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());
}
/**
- * This output is not part of the test but may help make sense of it...
+ * Generate annotations and add to dataset sequences and (optionally)
+ * sequences and/or alignment
*
- * @param shownTypes
- * @param hiddenTypes
+ * @param seqs
+ * @param addToSequence
+ * @param addToAlignment
*/
- protected void consoleDebug(Map>> shownTypes,
- Map>> hiddenTypes)
+ private void attachReferenceAnnotations(List seqs,
+ boolean addToSequence, boolean addToAlignment)
{
- for (String calcId : shownTypes.keySet())
+ // PDB.secondary structure on Sequence0
+ AlignmentAnnotation annotation = new AlignmentAnnotation(
+ "secondary structure", "", 0);
+ annotation.setCalcId("PDB");
+ seqs.get(0).getDatasetSequence().addAlignmentAnnotation(annotation);
+ if (addToSequence)
{
- System.out.println("Visible annotation types for calcId=" + calcId);
- for (List type : shownTypes.get(calcId))
- {
- System.out.println(" " + type);
- }
+ seqs.get(0).addAlignmentAnnotation(annotation);
}
- for (String calcId : hiddenTypes.keySet())
+ if (addToAlignment)
{
- System.out.println("Hidden annotation types for calcId=" + calcId);
- for (List type : hiddenTypes.get(calcId))
- {
- System.out.println(" " + type);
- }
+ this.alignment.addAnnotation(annotation);
}
+
+ // PDB.Temp on Sequence1
+ annotation = new AlignmentAnnotation("Temp", "", 0);
+ 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");
+ seqs.get(0).getDatasetSequence().addAlignmentAnnotation(annotation);
+ if (addToSequence)
+ {
+ seqs.get(0).addAlignmentAnnotation(annotation);
+ }
+ if (addToAlignment)
+ {
+ this.alignment.addAnnotation(annotation);
+ }
+ }
+
+ /**
+ * 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 case where there are 'grouped' annotations, visible and hidden, within
- * and without the selection group.
+ * Test for building menu options including 'show' and 'hide' annotation
+ * types.
*/
- @Test
- public void testGetAnnotationTypesForShowHide_withGraphGroups()
+ @Test(groups = { "Functional" })
+ public void testBuildAnnotationTypesMenus()
{
- final int GROUP_4 = 4;
- final int GROUP_5 = 5;
- final int GROUP_6 = 6;
-
- Map>> shownTypes = new HashMap>>();
- Map>> hiddenTypes = new HashMap>>();
- AlignmentAnnotation[] anns = alignment.getAlignmentAnnotation();
- BitSet visibleGraphGroups = new BitSet();
- visibleGraphGroups.set(GROUP_4);
- visibleGraphGroups.set(GROUP_6);
- selectSequences(0, 3);
- SequenceI[] seqs = parentPanel.getAlignment().getSequencesArray();
+ 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);
/*
- * Configure annotation properties for test (offsetting for auto-calculated
- * rows).
+ * Expect menu options to show "secondary structure" and "SSP", and to hide
+ * "secondary structure" and "Temp". Tooltip should be calcId.
