seqs = parentPanel.getAlignment().getSequences();
- seqs = parentPanel.getAlignment().getSequences();
// make up new annotations and add to dataset sequences
+ attachReferenceAnnotations(seqs, false, false);
+ testee.configureReferenceAnnotationsMenu(menu, seqs);
+ assertTrue(menu.isEnabled());
+ String s = MessageManager.getString("label.add_annotations_for");
+ String expected = ""
+ + s + "
Jmol/secondary structure
PDB/Temp
";
+ assertEquals(expected, menu.getToolTipText());
+ }
+
+ /**
+ * Test building the 'add reference annotations' menu for the case where
+ * several reference annotations are on the dataset and the sequences but not
+ * on the alignment. The menu item should be enabled, and acquire a tooltip
+ * which lists the annotation sources (calcIds) and type (labels).
+ */
+ @Test(groups = { "Functional" })
+ public void testConfigureReferenceAnnotationsMenu_notOnAlignment()
+ {
+ JMenuItem menu = new JMenuItem();
+ List seqs = parentPanel.getAlignment().getSequences();
+
+ // make up new annotations and add to dataset sequences and sequences
+ attachReferenceAnnotations(seqs, true, false);
+
+ testee.configureReferenceAnnotationsMenu(menu, seqs);
+ assertTrue(menu.isEnabled());
+ String s = MessageManager.getString("label.add_annotations_for");
+ String expected = ""
+ + s + "
Jmol/secondary structure
PDB/Temp
";
+ assertEquals(expected, menu.getToolTipText());
+ }
+
+ /**
+ * Generate annotations and add to dataset sequences and (optionally)
+ * sequences and/or alignment
+ *
+ * @param seqs
+ * @param addToSequence
+ * @param addToAlignment
+ */
+ private void attachReferenceAnnotations(List seqs,
+ boolean addToSequence, boolean addToAlignment)
+ {
// PDB.secondary structure on Sequence0
AlignmentAnnotation annotation = new AlignmentAnnotation(
"secondary structure", "", 0);
- annotation.setCalcId("PBD");
+ annotation.setCalcId("PDB");
seqs.get(0).getDatasetSequence().addAlignmentAnnotation(annotation);
+ if (addToSequence)
+ {
+ seqs.get(0).addAlignmentAnnotation(annotation);
+ }
+ if (addToAlignment)
+ {
+ this.alignment.addAnnotation(annotation);
+ }
// PDB.Temp on Sequence1
annotation = new AlignmentAnnotation("Temp", "", 0);
- annotation.setCalcId("PBD");
+ annotation.setCalcId("PDB");
seqs.get(1).getDatasetSequence().addAlignmentAnnotation(annotation);
+ if (addToSequence)
+ {
+ seqs.get(1).addAlignmentAnnotation(annotation);
+ }
+ if (addToAlignment)
+ {
+ this.alignment.addAnnotation(annotation);
+ }
// JMOL.secondary structure on Sequence0
annotation = new AlignmentAnnotation("secondary structure", "", 0);
- annotation.setCalcId("JMOL");
+ annotation.setCalcId("Jmol");
seqs.get(0).getDatasetSequence().addAlignmentAnnotation(annotation);
+ if (addToSequence)
+ {
+ seqs.get(0).addAlignmentAnnotation(annotation);
+ }
+ if (addToAlignment)
+ {
+ this.alignment.addAnnotation(annotation);
+ }
+ }
- testee.configureReferenceAnnotationsMenu(menu, seqs);
- assertTrue(menu.isEnabled());
- String expected = "Add annotations for
JMOL/secondary structure
PBD/Temp |
";
- assertEquals(expected, menu.getToolTipText());
+ /**
+ * Test building the 'add reference annotations' menu for the case where there
+ * are two alignment views:
+ *
+ * - in one view, reference annotations have been added (are on the
+ * datasets, sequences and alignment)
+ * - in the current view, reference annotations are on the dataset and
+ * sequence, but not the alignment
+ *
+ * The menu item should be enabled, and acquire a tooltip which lists the
+ * annotation sources (calcIds) and type (labels).
+ */
+ @Test(groups = { "Functional" })
+ public void testConfigureReferenceAnnotationsMenu_twoViews()
+ {
+ }
+
+ /**
+ * Test for building menu options including 'show' and 'hide' annotation
+ * types.
