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.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(groups = { "Functional" })
{
HiddenColumns cs = new HiddenColumns();
- Iterator<int[]> visible = cs.getVisContigsIterator(3, 10);
+ Iterator<int[]> visible = cs.getVisContigsIterator(3, 10, false);
int[] region = visible.next();
assertEquals("[3, 9]", Arrays.toString(region));
assertFalse(visible.hasNext());
// Test both ends visible region
// start position is inclusive, end position exclusive
- visible = cs.getVisContigsIterator(1, 13);
+ visible = cs.getVisContigsIterator(1, 13, false);
region = visible.next();
assertEquals("[1, 2]", Arrays.toString(region));
region = visible.next();
assertFalse(visible.hasNext());
// Test start hidden, end visible
- visible = cs.getVisContigsIterator(4, 14);
+ visible = cs.getVisContigsIterator(4, 14, false);
region = visible.next();
assertEquals("[7, 7]", Arrays.toString(region));
region = visible.next();
assertFalse(visible.hasNext());
// Test start hidden, end hidden
- visible = cs.getVisContigsIterator(3, 10);
+ 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);
+ visible = cs.getVisContigsIterator(0, 13, false);
region = visible.next();
assertEquals("[0, 2]", Arrays.toString(region));
region = visible.next();
assertFalse(visible.hasNext());
// Test empty result
- visible = cs.getVisContigsIterator(4, 6);
+ visible = cs.getVisContigsIterator(4, 6, false);
assertFalse(visible.hasNext());
}
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);
}
@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.hideList(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));
}
/**
}
@Test(groups = { "Functional" })
- public void testHideBitset()
+ public void testHideColumns_BitSet()
{
HiddenColumns cs;
// 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" })
- public void testMarkHiddenRegions()
+ public void hideColumns_BitSetAndRange()
{
- 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);
- }
+ HiddenColumns hc = new HiddenColumns();
+ hc.hideColumns(3, 5);
+ hc.hideColumns(15, 20);
+ hc.hideColumns(45, 60);
+
+ BitSet tohide = new BitSet();
+
+ // all unhidden if tohide is empty and range covers hidden
+ hc.hideColumns(tohide, 1, 70);
+ assertTrue(!hc.hasHiddenColumns());
+
+ hc.hideColumns(3, 5);
+ hc.hideColumns(15, 20);
+ hc.hideColumns(45, 60);
+
+ // but not if range does not cover hidden
+ hc.hideColumns(tohide, 23, 40);
+ assertTrue(hc.hasHiddenColumns());
+
+ // and partial unhide if range partially covers
+ hc.hideColumns(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());
}
@Test(groups = { "Functional" })
}
@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]);
- }
-
- @Test(groups = "Functional")
- public void testPropagateInsertions()
- {
- // create an alignment with no gaps - this will be the profile seq and other
- // JPRED seqs
- AlignmentGenerator gen = new AlignmentGenerator(false);
- AlignmentI al = gen.generate(25, 10, 1234, 0, 0);
-
- // get the profileseq
- SequenceI profileseq = al.getSequenceAt(0);
- SequenceI gappedseq = new Sequence(profileseq);
- gappedseq.insertCharAt(5, al.getGapCharacter());
- gappedseq.insertCharAt(6, al.getGapCharacter());
- gappedseq.insertCharAt(7, al.getGapCharacter());
- gappedseq.insertCharAt(8, al.getGapCharacter());
-
- // create an alignment view with the gapped sequence
- SequenceI[] seqs = new SequenceI[1];
- seqs[0] = gappedseq;
- AlignmentI newal = new Alignment(seqs);
- HiddenColumns hidden = new HiddenColumns();
- hidden.hideColumns(15, 17);
-
- AlignmentView view = new AlignmentView(newal, hidden, null, true, false,
- false);
-
- // confirm that original contigs are as expected
- Iterator<int[]> visible = hidden.getVisContigsIterator(0, 25);
- 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.getVisContigsIterator(0, 25);
- 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
- assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[10]));
- assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[11]));
- assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[12]));
- assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[13]));
- assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[14]));
-
- }
-
- @Test(groups = "Functional")
- public void testPropagateInsertionsOverlap()
- {
- // test propagateInsertions where gaps and hiddenColumns overlap
-
- // create an alignment with no gaps - this will be the profile seq and other
- // JPRED seqs
- AlignmentGenerator gen = new AlignmentGenerator(false);
