X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fgui%2FPopupMenuTest.java;h=edf320277fc35fe5d30c58cc9ac789862c627604;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=1d219df089e8d20c0ba0e43b6522ea918b74efbd;hpb=c46ac1bbccd595dfeb504220b465023d38815223;p=jalview.git

diff --git a/test/jalview/gui/PopupMenuTest.java b/test/jalview/gui/PopupMenuTest.java
index 1d219df..edf3202 100644
--- a/test/jalview/gui/PopupMenuTest.java
+++ b/test/jalview/gui/PopupMenuTest.java
@@ -1,12 +1,35 @@
+/*
+ * 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 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.SequenceI;
 import jalview.io.AppletFormatAdapter;
+import jalview.io.FormatAdapter;
 import jalview.util.MessageManager;
 
 import java.awt.Component;
@@ -19,8 +42,8 @@ import javax.swing.JMenuItem;
 import javax.swing.JPopupMenu;
 import javax.swing.JSeparator;
 
-import org.junit.Before;
-import org.junit.Test;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
 
 public class PopupMenuTest
 {
@@ -39,10 +62,10 @@ public class PopupMenuTest
 
   PopupMenu testee = null;
 
-  @Before
+  @BeforeMethod(alwaysRun = true)
   public void setUp() throws IOException
   {
-    alignment = new jalview.io.FormatAdapter().readFile(TEST_DATA,
+    alignment = new FormatAdapter().readFile(TEST_DATA,
             AppletFormatAdapter.PASTE, "FASTA");
     AlignFrame af = new AlignFrame(alignment, 700, 500);
     parentPanel = new AlignmentPanel(af, af.getViewport());
@@ -50,27 +73,24 @@ public class PopupMenuTest
     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();
     List<SequenceI> seqs = new ArrayList<SequenceI>();
     testee.configureReferenceAnnotationsMenu(menu, seqs);
     assertFalse(menu.isEnabled());
-    assertEquals(
-            MessageManager.getString("label.add_reference_annotations"),
-            menu.getText());
     // now try null list
     menu.setEnabled(true);
-    testee.configureReferenceAnnotationsMenu(menu, seqs);
+    testee.configureReferenceAnnotationsMenu(menu, null);
     assertFalse(menu.isEnabled());
   }
 
@@ -79,18 +99,17 @@ 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();
-    List<SequenceI> seqs = new ArrayList<SequenceI>();
 
     /*
      * Initial state is that sequences have annotations, and have dataset
      * sequences, but the dataset sequences have no annotations. Hence nothing
      * to add.
      */
-    seqs = parentPanel.getAlignment().getSequences();
+    List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
 
     testee.configureReferenceAnnotationsMenu(menu, seqs);
     assertFalse(menu.isEnabled());
@@ -101,16 +120,16 @@ 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();
-    List<SequenceI> seqs = new ArrayList<SequenceI>();
+    List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
+
+    // make up new annotations and add to dataset sequences, sequences and
+    // alignment
+    attachReferenceAnnotations(seqs, true, true);
 
-    seqs = parentPanel.getAlignment().getSequences();
-    // copy annotation from sequence to dataset
-    seqs.get(1).getDatasetSequence()
-            .addAlignmentAnnotation(seqs.get(1).getAnnotation()[0]);
     testee.configureReferenceAnnotationsMenu(menu, seqs);
     assertFalse(menu.isEnabled());
   }
@@ -121,40 +140,120 @@ 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();
     List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
+
     // make up new annotations and add to dataset sequences
+    attachReferenceAnnotations(seqs, false, false);
+
+    testee.configureReferenceAnnotationsMenu(menu, seqs);
+    assertTrue(menu.isEnabled());
+    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());
+  }
+
+  /**
+   * Test building the 'add reference annotations' menu for the case where
+   * several reference annotations are on the dataset and the sequences but not
+   * 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" })
+  public void testConfigureReferenceAnnotationsMenu_notOnAlignment()
+  {
+    JMenuItem menu = new JMenuItem();
+    List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
+
+    // make up new annotations and add to dataset sequences and sequences
+    attachReferenceAnnotations(seqs, true, false);
+
+    testee.configureReferenceAnnotationsMenu(menu, seqs);
+    assertTrue(menu.isEnabled());
+    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());
+  }
 