+ */
+ @Test(groups = { "Functional" })
+ public void testBuildAnnotationTypesMenus()
+ {
+ JMenu showMenu = new JMenu();
+ JMenu hideMenu = new JMenu();
+ List seqs = parentPanel.getAlignment().getSequences();
+
+ // make up new annotations and add to sequences and to the alignment
+
+ // PDB.secondary structure on Sequence0
+ AlignmentAnnotation annotation = new AlignmentAnnotation(
+ "secondary structure", "", new Annotation[] {});
+ annotation.setCalcId("PDB");
+ annotation.visible = true;
+ seqs.get(0).addAlignmentAnnotation(annotation);
+ parentPanel.getAlignment().addAnnotation(annotation);
+
+ // JMOL.secondary structure on Sequence0 - hidden
+ annotation = new AlignmentAnnotation("secondary structure", "",
+ new Annotation[] {});
+ annotation.setCalcId("JMOL");
+ annotation.visible = false;
+ seqs.get(0).addAlignmentAnnotation(annotation);
+ parentPanel.getAlignment().addAnnotation(annotation);
+
+ // Jpred.SSP on Sequence0 - hidden
+ annotation = new AlignmentAnnotation("SSP", "", new Annotation[] {});
+ annotation.setCalcId("JPred");
+ annotation.visible = false;
+ seqs.get(0).addAlignmentAnnotation(annotation);
+ parentPanel.getAlignment().addAnnotation(annotation);
+
+ // PDB.Temp on Sequence1
+ annotation = new AlignmentAnnotation("Temp", "", new Annotation[] {});
+ annotation.setCalcId("PDB");
+ annotation.visible = true;
+ seqs.get(1).addAlignmentAnnotation(annotation);
+ parentPanel.getAlignment().addAnnotation(annotation);
+
+ /*
+ * Expect menu options to show "secondary structure" and "SSP", and to hide
+ * "secondary structure" and "Temp". Tooltip should be calcId.
+ */
+ testee.buildAnnotationTypesMenus(showMenu, hideMenu, seqs);
+
+ assertTrue(showMenu.isEnabled());
+ assertTrue(hideMenu.isEnabled());
+
+ Component[] showOptions = showMenu.getMenuComponents();
+ Component[] hideOptions = hideMenu.getMenuComponents();
+
+ assertEquals(4, showOptions.length); // includes 'All' and separator
+ assertEquals(4, hideOptions.length);
+ String all = MessageManager.getString("label.all");
+ assertEquals(all, ((JMenuItem) showOptions[0]).getText());
+ assertTrue(showOptions[1] instanceof JPopupMenu.Separator);
+ assertEquals(JSeparator.HORIZONTAL,
+ ((JSeparator) showOptions[1]).getOrientation());
+ assertEquals("secondary structure",
+ ((JMenuItem) showOptions[2]).getText());
+ assertEquals("JMOL", ((JMenuItem) showOptions[2]).getToolTipText());
+ assertEquals("SSP", ((JMenuItem) showOptions[3]).getText());
+ assertEquals("JPred", ((JMenuItem) showOptions[3]).getToolTipText());
+
+ assertEquals(all, ((JMenuItem) hideOptions[0]).getText());
+ assertTrue(hideOptions[1] instanceof JPopupMenu.Separator);
+ assertEquals(JSeparator.HORIZONTAL,
+ ((JSeparator) hideOptions[1]).getOrientation());
+ assertEquals("secondary structure",
+ ((JMenuItem) hideOptions[2]).getText());
+ assertEquals("PDB", ((JMenuItem) hideOptions[2]).getToolTipText());
+ assertEquals("Temp", ((JMenuItem) hideOptions[3]).getText());
+ assertEquals("PDB", ((JMenuItem) hideOptions[3]).getToolTipText());
}
+
+ /**
+ * Test for building menu options with only 'hide' annotation types enabled.
+ */
+ @Test(groups = { "Functional" })
+ public void testBuildAnnotationTypesMenus_showDisabled()
+ {
+ JMenu showMenu = new JMenu();
+ JMenu hideMenu = new JMenu();
+ List seqs = parentPanel.getAlignment().getSequences();
+
+ // make up new annotations and add to sequences and to the alignment
+
+ // PDB.secondary structure on Sequence0
+ AlignmentAnnotation annotation = new AlignmentAnnotation(
+ "secondary structure", "", new Annotation[] {});
+ annotation.setCalcId("PDB");
+ annotation.visible = true;
+ seqs.get(0).addAlignmentAnnotation(annotation);
+ parentPanel.getAlignment().addAnnotation(annotation);
+
+ // PDB.Temp on Sequence1
+ annotation = new AlignmentAnnotation("Temp", "", new Annotation[] {});
+ annotation.setCalcId("PDB");
+ annotation.visible = true;
+ seqs.get(1).addAlignmentAnnotation(annotation);
+ parentPanel.getAlignment().addAnnotation(annotation);
+
+ /*
+ * Expect menu options to hide "secondary structure" and "Temp". Tooltip
+ * should be calcId. 'Show' menu should be disabled.
