--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+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.assertTrue;
+
+import jalview.analysis.AlignmentGenerator;
+import jalview.gui.JvOptionPane;
+
+import java.util.Arrays;
+import java.util.BitSet;
+import java.util.List;
+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
+ */
+ @Test(groups = { "Functional" })
+ public void testGetSize()
+ {
+ HiddenColumns hidden = new HiddenColumns();
+ assertEquals(0, hidden.getSize());
+
+ hidden.hideColumns(3, 5);
+ assertEquals(3, hidden.getSize());
+
+ hidden.hideColumns(8, 8);
+ assertEquals(4, hidden.getSize());
+
+ hidden.hideColumns(9, 14);
+ assertEquals(10, hidden.getSize());
+
+ ColumnSelection cs = new ColumnSelection();
+ hidden.revealAllHiddenColumns(cs);
+ assertEquals(0, hidden.getSize());
+ }
+
+ /**
+ * Test the method that finds the visible column position of an alignment
+ * column, allowing for hidden columns.
+ */
+ @Test(groups = { "Functional" })
+ public void testFindColumnPosition()
+ {
+ HiddenColumns cs = new HiddenColumns();
+ assertEquals(5, cs.findColumnPosition(5));
+
+ // hiding column 6 makes no difference
+ cs.hideColumns(6, 6);
+ assertEquals(5, cs.findColumnPosition(5));
+
+ // hiding column 4 moves column 5 to column 4
+ cs.hideColumns(4, 4);
+ assertEquals(4, cs.findColumnPosition(5));
+
+ // hiding column 4 moves column 4 to position 3
+ assertEquals(3, cs.findColumnPosition(4));
+
+ // hiding columns 1 and 2 moves column 5 to column 2
+ cs.hideColumns(1, 2);
+ assertEquals(2, cs.findColumnPosition(5));
+
+ // check with > 1 hidden column regions
+ // where some columns are in the hidden regions
+ HiddenColumns cs2 = new HiddenColumns();
+ cs2.hideColumns(5, 10);
+ cs2.hideColumns(20, 27);
+ cs2.hideColumns(40, 44);
+
+ // hiding columns 5-10 and 20-27 moves column 8 to column 4
+ assertEquals(4, cs2.findColumnPosition(8));
+
+ // and moves column 24 to 13
+ assertEquals(13, cs2.findColumnPosition(24));
+
+ // and moves column 28 to 14
+ assertEquals(14, cs2.findColumnPosition(28));
+
+ // and moves column 40 to 25
+ assertEquals(25, cs2.findColumnPosition(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));
+
+ }
+
+ /**
+ * Test the method that finds the visible column position a given distance
+ * before another column
+ */
+ @Test(groups = { "Functional" })
+ public void testFindColumnNToLeft()
+ {
+ 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);
+
+ // 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(groups = { "Functional" })
+ public void testEquals()
+ {
+ HiddenColumns cs = new HiddenColumns();
+ cs.hideColumns(5, 9);
+
+ // a different set of hidden columns
+ HiddenColumns cs2 = new HiddenColumns();
+
+ // with no hidden columns
+ assertFalse(cs.equals(cs2));
+ assertFalse(cs2.equals(cs));
+
+ // with hidden columns added in a different order
+ cs2.hideColumns(6, 9);
+ cs2.hideColumns(5, 8);
+
+ assertTrue(cs.equals(cs2));
+ assertTrue(cs.equals(cs));
+ assertTrue(cs2.equals(cs));
+ assertTrue(cs2.equals(cs2));
+ }
+
+ @Test(groups = "Functional")
+ public void testCopyConstructor()
+ {
+ HiddenColumns cs = new HiddenColumns();
+ cs.hideColumns(10, 11);
+ cs.hideColumns(5, 7);
+ assertEquals("[5, 7]",
+ Arrays.toString(cs.getHiddenColumnsCopy().get(0)));
+
+ HiddenColumns cs2 = new HiddenColumns(cs);
+ assertTrue(cs2.hasHiddenColumns());
+ assertEquals(2, cs2.getHiddenColumnsCopy().size());
+ // hidden columns are held in column order
+ assertEquals("[5, 7]",
+ Arrays.toString(cs2.getHiddenColumnsCopy().get(0)));
+ assertEquals("[10, 11]",
