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);
- assertEquals("-D",
- 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()
HiddenColumns h = new HiddenColumns();
// returns same value if no hidden cols
- assertEquals(3, h.getHiddenBoundaryLeft(3));
+ assertEquals(3, h.getNextHiddenBoundary(true, 3));
h.hideColumns(5, 10);
- assertEquals(10, h.getHiddenBoundaryLeft(15));
- assertEquals(3, h.getHiddenBoundaryLeft(3));
- assertEquals(7, h.getHiddenBoundaryLeft(7));
+ 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.getHiddenBoundaryLeft(15));
- assertEquals(20, h.getHiddenBoundaryLeft(21));
+ assertEquals(10, h.getNextHiddenBoundary(true, 15));
+ assertEquals(20, h.getNextHiddenBoundary(true, 21));
}
@Test(groups = "Functional")
- public void testGetHiddenBoundaryRight()
+ public void testGetNextHiddenBoundary()
{
HiddenColumns h = new HiddenColumns();
// returns same value if no hidden cols
- assertEquals(3, h.getHiddenBoundaryRight(3));
+ assertEquals(3, h.getNextHiddenBoundary(false, 3));
h.hideColumns(5, 10);
- assertEquals(5, h.getHiddenBoundaryRight(3));
- assertEquals(15, h.getHiddenBoundaryRight(15));
- assertEquals(7, h.getHiddenBoundaryRight(7));
+ 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.getHiddenBoundaryRight(7));
- assertEquals(15, h.getHiddenBoundaryRight(14));
+ 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.getHiddenBoundaryRight(22));
+ assertEquals(22, h.getNextHiddenBoundary(false, 22));
}
@Test(groups = "Functional")
assertFalse(result.hasNext());
}
- @Test(groups = "Functional")
+ /* @Test(groups = "Functional")
public void testGetVisibleSequenceStrings()
{
HiddenColumns h = new HiddenColumns();
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);
assertEquals("-D",
h.getVisibleSequenceStrings(0, 5, new SequenceI[]
{ seq })[0]);
- }
+ }*/
@Test(groups = "Functional")
public void testHideInsertionsFor()
git://source.jalview.org / jalview.git / blobdiff