- AlignmentI al = gen.generate(20, 10, 1234, 0, 0);
-
- // get the profileseq
- SequenceI profileseq = al.getSequenceAt(0);
- SequenceI gappedseq = new Sequence(profileseq);
- gappedseq.insertCharAt(5, al.getGapCharacter());
- gappedseq.insertCharAt(6, al.getGapCharacter());
- gappedseq.insertCharAt(7, al.getGapCharacter());
- gappedseq.insertCharAt(8, al.getGapCharacter());
-
- // create an alignment view with the gapped sequence
- SequenceI[] seqs = new SequenceI[1];
- seqs[0] = gappedseq;
- AlignmentI newal = new Alignment(seqs);
-
- // hide columns so that some overlap with the gaps
- HiddenColumns hidden = new HiddenColumns();
- hidden.hideColumns(7, 10);
-
- AlignmentView view = new AlignmentView(newal, hidden, null, true, false,
- false);
-
- // confirm that original contigs are as expected
- Iterator<int[]> visible = hidden.getVisContigsIterator(0, 20);
- 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.getVisContigsIterator(0, 20);
- 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
- assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[4]));
- assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[5]));
- assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[6]));
- assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[7]));
+ result = hc.getRegionWithEdgeAtRes(16);
+ assertNull(result);
}
@Test(groups = "Functional")
{
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.hideList(seq2.getInsertions());
assertTrue(h.equals(h2));
- h.hideInsertionsFor(seq1);
+ h.hideList(seq1.getInsertions());
h2.hideColumns(3, 5);
h2.hideColumns(9, 9);
h2.hideColumns(19, 20);
}
@Test(groups = "Functional")
- public void testHideMarkedBits()
+ public void testHideColumns_BitSet_range()
{
HiddenColumns h = new HiddenColumns();
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
+ // when setting bitset, first param is invlusive, second exclusive
tohide.set(3, 6);
tohide.set(9);
- tohide.set(19, 21);
- h.hideMarkedBits(tohide);
+ tohide.set(15, 21);
+ h.hideColumns(tohide, 5, 23);
- h2.hideColumns(3, 5);
+ h2.hideColumns(5, 5);
h2.hideColumns(9, 9);
- h2.hideColumns(19, 20);
+ h2.hideColumns(15, 20);
assertTrue(h.equals(h2));
- }
- @Test(groups = "Functional")
- public void testMakeVisibleAnnotation()
- {
- HiddenColumns h = new HiddenColumns();
- Annotation[] anns = new Annotation[] { null, null, new Annotation(1),
- new Annotation(2), new Annotation(3), null, null, new Annotation(4),
- new Annotation(5), new Annotation(6), new Annotation(7),
- new Annotation(8) };
- AlignmentAnnotation ann = new AlignmentAnnotation("an", "some an",
- anns);
-
- // without hidden cols, just truncates
- h.makeVisibleAnnotation(3, 5, ann);
- assertEquals(3, ann.annotations.length);
- assertEquals(2.0f, ann.annotations[0].value);
- assertEquals(3.0f, ann.annotations[1].value);
- assertNull(ann.annotations[2]);
-
- anns = new Annotation[] { null, null, new Annotation(1),
- new Annotation(2), new Annotation(3), null, null, new Annotation(4),
- new Annotation(5), new Annotation(6), new Annotation(7),
- new Annotation(8) };
- ann = new AlignmentAnnotation("an", "some an", anns);
- h.hideColumns(4, 7);
- h.makeVisibleAnnotation(1, 9, ann);
- assertEquals(5, ann.annotations.length);
- assertNull(ann.annotations[0]);
- assertEquals(1.0f, ann.annotations[1].value);
- assertEquals(2.0f, ann.annotations[2].value);
- assertEquals(5.0f, ann.annotations[3].value);
- assertEquals(6.0f, ann.annotations[4].value);
-
- anns = new Annotation[] { null, null, new Annotation(1),
- new Annotation(2), new Annotation(3), null, null, new Annotation(4),
- new Annotation(5), new Annotation(6), new Annotation(7),
- new Annotation(8) };
- ann = new AlignmentAnnotation("an", "some an", anns);
- h.hideColumns(1, 2);
- h.makeVisibleAnnotation(1, 9, ann);
- assertEquals(3, ann.annotations.length);
- assertEquals(2.0f, ann.annotations[0].value);
- assertEquals(5.0f, ann.annotations[1].value);
- assertEquals(6.0f, ann.annotations[2].value);
+ tohide.clear();
+ tohide.set(41);
+ h.hideColumns(tohide, 23, 30);
+ assertTrue(h.equals(h2));
+
+ tohide.set(41);
+ h.hideColumns(tohide, 30, 45);
+ h2.hideColumns(41, 41);
+ assertTrue(h.equals(h2));
+
+ tohide.clear();
+ tohide.set(25, 28);
+ h.hideColumns(tohide, 17, 50);
+ h2 = new HiddenColumns();
+ h2.hideColumns(17, 20);
+ h2.hideColumns(25, 27);
+ h2.hideColumns(41, 41);
}
@Test(groups = "Functional")
- public void testSubtractVisibleColumns()
+ public void testOffsetByVisibleColumns()
{
HiddenColumns h = new HiddenColumns();
- int result = h.subtractVisibleColumns(1, 10);
