X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fgui%2FPopupMenuTest.java;h=922d45758d1b2c784e40848d15fc3de0141716a8;hb=483e7163b1fb8d4bcb9393014816c944befce328;hp=e1f0708f4938cde53ffa6f23d4defc1d14c6e01a;hpb=001922aefa2bcf95471761473d25f4949635691c;p=jalview.git

diff --git a/test/jalview/gui/PopupMenuTest.java b/test/jalview/gui/PopupMenuTest.java
index e1f0708..922d457 100644
--- a/test/jalview/gui/PopupMenuTest.java
+++ b/test/jalview/gui/PopupMenuTest.java
@@ -1,8 +1,42 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.gui;
 
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertTrue;
+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;
+
+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.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FormatAdapter;
+import jalview.util.MessageManager;
 
 import java.awt.Component;
 import java.io.IOException;
@@ -14,18 +48,20 @@ import javax.swing.JMenuItem;
 import javax.swing.JPopupMenu;
 import javax.swing.JSeparator;
 
-import org.junit.Before;
-import org.junit.Test;
-
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.SequenceI;
-import jalview.io.AppletFormatAdapter;
-import jalview.io.FormatAdapter;
+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"
@@ -41,26 +77,26 @@ public class PopupMenuTest
 
   PopupMenu testee = null;
 
-  @Before
+  @BeforeMethod(alwaysRun = true)
   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);
     int i = 0;
     for (SequenceI seq : alignment.getSequences())
     {
-      final AlignmentAnnotation annotation = new AlignmentAnnotation("label" + i,
-              "desc" + i, i);
+      final AlignmentAnnotation annotation = new AlignmentAnnotation(
+              "label" + i, "desc" + i, i);
       annotation.setCalcId("calcId" + i);
       seq.addAlignmentAnnotation(annotation);
       annotation.setSequenceRef(seq);
     }
   }
 
-  @Test
+  @Test(groups = { "Functional" })
   public void testConfigureReferenceAnnotationsMenu_noSequenceSelected()
   {
     JMenuItem menu = new JMenuItem();
@@ -78,7 +114,7 @@ public class PopupMenuTest
    * are no reference annotations to add to the alignment. The menu item should
    * be disabled.
    */
-  @Test
+  @Test(groups = { "Functional" })
   public void testConfigureReferenceAnnotationsMenu_noReferenceAnnotations()
   {
     JMenuItem menu = new JMenuItem();
@@ -99,7 +135,7 @@ public class PopupMenuTest
    * reference annotations are already on the alignment. The menu item should be
    * disabled.
    */
-  @Test
+  @Test(groups = { "Functional" })
   public void testConfigureReferenceAnnotationsMenu_alreadyAdded()
   {
     JMenuItem menu = new JMenuItem();
@@ -119,7 +155,7 @@ public class PopupMenuTest
    * The menu item should be enabled, and acquire a tooltip which lists the
    * annotation sources (calcIds) and type (labels).
    */
-  @Test
+  @Test(groups = { "Functional" })
   public void testConfigureReferenceAnnotationsMenu()
   {
     JMenuItem menu = new JMenuItem();
@@ -130,7 +166,9 @@ public class PopupMenuTest
 
     testee.configureReferenceAnnotationsMenu(menu, seqs);
     assertTrue(menu.isEnabled());
-    String expected = "<html><table width=350 border=0><tr><td>Add annotations for<br/>JMOL/secondary structure<br/>PBD/Temp</td></tr></table></html>";
+    String s = MessageManager.getString("label.add_annotations_for");
+    String expected = "<html><style> p.ttip {width: 350; text-align: justify; word-wrap: break-word;}</style><p class=\"ttip\">"
+            + s + "<br/>Jmol/secondary structure<br/>PDB/Temp</p></html>";
     assertEquals(expected, menu.getToolTipText());
   }
 
@@ -140,7 +178,7 @@ 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
+  @Test(groups = { "Functional" })
   public void testConfigureReferenceAnnotationsMenu_notOnAlignment()
   {
     JMenuItem menu = new JMenuItem();
@@ -151,7 +189,9 @@ public class PopupMenuTest
 
     testee.configureReferenceAnnotationsMenu(menu, seqs);
     assertTrue(menu.isEnabled());
-    String expected = "<html><table width=350 border=0><tr><td>Add annotations for<br/>JMOL/secondary structure<br/>PBD/Temp</td></tr></table></html>";
+    String s = MessageManager.getString("label.add_annotations_for");
+    String expected = "<html><style> p.ttip {width: 350; text-align: justify; word-wrap: break-word;}</style><p class=\"ttip\">"
+            + s + "<br/>Jmol/secondary structure<br/>PDB/Temp</p></html>";
     assertEquals(expected, menu.getToolTipText());
   }
 
@@ -169,7 +209,7 @@ 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 +222,7 @@ 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 +235,7 @@ 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 +259,7 @@ public class PopupMenuTest
    * The menu item should be enabled, and acquire a tooltip which lists the
    * annotation sources (calcIds) and type (labels).
    */
-  @Test
+  @Test(groups = { "Functional" })
   public void testConfigureReferenceAnnotationsMenu_twoViews()
   {
   }
@@ -228,7 +268,7 @@ public class PopupMenuTest
    * Test for building menu options including 'show' and 'hide' annotation
    * types.
    */
-  @Test
+  @Test(groups = { "Functional" })
   public void testBuildAnnotationTypesMenus()
   {
     JMenu showMenu = new JMenu();
@@ -239,32 +279,29 @@ 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 +321,7 @@ public class PopupMenuTest
 
     assertEquals(4, showOptions.length); // includes 'All' and separator
     assertEquals(4, hideOptions.length);
-    assertEquals("All",
-            ((JMenuItem) showOptions[0]).getText());
+    assertEquals("All", ((JMenuItem) showOptions[0]).getText());
     assertTrue(showOptions[1] instanceof JPopupMenu.Separator);
     assertEquals(JSeparator.HORIZONTAL,
             ((JSeparator) showOptions[1]).getOrientation());
@@ -295,8 +331,7 @@ 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 +345,7 @@ public class PopupMenuTest
   /**
    * Test for building menu options with only 'hide' annotation types enabled.
    */
-  @Test
+  @Test(groups = { "Functional" })
   public void testBuildAnnotationTypesMenus_showDisabled()
   {
     JMenu showMenu = new JMenu();
@@ -321,16 +356,14 @@ 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);
@@ -369,7 +402,7 @@ public class PopupMenuTest
   /**
    * Test for building menu options with only 'show' annotation types enabled.
    */
-  @Test
+  @Test(groups = { "Functional" })
   public void testBuildAnnotationTypesMenus_hideDisabled()
   {
     JMenu showMenu = new JMenu();
@@ -380,16 +413,14 @@ 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);
@@ -424,4 +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());
+
+  }
 }