X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FHiddenColumnsTest.java;h=a31d52712063f6796a73a0fdf27484beb89f13b3;hb=2a66892874abea357a5e5d9ef2f69919453c31d0;hp=13cb52635445a0d9f261b518e75425b36176b07c;hpb=607a4aecda2f99866bb1acf7d364a6dde4e215bd;p=jalview.git diff --git a/test/jalview/datamodel/HiddenColumnsTest.java b/test/jalview/datamodel/HiddenColumnsTest.java index 13cb526..a31d527 100644 --- a/test/jalview/datamodel/HiddenColumnsTest.java +++ b/test/jalview/datamodel/HiddenColumnsTest.java @@ -26,26 +26,17 @@ import static org.testng.AssertJUnit.assertFalse; 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.List; +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 */ @@ -77,22 +68,22 @@ public class HiddenColumnsTest 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 @@ -102,105 +93,82 @@ public class HiddenColumnsTest 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); + Iterator visible = cs.getVisContigsIterator(3, 10, false); + int[] region = visible.next(); + assertEquals("[3, 9]", Arrays.toString(region)); + assertFalse(visible.hasNext()); - // 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); - - } - - @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" }) @@ -216,14 +184,31 @@ public class HiddenColumnsTest 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") @@ -232,24 +217,55 @@ public class HiddenColumnsTest HiddenColumns cs = new HiddenColumns(); cs.hideColumns(10, 11); cs.hideColumns(5, 7); + Iterator regions = cs.iterator(); assertEquals("[5, 7]", - Arrays.toString(cs.getHiddenColumnsCopyAsList().get(0))); + Arrays.toString(regions.next())); HiddenColumns cs2 = new HiddenColumns(cs); + regions = cs2.iterator(); assertTrue(cs2.hasHiddenColumns()); - assertEquals(2, cs2.getHiddenColumnsCopyAsList().size()); + assertEquals(2, cs2.getNumberOfRegions()); // hidden columns are held in column order assertEquals("[5, 7]", - Arrays.toString(cs2.getHiddenColumnsCopyAsList().get(0))); + Arrays.toString(regions.next())); assertEquals("[10, 11]", - Arrays.toString(cs2.getHiddenColumnsCopyAsList().get(1))); + Arrays.toString(regions.next())); + } + + @Test(groups = "Functional") + public void testCopyConstructor2() + { + HiddenColumns cs = new HiddenColumns(); + cs.hideColumns(10, 11); + cs.hideColumns(5, 7); + + HiddenColumns cs2 = new HiddenColumns(cs, 3, 9, 1); + assertTrue(cs2.hasHiddenColumns()); + Iterator regions = cs2.iterator(); + + // only [5,7] returned, offset by 1 + assertEquals("[4, 6]", + Arrays.toString(regions.next())); + assertEquals(3, cs2.getSize()); + + cs2 = new HiddenColumns(cs, 8, 15, 4); + regions = cs2.iterator(); + assertTrue(cs2.hasHiddenColumns()); + + // 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 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); @@ -262,71 +278,154 @@ public class HiddenColumnsTest 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))); + 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( - 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))); + 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( - 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))); + 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( - Arrays.toString(new int[] { 1, 1, 3, 3, - seq.findIndex(seq.getStart()) - 1, - seq.findIndex(seq.getEnd()) - 1 }), - Arrays.toString(cs.locateVisibleBoundsOfSequence(seq))); + 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( - Arrays.toString(new int[] { 0, 1, 0, 0, - seq.findIndex(seq.getStart()) - 1, - seq.findIndex(seq.getEnd()) - 1 }), - Arrays.toString(cs.locateVisibleBoundsOfSequence(seq))); + 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 testLocateVisibleBoundsPathologicals() + public void testLocateVisibleStartPathologicals() { // test some pathological cases we missed - AlignmentI al = new Alignment(new SequenceI[] { new Sequence( - "refseqGaptest", "KTDVTI----------NFI-----G----L") }); + 