import static org.testng.AssertJUnit.assertTrue;
import jalview.analysis.AlignmentGenerator;
-import jalview.util.Comparison;
import java.util.Arrays;
import java.util.BitSet;
import java.util.Iterator;
-import java.util.Random;
import org.testng.annotations.Test;
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.visibleToAbsoluteColumn(9)));
}
@Test(groups = { "Functional" })
- public void testHideBitset()
+ public void testHideColumns_BitSet()
{
HiddenColumns cs;
}
@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();
-
- 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());
- 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 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());
-
- // 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;
- 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, 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.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
- 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, 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.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
- assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[4]));
- assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[5]));
- assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[6]));
- assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[7]));
- }
-
- @Test(groups = "Functional")
public void testHasHiddenColumns()
{
HiddenColumns h = new HiddenColumns();
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();
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.hideColumns(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);
-
- // 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(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);
-
- 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]);
+ 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()
git://source.jalview.org / jalview.git / blobdiff