*/
- // annotations for selection group and graph group
- // hidden annotations Label2, Label3, in (hidden) group 5
- anns[AUTO_ANNS + 2].sequenceRef = seqs[3];
- anns[AUTO_ANNS + 2].visible = false;
- anns[AUTO_ANNS + 2].graph = AlignmentAnnotation.LINE_GRAPH;
- anns[AUTO_ANNS + 2].graphGroup = GROUP_5; // not a visible group
- anns[AUTO_ANNS + 3].sequenceRef = seqs[0];
- anns[AUTO_ANNS + 3].visible = false;
- anns[AUTO_ANNS + 3].graph = AlignmentAnnotation.LINE_GRAPH;
- anns[AUTO_ANNS + 3].graphGroup = GROUP_5;
- // need to ensure annotations have the same calcId as well
- anns[AUTO_ANNS + 3].setCalcId("CalcId2");
-
- // annotations Label1 (hidden), Label5 (visible) in group 6 (visible)
- anns[AUTO_ANNS + 1].sequenceRef = seqs[3];
- // being in a visible group should take precedence over this visibility
- anns[AUTO_ANNS + 1].visible = false;
- anns[AUTO_ANNS + 1].graph = AlignmentAnnotation.LINE_GRAPH;
- anns[AUTO_ANNS + 1].graphGroup = GROUP_6;
- anns[AUTO_ANNS + 5].sequenceRef = seqs[0];
- anns[AUTO_ANNS + 5].visible = true; // visibleGraphGroups overrides this
- anns[AUTO_ANNS + 5].graph = AlignmentAnnotation.LINE_GRAPH;
- anns[AUTO_ANNS + 5].graphGroup = GROUP_6;
- anns[AUTO_ANNS + 5].setCalcId("CalcId1");
-
- // annotations outwith selection group - should be ignored
- // hidden grouped annotations
- anns[AUTO_ANNS + 6].sequenceRef = seqs[2];
- anns[AUTO_ANNS + 6].visible = false;
- anns[AUTO_ANNS + 6].graph = AlignmentAnnotation.LINE_GRAPH;
- anns[AUTO_ANNS + 6].graphGroup = GROUP_4;
- anns[AUTO_ANNS + 8].sequenceRef = seqs[1];
- anns[AUTO_ANNS + 8].visible = false;
- anns[AUTO_ANNS + 8].graph = AlignmentAnnotation.LINE_GRAPH;
- anns[AUTO_ANNS + 8].graphGroup = GROUP_4;
- // visible grouped annotations Label7, Label9
- anns[AUTO_ANNS + 7].sequenceRef = seqs[2];
- anns[AUTO_ANNS + 7].visible = true;
- anns[AUTO_ANNS + 7].graph = AlignmentAnnotation.LINE_GRAPH;
- anns[AUTO_ANNS + 7].graphGroup = GROUP_4;
- anns[AUTO_ANNS + 9].sequenceRef = seqs[1];
- anns[AUTO_ANNS + 9].visible = true;
- anns[AUTO_ANNS + 9].graph = AlignmentAnnotation.LINE_GRAPH;
- anns[AUTO_ANNS + 9].graphGroup = GROUP_4;
-
- PopupMenu.getAnnotationTypesForShowHide(shownTypes, hiddenTypes,
- visibleGraphGroups, anns, parentPanel.av.getSelectionGroup());
-
- consoleDebug(shownTypes, hiddenTypes);
-
- // CalcId1 / Label1, Label5 (only) should be 'shown', as a compound type
- assertEquals(1, shownTypes.get("CalcId1").size());
- assertEquals(2, shownTypes.get("CalcId1").get(0).size());
- assertEquals("Label1", shownTypes.get("CalcId1").get(0).get(0));
- assertEquals("Label5", shownTypes.get("CalcId1").get(0).get(1));
-
- // CalcId2 / Label2, Label3 (only) should be 'hidden'
- assertEquals(1, hiddenTypes.get("CalcId2").size());
- assertEquals(2, hiddenTypes.get("CalcId2").get(0).size());
- assertEquals("Label2", hiddenTypes.get("CalcId2").get(0).get(0));
- assertEquals("Label3", hiddenTypes.get("CalcId2").get(0).get(1));
+ 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());
}
/**
- * Add a sequence group to the alignment with the specified sequences (base 0)
- * in it
- *
- * @param i
- * @param more
+ * Test for building menu options with only 'hide' annotation types enabled.
