.hideColumns(one);
+ assertEquals(1, cs.getNumberOfRegions());
+ assertEquals(3, cs.getSize());
// split
one.clear(2);
cs = new HiddenColumns();
- cs.hideMarkedBits(one);
- assertEquals(2, cs.getHiddenColumnsCopy().size());
+ cs.hideColumns(one);
+ assertEquals(2, cs.getNumberOfRegions());
+ assertEquals(2, cs.getSize());
- 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.getSize());
- assertEquals(1, cs.getHiddenColumnsCopy().size());
+ assertEquals(1, cs.getNumberOfRegions());
- assertEquals(0, cs.adjustForHiddenColumns(0));
- assertEquals(1, cs.adjustForHiddenColumns(1));
- assertEquals(2, cs.adjustForHiddenColumns(2));
- assertEquals(4, cs.adjustForHiddenColumns(3));
- }
-
- @Test(groups = { "Functional" })
- public void testGetBitset()
- {
- BitSet toMark, fromMark;
- long seed = -3241532;
- Random number = new Random(seed);
- for (int n = 0; n < 1000; n++)
- {
- // create a random bitfield
- toMark = BitSet.valueOf(new long[] { number.nextLong(),
- number.nextLong(), number.nextLong() });
- toMark.set(n * number.nextInt(10), n * (25 + number.nextInt(25)));
- HiddenColumns hc = new HiddenColumns();
- hc.hideMarkedBits(toMark);
-
- // see if we can recover bitfield
- hc.markHiddenRegions(fromMark = new BitSet());
- assertEquals(toMark, fromMark);
- }
- }
-
- @Test(groups = { "Functional" })
- public void testFindHiddenRegionPositions()
- {
- HiddenColumns hc = new HiddenColumns();
-
- List<Integer> 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());
+ assertEquals(0, cs.visibleToAbsoluteColumn(0));
+ assertEquals(1, cs.visibleToAbsoluteColumn(1));
+ assertEquals(2, cs.visibleToAbsoluteColumn(2));
+ assertEquals(4, cs.visibleToAbsoluteColumn(3));
}
@Test(groups = { "Functional" })
}
@Test(groups = "Functional")
- public void getVisibleStartAndEndIndexTest()
+ 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")
hc.hideColumns(10, 10);
hc.hideColumns(14, 15);
- result = hc.getRegionWithEdgeAtRes(3);
+ 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 testPropagateInsertions()
+ public void testHasHiddenColumns()
{
- // 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);
- 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, 20);
- int[] testcontigs = { 0, 14, 18, 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] = 10;
- testcontigs[2] = 14;
- assertTrue(Arrays.equals(newcontigs, testcontigs));
-
+ 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<int[]> result = h.iterator();
+ assertFalse(result.hasNext());
+
+ h.hideColumns(5, 10);
+ result = h.iterator();
+ int[] next = result.next();
+ assertEquals(5, next[0]);
+ assertEquals(10, next[1]);
+ assertFalse(result.hasNext());
+
+ h.hideColumns(22, 23);
+ result = h.iterator();
+ next = result.next();
+ assertEquals(5, next[0]);
+ assertEquals(10, next[1]);
+ next = result.next();
+ assertEquals(22, next[0]);
+ assertEquals(23, next[1]);
+ assertFalse(result.hasNext());
+
+ // test for only one hidden region at start of alignment
+ ColumnSelection sel = new ColumnSelection();
+ h.revealAllHiddenColumns(sel);
+ h.hideColumns(0, 1);
+ result = h.iterator();
+ next = result.next();
+ assertEquals(0, next[0]);
+ assertEquals(1, next[1]);
+ assertFalse(result.hasNext());
+ }
+
+ /* @Test(groups = "Functional")
+ public void testGetVisibleSequenceStrings()
+ {
+ HiddenColumns h = new HiddenColumns();
+ SequenceI seq1 = new Sequence("TEST1", "GALMFWKQESPVICYHRNDT");
+ SequenceI seq2 = new Sequence("TEST2", "VICYHRNDTGA");
+ SequenceI[] seqs = new SequenceI[2];
+ seqs[0] = seq1;
+ seqs[1] = seq2;
+ String[] result = h.getVisibleSequenceStrings(5, 10, seqs);
+ assertEquals(2, result.length);
+ assertEquals("WKQES", result[0]);
+ assertEquals("RNDTG", result[1]);
+
+ h.hideColumns(6, 8);
+ result = h.getVisibleSequenceStrings(5, 10, seqs);
+ assertEquals(2, result.length);
+ assertEquals("WS", result[0]);
+ assertEquals("RG", result[1]);
+
+ SequenceI seq = new Sequence("RefSeq", "-A-SD-ASD--E---");
+ ColumnSelection sel = new ColumnSelection();
+ h.revealAllHiddenColumns(sel);
+ h.hideColumns(1, 3);
+ h.hideColumns(6, 11);
+ assertEquals("-D",
+ h.getVisibleSequenceStrings(0, 5, new SequenceI[]
+ { seq })[0]);
+ }*/
+
+ @Test(groups = "Functional")
+ public void testHideInsertionsFor()
+ {
+ HiddenColumns h = new HiddenColumns();
+ HiddenColumns h2 = new HiddenColumns();
+ SequenceI seq1 = new Sequence("TEST1", "GAL---MFW-KQESPVICY--HRNDT");
+ SequenceI seq2 = new Sequence("TEST1", "GALMFWKQESPVICYHRNDT");
+
+ h.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<int[]> 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<int[]> it = h.getBoundedIterator(0, 10);
+
+ // no hidden columns = nothing to iterate over
+ assertFalse(it.hasNext());
+
+ // [start,end] contains all hidden columns
+ // all regions are returned
+ h.hideColumns(3, 10);
+ h.hideColumns(14, 16);
+ it = h.getBoundedIterator(0, 20);
+ assertTrue(it.hasNext());
+ int[] next = it.next();
+ assertEquals(3, next[0]);
+ assertEquals(10, next[1]);
+ next = it.next();
+ assertEquals(14, next[0]);
+ assertEquals(16, next[1]);
+ assertFalse(it.hasNext());
+
+ // [start,end] overlaps a region
+ // 1 region returned
+ it = h.getBoundedIterator(5, 7);
+ assertTrue(it.hasNext());
+ next = it.next();
+ assertEquals(3, next[0]);
+ assertEquals(10, next[1]);
+ assertFalse(it.hasNext());
+
+ // [start,end] fully contains 1 region and start of last
+ // - 2 regions returned
+ it = h.getBoundedIterator(3, 15);
+ assertTrue(it.hasNext());
+ next = it.next();
+ assertEquals(3, next[0]);
+ assertEquals(10, next[1]);
+ next = it.next();
+ assertEquals(14, next[0]);
+ assertEquals(16, next[1]);
+ assertFalse(it.hasNext());
+
+ // [start,end] contains end of first region and whole of last region
+ // - 2 regions returned
+ it = h.getBoundedIterator(4, 20);
+ assertTrue(it.hasNext());
+ next = it.next();
+ assertEquals(3, next[0]);
+ assertEquals(10, next[1]);
+ next = it.next();
+ assertEquals(14, next[0]);
+ assertEquals(16, next[1]);
+ assertFalse(it.hasNext());
+ }
+
+ @Test(groups = "Functional")
+ public void testBoundedStartIterator()
+ {
+ HiddenColumns h = new HiddenColumns();
+ Iterator<Integer> it = h.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<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);
+ 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<Integer> 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());
}
}
git://source.jalview.org / jalview.git / blobdiff