--- /dev/null
+package jalview.datamodel;
+
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertNotSame;
+import static org.testng.AssertJUnit.assertNull;
+import static org.testng.AssertJUnit.assertSame;
+import static org.testng.AssertJUnit.assertTrue;
+import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
+
+import jalview.gui.AlignViewport;
+
+import java.util.List;
+
+import org.testng.annotations.BeforeTest;
+import org.testng.annotations.Test;
+
+@Test(singleThreaded = true)
+public class HiddenSequencesTest
+{
+ static int SEQ_COUNT = 10;
+
+ SequenceI[] seqs;
+
+ /**
+ * Set up an alignment of 10 sequences
+ */
+ @BeforeTest(alwaysRun = true)
+ public void setUp()
+ {
+ seqs = new SequenceI[SEQ_COUNT];
+ for (int i = 0; i < SEQ_COUNT; i++)
+ {
+ // sequence lengths are 1, 2, ... 10
+ seqs[i] = new Sequence("Seq" + i, "abcdefghijk".substring(0, i + 1));
+ }
+ }
+
+ /**
+ * Test the method that converts sequence alignment index to what it would be
+ * if all sequences were unhidden
+ */
+ @Test(groups = "Functional")
+ public void testAdjustForHiddenSeqs()
+ {
+ AlignmentI al = new Alignment(seqs);
+ HiddenSequences hs = al.getHiddenSequences();
+ for (int i = 0; i < SEQ_COUNT; i++)
+ {
+ assertEquals(i, hs.adjustForHiddenSeqs(i));
+ }
+
+ // hide seq1 and seq5 and seq6
+ hs.hideSequence(seqs[1]);
+ hs.hideSequence(seqs[5]);
+ hs.hideSequence(seqs[6]);
+
+ /*
+ * alignment is now seq0/2/3/4/7/8/9
+ */
+ assertEquals(7, al.getHeight());
+ assertEquals(0, hs.adjustForHiddenSeqs(0));
+ assertEquals(2, hs.adjustForHiddenSeqs(1));
+ assertEquals(3, hs.adjustForHiddenSeqs(2));
+ assertEquals(4, hs.adjustForHiddenSeqs(3));
+ assertEquals(7, hs.adjustForHiddenSeqs(4));
+ assertEquals(8, hs.adjustForHiddenSeqs(5));
+ assertEquals(9, hs.adjustForHiddenSeqs(6));
+ }
+
+ /**
+ * Test the method that increments the internal array size if a sequence is
+ * added to the alignment (ugh this should not be exposed to the light of day)
+ */
+ @Test(groups = "Functional")
+ public void testAdjustHeightSequenceAdded()
+ {
+ AlignmentI al = new Alignment(seqs);
+ assertEquals(SEQ_COUNT, al.getHeight());
+
+ HiddenSequences hs = al.getHiddenSequences();
+ // initially does nothing
+ hs.adjustHeightSequenceAdded();
+ assertNull(hs.hiddenSequences);
+
+ // hide one sequence
+ hs.hideSequence(seqs[3]);
+ assertEquals(1, hs.getSize());
+ assertEquals(SEQ_COUNT - 1, al.getHeight());
+ assertEquals(SEQ_COUNT, hs.hiddenSequences.length);
+
+ /*
+ * add a sequence to the alignment
+ * - the safe way to call hs.adjustHeightSequenceAdded!
+ * (implementation depends on alignment height having
+ * been already updated for the added sequence)
+ */
+ al.addSequence(new Sequence("a", "b"));
+ assertEquals(1, hs.getSize());
+ assertEquals(SEQ_COUNT, al.getHeight());
+ assertEquals(SEQ_COUNT + 1, hs.hiddenSequences.length);
+ }
+
+ /**
+ * Test the method that decrements the internal array size if a sequence is
+ * deleted from the alignment (ugh this should not be exposed to the light of
+ * day)
+ */
+ @Test(groups = "Functional")
+ public void testAdjustHeightSequenceDeleted()
+ {
+ AlignmentI al = new Alignment(seqs);
+ assertEquals(SEQ_COUNT, al.getHeight());
+
+ HiddenSequences hs = al.getHiddenSequences();
+ // initially does nothing
+ hs.adjustHeightSequenceAdded();
+ assertNull(hs.hiddenSequences);
+
+ // hide two sequences
+ hs.hideSequence(seqs[3]);
+ hs.hideSequence(seqs[5]);
+ assertEquals(2, hs.getSize());
+ assertTrue(hs.isHidden(seqs[3]));
+ assertTrue(hs.isHidden(seqs[5]));
+ assertEquals(SEQ_COUNT - 2, al.getHeight());
+ assertEquals(SEQ_COUNT, hs.hiddenSequences.length);
+
+ /*
+ * delete a visible sequence from the alignment
+ * - the safe way to call hs.adjustHeightSequenceDeleted!
