X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fgui%2FAlignFrameTest.java;fp=test%2Fjalview%2Fgui%2FAlignFrameTest.java;h=2a768ff6e5942d0f8463e8d3f9368d9e4ffb8216;hb=9c98d4bd666346f6ad3892c5394b7da3be82d93e;hp=d362d35c1d5a2ee1bcb58f3f6db121fcaa2ae28e;hpb=c7b2143c9cf7c5e05ad63251f7d3910751b16d20;p=jalview.git

diff --git a/test/jalview/gui/AlignFrameTest.java b/test/jalview/gui/AlignFrameTest.java
index d362d35..2a768ff 100644
--- a/test/jalview/gui/AlignFrameTest.java
+++ b/test/jalview/gui/AlignFrameTest.java
@@ -79,8 +79,8 @@ public class AlignFrameTest
   }
 
   /**
-   * configure (read-only) properties for test to ensure Consensus is computed for
-   * colour Above PID testing
+   * configure (read-only) properties for test to ensure Consensus is computed
+   * for colour Above PID testing
    */
   @BeforeMethod(alwaysRun = true)
   public void setUp()
@@ -116,13 +116,14 @@ public class AlignFrameTest
   {
     SequenceI seq1 = new Sequence("Seq1", "ABCDEFGHIJ");
     SequenceI seq2 = new Sequence("Seq2", "ABCDEFGHIJ");
-    seq1.addSequenceFeature(new SequenceFeature("Metal", "", 1, 5, 0f, null));
-    seq2.addSequenceFeature(new SequenceFeature("Metal", "", 6, 10, 10f,
-            null));
-    seq1.addSequenceFeature(new SequenceFeature("Turn", "", 2, 4,
-            Float.NaN, null));
-    seq2.addSequenceFeature(new SequenceFeature("Turn", "", 7, 9,
-            Float.NaN, null));
+    seq1.addSequenceFeature(
+            new SequenceFeature("Metal", "", 1, 5, 0f, null));
+    seq2.addSequenceFeature(
+            new SequenceFeature("Metal", "", 6, 10, 10f, null));
+    seq1.addSequenceFeature(
+            new SequenceFeature("Turn", "", 2, 4, Float.NaN, null));
+    seq2.addSequenceFeature(
+            new SequenceFeature("Turn", "", 7, 9, Float.NaN, null));
     AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
     AlignFrame alignFrame = new AlignFrame(al, al.getWidth(),
             al.getHeight());
@@ -156,7 +157,6 @@ public class AlignFrameTest
     assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
             .getNumberOfRegions(), 0);
 