+ Arrays.toString(cs2.getHiddenColumnsCopy().get(1)));
+ }
+
+ /**
+ * Test the code used to locate the reference sequence ruler origin
+ */
+ @Test(groups = { "Functional" })
+ public void testLocateVisibleBoundsofSequence()
+ {
+ // create random alignment
+ AlignmentGenerator gen = new AlignmentGenerator(false);
+ AlignmentI al = gen.generate(50, 20, 123, 5, 5);
+
+ HiddenColumns cs = al.getHiddenColumns();
+ ColumnSelection colsel = new ColumnSelection();
+
+ SequenceI seq = new Sequence("RefSeq", "-A-SD-ASD--E---");
+ assertEquals(2, seq.findIndex(seq.getStart()));
+
+ // no hidden columns
+ assertEquals(
+ 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)));
+
+ // 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)));
+
+ 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)));
+
+ 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.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)));
+
+ }
+
+ @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") });
+ HiddenColumns cs = new HiddenColumns();
+ cs.hideInsertionsFor(al.getSequenceAt(0));
+ assertEquals(
+ "G",
+ ""
+ + al.getSequenceAt(0).getCharAt(
+ cs.adjustForHiddenColumns(9)));
+
+ }
+
+ @Test(groups = { "Functional" })
+ public void testHideColumns()
+ {
+ // create random alignment
+ AlignmentGenerator gen = new AlignmentGenerator(false);
+ AlignmentI al = gen.generate(50, 20, 123, 5, 5);
+
+ ColumnSelection colsel = new ColumnSelection();
+ HiddenColumns cs = al.getHiddenColumns();
+ colsel.hideSelectedColumns(5, al.getHiddenColumns());
+ List<int[]> hidden = cs.getHiddenColumnsCopy();
+ assertEquals(1, hidden.size());
+ assertEquals("[5, 5]", Arrays.toString(hidden.get(0)));
+
+ colsel.hideSelectedColumns(3, al.getHiddenColumns());
+ hidden = cs.getHiddenColumnsCopy();
+ assertEquals(2, hidden.size());
+ // two hidden ranges, in order:
+ assertEquals(hidden.size(), cs.getHiddenColumnsCopy().size());
+ assertEquals("[3, 3]", Arrays.toString(hidden.get(0)));
+ assertEquals("[5, 5]", Arrays.toString(hidden.get(1)));
+
+ // 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.getHiddenColumnsCopy();
+ assertEquals(1, hidden.size());
+ assertEquals("[3, 5]", Arrays.toString(hidden.get(0)));
+
+ // 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.getHiddenColumnsCopy().isEmpty());
+
+ cs.hideColumns(3, 6);
+ hidden = cs.getHiddenColumnsCopy();
+ int[] firstHiddenRange = hidden.get(0);
+ assertEquals("[3, 6]", Arrays.toString(firstHiddenRange));
+
+ // adding a subrange of already hidden should do nothing
+ cs.hideColumns(4, 5);
+ hidden = cs.getHiddenColumnsCopy();
+ assertEquals(1, hidden.size());
+ assertEquals("[3, 6]",
+ Arrays.toString(cs.getHiddenColumnsCopy().get(0)));
+ cs.hideColumns(3, 5);
+ hidden = cs.getHiddenColumnsCopy();
+ assertEquals(1, hidden.size());
+ assertEquals("[3, 6]",
+ Arrays.toString(cs.getHiddenColumnsCopy().get(0)));
+ cs.hideColumns(4, 6);
+ hidden = cs.getHiddenColumnsCopy();
+ assertEquals(1, hidden.size());
+ assertEquals("[3, 6]",
+ Arrays.toString(cs.getHiddenColumnsCopy().get(0)));
+ cs.hideColumns(3, 6);
+ hidden = cs.getHiddenColumnsCopy();
+ assertEquals(1, hidden.size());
+ assertEquals("[3, 6]",
+ Arrays.toString(cs.getHiddenColumnsCopy().get(0)));
+
+ cs.revealAllHiddenColumns(colsel);
+ cs.hideColumns(2, 4);
+ hidden = cs.getHiddenColumnsCopy();
+ assertEquals(1, hidden.size());
+ assertEquals("[2, 4]", Arrays.toString(hidden.get(0)));
+
+ // extend contiguous with 2 positions overlap
+ cs.hideColumns(3, 5);
+ hidden = cs.getHiddenColumnsCopy();
+ assertEquals(1, hidden.size());
