X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FHiddenColumnsTest.java;h=192a822aea8f56457ed687edd8f98671f23435e6;hb=04cb6a433a7ae367e57454c069222ccb830a03f1;hp=9f77eaa0fc685479713f3099b0b72ea115d13210;hpb=166a912dd82096db2777150675cf115bf8332b6c;p=jalview.git diff --git a/test/jalview/datamodel/HiddenColumnsTest.java b/test/jalview/datamodel/HiddenColumnsTest.java index 9f77eaa..192a822 100644 --- a/test/jalview/datamodel/HiddenColumnsTest.java +++ b/test/jalview/datamodel/HiddenColumnsTest.java @@ -20,17 +20,18 @@ */ package jalview.datamodel; +import static org.testng.Assert.assertNull; import static org.testng.AssertJUnit.assertEquals; import static org.testng.AssertJUnit.assertFalse; -import static org.testng.AssertJUnit.assertSame; 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; @@ -132,7 +133,7 @@ public class HiddenColumnsTest // test that without hidden columns, findColumnNToLeft returns // position n to left of provided position - int pos = cs.subtractVisibleColumns(3, 10); + long pos = cs.subtractVisibleColumns(3, 10); assertEquals(7, pos); // 0 returns same position @@ -182,25 +183,60 @@ public class HiddenColumnsTest } @Test(groups = { "Functional" }) - public void testGetVisibleContigs() + public void testVisibleContigsIterator() { HiddenColumns cs = new HiddenColumns(); + + Iterator visible = cs.getVisContigsIterator(3, 10); + int[] region = visible.next(); + assertEquals("[3, 9]", Arrays.toString(region)); + assertFalse(visible.hasNext()); + 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); + 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); + 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); + region = visible.next(); + assertEquals("[7, 7]", Arrays.toString(region)); + assertFalse(visible.hasNext()); + + // Test start visible, end hidden + visible = cs.getVisContigsIterator(0, 13); + 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); + assertFalse(visible.hasNext()); } @Test(groups = { "Functional" }) @@ -232,14 +268,48 @@ public class HiddenColumnsTest HiddenColumns cs = new HiddenColumns(); cs.hideColumns(10, 11); cs.hideColumns(5, 7); - assertEquals("[5, 7]", Arrays.toString(cs.getHiddenRegions().get(0))); + Iterator regions = cs.iterator(); + assertEquals("[5, 7]", + Arrays.toString(regions.next())); HiddenColumns cs2 = new HiddenColumns(cs); + regions = cs2.iterator(); assertTrue(cs2.hasHiddenColumns()); - assertEquals(2, cs2.getHiddenRegions().size()); + assertEquals(2, cs2.getNumberOfRegions()); // hidden columns are held in column order - assertEquals("[5, 7]", Arrays.toString(cs2.getHiddenRegions().get(0))); - assertEquals("[10, 11]", Arrays.toString(cs2.getHiddenRegions().get(1))); + assertEquals("[5, 7]", + Arrays.toString(regions.next())); + assertEquals("[10, 11]", + 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()); } /** @@ -260,19 +330,17 @@ public class HiddenColumnsTest // 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(new int[] + { seq.findIndex(seq.getStart()) - 1, seq.findIndex(seq.getStart()) - 1, + seq.findIndex(seq.getEnd()) - 1 }), Arrays.toString(cs.locateVisibleBoundsOfSequence(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(new int[] + { seq.findIndex(seq.getStart()) - 1, seq.findIndex(seq.getStart()) - 1, + seq.findIndex(seq.getEnd()) - 1 }), Arrays.toString(cs.locateVisibleBoundsOfSequence(seq))); cs.revealAllHiddenColumns(colsel); @@ -280,10 +348,9 @@ public class HiddenColumnsTest // 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(new int[] + { seq.findIndex(seq.getStart()) - 2, seq.findIndex(seq.getStart()) - 1, + seq.findIndex(seq.getEnd()) - 1 }), Arrays.toString(cs.locateVisibleBoundsOfSequence(seq))); cs.revealAllHiddenColumns(colsel); @@ -291,11 +358,14 @@ public class HiddenColumnsTest