+
+ /**
+ * Test that a mapping is not deregistered when a second view is closed but
+ * the first still holds a reference to the mapping
+ */
+ @Test(groups = { "Functional" })
+ public void testDeregisterMapping_onCloseView()
+ {
+ /*
+ * alignment with reference to mappings
+ */
+ AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
+ ">Seq1\nCAGT\n", DataSourceType.PASTE);
+
+ SequenceI s1 = af1.getViewport().getAlignment().getSequenceAt(0);
+ AlignedCodonFrame acf1 = new AlignedCodonFrame();
+ acf1.addMap(s1, s1, new MapList(new int[] { 1, 4 }, new int[] { 1, 4 },
+ 1, 1));
+ AlignedCodonFrame acf2 = new AlignedCodonFrame();
+ acf2.addMap(s1, s1, new MapList(new int[] { 1, 4 }, new int[] { 4, 1 },
+ 1, 1));
+
+ List<AlignedCodonFrame> mappings = new ArrayList<AlignedCodonFrame>();
+ mappings.add(acf1);
+ mappings.add(acf2);
+ af1.getViewport().getAlignment().setCodonFrames(mappings);
+ af1.newView_actionPerformed(null);
+
+ /*
+ * Verify that creating the alignment for the new View has registered the
+ * mappings
+ */
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ assertEquals(2, ssm.getSequenceMappings().size());
+ assertTrue(ssm.getSequenceMappings().contains(acf1));
+ assertTrue(ssm.getSequenceMappings().contains(acf2));
+
+ /*
+ * Close the second view. Verify that mappings are not removed as the first
+ * view still holds a reference to them.
+ */
+ af1.closeMenuItem_actionPerformed(false);
+ assertEquals(2, ssm.getSequenceMappings().size());
+ assertTrue(ssm.getSequenceMappings().contains(acf1));
+ assertTrue(ssm.getSequenceMappings().contains(acf2));
+ }
+
+ /**
+ * Test that a mapping is deregistered if no alignment holds a reference to it
+ */
+ @Test(groups = { "Functional" })
+ public void testDeregisterMapping_withNoReference()
+ {
+ Desktop d = Desktop.instance;
+ assertNotNull(d);
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ ssm.resetAll();
+
+ AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
+ ">Seq1\nRSVQ\n", DataSourceType.PASTE);
+ AlignFrame af2 = new FileLoader().LoadFileWaitTillLoaded(
+ ">Seq2\nDGEL\n", DataSourceType.PASTE);
+ SequenceI cs1 = new Sequence("cseq1", "CCCGGGTTTAAA");
+ SequenceI cs2 = new Sequence("cseq2", "CTTGAGTCTAGA");
+ SequenceI s1 = af1.getViewport().getAlignment().getSequenceAt(0);
+ SequenceI s2 = af2.getViewport().getAlignment().getSequenceAt(0);
+ // need to be distinct
+ AlignedCodonFrame acf1 = new AlignedCodonFrame();
+ acf1.addMap(cs1, s1, new MapList(new int[] { 1, 4 },
+ new int[] { 1, 12 }, 1, 3));
+ AlignedCodonFrame acf2 = new AlignedCodonFrame();
+ acf2.addMap(cs2, s2, new MapList(new int[] { 1, 4 },
+ new int[] { 1, 12 }, 1, 3));
+ AlignedCodonFrame acf3 = new AlignedCodonFrame();
+ acf3.addMap(cs2, cs2, new MapList(new int[] { 1, 12 }, new int[] { 1,
+ 12 }, 1, 1));
+
+ List<AlignedCodonFrame> mappings1 = new ArrayList<AlignedCodonFrame>();
+ mappings1.add(acf1);
+ af1.getViewport().getAlignment().setCodonFrames(mappings1);
+
+ List<AlignedCodonFrame> mappings2 = new ArrayList<AlignedCodonFrame>();
+ mappings2.add(acf2);
+ mappings2.add(acf3);
+ af2.getViewport().getAlignment().setCodonFrames(mappings2);
+
+ /*
+ * AlignFrame1 has mapping acf1, AlignFrame2 has acf2 and acf3
+ */
+
+ List<AlignedCodonFrame> ssmMappings = ssm.getSequenceMappings();
+ assertEquals(0, ssmMappings.size());
+ ssm.registerMapping(acf1);
+ assertEquals(1, ssmMappings.size());
+ ssm.registerMapping(acf2);
+ assertEquals(2, ssmMappings.size());
+ ssm.registerMapping(acf3);
+ assertEquals(3, ssmMappings.size());
+
+ /*
+ * Closing AlignFrame2 should remove its mappings from
+ * StructureSelectionManager, since AlignFrame1 has no reference to them
+ */
+ af2.closeMenuItem_actionPerformed(true);
+ assertEquals(1, ssmMappings.size());
+ assertTrue(ssmMappings.contains(acf1));
+ }
+
+ /**
+ * Test that a mapping is not deregistered if another alignment holds a
+ * reference to it
+ */
+ @Test(groups = { "Functional" })
+ public void testDeregisterMapping_withReference()
+ {
+ Desktop d = Desktop.instance;
+ assertNotNull(d);
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ ssm.resetAll();
+
+ AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
+ ">Seq1\nRSVQ\n", DataSourceType.PASTE);
+ AlignFrame af2 = new FileLoader().LoadFileWaitTillLoaded(
+ ">Seq2\nDGEL\n", DataSourceType.PASTE);
+ SequenceI cs1 = new Sequence("cseq1", "CCCGGGTTTAAA");