+ */
+ testee.buildAnnotationTypesMenus(showMenu, hideMenu, seqs);
+
+ assertFalse(showMenu.isEnabled());
+ assertTrue(hideMenu.isEnabled());
+
+ Component[] showOptions = showMenu.getMenuComponents();
+ Component[] hideOptions = hideMenu.getMenuComponents();
+
+ assertEquals(2, showOptions.length); // includes 'All' and separator
+ assertEquals(4, hideOptions.length);
+ String all = MessageManager.getString("label.all");
+ assertEquals(all, ((JMenuItem) showOptions[0]).getText());
+ assertTrue(showOptions[1] instanceof JPopupMenu.Separator);
+ assertEquals(JSeparator.HORIZONTAL,
+ ((JSeparator) showOptions[1]).getOrientation());
+
+ assertEquals(all, ((JMenuItem) hideOptions[0]).getText());
+ assertTrue(hideOptions[1] instanceof JPopupMenu.Separator);
+ assertEquals(JSeparator.HORIZONTAL,
+ ((JSeparator) hideOptions[1]).getOrientation());
+ assertEquals("secondary structure",
+ ((JMenuItem) hideOptions[2]).getText());
+ assertEquals("PDB", ((JMenuItem) hideOptions[2]).getToolTipText());
+ assertEquals("Temp", ((JMenuItem) hideOptions[3]).getText());
+ assertEquals("PDB", ((JMenuItem) hideOptions[3]).getToolTipText());
+ }
+
+ /**
+ * Test for building menu options with only 'show' annotation types enabled.
+ */
+ @Test(groups = { "Functional" })
+ public void testBuildAnnotationTypesMenus_hideDisabled()
+ {
+ JMenu showMenu = new JMenu();
+ JMenu hideMenu = new JMenu();
+ List seqs = parentPanel.getAlignment().getSequences();
+
+ // make up new annotations and add to sequences and to the alignment
+
+ // PDB.secondary structure on Sequence0
+ AlignmentAnnotation annotation = new AlignmentAnnotation(
+ "secondary structure", "", new Annotation[] {});
+ annotation.setCalcId("PDB");
+ annotation.visible = false;
+ seqs.get(0).addAlignmentAnnotation(annotation);
+ parentPanel.getAlignment().addAnnotation(annotation);
+
+ // PDB.Temp on Sequence1
+ annotation = new AlignmentAnnotation("Temp", "", new Annotation[] {});
+ annotation.setCalcId("PDB2");
+ annotation.visible = false;
+ seqs.get(1).addAlignmentAnnotation(annotation);
+ parentPanel.getAlignment().addAnnotation(annotation);
+
+ /*
+ * Expect menu options to show "secondary structure" and "Temp". Tooltip
+ * should be calcId. 'hide' menu should be disabled.
