JAL-2383 restore PID colour threshold from project; enable/disable

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

diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java
index 7d96618..cbbcf70 100755 (executable)
--- a/src/jalview/gui/RedundancyPanel.java
+++ b/src/jalview/gui/RedundancyPanel.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -82,6 +82,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
 
     slider.addChangeListener(new ChangeListener()
     {
+      @Override
       public void stateChanged(ChangeEvent evt)
       {
         valueField.setText(slider.getValue() + "");
@@ -105,6 +106,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
             false);
     frame.addInternalFrameListener(new InternalFrameAdapter()
     {
+      @Override
       public void internalFrameClosing(InternalFrameEvent evt)
       {
         ap.getIdPanel().getIdCanvas().setHighlighted(null);
@@ -125,6 +127,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public void run()
   {
     JProgressBar progress = new JProgressBar();
@@ -171,7 +174,8 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
     progress.setVisible(false);
     progress = null;
 
-    label.setText(MessageManager.getString("label.enter_redundancy_thereshold"));
+    label.setText(MessageManager
+            .getString("label.enter_redundancy_threshold"));
     slider.setVisible(true);
     applyButton.setEnabled(true);
     valueField.setVisible(true);
@@ -206,6 +210,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void applyButton_actionPerformed(ActionEvent e)
   {
     Vector del = new Vector();
@@ -240,7 +245,8 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
         }
       }
 
-      EditCommand cut = new EditCommand(MessageManager.getString("action.remove_redundancy"),
+      EditCommand cut = new EditCommand(
+              MessageManager.getString("action.remove_redundancy"),
               Action.CUT, deleted, 0, width, ap.av.getAlignment());
 
       for (int i = 0; i < del.size(); i++)
@@ -257,7 +263,8 @@ 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());
     }
 
   }
@@ -268,19 +275,22 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void undoButton_actionPerformed(ActionEvent e)
   {
-    if(historyList == null || historyList.isEmpty()){
-        undoButton.setEnabled(false);
-       return;
+    if (historyList == null || historyList.isEmpty())
+    {
+      undoButton.setEnabled(false);
+      return;
     }
-    
+
     CommandI command = historyList.pop();
-    if (ap.av.historyList.contains(command))
+    if (ap.av.getHistoryList().contains(command))
     {
       command.undoCommand(af.getViewAlignments());
-      ap.av.historyList.remove(command);
-      ap.av.firePropertyChange("alignment", null, ap.av.getAlignment().getSequences());
+      ap.av.getHistoryList().remove(command);
+      ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
+              .getSequences());
       af.updateEditMenuBar();
     }
 
@@ -292,22 +302,4 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
     }
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
-   */
-  public void valueField_actionPerformed(ActionEvent e)
-  {
-    try
-    {
-      int i = Integer.parseInt(valueField.getText());
-      slider.setValue(i);
-    } catch (Exception ex)
-    {
-      valueField.setText(slider.getValue() + "");
-    }
-  }
-
 }