cs.hideColumns(1, 3); cs.hideColumns(6, 11); assertEquals("-D", - cs.getVisibleSequenceStrings(0, 5, new SequenceI[] { seq })[0]); + 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( + new int[] + { 1, seq.findIndex(seq.getStart()) - 1, + seq.findIndex(seq.getEnd()) - 1 }), Arrays.toString(cs.locateVisibleBoundsOfSequence(seq))); cs.revealAllHiddenColumns(colsel); @@ -303,26 +373,193 @@ public class HiddenColumnsTest // 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( + new int[] + { 0, seq.findIndex(seq.getStart()) - 1, + seq.findIndex(seq.getEnd()) - 1 }), + Arrays.toString(cs.locateVisibleBoundsOfSequence(seq))); + + cs.revealAllHiddenColumns(colsel); + cs.hideColumns(0, 15); + assertEquals(Arrays + .toString(new int[] + { 0, seq.findIndex(seq.getStart()) - 1, + seq.findIndex(seq.getEnd()) - 1 }), Arrays.toString(cs.locateVisibleBoundsOfSequence(seq))); + SequenceI seq2 = new Sequence("RefSeq2", "-------A-SD-ASD--E---"); + + cs.revealAllHiddenColumns(colsel); + cs.hideColumns(7, 17); + assertEquals( + Arrays.toString( + new int[] + { 0, seq2.findIndex(seq2.getStart()) - 1, + seq2.findIndex(seq2.getEnd()) - 1 }), + Arrays.toString(cs.locateVisibleBoundsOfSequence(seq2))); + + cs.revealAllHiddenColumns(colsel); + cs.hideColumns(3, 17); + assertEquals( + Arrays.toString( + new int[] + { 0, seq2.findIndex(seq2.getStart()) - 1, + seq2.findIndex(seq2.getEnd()) - 1 }), + Arrays.toString(cs.locateVisibleBoundsOfSequence(seq2))); + + cs.revealAllHiddenColumns(colsel); + cs.hideColumns(3, 19); + assertEquals( + Arrays.toString( + new int[] + { 0, seq2.findIndex(seq2.getStart()) - 1, + seq2.findIndex(seq2.getEnd()) - 1 }), + Arrays.toString(cs.locateVisibleBoundsOfSequence(seq2))); + + cs.revealAllHiddenColumns(colsel); + cs.hideColumns(0, 0); + int[] test = cs.locateVisibleBoundsOfSequence(seq); + assertEquals(Arrays.toString(new int[] { 0, 1, 11 }), + Arrays.toString(test)); + + cs.revealAllHiddenColumns(colsel); + cs.hideColumns(0, 1); + test = cs.locateVisibleBoundsOfSequence(seq); + assertEquals(Arrays.toString(new int[] { 1, 1, 11 }), + Arrays.toString(test)); + + cs.revealAllHiddenColumns(colsel); + cs.hideColumns(0, 2); + test = cs.locateVisibleBoundsOfSequence(seq); + assertEquals(Arrays.toString(new int[] { 0, 1, 11 }), + Arrays.toString(test)); + + cs.revealAllHiddenColumns(colsel); + cs.hideColumns(1, 1); + test = cs.locateVisibleBoundsOfSequence(seq); + assertEquals(Arrays.toString(new int[] { 2, 1, 11 }), + Arrays.toString(test)); + + cs.revealAllHiddenColumns(colsel); + cs.hideColumns(1, 2); + test = cs.locateVisibleBoundsOfSequence(seq); + assertEquals(Arrays.toString(new int[] { 1, 1, 11 }), + Arrays.toString(test)); + + cs.revealAllHiddenColumns(colsel); + cs.hideColumns(1, 3); + test = cs.locateVisibleBoundsOfSequence(seq); + assertEquals(Arrays.toString(new int[] { 1, 1, 11 }), + Arrays.toString(test)); + + cs.revealAllHiddenColumns(colsel); + cs.hideColumns(0, 2); + cs.hideColumns(5, 6); + test = cs.locateVisibleBoundsOfSequence(seq); + assertEquals(Arrays.toString(new int[] { 0, 1, 11 }), + Arrays.toString(test)); + + cs.revealAllHiddenColumns(colsel); + cs.hideColumns(0, 2); + cs.hideColumns(5, 6); + cs.hideColumns(9, 10); + test = cs.locateVisibleBoundsOfSequence(seq); + assertEquals(Arrays.toString(new int[] { 0, 1, 11 }), + Arrays.toString(test)); + + cs.revealAllHiddenColumns(colsel); + cs.hideColumns(0, 2); + cs.hideColumns(7, 11); + test = cs.locateVisibleBoundsOfSequence(seq); + assertEquals(Arrays.toString(new int[] { 0, 1, 11 }), + Arrays.toString(test)); + + cs.revealAllHiddenColumns(colsel); + cs.hideColumns(2, 4); + cs.hideColumns(7, 11); + test = cs.locateVisibleBoundsOfSequence(seq); + assertEquals(Arrays.toString(new int[] { 1, 1, 11 }), + Arrays.toString(test)); + + cs.revealAllHiddenColumns(colsel); + cs.hideColumns(2, 4); + cs.hideColumns(7, 12); + test = cs.locateVisibleBoundsOfSequence(seq); + assertEquals(Arrays.toString(new int[] { 1, 1, 11 }), + Arrays.toString(test)); + + cs.revealAllHiddenColumns(colsel); + cs.hideColumns(1, 11); + test = cs.locateVisibleBoundsOfSequence(seq); + assertEquals(Arrays.toString(new int[] { 0, 1, 11 }), + Arrays.toString(test)); + + cs.revealAllHiddenColumns(colsel); + cs.hideColumns(0, 12); + test = cs.locateVisibleBoundsOfSequence(seq); + assertEquals(Arrays.toString(new int[] { 0, 1, 11 }), + Arrays.toString(test)); + + cs.revealAllHiddenColumns(colsel); + cs.hideColumns(0, 4); + cs.hideColumns(6, 12); + test = cs.locateVisibleBoundsOfSequence(seq); + assertEquals(Arrays.toString(new int[] { 0, 1, 11 }), + Arrays.toString(test)); + + cs.revealAllHiddenColumns(colsel); + cs.hideColumns(0, 1); + cs.hideColumns(3, 12); + test = cs.locateVisibleBoundsOfSequence(seq); + assertEquals(Arrays.toString(new int[] { 0, 1, 11 }), + Arrays.toString(test)); + + // These tests cover different behaviour to original + // locateVisibleBoundsOfSequence + // Previously first values of each were 3,9 and 6 respectively. + cs.revealAllHiddenColumns(colsel); + cs.hideColumns(3, 14); + cs.hideColumns(17, 19); + assertEquals( + Arrays.toString( + new int[] + { 3, seq2.findIndex(seq2.getStart()) - 1, + seq2.findIndex(seq2.getEnd()) - 1 }), + Arrays.toString(cs.locateVisibleBoundsOfSequence(seq2))); + + cs.revealAllHiddenColumns(colsel); + cs.hideColumns(3, 7); + cs.hideColumns(9, 14); + cs.hideColumns(17, 19); + assertEquals( + Arrays.toString( + new int[] + { 9, seq2.findIndex(seq2.getStart()) - 1, + seq2.findIndex(seq2.getEnd()) - 1 }), + Arrays.toString(cs.locateVisibleBoundsOfSequence(seq2))); + + cs.revealAllHiddenColumns(colsel); + cs.hideColumns(0, 1); + cs.hideColumns(3, 4); + cs.hideColumns(6, 8); + cs.hideColumns(10, 12); + test = cs.locateVisibleBoundsOfSequence(seq); + assertEquals(Arrays.toString(new int[] { 6, 1, 11 }), + Arrays.toString(test)); + } @Test(groups = { "Functional" }) public void testLocateVisibleBoundsPathologicals() { // 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))); + assertEquals("G", "" + + al.getSequenceAt(0).getCharAt(cs.adjustForHiddenColumns(9))); } @@ -336,68 +573,79 @@ public class HiddenColumnsTest ColumnSelection colsel = new ColumnSelection(); HiddenColumns cs = al.getHiddenColumns(); colsel.hideSelectedColumns(5, al.getHiddenColumns()); - List hidden = cs.getHiddenRegions(); - 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()); - assertEquals(2, hidden.size()); + regions = cs.iterator(); + assertEquals(2, cs.getNumberOfRegions()); // two hidden ranges, in order: - assertSame(hidden, cs.getHiddenRegions()); - 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.getHiddenRegions(); - 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.getHiddenRegions().isEmpty()); + assertEquals(0, cs.getNumberOfRegions()); cs.hideColumns(3, 6); - hidden = cs.getHiddenRegions(); - 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); - assertEquals(1, hidden.size()); - assertSame(firstHiddenRange, cs.getHiddenRegions().get(0)); + regions = cs.iterator(); + assertEquals(1, cs.getNumberOfRegions()); + assertEquals("[3, 6]", + Arrays.toString(regions.next())); cs.hideColumns(3, 5); - assertEquals(1, hidden.size()); - assertSame(firstHiddenRange, cs.getHiddenRegions().get(0)); + regions = cs.iterator(); + assertEquals(1, cs.getNumberOfRegions()); + assertEquals("[3, 6]", + Arrays.toString(regions.next())); cs.hideColumns(4, 6); - assertEquals(1, hidden.size()); - assertSame(firstHiddenRange, cs.getHiddenRegions().get(0)); + regions = cs.iterator(); + assertEquals(1, cs.getNumberOfRegions()); + assertEquals("[3, 