*/
- private void selectSequences(int... selected)
+ @Test(groups = { "Functional" })
+ public void testBuildAnnotationTypesMenus_showDisabled()
{
- SequenceI[] seqs = parentPanel.getAlignment().getSequencesArray();
- SequenceGroup sg = new SequenceGroup();
- for (int i : selected)
+ 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());
+ }
+
+ /**
+ * Test for adding feature links
+ */
+ @Test(groups = { "Functional" })
+ public void testAddFeatureLinks()
+ {
+ // sequences from the alignment
+ List seqs = parentPanel.getAlignment().getSequences();
+
+ // create list of links and list of DBRefs
+ List links = new ArrayList();
+ List refs = new ArrayList();
+
+ // links as might be added into Preferences | Connections dialog
+ links.add("EMBL-EBI Search | http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$"
+ + SEQUENCE_ID + "$");
+ links.add("UNIPROT | http://www.uniprot.org/uniprot/$" + DB_ACCESSION
+ + "$");
+ links.add("INTERPRO | http://www.ebi.ac.uk/interpro/entry/$"
+ + DB_ACCESSION + "$");
+ // Gene3D entry tests for case (in)sensitivity
+ links.add("Gene3D | http://gene3d.biochem.ucl.ac.uk/Gene3D/search?sterm=$"
+ + DB_ACCESSION + "$&mode=protein");
+
+ // make seq0 dbrefs
+ refs.add(new DBRefEntry(DBRefSource.UNIPROT, "1", "P83527"));
+ refs.add(new DBRefEntry("INTERPRO", "1", "IPR001041"));
+ refs.add(new DBRefEntry("INTERPRO", "1", "IPR006058"));
+ refs.add(new DBRefEntry("INTERPRO", "1", "IPR012675"));
+
+ // make seq1 dbrefs
+ refs.add(new DBRefEntry(DBRefSource.UNIPROT, "1", "Q9ZTS2"));
+ refs.add(new DBRefEntry("GENE3D", "1", "3.10.20.30"));
+
+ // add all the dbrefs to the sequences: Uniprot 1 each, Interpro all 3 to
+ // seq0, Gene3D to seq1
+ seqs.get(0).addDBRef(refs.get(0));
+
+ seqs.get(0).addDBRef(refs.get(1));
+ seqs.get(0).addDBRef(refs.get(2));
+ seqs.get(0).addDBRef(refs.get(3));
+
+ seqs.get(1).addDBRef(refs.get(4));
+ seqs.get(1).addDBRef(refs.get(5));
+
+ // get the Popup Menu for first sequence
+ testee = new PopupMenu(parentPanel, (Sequence) seqs.get(0), links);
+ Component[] seqItems = testee.sequenceMenu.getMenuComponents();
+ JMenu linkMenu = (JMenu) seqItems[6];
+ Component[] linkItems = linkMenu.getMenuComponents();
+
+ // check the number of links are the expected number
+ assertEquals(5, linkItems.length);
+
+ // first entry is EMBL-EBI which just uses sequence id not accession id?
+ assertEquals("EMBL-EBI Search", ((JMenuItem) linkItems[0]).getText());
+
+ // sequence id for each link should match corresponding DB accession id
+ for (int i = 1; i < 4; i++)
{
- sg.addSequence(seqs[i], false);
+ assertEquals(refs.get(i - 1).getSource(), ((JMenuItem) linkItems[i])
+ .getText().split("\\|")[0]);
+ assertEquals(refs.get(i - 1).getAccessionId(),
+ ((JMenuItem) linkItems[i])
+ .getText().split("\\|")[1]);
}
- parentPanel.av.setSelectionGroup(sg);
+
+ // get the Popup Menu for second sequence
+ testee = new PopupMenu(parentPanel, (Sequence) seqs.get(1), links);
+ seqItems = testee.sequenceMenu.getMenuComponents();
+ linkMenu = (JMenu) seqItems[6];
+ linkItems = linkMenu.getMenuComponents();
+
+ // check the number of links are the expected number
+ assertEquals(3, linkItems.length);
+
+ // first entry is EMBL-EBI which just uses sequence id not accession id?
+ assertEquals("EMBL-EBI Search", ((JMenuItem) linkItems[0]).getText());
+
+ // sequence id for each link should match corresponding DB accession id
+ for (int i = 1; i < 3; i++)
+ {
+ assertEquals(refs.get(i + 3).getSource(), ((JMenuItem) linkItems[i])
+ .getText().split("\\|")[0].toUpperCase());
+ assertEquals(refs.get(i + 3).getAccessionId(),
+ ((JMenuItem) linkItems[i]).getText().split("\\|")[1]);
+ }
+
+ // if there are no valid links the Links submenu is disabled
+ List nomatchlinks = new ArrayList();
+ nomatchlinks.add("NOMATCH | http://www.uniprot.org/uniprot/$"
+ + DB_ACCESSION + "$");
+
+ testee = new PopupMenu(parentPanel, (Sequence) seqs.get(0),
+ nomatchlinks);
+ seqItems = testee.sequenceMenu.getMenuComponents();
+ linkMenu = (JMenu) seqItems[6];
+ assertFalse(linkMenu.isEnabled());
+
}
}