assertFalse(cs2.hasHiddenColumns());
}
- /**
- * Test the code used to locate the reference sequence ruler origin
- */
- @Test(groups = { "Functional" })
- public void testLocateVisibleStartofSequence()
- {
- // create random alignment
- AlignmentGenerator gen = new AlignmentGenerator(false);
- AlignmentI al = gen.generate(50, 20, 123, 5, 5);
-
- HiddenColumns cs = al.getHiddenColumns();
- ColumnSelection colsel = new ColumnSelection();
-
- SequenceI seq = new Sequence("RefSeq", "-A-SD-ASD--E---");
- assertEquals(2, seq.findIndex(seq.getStart()));
-
- // no hidden columns
- 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(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(seq.findIndex(seq.getStart()) - 2,cs.locateVisibleStartOfSequence(seq));
-
- cs.revealAllHiddenColumns(colsel);
- // hide columns around most of sequence - leave one residue remaining
- cs.hideColumns(1, 3);
- cs.hideColumns(6, 11);
-
- Iterator<int[]> it = cs.getVisContigsIterator(0, 6, false);
-
- assertEquals("-D", seq.getSequenceStringFromIterator(it));
- // cs.getVisibleSequenceStrings(0, 5, new SequenceI[]
- // { seq })[0]);
-
- 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(0,cs.locateVisibleStartOfSequence(seq));
-
- cs.revealAllHiddenColumns(colsel);
- cs.hideColumns(0, 15);
- assertEquals(0,cs.locateVisibleStartOfSequence(seq));
-
- SequenceI seq2 = new Sequence("RefSeq2", "-------A-SD-ASD--E---");
-
- cs.revealAllHiddenColumns(colsel);
- cs.hideColumns(7, 17);
- assertEquals(0,cs.locateVisibleStartOfSequence(seq2));
-
- cs.revealAllHiddenColumns(colsel);
- cs.hideColumns(3, 17);
- assertEquals(0,cs.locateVisibleStartOfSequence(seq2));
-
- cs.revealAllHiddenColumns(colsel);
- cs.hideColumns(3, 19);
- assertEquals(0,cs.locateVisibleStartOfSequence(seq2));
-
- cs.revealAllHiddenColumns(colsel);
- cs.hideColumns(0, 0);
- assertEquals(0,cs.locateVisibleStartOfSequence(seq));
-
- cs.revealAllHiddenColumns(colsel);
- cs.hideColumns(0, 1);
- assertEquals(1,cs.locateVisibleStartOfSequence(seq));
-
- cs.revealAllHiddenColumns(colsel);
- cs.hideColumns(0, 2);
- assertEquals(0,cs.locateVisibleStartOfSequence(seq));
-
- cs.revealAllHiddenColumns(colsel);
- cs.hideColumns(1, 1);
- assertEquals(2,cs.locateVisibleStartOfSequence(seq));
-
- cs.revealAllHiddenColumns(colsel);
- cs.hideColumns(1, 2);
- assertEquals(1,cs.locateVisibleStartOfSequence(seq));
-
- cs.revealAllHiddenColumns(colsel);
- cs.hideColumns(1, 3);
- assertEquals(1,cs.locateVisibleStartOfSequence(seq));
-
- cs.revealAllHiddenColumns(colsel);
- cs.hideColumns(0, 2);
- cs.hideColumns(5, 6);
- assertEquals(0,cs.locateVisibleStartOfSequence(seq));
-
- cs.revealAllHiddenColumns(colsel);
- cs.hideColumns(0, 2);
- cs.hideColumns(5, 6);
- cs.hideColumns(9, 10);
- assertEquals(0,cs.locateVisibleStartOfSequence(seq));
-
- cs.revealAllHiddenColumns(colsel);
- cs.hideColumns(0, 2);
- cs.hideColumns(7, 11);
- assertEquals(0,cs.locateVisibleStartOfSequence(seq));
-
- cs.revealAllHiddenColumns(colsel);
- cs.hideColumns(2, 4);
- cs.hideColumns(7, 11);
- assertEquals(1,cs.locateVisibleStartOfSequence(seq));
-
- cs.revealAllHiddenColumns(colsel);
- cs.hideColumns(2, 4);
- cs.hideColumns(7, 12);
- assertEquals(1,cs.locateVisibleStartOfSequence(seq));
-
- cs.revealAllHiddenColumns(colsel);
- cs.hideColumns(1, 11);
- assertEquals(0,cs.locateVisibleStartOfSequence(seq));
-
- cs.revealAllHiddenColumns(colsel);