+ assertEquals("[2, 5]", Arrays.toString(hidden.get(0)));
+
+ // extend contiguous with 1 position overlap
+ cs.hideColumns(5, 6);
+ hidden = cs.getHiddenColumnsCopy();
+ assertEquals(1, hidden.size());
+ assertEquals("[2, 6]", Arrays.toString(hidden.get(0)));
+
+ // extend contiguous with overlap both ends:
+ cs.hideColumns(1, 7);
+ hidden = cs.getHiddenColumnsCopy();
+ assertEquals(1, hidden.size());
+ assertEquals("[1, 7]", Arrays.toString(hidden.get(0)));
+ }
+
+ /**
+ * Test the method that reveals a range of hidden columns given the start
+ * column of the range
+ */
+ @Test(groups = { "Functional" })
+ public void testRevealHiddenColumns()
+ {
+ ColumnSelection colsel = new ColumnSelection();
+ HiddenColumns cs = new HiddenColumns();
+ cs.hideColumns(5, 8);
+ colsel.addElement(10);
+ cs.revealHiddenColumns(5, colsel);
+ // hidden columns list now null but getter returns empty list:
+ assertTrue(cs.getHiddenColumnsCopy().isEmpty());
+ // revealed columns are marked as selected (added to selection):
+ assertEquals("[10, 5, 6, 7, 8]", colsel.getSelected().toString());
+
+ // calling with a column other than the range start does nothing:
+ colsel = new ColumnSelection();
+ cs = new HiddenColumns();
+ cs.hideColumns(5, 8);
+ List<int[]> hidden = cs.getHiddenColumnsCopy();
+ cs.revealHiddenColumns(6, colsel);
+ assertEquals(hidden.size(), cs.getHiddenColumnsCopy().size());
+ assertTrue(colsel.getSelected().isEmpty());
+ }
+
+ @Test(groups = { "Functional" })
+ public void testRevealAllHiddenColumns()
+ {
+ HiddenColumns cs = new HiddenColumns();
+ ColumnSelection colsel = new ColumnSelection();
+ cs.hideColumns(5, 8);
+ cs.hideColumns(2, 3);
+ colsel.addElement(11);
+ colsel.addElement(1);
+ cs.revealAllHiddenColumns(colsel);
+
+ /*
+ * revealing hidden columns adds them (in order) to the (unordered)
+ * selection list
+ */
+ assertTrue(cs.getHiddenColumnsCopy().isEmpty());
+ assertEquals("[11, 1, 2, 3, 5, 6, 7, 8]", colsel.getSelected()
+ .toString());
+ }
+
+ @Test(groups = { "Functional" })
+ public void testIsVisible()
+ {
+ HiddenColumns cs = new HiddenColumns();
+ cs.hideColumns(2, 4);
+ cs.hideColumns(6, 7);
+ assertTrue(cs.isVisible(0));
+ assertTrue(cs.isVisible(-99));
+ assertTrue(cs.isVisible(1));
+ assertFalse(cs.isVisible(2));
+ assertFalse(cs.isVisible(3));
+ assertFalse(cs.isVisible(4));
+ assertTrue(cs.isVisible(5));
+ assertFalse(cs.isVisible(6));
+ assertFalse(cs.isVisible(7));
+ }
+
+ /**
+ * Test for the case when a hidden range encloses more one already hidden
+ * range
+ */
+ @Test(groups = { "Functional" })
+ public void testHideColumns_subsumingHidden()
+ {
+ /*
+ * JAL-2370 bug scenario:
+ * two hidden ranges subsumed by a third
+ */
+ HiddenColumns cs = new HiddenColumns();
+ cs.hideColumns(49, 59);
+ cs.hideColumns(69, 79);
+ List<int[]> hidden = cs.getHiddenColumnsCopy();
+ assertEquals(2, hidden.size());
+ assertEquals("[49, 59]", Arrays.toString(hidden.get(0)));
+ assertEquals("[69, 79]", Arrays.toString(hidden.get(1)));
+
+ cs.hideColumns(48, 80);
+ hidden = cs.getHiddenColumnsCopy();
+ assertEquals(1, hidden.size());
+ assertEquals("[48, 80]", Arrays.toString(hidden.get(0)));
+
+ /*
+ * another...joining hidden ranges
+ */
+ cs = new HiddenColumns();
+ cs.hideColumns(10, 20);
+ cs.hideColumns(30, 40);
+ cs.hideColumns(50, 60);
+ // hiding 21-49 should merge to one range
+ cs.hideColumns(21, 49);
+ hidden = cs.getHiddenColumnsCopy();
+ assertEquals(1, hidden.size());
+ assertEquals("[10, 60]", Arrays.toString(hidden.get(0)));
+
+ /*
+ * another...left overlap, subsumption, right overlap,