+ * (implementation depends on alignment height having
+ * been already updated for the removed sequence)
+ */
+ al.deleteSequence(seqs[2]);
+ assertEquals(2, hs.getSize());
+ // the visible alignment is unchanged:
+ assertEquals(SEQ_COUNT - 3, al.getHeight());
+ // sequences array size has decremented:
+ assertEquals(SEQ_COUNT - 1, hs.hiddenSequences.length);
+ }
+
+ /**
+ * Test the method that converts a 'full alignment' sequence index into the
+ * equivalent in the alignment with sequences hidden
+ */
+ @Test(groups = "Functional")
+ public void testFindIndexWithoutHiddenSeqs()
+ {
+ AlignmentI al = new Alignment(seqs);
+ HiddenSequences hs = al.getHiddenSequences();
+ for (int i = 0; i < SEQ_COUNT; i++)
+ {
+ assertEquals(i, hs.findIndexWithoutHiddenSeqs(i));
+ }
+
+ // hide seq1 and seq5 and seq6
+ hs.hideSequence(seqs[1]);
+ hs.hideSequence(seqs[5]);
+ hs.hideSequence(seqs[6]);
+
+ /*
+ * alignment is now seq0/2/3/4/7/8/9
+ */
+ assertEquals(7, al.getHeight());
+ assertEquals(0, hs.findIndexWithoutHiddenSeqs(0));
+ assertEquals(0, hs.findIndexWithoutHiddenSeqs(1));
+ assertEquals(1, hs.findIndexWithoutHiddenSeqs(2));
+ assertEquals(2, hs.findIndexWithoutHiddenSeqs(3));
+ assertEquals(3, hs.findIndexWithoutHiddenSeqs(4));
+ assertEquals(3, hs.findIndexWithoutHiddenSeqs(5));
+ assertEquals(3, hs.findIndexWithoutHiddenSeqs(6));
+ assertEquals(4, hs.findIndexWithoutHiddenSeqs(7));
+ assertEquals(5, hs.findIndexWithoutHiddenSeqs(8));
+ assertEquals(6, hs.findIndexWithoutHiddenSeqs(9));
+ }
+
+ /**
+ * Test the method that reconstructs (sort of) the full alignment including
+ * hidden sequences
+ */
+ @Test(groups = "Functional")
+ public void testGetFullAlignment()
+ {
+ AlignmentI al = new Alignment(seqs);
+ assertArrayEquals(seqs, al.getSequencesArray());
+ al.setProperty("a", "b");
+ al.addAnnotation(new AlignmentAnnotation("ann", "label", 12f));
+ al.setSeqrep(seqs[4]);
+ SequenceGroup sg = new SequenceGroup();
+ sg.addSequence(seqs[8], false);
+ al.addGroup(sg);
+ ((Alignment) al).hasRNAStructure = true;
+
+ HiddenSequences hs = al.getHiddenSequences();
+ AlignmentI al2 = hs.getFullAlignment();
+ // new alignment but with original sequences
+ assertNotSame(al, al2);
+ assertArrayEquals(al.getSequencesArray(), al2.getSequencesArray());
+
+ hs.hideSequence(seqs[4]);
+ hs.hideSequence(seqs[9]);
+ al2 = hs.getFullAlignment();
+ assertNotSame(al, al2);
+ assertArrayEquals(seqs, al2.getSequencesArray());
+ assertNotNull(al2.getProperties());
+ assertSame(al.getProperties(), al2.getProperties());
+ assertNotNull(al2.getAlignmentAnnotation());
+ assertSame(al.getAlignmentAnnotation(), al2.getAlignmentAnnotation());
+ assertSame(seqs[4], al2.getSeqrep());
+ assertNotNull(al2.getGroups());
+ assertSame(al.getGroups(), al2.getGroups());
+ assertTrue(al2.hasRNAStructure());
+ }
+
+ /**
+ * Test the method that returns the hidden sequence at a given index in the
+ * full alignment
+ *
+ * @return either the sequence (if hidden) or null (if not hidden)
+ */
+ @Test(groups = "Functional")
+ public void testGetHiddenSequence()
+ {
+ AlignmentI al = new Alignment(seqs);
+ HiddenSequences hs = al.getHiddenSequences();
+ assertNull(hs.getHiddenSequence(0));
+ hs.hideSequence(seqs[3]);
+ assertSame(seqs[3], hs.getHiddenSequence(3));
+ assertNull(hs.getHiddenSequence(2));
+ assertNull(hs.getHiddenSequence(4));
+ }
+
+ @Test(groups = "Functional")
+ public void testGetSize()
+ {
+ }
+
+ @Test(groups = "Functional")
+ public void testGetWidth()
+ {
+ AlignmentI al = new Alignment(seqs);
+ HiddenSequences hs = al.getHiddenSequences();
+ assertEquals(0, hs.getWidth());
+ hs.hideSequence(seqs[6]);
+ hs.hideSequence(seqs[8]);
+ assertEquals(9, hs.getWidth());
+ }
+
+ /**
+ * Test the method that adds a sequence to the hidden sequences and deletes it