- cs.hideColumns(0, 12);
- assertEquals(0,cs.locateVisibleStartOfSequence(seq));
-
- cs.revealAllHiddenColumns(colsel);
- cs.hideColumns(0, 4);
- cs.hideColumns(6, 12);
- assertEquals(0,cs.locateVisibleStartOfSequence(seq));
-
- cs.revealAllHiddenColumns(colsel);
- cs.hideColumns(0, 1);
- cs.hideColumns(3, 12);
- assertEquals(0,cs.locateVisibleStartOfSequence(seq));
-
- cs.revealAllHiddenColumns(colsel);
- cs.hideColumns(3, 14);
- cs.hideColumns(17, 19);
- assertEquals(3,cs.locateVisibleStartOfSequence(seq2));
-
- cs.revealAllHiddenColumns(colsel);
- cs.hideColumns(3, 7);
- cs.hideColumns(9, 14);
- cs.hideColumns(17, 19);
- assertEquals(9,cs.locateVisibleStartOfSequence(seq2));
-
- cs.revealAllHiddenColumns(colsel);
- cs.hideColumns(0, 1);
- cs.hideColumns(3, 4);
- cs.hideColumns(6, 8);
- cs.hideColumns(10, 12);
- assertEquals(6, cs.locateVisibleStartOfSequence(seq));
-
- }
-
- @Test(groups = { "Functional" })
- 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.hideList(al.getSequenceAt(0).getInsertions());
- assertEquals("G", ""
- + 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" })
public void testHideColumns()
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());
regions = cs.iterator();
// two hidden ranges, in order:
assertEquals("[3, 3]", Arrays.toString(regions.next()));
assertEquals("[5, 5]", Arrays.toString(regions.next()));
+ assertEquals(cs.getSize(), 2);
// hiding column 4 expands [3, 3] to [3, 4]
// and merges to [5, 5] to make [3, 5]
regions = cs.iterator();
assertEquals(1, cs.getNumberOfRegions());
assertEquals("[3, 5]", Arrays.toString(regions.next()));
+ assertEquals(cs.getSize(), 3);
// clear hidden columns (note they are added to selected)
cs.revealAllHiddenColumns(colsel);
// it is now actually null but getter returns an empty list
assertEquals(0, cs.getNumberOfRegions());
+ assertEquals(cs.getSize(), 0);
cs.hideColumns(3, 6);
regions = cs.iterator();
int[] firstHiddenRange = regions.next();
assertEquals("[3, 6]", Arrays.toString(firstHiddenRange));
+ assertEquals(cs.getSize(), 4);
// adding a subrange of already hidden should do nothing
cs.hideColumns(4, 5);
assertEquals(1, cs.getNumberOfRegions());
assertEquals("[3, 6]",
Arrays.toString(regions.next()));
+ assertEquals(cs.getSize(), 4);
cs.hideColumns(3, 5);
regions = cs.iterator();
assertEquals(1, cs.getNumberOfRegions());
assertEquals("[3, 6]",
Arrays.toString(regions.next()));
+ assertEquals(cs.getSize(), 4);
cs.hideColumns(4, 6);
regions = cs.iterator();
assertEquals(1, cs.getNumberOfRegions());
assertEquals("[3, 6]",
Arrays.toString(regions.next()));
+ assertEquals(cs.getSize(), 4);
cs.hideColumns(3, 6);
regions = cs.iterator();
assertEquals(1, cs.getNumberOfRegions());
assertEquals("[3, 6]",
Arrays.toString(regions.next()));
+ assertEquals(cs.getSize(), 4);
cs.revealAllHiddenColumns(colsel);
cs.hideColumns(2, 4);
regions = cs.iterator();
assertEquals(1, cs.getNumberOfRegions());
assertEquals("[2, 4]", Arrays.toString(regions.next()));
+ assertEquals(cs.getSize(), 3);
// extend contiguous with 2 positions overlap
cs.hideColumns(3, 5);
regions = cs.iterator();
assertEquals(1, cs.getNumberOfRegions());
assertEquals("[2, 5]", Arrays.toString(regions.next()));
+ assertEquals(cs.getSize(), 4);
// extend contiguous with 1 position overlap
cs.hideColumns(5, 6);
regions = cs.iterator();
assertEquals(1, cs.getNumberOfRegions());
assertEquals("[2, 6]", Arrays.toString(regions.next()));