+ */
+ testee.buildAnnotationTypesMenus(showMenu, hideMenu, seqs);
+
+ assertTrue(showMenu.isEnabled());
+ assertFalse(hideMenu.isEnabled());
+
+ Component[] showOptions = showMenu.getMenuComponents();
+ Component[] hideOptions = hideMenu.getMenuComponents();
+
+ assertEquals(4, showOptions.length); // includes 'All' and separator
+ assertEquals(2, hideOptions.length);
+ String all = MessageManager.getString("label.all");
+ assertEquals(all, ((JMenuItem) showOptions[0]).getText());
+ assertTrue(showOptions[1] instanceof JPopupMenu.Separator);
+ assertEquals(JSeparator.HORIZONTAL,
+ ((JSeparator) showOptions[1]).getOrientation());
+ assertEquals("secondary structure",
+ ((JMenuItem) showOptions[2]).getText());
+ assertEquals("PDB", ((JMenuItem) showOptions[2]).getToolTipText());
+ assertEquals("Temp", ((JMenuItem) showOptions[3]).getText());
+ assertEquals("PDB2", ((JMenuItem) showOptions[3]).getToolTipText());
+
+ assertEquals(all, ((JMenuItem) hideOptions[0]).getText());
+ assertTrue(hideOptions[1] instanceof JPopupMenu.Separator);
+ assertEquals(JSeparator.HORIZONTAL,
+ ((JSeparator) hideOptions[1]).getOrientation());
+ }
+
+ /**
+ * Test for adding sequence id, dbref and feature links
+ */
+ @Test(groups = { "Functional" })
+ public void testConstructor_links()
+ {
+ List seqs = parentPanel.getAlignment().getSequences();
+ final SequenceI seq0 = seqs.get(0);
+ final SequenceI seq1 = seqs.get(1);
+ final List noFeatures = Collections
+ . emptyList();
+ final String linkText = MessageManager.getString("action.link");
+
+ seq0.addDBRef(new DBRefEntry(DBRefSource.UNIPROT, "1", "P83527"));
+ seq0.addDBRef(new DBRefEntry("INTERPRO", "1", "IPR001041"));
+ seq0.addDBRef(new DBRefEntry("INTERPRO", "1", "IPR012675"));
+ seq0.addDBRef(new DBRefEntry("INTERPRO", "1", "IPR006058"));
+ seq1.addDBRef(new DBRefEntry(DBRefSource.UNIPROT, "1", "Q9ZTS2"));
+ seq1.addDBRef(new DBRefEntry("GENE3D", "1", "3.10.20.30"));
+
+ /*
+ * check the Popup Menu for the first sequence
+ */
+ testee = new PopupMenu(parentPanel, seq0, noFeatures);
+ Component[] seqItems = testee.sequenceMenu.getMenuComponents();
+ JMenu linkMenu = (JMenu) seqItems[6];
+ assertEquals(linkText, linkMenu.getText());
+ Component[] linkItems = linkMenu.getMenuComponents();
+
+ /*
+ * menu items are ordered: SEQUENCE_ID search first, then dbrefs in order
+ * of database name (and within that by order of dbref addition)
+ */
+ assertEquals(5, linkItems.length);
+ assertEquals("EMBL-EBI Search", ((JMenuItem) linkItems[0]).getText());
+ assertEquals("INTERPRO|IPR001041",
+ ((JMenuItem) linkItems[1]).getText());
+ assertEquals("INTERPRO|IPR012675",
+ ((JMenuItem) linkItems[2]).getText());
+ assertEquals("INTERPRO|IPR006058",
+ ((JMenuItem) linkItems[3]).getText());
+ assertEquals("UNIPROT|P83527", ((JMenuItem) linkItems[4]).getText());
+
+ /*
+ * check the Popup Menu for second sequence
+ * note dbref GENE3D is matched to link Gene3D, the latter is displayed
+ */
+ testee = new PopupMenu(parentPanel, seq1, noFeatures);
+ seqItems = testee.sequenceMenu.getMenuComponents();
+ linkMenu = (JMenu) seqItems[6];
+ assertEquals(linkText, linkMenu.getText());
+ linkItems = linkMenu.getMenuComponents();
+ assertEquals(3, linkItems.length);
+ assertEquals("EMBL-EBI Search", ((JMenuItem) linkItems[0]).getText());
+ assertEquals("Gene3D|3.10.20.30", ((JMenuItem) linkItems[1]).getText());
+ assertEquals("UNIPROT|Q9ZTS2", ((JMenuItem) linkItems[2]).getText());
+
+ /*
+ * if there are no valid links the Links submenu is still shown, but
+ * reduced to the EMBL-EBI lookup only (inserted by
+ * CustomUrlProvider.choosePrimaryUrl())
+ */
+ String unmatched = "NOMATCH|http://www.uniprot.org/uniprot/$"
+ + DB_ACCESSION + "$";
+ UrlProviderFactoryI factory = new DesktopUrlProviderFactory(null,
+ unmatched, "");
+ Preferences.sequenceUrlLinks = factory.createUrlProvider();
+
+ testee = new PopupMenu(parentPanel, seq1, noFeatures);
+ seqItems = testee.sequenceMenu.getMenuComponents();
+ linkMenu = (JMenu) seqItems[6];
+ assertEquals(linkText, linkMenu.getText());
+ linkItems = linkMenu.getMenuComponents();
+ assertEquals(1, linkItems.length);
+ assertEquals("EMBL-EBI Search", ((JMenuItem) linkItems[0]).getText());
+ }
+
+ @Test(groups = { "Functional" })
+ public void testHideInsertions()
+ {
+ // get sequences from the alignment
+ List seqs = parentPanel.getAlignment().getSequences();
+
+ // add our own seqs to avoid problems with changes to existing sequences
+ // (gap at end of sequences varies depending on how tests are run!)