+ * no overlap of existing hidden ranges
+ */
+ cs = new HiddenColumns();
+ cs.hideColumns(10, 20);
+ cs.hideColumns(10, 20);
+ cs.hideColumns(30, 35);
+ cs.hideColumns(40, 50);
+ cs.hideColumns(60, 70);
+
+ cs.hideColumns(15, 45);
+ hidden = cs.getHiddenColumnsCopy();
+ assertEquals(2, hidden.size());
+ assertEquals("[10, 50]", Arrays.toString(hidden.get(0)));
+ assertEquals("[60, 70]", Arrays.toString(hidden.get(1)));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testHideBitset()
+ {
+ HiddenColumns cs;
+
+ BitSet one = new BitSet();
+
+ // one hidden range
+ one.set(1);
+ cs = new HiddenColumns();
+ cs.hideMarkedBits(one);
+ assertEquals(1, cs.getHiddenColumnsCopy().size());
+
+ one.set(2);
+ cs = new HiddenColumns();
+ cs.hideMarkedBits(one);
+ assertEquals(1, cs.getHiddenColumnsCopy().size());
+
+ one.set(3);
+ cs = new HiddenColumns();
+ cs.hideMarkedBits(one);
+ assertEquals(1, cs.getHiddenColumnsCopy().size());
+
+ // split
+ one.clear(2);
+ cs = new HiddenColumns();
+ cs.hideMarkedBits(one);
+ assertEquals(2, cs.getHiddenColumnsCopy().size());
+
+ assertEquals(0, cs.adjustForHiddenColumns(0));
+ assertEquals(2, cs.adjustForHiddenColumns(1));
+ assertEquals(4, cs.adjustForHiddenColumns(2));
+
+ // one again
+ one.clear(1);
+ cs = new HiddenColumns();
+ cs.hideMarkedBits(one);
+
+ assertEquals(1, cs.getHiddenColumnsCopy().size());
+
+ assertEquals(0, cs.adjustForHiddenColumns(0));
+ assertEquals(1, cs.adjustForHiddenColumns(1));
+ assertEquals(2, cs.adjustForHiddenColumns(2));
+ assertEquals(4, cs.adjustForHiddenColumns(3));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testGetBitset()
+ {
+ BitSet toMark, fromMark;
+ long seed = -3241532;
+ Random number = new Random(seed);
+ for (int n = 0; n < 1000; n++)
+ {
+ // create a random bitfield
+ toMark = BitSet.valueOf(new long[] { number.nextLong(),
+ number.nextLong(), number.nextLong() });
+ toMark.set(n * number.nextInt(10), n * (25 + number.nextInt(25)));
+ HiddenColumns hc = new HiddenColumns();
+ hc.hideMarkedBits(toMark);
+
+ // see if we can recover bitfield
+ hc.markHiddenRegions(fromMark = new BitSet());
+ assertEquals(toMark, fromMark);
+ }
+ }
+
+ @Test(groups = { "Functional" })
+ public void testFindHiddenRegionPositions()
+ {
+ HiddenColumns hc = new HiddenColumns();
+
+ List<Integer> 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();
+
+ String result = hc.regionsToString(",", "--");
+ assertEquals("", result);
+
+ hc.hideColumns(3, 7);
+ hc.hideColumns(10, 10);
+ hc.hideColumns(14, 15);
+
+ result = hc.regionsToString(",", "--");
+ assertEquals("3--7,10--10,14--15", result);
+ }
+
+ @Test(groups = "Functional")
+ public void getVisibleStartAndEndIndexTest()
+ {
+ 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);
+
+ result = hc.getRegionWithEdgeAtRes(3);
+ 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);
+ }
+
+ @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(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);
+ 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
+ int[] oldcontigs = hidden.getVisibleContigs(0, 20);
+ int[] testcontigs = { 0, 14, 18, 19 };
+ assertTrue(Arrays.equals(oldcontigs, testcontigs));
+
+ // propagate insertions
+ HiddenColumns result = HiddenColumns.propagateInsertions(profileseq, al,
+ view);
+
+ // confirm that the contigs have changed to account for the gaps
+ int[] newcontigs = result.getVisibleContigs(0, 20);
+ testcontigs[1] = 10;
+ testcontigs[2] = 14;
+ assertTrue(Arrays.equals(newcontigs, testcontigs));
+
+ }
+}
git://source.jalview.org / jalview.git / blobdiff