seqs = new ArrayList<>();
testee.configureReferenceAnnotationsMenu(menu, seqs);
assertFalse(menu.isEnabled());
// now try null list
@@ -78,7 +146,7 @@ public class PopupMenuTest
* are no reference annotations to add to the alignment. The menu item should
* be disabled.
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testConfigureReferenceAnnotationsMenu_noReferenceAnnotations()
{
JMenuItem menu = new JMenuItem();
@@ -99,7 +167,7 @@ public class PopupMenuTest
* reference annotations are already on the alignment. The menu item should be
* disabled.
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testConfigureReferenceAnnotationsMenu_alreadyAdded()
{
JMenuItem menu = new JMenuItem();
@@ -119,7 +187,7 @@ public class PopupMenuTest
* The menu item should be enabled, and acquire a tooltip which lists the
* annotation sources (calcIds) and type (labels).
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testConfigureReferenceAnnotationsMenu()
{
JMenuItem menu = new JMenuItem();
@@ -130,7 +198,10 @@ public class PopupMenuTest
testee.configureReferenceAnnotationsMenu(menu, seqs);
assertTrue(menu.isEnabled());
- String expected = "Add annotations for
JMOL/secondary structure
PBD/Temp |
";
+ String s = MessageManager.getString("label.add_annotations_for");
+ String expected = ""
+ + "" + s
+ + "
Jmol/secondary structure
PDB/Temp
";
assertEquals(expected, menu.getToolTipText());
}
@@ -140,7 +211,7 @@ public class PopupMenuTest
* 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" })
+ @Test(groups = { "Functional" })
public void testConfigureReferenceAnnotationsMenu_notOnAlignment()
{
JMenuItem menu = new JMenuItem();
@@ -151,7 +222,10 @@ public class PopupMenuTest
testee.configureReferenceAnnotationsMenu(menu, seqs);
assertTrue(menu.isEnabled());
- String expected = "Add annotations for
JMOL/secondary structure
PBD/Temp |
";
+ String s = MessageManager.getString("label.add_annotations_for");
+ String expected = ""
+ + "" + s
+ + "
Jmol/secondary structure
PDB/Temp
";
assertEquals(expected, menu.getToolTipText());
}
@@ -169,7 +243,7 @@ public class PopupMenuTest
// 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)
{
@@ -182,7 +256,7 @@ public class PopupMenuTest
// PDB.Temp on Sequence1
annotation = new AlignmentAnnotation("Temp", "", 0);
- annotation.setCalcId("PBD");
+ annotation.setCalcId("PDB");
seqs.get(1).getDatasetSequence().addAlignmentAnnotation(annotation);
if (addToSequence)
{
@@ -195,7 +269,7 @@ public class PopupMenuTest
// 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)
{
@@ -219,7 +293,7 @@ public class PopupMenuTest
* The menu item should be enabled, and acquire a tooltip which lists the
* annotation sources (calcIds) and type (labels).
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testConfigureReferenceAnnotationsMenu_twoViews()
{
}
@@ -228,7 +302,7 @@ public class PopupMenuTest
* Test for building menu options including 'show' and 'hide' annotation
* types.
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testBuildAnnotationTypesMenus()
{
JMenu showMenu = new JMenu();
@@ -239,32 +313,29 @@ public class PopupMenuTest
// PDB.secondary structure on Sequence0
AlignmentAnnotation annotation = new AlignmentAnnotation(
- "secondary structure", "", new Annotation[]
- {});
+ "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 = 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 = 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 = new AlignmentAnnotation("Temp", "", new Annotation[] {});
annotation.setCalcId("PDB");
annotation.visible = true;
seqs.get(1).addAlignmentAnnotation(annotation);
@@ -284,8 +355,8 @@ public class PopupMenuTest
assertEquals(4, showOptions.length); // includes 'All' and separator
assertEquals(4, hideOptions.length);
- assertEquals("All",
- ((JMenuItem) showOptions[0]).getText());
+ 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());
@@ -295,8 +366,7 @@ public class PopupMenuTest
assertEquals("SSP", ((JMenuItem) showOptions[3]).getText());
assertEquals("JPred", ((JMenuItem) showOptions[3]).getToolTipText());
- assertEquals("All",
- ((JMenuItem) hideOptions[0]).getText());
+ assertEquals(all, ((JMenuItem) hideOptions[0]).getText());
assertTrue(hideOptions[1] instanceof JPopupMenu.Separator);
assertEquals(JSeparator.HORIZONTAL,
((JSeparator) hideOptions[1]).getOrientation());
@@ -310,7 +380,7 @@ public class PopupMenuTest
/**
* Test for building menu options with only 'hide' annotation types enabled.
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testBuildAnnotationTypesMenus_showDisabled()
{
JMenu showMenu = new JMenu();
@@ -321,16 +391,14 @@ public class PopupMenuTest
// PDB.secondary structure on Sequence0
AlignmentAnnotation annotation = new AlignmentAnnotation(
- "secondary structure", "", new Annotation[]
- {});
+ "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 = new AlignmentAnnotation("Temp", "", new Annotation[] {});
annotation.setCalcId("PDB");
annotation.visible = true;
seqs.get(1).addAlignmentAnnotation(annotation);
@@ -350,12 +418,13 @@ public class PopupMenuTest
assertEquals(2, showOptions.length); // includes 'All' and separator
assertEquals(4, hideOptions.length);
- assertEquals("All", ((JMenuItem) showOptions[0]).getText());
+ 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());
+ assertEquals(all, ((JMenuItem) hideOptions[0]).getText());
assertTrue(hideOptions[1] instanceof JPopupMenu.Separator);
assertEquals(JSeparator.HORIZONTAL,
((JSeparator) hideOptions[1]).getOrientation());
@@ -369,7 +438,7 @@ public class PopupMenuTest
/**
* Test for building menu options with only 'show' annotation types enabled.