+ Sequence seqGap1 = new Sequence("GappySeq",
+ "AAAA----AA-AAAAAAA---AAA-----------AAAAAAAAAA--");
+ seqGap1.createDatasetSequence();
+ seqs.add(seqGap1);
+ Sequence seqGap2 = new Sequence("LessGappySeq",
+ "AAAAAA-AAAAA---AAA--AAAAA--AAAAAAA-AAAAAA");
+ seqGap2.createDatasetSequence();
+ seqs.add(seqGap2);
+ Sequence seqGap3 = new Sequence("AnotherGapSeq",
+ "AAAAAA-AAAAAA--AAAAAA-AAAAAAAAAAA---AAAAAAAA");
+ seqGap3.createDatasetSequence();
+ seqs.add(seqGap3);
+ Sequence seqGap4 = new Sequence("NoGaps",
+ "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA");
+ seqGap4.createDatasetSequence();
+ seqs.add(seqGap4);
+
+ ColumnSelection sel = new ColumnSelection();
+ parentPanel.av.getAlignment().getHiddenColumns()
+ .revealAllHiddenColumns(sel);
+
+ // get the Popup Menu for 7th sequence - no insertions
+ testee = new PopupMenu(parentPanel, seqs.get(7), null);
+ testee.hideInsertions_actionPerformed(null);
+
+ HiddenColumns hidden = parentPanel.av.getAlignment().getHiddenColumns();
+ Iterator it = hidden.iterator();
+ assertFalse(it.hasNext());
+
+ // get the Popup Menu for GappySeq - this time we have insertions
+ testee = new PopupMenu(parentPanel, seqs.get(4), null);
+ testee.hideInsertions_actionPerformed(null);
+ hidden = parentPanel.av.getAlignment().getHiddenColumns();
+ it = hidden.iterator();
+
+ assertTrue(it.hasNext());
+ int[] region = it.next();
+ assertEquals(region[0], 4);
+ assertEquals(region[1], 7);
+
+ assertTrue(it.hasNext());
+ region = it.next();
+ assertEquals(region[0], 10);
+ assertEquals(region[1], 10);
+
+ assertTrue(it.hasNext());
+ region = it.next();
+ assertEquals(region[0], 18);
+ assertEquals(region[1], 20);
+
+ assertTrue(it.hasNext());
+ region = it.next();
+ assertEquals(region[0], 24);
+ assertEquals(region[1], 34);
+
+ assertTrue(it.hasNext());
+ region = it.next();
+ assertEquals(region[0], 45);
+ assertEquals(region[1], 46);
+
+ assertFalse(it.hasNext());
+
+ sel = new ColumnSelection();
+ hidden.revealAllHiddenColumns(sel);
+
+ // make a sequence group and hide insertions within the group
+ SequenceGroup sg = new SequenceGroup();
+ sg.setStartRes(8);
+ sg.setEndRes(42);
+ sg.addSequence(seqGap2, false);
+ sg.addSequence(seqGap3, false);
+ parentPanel.av.setSelectionGroup(sg);
+
+ // hide columns outside and within selection
+ // only hidden columns outside the collection will be retained (unless also
+ // gaps in the selection)
+ hidden.hideColumns(1, 10);
+ hidden.hideColumns(31, 40);
+
+ // get the Popup Menu for LessGappySeq in the sequence group
+ testee = new PopupMenu(parentPanel, seqs.get(5), null);
+ testee.hideInsertions_actionPerformed(null);
+ hidden = parentPanel.av.getAlignment().getHiddenColumns();
+ it = hidden.iterator();
+
+ assertTrue(it.hasNext());
+ region = it.next();
+ assertEquals(region[0], 1);
+ assertEquals(region[1], 7);
+
+ assertTrue(it.hasNext());
+ region = it.next();
+ assertEquals(region[0], 13);
+ assertEquals(region[1], 14);
+
+ assertTrue(it.hasNext());
+ region = it.next();
+ assertEquals(region[0], 34);
+ assertEquals(region[1], 34);
+ }
+
}