+ SequenceI cs2 = new Sequence("cseq2", "CTTGAGTCTAGA");
+ SequenceI s1 = af1.getViewport().getAlignment().getSequenceAt(0);
+ SequenceI s2 = af2.getViewport().getAlignment().getSequenceAt(0);
+ // need to be distinct
+ AlignedCodonFrame acf1 = new AlignedCodonFrame();
+ acf1.addMap(cs1, s1, new MapList(new int[] { 1, 4 },
+ new int[] { 1, 12 }, 1, 3));
+ AlignedCodonFrame acf2 = new AlignedCodonFrame();
+ acf2.addMap(cs2, s2, new MapList(new int[] { 1, 4 },
+ new int[] { 1, 12 }, 1, 3));
+ AlignedCodonFrame acf3 = new AlignedCodonFrame();
+ acf3.addMap(cs2, cs2, new MapList(new int[] { 1, 12 }, new int[] { 1,
+ 12 }, 1, 1));
+
+ List<AlignedCodonFrame> mappings1 = new ArrayList<AlignedCodonFrame>();
+ mappings1.add(acf1);
+ mappings1.add(acf2);
+ af1.getViewport().getAlignment().setCodonFrames(mappings1);
+
+ List<AlignedCodonFrame> mappings2 = new ArrayList<AlignedCodonFrame>();
+ mappings2.add(acf2);
+ mappings2.add(acf3);
+ af2.getViewport().getAlignment().setCodonFrames(mappings2);
+
+ /*
+ * AlignFrame1 has mappings acf1 and acf2, AlignFrame2 has acf2 and acf3
+ */
+
+ List<AlignedCodonFrame> ssmMappings = ssm.getSequenceMappings();
+ assertEquals(0, ssmMappings.size());
+ ssm.registerMapping(acf1);
+ assertEquals(1, ssmMappings.size());
+ ssm.registerMapping(acf2);
+ assertEquals(2, ssmMappings.size());
+ ssm.registerMapping(acf3);
+ assertEquals(3, ssmMappings.size());
+
+ /*
+ * Closing AlignFrame2 should remove mapping acf3 from
+ * StructureSelectionManager, but not acf2, since AlignFrame1 still has a
+ * reference to it
+ */
+ af2.closeMenuItem_actionPerformed(true);
+ assertEquals(2, ssmMappings.size());
+ assertTrue(ssmMappings.contains(acf1));
+ assertTrue(ssmMappings.contains(acf2));
+ assertFalse(ssmMappings.contains(acf3));
+ }
+
+ /**
+ * Test for JAL-1306 - conservation thread should run even when only Quality
+ * (and not Conservation) is enabled in Preferences
+ */
+ @Test(groups = { "Functional" })
+ public void testUpdateConservation_qualityOnly()
+ {
+ Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
+ Boolean.TRUE.toString());
+ Cache.applicationProperties.setProperty("SHOW_QUALITY",
+ Boolean.TRUE.toString());
+ Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
+ Boolean.FALSE.toString());
+ Cache.applicationProperties.setProperty("SHOW_IDENTITY",
+ Boolean.FALSE.toString());
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ "examples/uniref50.fa", DataSourceType.FILE);
+ AlignmentAnnotation[] anns = af.viewport.getAlignment()
+ .getAlignmentAnnotation();
+ assertNotNull("No annotations found", anns);
+ assertEquals("More than one annotation found", 1, anns.length);
+ assertTrue("Annotation is not Quality",
+ anns[0].description.startsWith("Alignment Quality"));
+ Annotation[] annotations = anns[0].annotations;
+ assertNotNull("Quality annotations are null", annotations);
+ assertNotNull("Quality in column 1 is null", annotations[0]);
+ assertTrue("No quality value in column 1", annotations[0].value > 10f);
+ }
+
+ @Test(groups = { "Functional" })
+ public void testSetGlobalColourScheme()
+ {
+ /*
+ * test for JAL-2283: don't inadvertently turn on colour by conservation
+ */
+ Cache.applicationProperties.setProperty("DEFAULT_COLOUR_PROT", "None");
+ Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
+ Boolean.TRUE.toString());
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ "examples/uniref50.fa", DataSourceType.FILE);
+ ColourSchemeI cs = new PIDColourScheme();
+ af.getViewport().setGlobalColourScheme(cs);
+ assertFalse(af.getViewport().getResidueShading()
+ .conservationApplied());
+ }
+
+ @Test(groups = { "Functional" })
+ public void testSetGetHasSearchResults()
+ {
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ "examples/uniref50.fa", DataSourceType.FILE);
+ SearchResultsI sr = new SearchResults();
+ SequenceI s1 = af.getViewport().getAlignment().getSequenceAt(0);
+
+ // create arbitrary range on first sequence
+ sr.addResult(s1, s1.getStart() + 10, s1.getStart() + 15);
+
+ // test set
+ af.getViewport().setSearchResults(sr);
+ // has -> true
+ assertTrue(af.getViewport().hasSearchResults());
+ // get == original
+ assertEquals(sr, af.getViewport().getSearchResults());
+
+ // set(null) results in has -> false
+
+ af.getViewport().setSearchResults(null);
+ assertFalse(af.getViewport().hasSearchResults());
+ }