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))); + cs.hideInsertionsFor(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" }) @@ -339,80 +438,89 @@ public class HiddenColumnsTest ColumnSelection colsel = new ColumnSelection(); HiddenColumns cs = al.getHiddenColumns(); colsel.hideSelectedColumns(5, al.getHiddenColumns()); - List hidden = cs.getHiddenColumnsCopyAsList(); - assertEquals(1, hidden.size()); - assertEquals("[5, 5]", Arrays.toString(hidden.get(0))); + Iterator regions = cs.iterator(); + assertEquals(1, cs.getNumberOfRegions()); + assertEquals("[5, 5]", Arrays.toString(regions.next())); colsel.hideSelectedColumns(3, al.getHiddenColumns()); - hidden = cs.getHiddenColumnsCopyAsList(); - assertEquals(2, hidden.size()); + regions = cs.iterator(); + assertEquals(2, cs.getNumberOfRegions()); // two hidden ranges, in order: - assertEquals(hidden.size(), cs.getHiddenColumnsCopyAsList().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())); // 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.getHiddenColumnsCopyAsList(); - 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())); // 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.getHiddenColumnsCopyAsList().isEmpty()); + assertEquals(0, cs.getNumberOfRegions()); cs.hideColumns(3, 6); - hidden = cs.getHiddenColumnsCopyAsList(); - int[] firstHiddenRange = hidden.get(0); + regions = cs.iterator(); + int[] firstHiddenRange = regions.next(); assertEquals("[3, 6]", Arrays.toString(firstHiddenRange)); // adding a subrange of already hidden should do nothing cs.hideColumns(4, 5); - hidden = cs.getHiddenColumnsCopyAsList(); - assertEquals(1, hidden.size()); + regions = cs.iterator(); + assertEquals(1, cs.getNumberOfRegions()); assertEquals("[3, 6]", - Arrays.toString(cs.getHiddenColumnsCopyAsList().get(0))); + Arrays.toString(regions.next())); cs.hideColumns(3, 5); - hidden = cs.getHiddenColumnsCopyAsList(); - assertEquals(1, hidden.size()); + regions = cs.iterator(); + assertEquals(1, cs.getNumberOfRegions()); assertEquals("[3, 6]", - Arrays.toString(cs.getHiddenColumnsCopyAsList().get(0))); + Arrays.toString(regions.next())); cs.hideColumns(4, 6); - hidden = cs.getHiddenColumnsCopyAsList(); - assertEquals(1, hidden.size()); + regions = cs.iterator(); + assertEquals(1, cs.getNumberOfRegions()); assertEquals("[3, 6]", - Arrays.toString(cs.getHiddenColumnsCopyAsList().get(0))); + Arrays.toString(regions.next())); cs.hideColumns(3, 6); - hidden = cs.getHiddenColumnsCopyAsList(); - assertEquals(1, hidden.size()); + regions = cs.iterator(); + assertEquals(1, cs.getNumberOfRegions()); assertEquals("[3, 6]", - Arrays.toString(cs.getHiddenColumnsCopyAsList().get(0))); + Arrays.toString(regions.next())); cs.revealAllHiddenColumns(colsel); cs.hideColumns(2, 4); - hidden = cs.getHiddenColumnsCopyAsList(); - 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())); // extend contiguous with 2 positions overlap cs.hideColumns(3, 5); - hidden = cs.getHiddenColumnsCopyAsList(); - 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())); // extend contiguous with 1 position overlap cs.hideColumns(5, 6); - hidden = cs.getHiddenColumnsCopyAsList(); - 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())); // extend contiguous with overlap both ends: cs.hideColumns(1, 7); - hidden = cs.getHiddenColumnsCopyAsList(); - 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())); + + 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())); } /** @@ -424,11 +532,18 @@ public class HiddenColumnsTest { 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.getHiddenColumnsCopyAsList().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()); @@ -436,30 +551,59 @@ public class HiddenColumnsTest colsel = new ColumnSelection(); cs = new HiddenColumns(); cs.hideColumns(5, 8); - List hidden = cs.getHiddenColumnsCopyAsList(); + + int prevSize = cs.getSize(); cs.revealHiddenColumns(6, colsel); - assertEquals(hidden.size(), cs.getHiddenColumnsCopyAsList().