seqs = new ArrayList<>();
testee.configureReferenceAnnotationsMenu(menu, seqs);
assertFalse(menu.isEnabled());
// now try null list
@@ -78,7 +143,7 @@ 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 +164,7 @@ 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 +184,7 @@ 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 +195,9 @@ 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 +207,7 @@ 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 +218,9 @@ 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 +238,7 @@ 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 +251,7 @@ 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 +264,7 @@ 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 +288,7 @@ 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 +297,7 @@ 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 +308,29 @@ 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 +350,8 @@ 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 +361,7 @@ 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 +375,7 @@ 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 +386,14 @@ 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 +413,13 @@ 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 +433,7 @@ 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 +444,14 @@ 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 +471,8 @@ 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 +482,229 @@ 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 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
+ SequenceI seq = seqs.get(0);
+ seq.addDBRef(refs.get(0));
+
+ seq.addDBRef(refs.get(1));
+ seq.addDBRef(refs.get(2));
+ seq.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
+ List noFeatures = Collections. emptyList();
+ testee = new PopupMenu(parentPanel, seq, noFeatures);
+ 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++)
+ {
+ String msg = seq.getName() + " link[" + i + "]";
+ assertEquals(msg, refs.get(i - 1).getSource(),
+ ((JMenuItem) linkItems[i])
+ .getText().split("\\|")[0]);
+ assertEquals(msg, refs.get(i - 1).getAccessionId(),
+ ((JMenuItem) linkItems[i])
+ .getText().split("\\|")[1]);
+ }
+
+ // get the Popup Menu for second sequence
+ seq = seqs.get(1);
+ testee = new PopupMenu(parentPanel, seq, noFeatures);
+ 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++)
+ {
+ String msg = seq.getName() + " link[" + i + "]";
+ assertEquals(msg, refs.get(i + 3).getSource(),
+ ((JMenuItem) linkItems[i])
+ .getText().split("\\|")[0].toUpperCase());
+ assertEquals(msg, 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, seq, noFeatures);
+ seqItems = testee.sequenceMenu.getMenuComponents();
+ linkMenu = (JMenu) seqItems[6];
+ assertFalse(linkMenu.isEnabled());
+
+ }
+
+ /**
+ * Test for adding feature links
+ */
+ @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);
+ }
+
}