6]", + Arrays.toString(regions.next())); cs.hideColumns(3, 6); - assertEquals(1, hidden.size()); - assertSame(firstHiddenRange, cs.getHiddenRegions().get(0)); + regions = cs.iterator(); + assertEquals(1, cs.getNumberOfRegions()); + assertEquals("[3, 6]", + Arrays.toString(regions.next())); cs.revealAllHiddenColumns(colsel); cs.hideColumns(2, 4); - hidden = cs.getHiddenRegions(); - 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); - 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); - 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); - 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())); } /** @@ -412,8 +660,10 @@ public class HiddenColumnsTest cs.hideColumns(5, 8); colsel.addElement(10); cs.revealHiddenColumns(5, colsel); - // hidden columns list now null but getter returns empty list: - assertTrue(cs.getHiddenRegions().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()); @@ -421,30 +671,34 @@ public class HiddenColumnsTest colsel = new ColumnSelection(); cs = new HiddenColumns(); cs.hideColumns(5, 8); - List hidden = cs.getHiddenRegions(); + + int prevSize = cs.getSize(); cs.revealHiddenColumns(6, colsel); - assertSame(hidden, cs.getHiddenRegions()); + assertEquals(prevSize, cs.getSize()); 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); + 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.getHiddenRegions().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" }) @@ -478,15 +732,15 @@ public class HiddenColumnsTest HiddenColumns cs = new HiddenColumns(); cs.hideColumns(49, 59); cs.hideColumns(69, 79); - List hidden = cs.getHiddenRegions(); - 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.getHiddenRegions(); - 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 @@ -497,9 +751,9 @@ public class HiddenColumnsTest cs.hideColumns(50, 60); // hiding 21-49 should merge to one range cs.hideColumns(21, 49); - hidden = cs.getHiddenRegions(); - 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, @@ -513,10 +767,10 @@ public class HiddenColumnsTest cs.hideColumns(60, 70); cs.hideColumns(15, 45); - hidden = cs.getHiddenRegions(); - 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" }) @@ -530,23 +784,23 @@ public class HiddenColumnsTest one.set(1); cs = new HiddenColumns(); cs.hideMarkedBits(one); - assertEquals(1, cs.getHiddenRegions().size()); + assertEquals(1, cs.getNumberOfRegions()); one.set(2); cs = new HiddenColumns(); cs.hideMarkedBits(one); - assertEquals(1, cs.getHiddenRegions().size()); + assertEquals(1, cs.getNumberOfRegions()); one.set(3); cs = new HiddenColumns(); cs.hideMarkedBits(one); - assertEquals(1, cs.getHiddenRegions().size()); + assertEquals(1, cs.getNumberOfRegions()); // split one.clear(2); cs = new HiddenColumns(); cs.hideMarkedBits(one); - assertEquals(2, cs.getHiddenRegions().size()); + assertEquals(2, cs.getNumberOfRegions()); assertEquals(0, cs.adjustForHiddenColumns(0)); assertEquals(2, cs.adjustForHiddenColumns(1)); @@ -557,7 +811,7 @@ public class HiddenColumnsTest cs = new HiddenColumns(); cs.hideMarkedBits(one); - assertEquals(1, cs.getHiddenRegions().size()); + assertEquals(1, cs.getNumberOfRegions()); assertEquals(0, cs.adjustForHiddenColumns(0)); assertEquals(1, cs.adjustForHiddenColumns(1)); @@ -566,7 +820,7 @@ public class HiddenColumnsTest } @Test(groups = { "Functional" }) - public void testGetBitset() + public void testMarkHiddenRegions() { BitSet toMark, fromMark; long seed = -3241532; @@ -574,8 +828,9 @@ 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); @@ -587,29 +842,578 @@ public class HiddenColumnsTest } @Test(groups = { "Functional" }) - public void testFindHiddenRegionPositions() + public void testRegionsToString() { HiddenColumns hc = new HiddenColumns(); + + String result = hc.regionsToString(",", "--"); + assertEquals("", result); + hc.hideColumns(3, 7); hc.hideColumns(10, 10); hc.hideColumns(14, 15); - List 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()); + result = hc.regionsToString(",", "--"); + assertEquals("3--7,10--10,14--15", result); } - @Test(groups = { "Functional" }) - public void testRegionsToString() + @Test(groups = "Functional") + public void testGetVisibleStartAndEndIndexTest() + { + Sequence seq = new Sequence("testSeq", "ABCDEFGHIJKLMNOPQRSTUVWXYZ"); + AlignmentI align = new Alignment(new SequenceI[] { seq }); + HiddenColumns hc = new HiddenColumns(); + + int[] startEnd = hc.getVisibleStartAndEndIndex(align.getWidth()); + assertEquals(0, startEnd[0]); + assertEquals(25, startEnd[1]); + + hc.hideColumns(0, 0); + startEnd = hc.getVisibleStartAndEndIndex(align.getWidth()); + assertEquals(1, startEnd[0]); + assertEquals(25, startEnd[1]); + + hc.hideColumns(6, 9); + hc.hideColumns(11, 12); + startEnd = hc.getVisibleStartAndEndIndex(align.getWidth()); + assertEquals(1, startEnd[0]); + assertEquals(25, startEnd[1]); + + hc.hideColumns(24, 25); + startEnd = hc.getVisibleStartAndEndIndex(align.getWidth()); + System.out.println(startEnd[0] + " : " + startEnd[1]); + assertEquals(1, startEnd[0]); + assertEquals(23, startEnd[1]); + } + + @Test(groups = "Functional") + public void testGetRegionWithEdgeAtRes() { HiddenColumns hc = new HiddenColumns(); + + int[] result = hc.getRegionWithEdgeAtRes(5); + assertNull(result); + hc.hideColumns(3, 7); hc.hideColumns(10, 10); hc.hideColumns(14, 15); - String result = hc.regionsToString(",", "--"); - assertEquals("3--7,10--10,14--15", result); + result = hc.getRegionWithEdgeAtRes(2); + assertEquals(3, result[0]); + assertEquals(7, 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]); + } + + @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 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 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])); + } + + @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(); + + // new HiddenColumns2 has no hidden cols + assertFalse(h.hasManyHiddenColumns()); + + // one set of columns hidden, returns false + h.hideColumns(5, 10); + assertFalse(h.hasManyHiddenColumns()); + + // two sets hidden, returns true + h.hideColumns(15, 17); + assertTrue(h.hasManyHiddenColumns()); + + // back to one block, asserts false + h.hideColumns(11, 14); + assertFalse(h.hasManyHiddenColumns()); + } + + @Test(groups = "Functional") + public void testAdjustForHiddenColumns() + { + HiddenColumns h = new HiddenColumns(); + // returns input value when there are no hidden columns + assertEquals(10, h.adjustForHiddenColumns(10)); + + h.hideColumns(20, 30); + assertEquals(10, h.adjustForHiddenColumns(10)); + assertEquals(20 + 11, h.adjustForHiddenColumns(20)); + assertEquals(35 + 11, h.adjustForHiddenColumns(35)); + + h.hideColumns(5, 7); + assertEquals(10 + 3, h.adjustForHiddenColumns(10)); + assertEquals(20 + 14, h.adjustForHiddenColumns(20)); + assertEquals(35 + 14, h.adjustForHiddenColumns(35)); + + ColumnSelection sel = new ColumnSelection(); + h.revealAllHiddenColumns(sel); + h.hideColumns(0, 1); + assertEquals(4, h.adjustForHiddenColumns(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)); + } + + @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); + assertTrue(h.equals(h2)); + + h.hideInsertionsFor(seq1); + 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.hideMarkedBits(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.hideMarkedBits(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); + + // 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); + } + + @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); + } + + @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()); } }