JAL-3116 parse EMBL XML with JAXB (todo: update unit tests)

[jalview.git] / src / jalview / gui / RedundancyPanel.java

diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java
index cbbcf70..c4390c0 100755 (executable)
--- a/src/jalview/gui/RedundancyPanel.java
+++ b/src/jalview/gui/RedundancyPanel.java
@@ -54,7 +54,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
 
   AlignmentPanel ap;
 
-  Stack<CommandI> historyList = new Stack<CommandI>();
+  Stack<CommandI> historyList = new Stack<>();
 
   // simpler than synching with alignFrame.
 
@@ -101,9 +101,10 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
 
     frame = new JInternalFrame();
     frame.setContentPane(this);
-    Desktop.addInternalFrame(frame, MessageManager
-            .getString("label.redundancy_threshold_selection"), 400, 100,
-            false);
+    Desktop.addInternalFrame(frame,
+            MessageManager
+                    .getString("label.redundancy_threshold_selection"),
+            400, 100, false);
     frame.addInternalFrameListener(new InternalFrameAdapter()
     {
       @Override
@@ -174,8 +175,8 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
     progress.setVisible(false);
     progress = null;
 
-    label.setText(MessageManager
-            .getString("label.enter_redundancy_threshold"));
+    label.setText(
+            MessageManager.getString("label.enter_redundancy_threshold"));
     slider.setVisible(true);
     applyButton.setEnabled(true);
     valueField.setVisible(true);
@@ -193,7 +194,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
     }
 
     float value = slider.getValue();
-    List<SequenceI> redundantSequences = new ArrayList<SequenceI>();
+    List<SequenceI> redundantSequences = new ArrayList<>();
     for (int i = 0; i < redundancy.length; i++)
     {
       if (value <= redundancy[i])
@@ -263,8 +264,8 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
       ap.alignFrame.addHistoryItem(cut);
 
       PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true);
-      ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
-              .getSequences());
+      ap.av.firePropertyChange("alignment", null,
+              ap.av.getAlignment().getSequences());
     }
 
   }
@@ -289,12 +290,12 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
     {
       command.undoCommand(af.getViewAlignments());
       ap.av.getHistoryList().remove(command);
-      ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
-              .getSequences());
+      ap.av.firePropertyChange("alignment", null,
+              ap.av.getAlignment().getSequences());
       af.updateEditMenuBar();
     }
 
-    ap.paintAlignment(true);
+    ap.paintAlignment(true, true);
 
     if (historyList.size() == 0)
     {