*/
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;
HiddenColumns cs = new HiddenColumns();
cs.hideColumns(10, 11);
cs.hideColumns(5, 7);
- assertEquals("[5, 7]", Arrays.toString(cs.getHiddenRegions().get(0)));
+ assertEquals("[5, 7]",
+ Arrays.toString(cs.getHiddenColumnsCopy().get(0)));
HiddenColumns cs2 = new HiddenColumns(cs);
assertTrue(cs2.hasHiddenColumns());
- assertEquals(2, cs2.getHiddenRegions().size());
+ assertEquals(2, cs2.getHiddenColumnsCopy().size());
// 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(cs2.getHiddenColumnsCopy().get(0)));
+ assertEquals("[10, 11]",
+ Arrays.toString(cs2.getHiddenColumnsCopy().get(1)));
}
/**
ColumnSelection colsel = new ColumnSelection();
HiddenColumns cs = al.getHiddenColumns();
colsel.hideSelectedColumns(5, al.getHiddenColumns());
- List<int[]> hidden = cs.getHiddenRegions();
+ 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:
- assertSame(hidden, cs.getHiddenRegions());
+ 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.getHiddenRegions();
+ 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.getHiddenRegions().isEmpty());
+ assertTrue(cs.getHiddenColumnsCopy().isEmpty());
cs.hideColumns(3, 6);
- hidden = cs.getHiddenRegions();
+ 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());
- assertSame(firstHiddenRange, cs.getHiddenRegions().get(0));
+ assertEquals("[3, 6]",
+ Arrays.toString(cs.getHiddenColumnsCopy().get(0)));
cs.hideColumns(3, 5);
+ hidden = cs.getHiddenColumnsCopy();
assertEquals(1, hidden.size());
- assertSame(firstHiddenRange, cs.getHiddenRegions().get(0));
+ assertEquals("[3, 6]",
+ Arrays.toString(cs.getHiddenColumnsCopy().get(0)));
cs.hideColumns(4, 6);
+ hidden = cs.getHiddenColumnsCopy();
assertEquals(1, hidden.size());
- assertSame(firstHiddenRange, cs.getHiddenRegions().get(0));
+ assertEquals("[3, 6]",
+ Arrays.toString(cs.getHiddenColumnsCopy().get(0)));
cs.hideColumns(3, 6);
+ hidden = cs.getHiddenColumnsCopy();
assertEquals(1, hidden.size());
- assertSame(firstHiddenRange, cs.getHiddenRegions().get(0));
+ assertEquals("[3, 6]",
+ Arrays.toString(cs.getHiddenColumnsCopy().get(0)));
cs.revealAllHiddenColumns(colsel);
cs.hideColumns(2, 4);
- hidden = cs.getHiddenRegions();
+ 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)));
}
colsel.addElement(10);
cs.revealHiddenColumns(5, colsel);
// hidden columns list now null but getter returns empty list:
- assertTrue(cs.getHiddenRegions().isEmpty());
+ assertTrue(cs.getHiddenColumnsCopy().isEmpty());
// revealed columns are marked as selected (added to selection):
assertEquals("[10, 5, 6, 7, 8]", colsel.getSelected().toString());
colsel = new ColumnSelection();
cs = new HiddenColumns();
cs.hideColumns(5, 8);
- List<int[]> hidden = cs.getHiddenRegions();
+ List<int[]> hidden = cs.getHiddenColumnsCopy();
cs.revealHiddenColumns(6, colsel);
- assertSame(hidden, cs.getHiddenRegions());
+ assertEquals(hidden.size(), cs.getHiddenColumnsCopy().size());
assertTrue(colsel.getSelected().isEmpty());
}
* revealing hidden columns adds them (in order) to the (unordered)
* selection list
*/
- assertTrue(cs.getHiddenRegions().isEmpty());
+ assertTrue(cs.getHiddenColumnsCopy().isEmpty());
assertEquals("[11, 1, 2, 3, 5, 6, 7, 8]", colsel.getSelected()
.toString());
}
HiddenColumns cs = new HiddenColumns();
cs.hideColumns(49, 59);
cs.hideColumns(69, 79);
- List<int[]> hidden = cs.getHiddenRegions();
+ 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.getHiddenRegions();
+ hidden = cs.getHiddenColumnsCopy();
assertEquals(1, hidden.size());
assertEquals("[48, 80]", Arrays.toString(hidden.get(0)));
cs.hideColumns(50, 60);
// hiding 21-49 should merge to one range
cs.hideColumns(21, 49);
- hidden = cs.getHiddenRegions();
+ hidden = cs.getHiddenColumnsCopy();
assertEquals(1, hidden.size());
assertEquals("[10, 60]", Arrays.toString(hidden.get(0)));
cs.hideColumns(60, 70);
cs.hideColumns(15, 45);
- hidden = cs.getHiddenRegions();
+ hidden = cs.getHiddenColumnsCopy();
assertEquals(2, hidden.size());
assertEquals("[10, 50]", Arrays.toString(hidden.get(0)));
assertEquals("[60, 70]", Arrays.toString(hidden.get(1)));
one.set(1);
cs = new HiddenColumns();
cs.hideMarkedBits(one);
- assertEquals(1, cs.getHiddenRegions().size());
+ assertEquals(1, cs.getHiddenColumnsCopy().size());
one.set(2);
cs = new HiddenColumns();
cs.hideMarkedBits(one);
- assertEquals(1, cs.getHiddenRegions().size());
+ assertEquals(1, cs.getHiddenColumnsCopy().size());
one.set(3);
cs = new HiddenColumns();
cs.hideMarkedBits(one);
- assertEquals(1, cs.getHiddenRegions().size());
+ assertEquals(1, cs.getHiddenColumnsCopy().size());
// split
one.clear(2);
cs = new HiddenColumns();
cs.hideMarkedBits(one);
- assertEquals(2, cs.getHiddenRegions().size());
+ assertEquals(2, cs.getHiddenColumnsCopy().size());
assertEquals(0, cs.adjustForHiddenColumns(0));
assertEquals(2, cs.adjustForHiddenColumns(1));
cs = new HiddenColumns();
cs.hideMarkedBits(one);
- assertEquals(1, cs.getHiddenRegions().size());
+ assertEquals(1, cs.getHiddenColumnsCopy().size());
assertEquals(0, cs.adjustForHiddenColumns(0));
assertEquals(1, cs.adjustForHiddenColumns(1));
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);
- List<Integer> positions = hc.findHiddenRegionPositions();
+ positions = hc.findHiddenRegionPositions();
assertEquals(3, positions.size());
assertEquals(3, positions.get(0).intValue());
assertEquals(5, positions.get(1).intValue());
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);
- String result = hc.regionsToString(",", "--");
+ 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));
+
+ }
}