X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fgui%2FPopupMenuTest.java;h=922d45758d1b2c784e40848d15fc3de0141716a8;hb=483e7163b1fb8d4bcb9393014816c944befce328;hp=0ac7a7edb441f2e760e1459681cfa18d3f744be8;hpb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;p=jalview.git

diff --git a/test/jalview/gui/PopupMenuTest.java b/test/jalview/gui/PopupMenuTest.java
index 0ac7a7e..922d457 100644
--- a/test/jalview/gui/PopupMenuTest.java
+++ b/test/jalview/gui/PopupMenuTest.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,6 +20,8 @@
  */
 package jalview.gui;
 
+import static jalview.util.UrlConstants.DB_ACCESSION;
+import static jalview.util.UrlConstants.SEQUENCE_ID;
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertTrue;
@@ -27,8 +29,12 @@ 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.DataSourceType;
+import jalview.io.FileFormat;
 import jalview.io.FormatAdapter;
 import jalview.util.MessageManager;
 
@@ -42,11 +48,20 @@ import javax.swing.JMenuItem;
 import javax.swing.JPopupMenu;
 import javax.swing.JSeparator;
 
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
 public class PopupMenuTest
 {
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   // 4 sequences x 13 positions
   final static String TEST_DATA = ">FER_CAPAA Ferredoxin\n"
           + "TIETHKEAELVG-\n"
@@ -66,7 +81,7 @@ public class PopupMenuTest
   public void setUp() throws IOException
   {
     alignment = new FormatAdapter().readFile(TEST_DATA,
-            AppletFormatAdapter.PASTE, "FASTA");
+            DataSourceType.PASTE, FileFormat.Fasta);
     AlignFrame af = new AlignFrame(alignment, 700, 500);
     parentPanel = new AlignmentPanel(af, af.getViewport());
     testee = new PopupMenu(parentPanel, null, null);
@@ -440,4 +455,105 @@ 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/$" + DB_ACCESSION
+            + "$");
+    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++)
+    {
+      assertEquals(refs.get(i - 1).getSource(), ((JMenuItem) linkItems[i])
+              .getText().split("\\|")[0]);
+      assertEquals(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);
+    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<String> nomatchlinks = new ArrayList<String>();
+    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());
+
+  }
 }