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.assertNotSame; 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.analysis.Conservation; import jalview.schemes.NucleotideColourScheme; import jalview.schemes.PIDColourScheme; import java.awt.Color; import java.util.Collections; 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, false); // circular reference in sg2 fail("Expected exception"); } catch (IllegalArgumentException e) { // expected assertNull(sg3.getContext()); } // test isDefined setting behaviour sg2 = new SequenceGroup(); sg1.setContext(null, false); assertFalse(sg1.isDefined()); sg1.setContext(sg2, false); assertFalse(sg1.isDefined()); sg1.setContext(sg2, true); assertTrue(sg1.isDefined()); // setContext without defined parameter does not change isDefined sg1.setContext(null); assertTrue(sg1.isDefined()); sg1.setContext(null, false); sg1.setContext(sg2); assertFalse(sg1.isDefined()); } @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)); } @Test(groups = { "Functional" }) public void testCopyConstructor() { SequenceI seq = new Sequence("seq", "ABC"); SequenceGroup sg = new SequenceGroup(); sg.addSequence(seq, false); sg.setName("g1"); sg.setDescription("desc"); sg.setColourScheme(new PIDColourScheme()); Conservation cons = new Conservation("Cons", 2, Collections. emptyList(), 3, 12); PA.setValue(cons, "consSequence", new Sequence("s", "abc")); sg.getGroupColourScheme().setConservation(cons); sg.getGroupColourScheme().setConsensus(new Profiles(null)); sg.setDisplayBoxes(false); sg.setDisplayText(false); sg.setColourText(true); sg.isDefined = true; sg.setShowNonconserved(true); sg.setOutlineColour(Color.red); sg.setIdColour(Color.blue); sg.thresholdTextColour = 1; sg.textColour = Color.orange; sg.textColour2 = Color.yellow; sg.setIgnoreGapsConsensus(false); sg.setshowSequenceLogo(true); sg.setNormaliseSequenceLogo(true); sg.setHidereps(true); sg.setHideCols(true); sg.setShowConsensusHistogram(true); sg.setContext(new SequenceGroup()); SequenceGroup sg2 = new SequenceGroup(sg); assertEquals(sg2.getName(), sg.getName()); assertEquals(sg2.getDescription(), sg.getDescription()); assertNotSame(sg2.getGroupColourScheme(), sg.getGroupColourScheme()); assertSame(sg2.getColourScheme(), sg.getColourScheme()); assertSame(PA.getValue(sg2.getGroupColourScheme(), "consensus"), PA.getValue(sg.getGroupColourScheme(), "consensus")); assertSame(PA.getValue(sg2.getGroupColourScheme(), "conservation"), PA.getValue(sg.getGroupColourScheme(), "conservation")); assertEquals(sg2.getDisplayBoxes(), sg.getDisplayBoxes()); assertEquals(sg2.getDisplayText(), sg.getDisplayText()); assertEquals(sg2.getColourText(), sg.getColourText()); assertEquals(sg2.getShowNonconserved(), sg.getShowNonconserved()); assertEquals(sg2.getOutlineColour(), sg.getOutlineColour()); assertEquals(sg2.getIdColour(), sg.getIdColour()); assertEquals(sg2.thresholdTextColour, sg.thresholdTextColour); assertEquals(sg2.textColour, sg.textColour); assertEquals(sg2.textColour2, sg.textColour2); assertEquals(sg2.getIgnoreGapsConsensus(), sg.getIgnoreGapsConsensus()); assertEquals(sg2.isShowSequenceLogo(), sg.isShowSequenceLogo()); assertEquals(sg2.isNormaliseSequenceLogo(), sg.isNormaliseSequenceLogo()); assertEquals(sg2.isHidereps(), sg.isHidereps()); assertEquals(sg2.isHideCols(), sg.isHideCols()); assertEquals(sg2.isShowConsensusHistogram(), sg.isShowConsensusHistogram()); /* * copy of sequences */ assertNotSame(sg2.getSequences(), sg.getSequences()); assertEquals(sg2.getSequences(), sg.getSequences()); /* * isDefined should only be set true when a new group is added to * an alignment, not in the copy constructor */ assertFalse(sg2.isDefined()); /* * context should be set explicitly, not by copy */ assertNull(sg2.getContext()); } }