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.getHiddenColumnsCopyAsList().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" }) @@ -477,6 +621,7 @@ public class HiddenColumnsTest assertTrue(cs.isVisible(5)); assertFalse(cs.isVisible(6)); assertFalse(cs.isVisible(7)); + assertTrue(cs.isVisible(8)); } /** @@ -493,15 +638,15 @@ public class HiddenColumnsTest HiddenColumns cs = new HiddenColumns(); cs.hideColumns(49, 59); cs.hideColumns(69, 79); - List hidden = cs.getHiddenColumnsCopyAsList(); - assertEquals(2, hidden.size()); - assertEquals("[49, 59]", Arrays.toString(hidden.get(0))); - assertEquals("[69, 79]", Arrays.toString(hidden.get(1))); + Iterator regions = cs.iterator(); + assertEquals(2, cs.getNumberOfRegions()); + assertEquals("[49, 59]", Arrays.toString(regions.next())); + assertEquals("[69, 79]", Arrays.toString(regions.next())); cs.hideColumns(48, 80); - hidden = cs.getHiddenColumnsCopyAsList(); - 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())); /* * another...joining hidden ranges @@ -512,9 +657,9 @@ public class HiddenColumnsTest cs.hideColumns(50, 60); // hiding 21-49 should merge to one range cs.hideColumns(21, 49); - hidden = cs.getHiddenColumnsCopyAsList(); - 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())); /* * another...left overlap, subsumption, right overlap, @@ -528,10 +673,10 @@ public class HiddenColumnsTest cs.hideColumns(60, 70); cs.hideColumns(15, 45); - hidden = cs.getHiddenColumnsCopyAsList(); - 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())); } @Test(groups = { "Functional" }) @@ -544,44 +689,44 @@ public class HiddenColumnsTest // one hidden range one.set(1); cs = new HiddenColumns(); - cs.hideMarkedBits(one); - assertEquals(1, cs.getHiddenColumnsCopyAsList().size()); + cs.hideColumns(one); + assertEquals(1, cs.getNumberOfRegions()); one.set(2); cs = new HiddenColumns(); - cs.hideMarkedBits(one); - assertEquals(1, cs.getHiddenColumnsCopyAsList().size()); + cs.hideColumns(one); + assertEquals(1, cs.getNumberOfRegions()); one.set(3); cs = new HiddenColumns(); - cs.hideMarkedBits(one); - assertEquals(1, cs.getHiddenColumnsCopyAsList().size()); + cs.hideColumns(one); + assertEquals(1, cs.getNumberOfRegions()); // split one.clear(2); cs = new HiddenColumns(); - cs.hideMarkedBits(one); - assertEquals(2, cs.getHiddenColumnsCopyAsList().size()); + 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.getHiddenColumnsCopyAsList().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)); + 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 testGetBitset() + public void testMarkHiddenRegions() { BitSet toMark, fromMark; long seed = -3241532; @@ -589,11 +734,19 @@ public class HiddenColumnsTest for (int n = 0; n < 1000; n++) { // create a random bitfield - toMark = BitSet.valueOf(new long[] { number.nextLong(), - number.nextLong(), number.nextLong() }); + 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); + + 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()); @@ -602,25 +755,6 @@ public class HiddenColumnsTest } @Test(groups = { "Functional" }) - public void testFindHiddenRegionPositions() - { - HiddenColumns hc = new HiddenColumns(); - - List 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()); - } - - @Test(groups = { "Functional" }) public void testRegionsToString() { HiddenColumns hc = new HiddenColumns(); @@ -637,7 +771,7 @@ public class HiddenColumnsTest } @Test(groups = "Functional") - public void getVisibleStartAndEndIndexTest() + public void testGetVisibleStartAndEndIndex() { Sequence seq = new Sequence("testSeq", "ABCDEFGHIJKLMNOPQRSTUVWXYZ"); AlignmentI align = new Alignment(new SequenceI[] { seq }); @@ -663,6 +797,13 @@ public class HiddenColumnsTest 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") @@ -677,16 +818,796 @@ public class HiddenColumnsTest 