+package jalview.datamodel;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertNotNull;
+import static org.testng.Assert.assertNull;
+import static org.testng.Assert.assertSame;
+import static org.testng.Assert.assertTrue;
+import static org.testng.Assert.fail;
+
+import jalview.schemes.NucleotideColourScheme;
+
+import junit.extensions.PA;
+
+import org.testng.annotations.Test;
+
+public class SequenceGroupTest
+{
+ @Test(groups={"Functional"})
+ public void testAddSequence()
+ {
+ SequenceGroup sg = new SequenceGroup();
+ assertTrue(sg.getSequences().isEmpty());
+
+ SequenceI seq1 = new Sequence("seq1", "abc");
+ SequenceI seq2 = new Sequence("seq2", "abc");
+ SequenceI seq3 = new Sequence(seq1);
+
+ sg.addSequence(null, false);
+ assertTrue(sg.getSequences().isEmpty());
+ sg.addSequence(seq1, false);
+ assertEquals(sg.getSequences().size(), 1);
+ assertTrue(sg.getSequences().contains(seq1));
+ // adding the same sequence again does nothing
+ sg.addSequence(seq1, false);
+ assertEquals(sg.getSequences().size(), 1);
+ assertTrue(sg.getSequences().contains(seq1));
+ sg.addSequence(seq2, false);
+ sg.addSequence(seq2, false);
+ sg.addSequence(seq3, false);
+ assertEquals(sg.getSequences().size(), 3);
+ assertTrue(sg.getSequences().contains(seq1));
+ assertTrue(sg.getSequences().contains(seq2));
+ assertTrue(sg.getSequences().contains(seq3));
+ }
+
+ @Test(groups={"Functional"})
+ public void testAddOrRemove()
+ {
+ SequenceGroup sg = new SequenceGroup();
+ assertTrue(sg.getSequences().isEmpty());
+
+ SequenceI seq1 = new Sequence("seq1", "abc");
+ SequenceI seq2 = new Sequence("seq2", "abc");
+ SequenceI seq3 = new Sequence(seq1);
+
+ sg.addOrRemove(seq1, false);
+ assertEquals(sg.getSequences().size(), 1);
+ sg.addOrRemove(seq2, false);
+ assertEquals(sg.getSequences().size(), 2);
+ sg.addOrRemove(seq3, false);
+ assertEquals(sg.getSequences().size(), 3);
+ assertTrue(sg.getSequences().contains(seq1));
+ assertTrue(sg.getSequences().contains(seq2));
+ assertTrue(sg.getSequences().contains(seq3));
+ sg.addOrRemove(seq1, false);
+ assertEquals(sg.getSequences().size(), 2);
+ assertFalse(sg.getSequences().contains(seq1));
+ }
+
+ @Test(groups={"Functional"})
+ public void testGetColourScheme()
+ {
+ SequenceGroup sg = new SequenceGroup();
+ assertNotNull(sg.getGroupColourScheme());
+ assertNull(sg.getColourScheme());
+
+ sg.setGroupColourScheme(null);
+ assertNull(sg.getColourScheme());
+
+ NucleotideColourScheme scheme = new NucleotideColourScheme();
+ sg.setColourScheme(scheme);
+ assertSame(scheme, sg.getColourScheme());
+ }
+
+ @Test(groups={"Functional"})
+ public void testSetContext()
+ {
+ SequenceGroup sg1 = new SequenceGroup();
+ SequenceGroup sg2 = new SequenceGroup();
+ SequenceGroup sg3 = new SequenceGroup();
+ assertNull(sg1.getContext());
+ sg1.setContext(null);
+ assertNull(sg1.getContext());
+ try
+ {
+ sg1.setContext(sg1); // self-reference :-O
+ fail("Expected exception");
+ } catch (IllegalArgumentException e)
+ {
+ // expected
+ assertNull(sg1.getContext());
+ }
+ sg1.setContext(sg2);
+ assertSame(sg2, sg1.getContext());
+ sg2.setContext(sg3);
+ try
+ {
+ sg3.setContext(sg1); // circular reference :-O
+ fail("Expected exception");
+ } catch (IllegalArgumentException e)
+ {
+ // expected
+ assertNull(sg3.getContext());
+ }
+
+ /*
+ * use PrivilegedAccessor to 'force' a SequenceGroup with
+ * a circular context reference
+ */
+ PA.setValue(sg2, "context", sg2);
+ try
+ {
+ sg3.setContext(sg2); // circular reference in sg2
+ fail("Expected exception");
+ } catch (IllegalArgumentException e)
+ {
+ // expected
+ assertNull(sg3.getContext());
+ }
+ }
+
+ @Test(groups = { "Functional" })
+ public void testContains()
+ {
+ /*
+ * essentially the same tests as AlignmentI.findGroup
+ * but from a particular group's perspective
+ */
+
+ SequenceI seq1 = new Sequence("seq1", "ABCDEF---GHI");
+ SequenceI seq2 = new Sequence("seq2", "---JKLMNO---");
+ AlignmentI a = new Alignment(new SequenceI[] { seq1, seq2 });
+ /*
+ * add a group consisting of just "DEF"
+ */
+ SequenceGroup sg1 = new SequenceGroup();
+ sg1.addSequence(seq1, false);
+ sg1.setStartRes(3);
+ sg1.setEndRes(5);
+
+ /*
+ * test sequence membership
+ */
+ assertTrue(sg1.contains(seq1));
+ assertFalse(sg1.contains(seq2));
+
+ /*
+ * test sequence+position
+ */
+
+ assertFalse(sg1.contains(seq1, 2)); // position not in group
+ assertFalse(sg1.contains(seq1, 6)); // position not in group
+ assertFalse(sg1.contains(seq2, 5)); // sequence not in group
+ assertTrue(sg1.contains(seq1, 3)); // yes
+ assertTrue(sg1.contains(seq1, 4));
+ assertTrue(sg1.contains(seq1, 5));
+
+ /*
+ * add a group consisting of
+ * EF--
+ * KLMN
+ */
+ SequenceGroup sg2 = new SequenceGroup();
+ sg2.addSequence(seq1, false);
+ sg2.addSequence(seq2, false);
+ sg2.setStartRes(4);
+ sg2.setEndRes(7);
+ a.addGroup(sg2);
+
+ /*
+ * if a residue is in more than one group, method returns
+ * the first found (in order groups were added)
+ */
+ assertTrue(sg2.contains(seq1, 4));
+ assertTrue(sg2.contains(seq1, 5));
+
+ /*
+ * seq2 only belongs to the second group
+ */
+ assertTrue(sg2.contains(seq2, 4));
+ assertTrue(sg2.contains(seq2, 5));
+ assertTrue(sg2.contains(seq2, 6));
+ assertTrue(sg2.contains(seq2, 7));
+ assertFalse(sg2.contains(seq2, 3));
+ assertFalse(sg2.contains(seq2, 8));
+ sg2.setEndRes(8);
+ assertTrue(sg2.contains(seq2, 8));
+ sg2.deleteSequence(seq2, false);
+ assertFalse(sg2.contains(seq2));
+
+ }
+}