+  /**
+   * Generate annotations and add to dataset sequences and (optionally)
+   * sequences and/or alignment
+   * 
+   * @param seqs
+   * @param addToSequence
+   * @param addToAlignment
+   */
+  private void attachReferenceAnnotations(List<SequenceI> seqs,
+          boolean addToSequence, boolean addToAlignment)
+  {
     // 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)
+    {
+      seqs.get(0).addAlignmentAnnotation(annotation);
+    }
+    if (addToAlignment)
+    {
+      this.alignment.addAnnotation(annotation);
+    }
 
     // PDB.Temp on Sequence1
     annotation = new AlignmentAnnotation("Temp", "", 0);
-    annotation.setCalcId("PBD");
+    annotation.setCalcId("PDB");
     seqs.get(1).getDatasetSequence().addAlignmentAnnotation(annotation);
+    if (addToSequence)
+    {
+      seqs.get(1).addAlignmentAnnotation(annotation);
+    }
+    if (addToAlignment)
+    {
+      this.alignment.addAnnotation(annotation);
+    }
 
     // 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)
+    {
+      seqs.get(0).addAlignmentAnnotation(annotation);
+    }
+    if (addToAlignment)
+    {
+      this.alignment.addAnnotation(annotation);
+    }
+  }
 
-    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>";
-    assertEquals(expected, menu.getToolTipText());
+  /**
+   * Test building the 'add reference annotations' menu for the case where there
+   * are two alignment views:
+   * <ul>
+   * <li>in one view, reference annotations have been added (are on the
+   * datasets, sequences and alignment)</li>
+   * <li>in the current view, reference annotations are on the dataset and
+   * sequence, but not the alignment</li>
+   * </ul>
+   * The menu item should be enabled, and acquire a tooltip which lists the
+   * annotation sources (calcIds) and type (labels).
+   */
+  @Test(groups = { "Functional" })
+  public void testConfigureReferenceAnnotationsMenu_twoViews()
+  {
   }
 
   /**
    * Test for building menu options including 'show' and 'hide' annotation
    * types.
    */
-  @Test
+  @Test(groups = { "Functional" })
   public void testBuildAnnotationTypesMenus()
   {
     JMenu showMenu = new JMenu();
@@ -165,28 +264,29 @@ public class PopupMenuTest
 
     // PDB.secondary structure on Sequence0
     AlignmentAnnotation annotation = new AlignmentAnnotation(
-            "secondary structure", "", 0);
+            "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", "", 0);
+    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", "", 0);
+    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", "", 0);
+    annotation = new AlignmentAnnotation("Temp", "", new Annotation[] {});
     annotation.setCalcId("PDB");
     annotation.visible = true;
     seqs.get(1).addAlignmentAnnotation(annotation);
@@ -206,8 +306,7 @@ 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());
@@ -217,8 +316,7 @@ 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());
@@ -232,7 +330,7 @@ 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();
@@ -243,14 +341,14 @@ public class PopupMenuTest
 
     // PDB.secondary structure on Sequence0
     AlignmentAnnotation annotation = new AlignmentAnnotation(
-            "secondary structure", "", 0);
+            "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", "", 0);
+    annotation = new AlignmentAnnotation("Temp", "", new Annotation[] {});
     annotation.setCalcId("PDB");
     annotation.visible = true;
     seqs.get(1).addAlignmentAnnotation(annotation);
@@ -289,7 +387,7 @@ 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();
@@ -300,14 +398,14 @@ public class PopupMenuTest
 
     // PDB.secondary structure on Sequence0
     AlignmentAnnotation annotation = new AlignmentAnnotation(
-            "secondary structure", "", 0);
+            "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", "", 0);
+    annotation = new AlignmentAnnotation("Temp", "", new Annotation[] {});
     annotation.setCalcId("PDB2");
     annotation.visible = false;
     seqs.get(1).addAlignmentAnnotation(annotation);