JAL-2089 patch broken merge to master for Release 2.10.0b1

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

diff --git a/test/jalview/gui/PopupMenuTest.java b/test/jalview/gui/PopupMenuTest.java
index 82fcbc8..edf3202 100644 (file)
--- a/test/jalview/gui/PopupMenuTest.java
+++ b/test/jalview/gui/PopupMenuTest.java
@@ -1,3 +1,23 @@
+/*
+ * 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.testng.AssertJUnit.assertEquals;
@@ -42,7 +62,7 @@ public class PopupMenuTest
 
   PopupMenu testee = null;
 
- @BeforeMethod(alwaysRun = true)
+  @BeforeMethod(alwaysRun = true)
   public void setUp() throws IOException
   {
     alignment = new FormatAdapter().readFile(TEST_DATA,
@@ -53,15 +73,15 @@ 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(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testConfigureReferenceAnnotationsMenu_noSequenceSelected()
   {
     JMenuItem menu = new JMenuItem();
@@ -79,7 +99,7 @@ public class PopupMenuTest
    * are no reference annotations to add to the alignment. The menu item should
    * be disabled.
    */
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testConfigureReferenceAnnotationsMenu_noReferenceAnnotations()
   {
     JMenuItem menu = new JMenuItem();
@@ -100,7 +120,7 @@ public class PopupMenuTest
    * reference annotations are already on the alignment. The menu item should be
    * disabled.
    */
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testConfigureReferenceAnnotationsMenu_alreadyAdded()
   {
     JMenuItem menu = new JMenuItem();
@@ -120,7 +140,7 @@ public class PopupMenuTest
    * The menu item should be enabled, and acquire a tooltip which lists the
    * annotation sources (calcIds) and type (labels).
    */
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testConfigureReferenceAnnotationsMenu()
   {
     JMenuItem menu = new JMenuItem();
@@ -143,7 +163,7 @@ 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(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testConfigureReferenceAnnotationsMenu_notOnAlignment()
   {
     JMenuItem menu = new JMenuItem();
@@ -224,7 +244,7 @@ public class PopupMenuTest
    * The menu item should be enabled, and acquire a tooltip which lists the
    * annotation sources (calcIds) and type (labels).
    */
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testConfigureReferenceAnnotationsMenu_twoViews()
   {
   }
@@ -233,7 +253,7 @@ public class PopupMenuTest
    * Test for building menu options including 'show' and 'hide' annotation
    * types.
    */
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testBuildAnnotationTypesMenus()
   {
     JMenu showMenu = new JMenu();
@@ -244,32 +264,29 @@ 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);
@@ -289,8 +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());
@@ -300,8 +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());
@@ -315,7 +330,7 @@ public class PopupMenuTest
   /**
    * Test for building menu options with only 'hide' annotation types enabled.
    */
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testBuildAnnotationTypesMenus_showDisabled()
   {
     JMenu showMenu = new JMenu();
@@ -326,16 +341,14 @@ 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);
@@ -374,7 +387,7 @@ public class PopupMenuTest
   /**
    * Test for building menu options with only 'show' annotation types enabled.
    */
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testBuildAnnotationTypesMenus_hideDisabled()
   {
     JMenu showMenu = new JMenu();
@@ -385,16 +398,14 @@ 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);