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);
+ 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);
+ 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);
+ 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());
}
}