+ int result = h.offsetByVisibleColumns(-1, 10);
assertEquals(9, result);
h.hideColumns(7, 9);
- result = h.subtractVisibleColumns(4, 10);
+ result = h.offsetByVisibleColumns(-4, 10);
assertEquals(3, result);
h.hideColumns(14, 15);
- result = h.subtractVisibleColumns(4, 10);
+ result = h.offsetByVisibleColumns(-4, 10);
assertEquals(3, result);
- result = h.subtractVisibleColumns(10, 17);
+ result = h.offsetByVisibleColumns(-10, 17);
assertEquals(2, result);
- result = h.subtractVisibleColumns(1, 7);
+ result = h.offsetByVisibleColumns(-1, 7);
assertEquals(5, result);
- result = h.subtractVisibleColumns(1, 8);
+ result = h.offsetByVisibleColumns(-1, 8);
assertEquals(5, result);
- result = h.subtractVisibleColumns(3, 15);
+ result = h.offsetByVisibleColumns(-3, 15);
assertEquals(10, result);
ColumnSelection sel = new ColumnSelection();
h.revealAllHiddenColumns(sel);
h.hideColumns(0, 30);
- result = h.subtractVisibleColumns(31, 0);
+ result = h.offsetByVisibleColumns(-31, 0);
assertEquals(-31, result);
HiddenColumns cs = new HiddenColumns();
- // test that without hidden columns, findColumnNToLeft returns
+ // test that without hidden columns, offsetByVisibleColumns returns
// position n to left of provided position
- long pos = cs.subtractVisibleColumns(3, 10);
+ long pos = cs.offsetByVisibleColumns(-3, 10);
assertEquals(7, pos);
// 0 returns same position
- pos = cs.subtractVisibleColumns(0, 10);
+ pos = cs.offsetByVisibleColumns(0, 10);
assertEquals(10, pos);
// overflow to left returns negative number
- pos = cs.subtractVisibleColumns(3, 0);
+ pos = cs.offsetByVisibleColumns(-3, 0);
assertEquals(-3, pos);
// test that with hidden columns to left of result column
cs.hideColumns(1, 3);
// position n to left of provided position
- pos = cs.subtractVisibleColumns(3, 10);
+ pos = cs.offsetByVisibleColumns(-3, 10);
assertEquals(7, pos);
// 0 returns same position
- pos = cs.subtractVisibleColumns(0, 10);
+ 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.subtractVisibleColumns(8, 17);
+ 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.subtractVisibleColumns(8, 23);
+ pos = cs.offsetByVisibleColumns(-8, 23);
assertEquals(9, pos);
// repeat last 2 tests with no hidden columns to left of required position
// test with one set of hidden columns between start and required position
cs.hideColumns(12, 15);
- pos = cs.subtractVisibleColumns(8, 17);
+ 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.subtractVisibleColumns(8, 23);
+ 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()
public void testVisibleBlocksVisBoundsIterator()
{
HiddenColumns h = new HiddenColumns();
- Iterator<int[]> regions = h.getVisibleBlocksIterator(0, 30, true);
+ Iterator<int[]> regions = h.getVisContigsIterator(0, 31, true);
// only 1 visible region spanning 0-30 if nothing is hidden
assertTrue(regions.hasNext());
// 2 regions one on either side
// second region boundary accounts for hidden columns
h.hideColumns(10, 15);
- regions = h.getVisibleBlocksIterator(0, 30, true);
+ regions = h.getVisContigsIterator(0, 31, true);
assertTrue(regions.hasNext());
region = regions.next();
// single hidden region at left
h = new HiddenColumns();
h.hideColumns(0, 5);
- regions = h.getVisibleBlocksIterator(0, 30, true);
+ regions = h.getVisContigsIterator(0, 31, true);
assertTrue(regions.hasNext());
region = regions.next();
// single hidden region at right
h = new HiddenColumns();
h.hideColumns(27, 30);
- regions = h.getVisibleBlocksIterator(0, 30, true);
+ regions = h.getVisContigsIterator(0, 31, true);
assertTrue(regions.hasNext());
region = regions.next();
h = new HiddenColumns();
h.hideColumns(0, 5);
h.hideColumns(23, 25);
- regions = h.getVisibleBlocksIterator(0, 30, true);
+ regions = h.getVisContigsIterator(0, 31, true);
assertTrue(regions.hasNext());
region = regions.next();
h = new HiddenColumns();
h.hideColumns(27, 30);
h.hideColumns(11, 14);
- regions = h.getVisibleBlocksIterator(0, 30, true);
+ regions = h.getVisContigsIterator(0, 31, true);
assertTrue(regions.hasNext());
region = regions.next();
h = new HiddenColumns();
h.hideColumns(27, 35);
h.hideColumns(0, 4);
- regions = h.getVisibleBlocksIterator(0, 30, true);
+ regions = h.getVisContigsIterator(0, 31, true);
assertTrue(regions.hasNext());
region = regions.next();
h.hideColumns(9, 11);
h.hideColumns(22, 26);
- regions = h.getVisibleBlocksIterator(0, 30, true);
+ regions = h.getVisContigsIterator(0, 31, true);
assertTrue(regions.hasNext());
region = regions.next();
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