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testBuildAnnotationTypesMenus_hideDisabled()
{
JMenu showMenu = new JMenu();
@@ -380,16 +449,14 @@ public class PopupMenuTest
// PDB.secondary structure on Sequence0
AlignmentAnnotation annotation = new AlignmentAnnotation(
- "secondary structure", "", new Annotation[]
- {});
+ "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 = new AlignmentAnnotation("Temp", "", new Annotation[] {});
annotation.setCalcId("PDB2");
annotation.visible = false;
seqs.get(1).addAlignmentAnnotation(annotation);
@@ -409,7 +476,8 @@ public class PopupMenuTest
assertEquals(4, showOptions.length); // includes 'All' and separator
assertEquals(2, hideOptions.length);
- assertEquals("All", ((JMenuItem) showOptions[0]).getText());
+ 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());
@@ -419,9 +487,280 @@ public class PopupMenuTest
assertEquals("Temp", ((JMenuItem) showOptions[3]).getText());
assertEquals("PDB2", ((JMenuItem) showOptions[3]).getToolTipText());
- assertEquals("All", ((JMenuItem) hideOptions[0]).getText());
+ 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 testBuildLinkMenu()
+ {
+ 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 Link Menu for the first sequence
+ */
+ JMenu linkMenu = PopupMenu.buildLinkMenu(seq0, noFeatures);
+ 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 Link Menu for the second sequence
+ * note dbref GENE3D is matched to link Gene3D, the latter is displayed
+ */
+ linkMenu = PopupMenu.buildLinkMenu(seq1, noFeatures);
+ 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();
+
+ linkMenu = PopupMenu.buildLinkMenu(seq1, noFeatures);
+ linkItems = linkMenu.getMenuComponents();
+ assertEquals(1, linkItems.length);
+ assertEquals("EMBL-EBI Search", ((JMenuItem) linkItems[0]).getText());
+
+ /*
+ * if sequence is null, only feature links are shown (alignment popup submenu)
+ */
+ linkMenu = PopupMenu.buildLinkMenu(null, noFeatures);
+ linkItems = linkMenu.getMenuComponents();
+ assertEquals(0, linkItems.length);
+
+ List features = new ArrayList<>();
+ SequenceFeature sf = new SequenceFeature("type", "desc", 1, 20, null);
+ features.add(sf);
+ linkMenu = PopupMenu.buildLinkMenu(null, features);
+ linkItems = linkMenu.getMenuComponents();
+ assertEquals(0, linkItems.length); // feature has no links
+
+ sf.addLink("Pfam family|http://pfam.xfam.org/family/PF00111");
+ linkMenu = PopupMenu.buildLinkMenu(null, features);
+ linkItems = linkMenu.getMenuComponents();
+ assertEquals(1, linkItems.length);
+ JMenuItem item = (JMenuItem) linkItems[0];
+ assertEquals("Pfam family", item.getText());
+ // ? no way to verify URL, compiled into link's actionListener
+ }
+
+ @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);
+ }
+
+ @Test(groups = { "Functional" })
+ public void testAddFeatureDetails()
+ {
+ String menuText = MessageManager.getString("label.feature_details");
+
+ /*
+ * with no features, sub-menu should not be created
+ */
+ List features = new ArrayList<>();
+ SequenceI seq = this.alignment.getSequenceAt(0); // FER_CAPAA/1-12
+ testee.addFeatureDetails(features, seq, 10);
+ JMenu menu = findMenu(testee, menuText);
+ assertNull(menu);
+
+ /*
+ * add some features; the menu item text is wrapped in html, and includes
+ * feature type, position, description, group (if not null)
+ */
+ SequenceFeature sf1 = new SequenceFeature("helix", "curly", 2, 6, null);
+ SequenceFeature sf2 = new SequenceFeature("chain", "straight", 1, 1,
+ "uniprot");
+ features.add(sf1);
+ features.add(sf2);
+ testee.addFeatureDetails(features, seq, 10);
+ menu = findMenu(testee, menuText);
+ assertNotNull(menu);
+ assertEquals(2, menu.getItemCount());
+ JMenuItem item = menu.getItem(0);
+ assertEquals("helix 2-6 curly", item.getText());
+ item = menu.getItem(1);
+ assertEquals("chain 1 straight (uniprot)", item.getText());
+
+ /*
+ * long feature descriptions are truncated to 40 characters
+ */
+ sf1.setDescription("this is a quite extraordinarily long description");
+ testee.remove(menu); // don't create the sub-menu twice
+ testee.addFeatureDetails(features, seq, 10);
+ menu = findMenu(testee, menuText);
+ item = menu.getItem(0);
+ assertEquals(
+ "helix 2-6 this is a quite extraordinarily long des...",
+ item.getText());
+ }
+
+ /**
+ * Returns the first component which is a JMenu with the given text
+ *
+ * @param c
+ * @param text
+ * @return
+ */
+ private JMenu findMenu(Container c, String text)
+ {
+ for (int i = 0; i < c.getComponentCount(); i++)
+ {
+ Component comp = c.getComponent(i);
+ if ((comp instanceof JMenu) && ((JMenu) comp).getText().equals(text))
+ {
+ return (JMenu) comp;
+ }
+ }
+ return null;
+ }
+
+ @Test(groups = { "Functional" })
+ public void testAddFeatureDetails_linkedFeatures()
+ {
+ // todo tests that verify menu items for complement features
+ }
}