From 0a9a0c390bce6a5b374f4d559d0b93797e5d36d0 Mon Sep 17 00:00:00 2001
From: kiramt <k.mourao@dundee.ac.uk>
Date: Fri, 21 Oct 2016 08:08:23 +0100
Subject: [PATCH] Created (failing) unit test for addFeatureLinks

---
 test/jalview/gui/PopupMenuTest.java |   89 +++++++++++++++++++++++++++++++++++
 1 file changed, 89 insertions(+)

diff --git a/test/jalview/gui/PopupMenuTest.java b/test/jalview/gui/PopupMenuTest.java
index edf3202..fe52e92 100644
--- a/test/jalview/gui/PopupMenuTest.java
+++ b/test/jalview/gui/PopupMenuTest.java
@@ -27,6 +27,9 @@ import static org.testng.AssertJUnit.assertTrue;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.FormatAdapter;
@@ -440,4 +443,90 @@ public class PopupMenuTest
     assertEquals(JSeparator.HORIZONTAL,
             ((JSeparator) hideOptions[1]).getOrientation());
   }
+
+  /**
+   * Test for adding feature links
+   */
+  @Test(groups = { "Functional" })
+  public void testAddFeatureLinks()
+  {
+    // sequences from the alignment
+    List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
+
+    // create list of links and list of DBRefs
+    List<String> links = new ArrayList<String>();
+    List<DBRefEntry> refs = new ArrayList<DBRefEntry>();
+
+    // 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/$SEQUENCE_ID$");
+    links.add("INTERPRO | http://www.ebi.ac.uk/interpro/entry/$SEQUENCE_ID$");
+    // Gene3D entry tests for case (in)sensitivity
+    links.add("Gene3D | http://gene3d.biochem.ucl.ac.uk/Gene3D/search?sterm=$SEQUENCE_ID$&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++)
+    {
+      assertEquals(refs.get(i).getSource(), ((JMenuItem) linkItems[i])
+              .getText().split(" \\|")[0]);
+      assertEquals(refs.get(i).getAccessionId(), ((JMenuItem) linkItems[i])
+              .getText().split(" \\|")[1]);
+    }
+
+    // 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 = 5; i < 7; i++)
+    {
+      assertEquals(refs.get(i).getSource(), ((JMenuItem) linkItems[i - 4])
+              .getText().split(" \\|")[0]);
+      assertEquals(refs.get(i).getAccessionId(),
+              ((JMenuItem) linkItems[i - 4]).getText().split(" \\|")[1]);
+    }
+
+
+  }
 }
-- 
1.7.10.2