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() + { + // 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 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 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(); + + // 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 testGetHiddenBoundaryLeft() + { + HiddenColumns h = new HiddenColumns(); + + // returns same value if no hidden cols + assertEquals(3, h.getHiddenBoundaryLeft(3)); + + h.hideColumns(5, 10); + assertEquals(10, h.getHiddenBoundaryLeft(15)); + assertEquals(3, h.getHiddenBoundaryLeft(3)); + assertEquals(7, h.getHiddenBoundaryLeft(7)); + + h.hideColumns(15, 20); + assertEquals(10, h.getHiddenBoundaryLeft(15)); + assertEquals(20, h.getHiddenBoundaryLeft(21)); + } + + @Test(groups = "Functional") + public void testGetHiddenBoundaryRight() + { + HiddenColumns h = new HiddenColumns(); + + // returns same value if no hidden cols + assertEquals(3, h.getHiddenBoundaryRight(3)); + + h.hideColumns(5, 10); + assertEquals(5, h.getHiddenBoundaryRight(3)); + assertEquals(15, h.getHiddenBoundaryRight(15)); + assertEquals(7, h.getHiddenBoundaryRight(7)); + + 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") + public void testIterator() + { + HiddenColumns h = new HiddenColumns(); + Iterator 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.hideInsertionsFor(seq2.getInsertions()); + assertTrue(h.equals(h2)); + + h.hideInsertionsFor(seq1.getInsertions()); + h2.hideColumns(3, 5); + h2.hideColumns(9, 9); + h2.hideColumns(19, 20); + assertTrue(h.equals(h2)); + } + + @Test(groups = "Functional") + public void testHideMarkedBits() + { + HiddenColumns h = new HiddenColumns(); + HiddenColumns h2 = new HiddenColumns(); + + BitSet tohide = new BitSet(21); + h.hideColumns(tohide); + assertTrue(h.equals(h2)); + + // NB in hideMarkedBits, the last bit is not set to hidden + tohide.set(3, 6); + tohide.set(9); + tohide.set(19, 21); + h.hideColumns(tohide); + + h2.hideColumns(3, 5); + h2.hideColumns(9, 9); + h2.hideColumns(19, 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]); } + @Test(groups = "Functional") + public void testSubtractVisibleColumns() + { + HiddenColumns h = new HiddenColumns(); + int result = h.subtractVisibleColumns(1, 10); + assertEquals(9, result); + + h.hideColumns(7, 9); + result = h.subtractVisibleColumns(4, 10); + assertEquals(3, result); + + h.hideColumns(14, 15); + result = h.subtractVisibleColumns(4, 10); + assertEquals(3, result); + + result = h.subtractVisibleColumns(10, 17); + assertEquals(2, result); + + result = h.subtractVisibleColumns(1, 7); + assertEquals(5, result); + + result = h.subtractVisibleColumns(1, 8); + assertEquals(5, result); + + result = h.subtractVisibleColumns(3, 15); + assertEquals(10, result); + + ColumnSelection sel = new ColumnSelection(); + h.revealAllHiddenColumns(sel); + h.hideColumns(0, 30); + result = h.subtractVisibleColumns(31, 0); + assertEquals(-31, result); + + HiddenColumns cs = new HiddenColumns(); + + // test that without hidden columns, findColumnNToLeft returns + // position n to left of provided position + long 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); + + } + + + @Test(groups = "Functional") + public void testBoundedIterator() + { + HiddenColumns h = new HiddenColumns(); + Iterator 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 it = h.getBoundedStartIterator(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.getBoundedStartIterator(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.getBoundedStartIterator(4, 5); + assertFalse(it.hasNext()); + + // [start,end] fully contains 1 region and start of last + // - 2 regions returned + it = h.getBoundedStartIterator(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.getBoundedStartIterator(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 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 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()); + } }