+ * from the alignment, and its converse
+ */
+ @Test(groups = "Functional")
+ public void testHideShowSequence()
+ {
+ AlignmentI al = new Alignment(seqs);
+ assertTrue(al.getSequences().contains(seqs[1]));
+ HiddenSequences hs = al.getHiddenSequences();
+ assertEquals(0, hs.getSize());
+ assertEquals(10, al.getHeight());
+
+ /*
+ * hide the second sequence in the alignment
+ */
+ hs.hideSequence(seqs[1]);
+ assertFalse(hs.isHidden(seqs[0]));
+ assertTrue(hs.isHidden(seqs[1]));
+ assertFalse(al.getSequences().contains(seqs[1]));
+ assertEquals(1, hs.getSize());
+ assertEquals(9, al.getHeight());
+ assertSame(seqs[2], al.getSequenceAt(1));
+
+ /*
+ * hide what is now the second sequence in the alignment
+ */
+ hs.hideSequence(seqs[2]);
+ assertFalse(hs.isHidden(seqs[0]));
+ assertTrue(hs.isHidden(seqs[1]));
+ assertTrue(hs.isHidden(seqs[2]));
+ assertFalse(al.getSequences().contains(seqs[1]));
+ assertFalse(al.getSequences().contains(seqs[2]));
+ assertEquals(2, hs.getSize());
+ assertEquals(8, al.getHeight());
+
+ /*
+ * perform 'reveal' on what is now the second sequence in the alignment
+ * this should unhide the two sequences that precede it
+ */
+ List<SequenceI> revealed = hs.showSequence(1, null);
+ assertEquals(2, revealed.size());
+ assertTrue(revealed.contains(seqs[1]));
+ assertTrue(revealed.contains(seqs[2]));
+ assertEquals(0, hs.getSize());
+ assertEquals(10, al.getHeight());
+ }
+
+ @Test(groups = "Functional")
+ public void testIsHidden()
+ {
+ AlignmentI al = new Alignment(seqs);
+ HiddenSequences hs = al.getHiddenSequences();
+ hs.hideSequence(seqs[7]);
+ hs.hideSequence(seqs[4]);
+ assertTrue(hs.isHidden(seqs[4]));
+ assertFalse(hs.isHidden(seqs[5]));
+ assertFalse(hs.isHidden(seqs[6]));
+ assertTrue(hs.isHidden(seqs[7]));
+ assertFalse(hs.isHidden(null));
+ assertFalse(hs.isHidden(new Sequence("", "")));
+ }
+
+ /**
+ * Test hiding and unhiding a group with a representative sequence. The
+ * representative should be left visible when the group is hidden, and
+ * included in the selected group when it is unhidden.
+ */
+ @Test(groups = "Functional")
+ public void testHideShowSequence_withHiddenRepSequence()
+ {
+ AlignmentI al = new Alignment(seqs);
+
+ /*
+ * represent seqs 2-4 with seq3
+ * this hides seq2 and seq4 but not seq3
+ */
+ AlignViewport av = new AlignViewport(al);
+ SequenceGroup sg = new SequenceGroup();
+ sg.addSequence(seqs[1], false);
+ sg.addSequence(seqs[2], false);
+ sg.addSequence(seqs[3], false);
+ av.setSelectionGroup(sg);
+
+ /*
+ * hiding group with reference sequence is done via AlignViewport
+ */
+ av.hideSequences(seqs[2], true);
+ HiddenSequences hs = al.getHiddenSequences();
+ assertEquals(2, hs.getSize());
+ assertTrue(hs.isHidden(seqs[1]));
+ assertFalse(hs.isHidden(seqs[2]));
+ assertTrue(hs.isHidden(seqs[3]));
+
+ /*
+ * should now be no sequences selected in the alignment
+ */
+ assertNull(av.getSelectionGroup());
+
+ /*
+ * visible alignment is now seq0/2/4/5/6/7/8/9
+ * 'reveal sequences' at the representative sequence (index = 1)
+ * this should unhide the one above i.e. seq1
+ * and return a selection list including seq2
+ *
+ * note have to call via AlignViewport to get the expected
+ * resulting sequence selection
+ */
+ av.showSequence(1);
+
+ /*
+ * only seq3 is now hidden
+ */
+ assertEquals(1, hs.getSize());
+ assertTrue(hs.isHidden(seqs[3]));
+ assertEquals(SEQ_COUNT - 1, al.getHeight());
+ sg = av.getSelectionGroup();
+
+ /*
+ * unhidden and representative sequence selected
+ * (this behaviour may change! JAL-2133)
+ */
+ assertEquals(2, sg.getSize());
+ assertTrue(sg.getSequences().contains(seqs[1]));
+ assertTrue(sg.getSequences().contains(seqs[2]));
+ assertFalse(sg.getSequences().contains(seqs[3]));
+ }
+}
git://source.jalview.org / jalview.git / blobdiff