Merge branch 'develop' into releases/Release_2_11_Branch

[jalview.git] / test / jalview / gui / PopupMenuTest.java

diff --git a/test/jalview/gui/PopupMenuTest.java b/test/jalview/gui/PopupMenuTest.java
index 8f60021..6f60588 100644 (file)
--- a/test/jalview/gui/PopupMenuTest.java
+++ b/test/jalview/gui/PopupMenuTest.java
@@ -26,6 +26,7 @@ import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertTrue;
 
+import jalview.bin.Cache;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
@@ -34,16 +35,21 @@ import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.io.DataSourceType;
 import jalview.io.FileFormat;
 import jalview.io.FormatAdapter;
+import jalview.urls.api.UrlProviderFactoryI;
+import jalview.urls.desktop.DesktopUrlProviderFactory;
 import jalview.util.MessageManager;
+import jalview.util.UrlConstants;
 
 import java.awt.Component;
 import java.io.IOException;
 import java.util.ArrayList;
+import java.util.Collections;
 import java.util.Iterator;
 import java.util.List;
 
@@ -84,6 +90,25 @@ public class PopupMenuTest
   @BeforeMethod(alwaysRun = true)
   public void setUp() throws IOException
   {
+    Cache.loadProperties("test/jalview/io/testProps.jvprops");
+    String inMenuString = ("EMBL-EBI Search | http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$"
+            + SEQUENCE_ID
+            + "$"
+            + "|"
+            + "UNIPROT | http://www.uniprot.org/uniprot/$" + DB_ACCESSION + "$")
+            + "|"
+            + ("INTERPRO | http://www.ebi.ac.uk/interpro/entry/$"
+                    + DB_ACCESSION + "$")
+            + "|"
+            +
+            // Gene3D entry tests for case (in)sensitivity
+            ("Gene3D | http://gene3d.biochem.ucl.ac.uk/Gene3D/search?sterm=$"
+                    + DB_ACCESSION + "$&mode=protein");
+
+    UrlProviderFactoryI factory = new DesktopUrlProviderFactory(
+            UrlConstants.DEFAULT_LABEL, inMenuString, "");
+    Preferences.sequenceUrlLinks = factory.createUrlProvider();
+
     alignment = new FormatAdapter().readFile(TEST_DATA,
             DataSourceType.PASTE, FileFormat.Fasta);
     AlignFrame af = new AlignFrame(alignment, 700, 500);
@@ -499,17 +524,19 @@ public class PopupMenuTest
 
     // 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));
+    SequenceI seq = seqs.get(0);
+    seq.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));
+    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
-    testee = new PopupMenu(parentPanel, (Sequence) seqs.get(0), links);
+    List<SequenceFeature> noFeatures = Collections.<SequenceFeature> emptyList();
+    testee = new PopupMenu(parentPanel, seq, noFeatures);
     Component[] seqItems = testee.sequenceMenu.getMenuComponents();
     JMenu linkMenu = (JMenu) seqItems[6];
     Component[] linkItems = linkMenu.getMenuComponents();
@@ -523,15 +550,18 @@ public class PopupMenuTest
     // sequence id for each link should match corresponding DB accession id
     for (int i = 1; i < 4; i++)
     {
-      assertEquals(refs.get(i - 1).getSource(), ((JMenuItem) linkItems[i])
+      String msg = seq.getName() + " link[" + i + "]";
+      assertEquals(msg, refs.get(i - 1).getSource(),
+              ((JMenuItem) linkItems[i])
               .getText().split("\\|")[0]);
-      assertEquals(refs.get(i - 1).getAccessionId(),
+      assertEquals(msg, refs.get(i - 1).getAccessionId(),
               ((JMenuItem) linkItems[i])
               .getText().split("\\|")[1]);
     }
 
     // get the Popup Menu for second sequence
-    testee = new PopupMenu(parentPanel, (Sequence) seqs.get(1), links);
+    seq = seqs.get(1);
+    testee = new PopupMenu(parentPanel, seq, noFeatures);
     seqItems = testee.sequenceMenu.getMenuComponents();
     linkMenu = (JMenu) seqItems[6];
     linkItems = linkMenu.getMenuComponents();
@@ -545,9 +575,11 @@ public class PopupMenuTest
     // 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])
+      String msg = seq.getName() + " link[" + i + "]";
+      assertEquals(msg, refs.get(i + 3).getSource(),
+              ((JMenuItem) linkItems[i])
               .getText().split("\\|")[0].toUpperCase());
-      assertEquals(refs.get(i + 3).getAccessionId(),
+      assertEquals(msg, refs.get(i + 3).getAccessionId(),
               ((JMenuItem) linkItems[i]).getText().split("\\|")[1]);
     }
 
@@ -556,8 +588,7 @@ public class PopupMenuTest
     nomatchlinks.add("NOMATCH | http://www.uniprot.org/uniprot/$"
             + DB_ACCESSION + "$");
 
-    testee = new PopupMenu(parentPanel, (Sequence) seqs.get(0),
-            nomatchlinks);
+    testee = new PopupMenu(parentPanel, seq, noFeatures);
     seqItems = testee.sequenceMenu.getMenuComponents();
     linkMenu = (JMenu) seqItems[6];
     assertFalse(linkMenu.isEnabled());
@@ -597,7 +628,7 @@ public class PopupMenuTest
             .revealAllHiddenColumns(sel);
 
     // get the Popup Menu for 7th sequence - no insertions
-    testee = new PopupMenu(parentPanel, (Sequence) seqs.get(7), null);
+    testee = new PopupMenu(parentPanel, seqs.get(7), null);
     testee.hideInsertions_actionPerformed(null);
     
     HiddenColumns hidden = parentPanel.av.getAlignment().getHiddenColumns();
@@ -605,7 +636,7 @@ public class PopupMenuTest
     assertFalse(it.hasNext());
 
     // get the Popup Menu for GappySeq - this time we have insertions
-    testee = new PopupMenu(parentPanel, (Sequence) seqs.get(4), null);
+    testee = new PopupMenu(parentPanel, seqs.get(4), null);
     testee.hideInsertions_actionPerformed(null);
     hidden = parentPanel.av.getAlignment().getHiddenColumns();
     it = hidden.iterator();
@@ -655,7 +686,7 @@ public class PopupMenuTest
     hidden.hideColumns(31, 40);
 
     // get the Popup Menu for LessGappySeq in the sequence group
-    testee = new PopupMenu(parentPanel, (Sequence) seqs.get(5), null);
+    testee = new PopupMenu(parentPanel, seqs.get(5), null);
     testee.hideInsertions_actionPerformed(null);
     hidden = parentPanel.av.getAlignment().getHiddenColumns();
     it = hidden.iterator();