-
     /*
      * threshold Metal to hide features where score < 5
      * seq1 feature in columns 1-5 is hidden
@@ -168,7 +168,8 @@ public class AlignFrameTest
     fc.setThreshold(5f);
     alignFrame.getFeatureRenderer().setColour("Metal", fc);
     assertTrue(alignFrame.hideFeatureColumns("Metal", true));
-    HiddenColumns hidden = alignFrame.getViewport().getAlignment().getHiddenColumns();
+    HiddenColumns hidden = alignFrame.getViewport().getAlignment()
+            .getHiddenColumns();
     assertEquals(hidden.getNumberOfRegions(), 1);
     Iterator<int[]> regions = hidden.iterator();
     int[] next = regions.next();
@@ -182,8 +183,8 @@ public class AlignFrameTest
      */
     alignFrame.getViewport().showAllHiddenColumns();
     assertTrue(alignFrame.hideFeatureColumns("Turn", true));
-    regions = alignFrame.getViewport().getAlignment()
-            .getHiddenColumns().iterator();
+    regions = alignFrame.getViewport().getAlignment().getHiddenColumns()
+            .iterator();
     assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
             .getNumberOfRegions(), 2);
     next = regions.next();
@@ -199,7 +200,8 @@ public class AlignFrameTest
    * <ul>
    * <li>with Apply Colour to All Groups not selected, does not change group
    * colours</li>
-   * <li>with Apply Colour to All Groups selected, does change group colours</li>
+   * <li>with Apply Colour to All Groups selected, does change group
+   * colours</li>
    * <li>in neither case, changes alignment or group colour thresholds (PID or
    * Conservation)</li>
    * </ul>
@@ -225,8 +227,8 @@ public class AlignFrameTest
     af.conservationMenuItem_actionPerformed(true);
     SliderPanel sp = SliderPanel.getSliderPanel();
     assertEquals(sp.getTitle(), MessageManager.formatMessage(
-            "label.conservation_colour_increment",
-            new String[] { "Background" }));
+            "label.conservation_colour_increment", new String[]
+            { "Background" }));
     assertTrue(sp.isForConservation());
     sp.valueChanged(20);
     assertTrue(av.getResidueShading().conservationApplied());
@@ -239,8 +241,8 @@ public class AlignFrameTest
     sp = SliderPanel.getSliderPanel();
     assertFalse(sp.isForConservation());
     assertEquals(sp.getTitle(), MessageManager.formatMessage(
-            "label.percentage_identity_threshold",
-            new String[] { "Background" }));
+            "label.percentage_identity_threshold", new String[]
+            { "Background" }));
     sp.valueChanged(10);
     assertEquals(av.getResidueShading().getThreshold(), 10);
     assertTrue(av.getResidueShading().conservationApplied());
@@ -263,8 +265,8 @@ public class AlignFrameTest
      */
     PopupMenu popupMenu = new PopupMenu(af.alignPanel, al.getSequenceAt(2),
             null);
-    popupMenu.changeColour_actionPerformed(JalviewColourScheme.Strand
-            .toString());
+    popupMenu.changeColour_actionPerformed(
+            JalviewColourScheme.Strand.toString());
     assertTrue(sg.getColourScheme() instanceof StrandColourScheme);
     assertEquals(al.getGroups().size(), 1);
     assertSame(al.getGroups().get(0), sg);
@@ -272,8 +274,8 @@ public class AlignFrameTest
     sp = SliderPanel.getSliderPanel();
     assertTrue(sp.isForConservation());
     assertEquals(sp.getTitle(), MessageManager.formatMessage(
-            "label.conservation_colour_increment",
-            new String[] { sg.getName() }));
+            "label.conservation_colour_increment", new String[]
+            { sg.getName() }));
     sp.valueChanged(30);
     assertTrue(sg.getGroupColourScheme().conservationApplied());
     assertEquals(sg.getGroupColourScheme().getConservationInc(), 30);
@@ -285,8 +287,8 @@ public class AlignFrameTest
     sp = SliderPanel.getSliderPanel();
     assertFalse(sp.isForConservation());
     assertEquals(sp.getTitle(), MessageManager.formatMessage(
-            "label.percentage_identity_threshold",
-            new String[] { sg.getName() }));
+            "label.percentage_identity_threshold", new String[]
+            { sg.getName() }));
     sp.valueChanged(40);
     assertEquals(sg.getGroupColourScheme().getThreshold(), 40);
     // conservation threshold is unchanged:
@@ -546,8 +548,8 @@ public class AlignFrameTest
     av.setSelectionGroup(sg);
     PopupMenu popupMenu = new PopupMenu(af.alignPanel, al.getSequenceAt(0),
             null);
-    popupMenu.changeColour_actionPerformed(JalviewColourScheme.Strand
-            .toString());
+    popupMenu.changeColour_actionPerformed(
+            JalviewColourScheme.Strand.toString());
     assertTrue(sg.getColourScheme() instanceof StrandColourScheme);
     assertEquals(al.getGroups().size(), 1);
     assertSame(al.getGroups().get(0), sg);
@@ -571,8 +573,8 @@ public class AlignFrameTest
     sp = SliderPanel.getSliderPanel();
     assertTrue(sp.isForConservation());
     assertEquals(sp.getTitle(), MessageManager.formatMessage(
-            "label.conservation_colour_increment",
-            new String[] { "Background" }));
+            "label.conservation_colour_increment", new String[]
+            { "Background" }));
 
     /*
      * make a new View, verify alignment and group colour schemes
@@ -601,8 +603,8 @@ public class AlignFrameTest
     sp = SliderPanel.getSliderPanel();
     assertTrue(sp.isForConservation());
     assertEquals(sp.getTitle(), MessageManager.formatMessage(
-            "label.conservation_colour_increment",
-            new String[] { "View 1" }));
+            "label.conservation_colour_increment", new String[]
+            { "View 1" }));
     sp.valueChanged(22);
     assertEquals(av2.getResidueShading().getConservationInc(), 22);
   }