X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FRedundancyPanel.java;h=a5b652fb40d0da1b6423373c08e379b6806c7802;hb=c932f0e85a8852824cdd8ce790af68682732c85c;hp=6be416c59ddddbee6d9bc979bc2df0ed9528badd;hpb=7dc7fb2a35c435d825bc91c5ae60ec6073419a69;p=jalview.git

diff --git a/src/jalview/appletgui/RedundancyPanel.java b/src/jalview/appletgui/RedundancyPanel.java
index 6be416c..a5b652f 100644
--- a/src/jalview/appletgui/RedundancyPanel.java
+++ b/src/jalview/appletgui/RedundancyPanel.java
@@ -40,8 +40,8 @@ import java.util.List;
 import java.util.Stack;
 import java.util.Vector;
 
-public class RedundancyPanel extends SliderPanel implements Runnable,
-        WindowListener
+public class RedundancyPanel extends SliderPanel
+        implements Runnable, WindowListener
 {
   Stack historyList = new Stack(); // simpler than synching with alignFrame.
 
@@ -63,8 +63,8 @@ public class RedundancyPanel extends SliderPanel implements Runnable,
     applyButton.setVisible(true);
     allGroupsCheck.setVisible(false);
 
-    label.setText(MessageManager
-            .getString("label.enter_redundancy_threshold"));
+    label.setText(
+            MessageManager.getString("label.enter_redundancy_threshold"));
     valueField.setText("100");
 
     slider.setVisibleAmount(1);
@@ -140,15 +140,15 @@ public class RedundancyPanel extends SliderPanel implements Runnable,
 
     redundancy = AlignSeq.computeRedundancyMatrix(originalSequences,
             omitHidden, start, end, false);
-    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);
 
     validate();
     sliderValueChanged();
-    // System.out.println("blob done "+ (System.currentTimeMillis()-start));
+    // jalview.bin.Console.outPrintln("blob done "+ (System.currentTimeMillis()-start));
   }
 
   void sliderValueChanged()
@@ -160,7 +160,7 @@ public class RedundancyPanel extends SliderPanel 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])
@@ -227,8 +227,8 @@ public class RedundancyPanel extends SliderPanel 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());
     }
 
   }
@@ -243,11 +243,11 @@ public class RedundancyPanel extends SliderPanel implements Runnable,
     {
       ap.av.getHistoryList().remove(command);
       ap.alignFrame.updateEditMenuBar();
-      ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
-              .getSequences());
+      ap.av.firePropertyChange("alignment", null,
+              ap.av.getAlignment().getSequences());
     }
 
-    ap.paintAlignment(true);
+    ap.paintAlignment(true, true);
 
     if (historyList.size() == 0)
     {