+ assertEquals(cs.getSize(), 5);
// extend contiguous with overlap both ends:
cs.hideColumns(1, 7);
regions = cs.iterator();
assertEquals(1, cs.getNumberOfRegions());
assertEquals("[1, 7]", Arrays.toString(regions.next()));
+ assertEquals(cs.getSize(), 7);
cs.revealAllHiddenColumns(colsel);
cs.hideColumns(15, 18);
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);
}
/**
assertEquals(2, cs.getNumberOfRegions());
assertEquals("[49, 59]", Arrays.toString(regions.next()));
assertEquals("[69, 79]", Arrays.toString(regions.next()));
+ assertEquals(22, cs.getSize());
cs.hideColumns(48, 80);
regions = cs.iterator();
assertEquals(1, cs.getNumberOfRegions());
assertEquals("[48, 80]", Arrays.toString(regions.next()));
+ assertEquals(33, cs.getSize());
/*
* another...joining hidden ranges
regions = cs.iterator();
assertEquals(1, cs.getNumberOfRegions());
assertEquals("[10, 60]", Arrays.toString(regions.next()));
+ assertEquals(51, cs.getSize());
/*
* another...left overlap, subsumption, right overlap,
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" })
cs = new HiddenColumns();
cs.hideColumns(one);
assertEquals(1, cs.getNumberOfRegions());
+ assertEquals(1, cs.getSize());
one.set(2);
cs = new HiddenColumns();
cs.hideColumns(one);
assertEquals(1, cs.getNumberOfRegions());
+ assertEquals(2, cs.getSize());
one.set(3);
cs = new HiddenColumns();
cs.hideColumns(one);
assertEquals(1, cs.getNumberOfRegions());
+ assertEquals(3, cs.getSize());
// split
one.clear(2);
cs = new HiddenColumns();
cs.hideColumns(one);
assertEquals(2, cs.getNumberOfRegions());
+ assertEquals(2, cs.getSize());
assertEquals(0, cs.visibleToAbsoluteColumn(0));
assertEquals(2, cs.visibleToAbsoluteColumn(1));
one.clear(1);
cs = new HiddenColumns();
cs.hideColumns(one);
+ assertEquals(1, cs.getSize());
assertEquals(1, cs.getNumberOfRegions());
}
@Test(groups = { "Functional" })
- public void hideColumns_BitSetAndRange()
- {
- 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" })
public void testRegionsToString()
{
HiddenColumns hc = new HiddenColumns();
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")
h.hideColumns(tohide);
assertTrue(h.equals(h2));
- // when setting bitset, first param is invlusive, second exclusive
+ // when setting bitset, first param is inclusive, second exclusive
tohide.set(3, 6);
tohide.set(9);
tohide.set(15, 21);
h2.hideColumns(9, 9);
h2.hideColumns(15, 20);
assertTrue(h.equals(h2));
+ assertEquals(h.getSize(), h2.getSize());
tohide.clear();
tohide.set(41);
h.hideColumns(tohide, 23, 30);
assertTrue(h.equals(h2));
+ assertEquals(h.getSize(), h2.getSize());
tohide.set(41);
h.hideColumns(tohide, 30, 45);
h2.hideColumns(41, 41);
assertTrue(h.equals(h2));
+ assertEquals(h.getSize(), h2.getSize());
tohide.clear();
tohide.set(25, 28);
h.hideColumns(tohide, 17, 50);
h2 = new HiddenColumns();
- h2.hideColumns(17, 20);
+ h2.hideColumns(5, 5);
+ h2.hideColumns(9, 9);
+ h2.hideColumns(15, 16);
h2.hideColumns(25, 27);
- h2.hideColumns(41, 41);
+ 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.hideColumns(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.hideColumns(tohide, 23, 40);
+ assertTrue(hc.hasHiddenColumns());
+ assertEquals(25, hc.getSize());
+
+ // 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());
+ assertEquals(19, hc.getSize());
}
@Test(groups = "Functional")
git://source.jalview.org / jalview.git / blobdiff