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

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

diff --git a/src/jalview/gui/SliderPanel.java b/src/jalview/gui/SliderPanel.java
index 81b3bd3..af77c48 100755 (executable)
--- a/src/jalview/gui/SliderPanel.java
+++ b/src/jalview/gui/SliderPanel.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * 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.
  * 
@@ -20,16 +20,20 @@
  */
 package jalview.gui;
 
-import java.util.*;
+import jalview.datamodel.SequenceGroup;
+import jalview.jbgui.GSliderPanel;
+import jalview.schemes.ColourSchemeI;
+import jalview.util.MessageManager;
 
-import java.awt.event.*;
-import javax.swing.*;
-import javax.swing.event.*;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.beans.PropertyVetoException;
+import java.util.Iterator;
 
-import jalview.datamodel.*;
-import jalview.jbgui.*;
-import jalview.schemes.*;
-import jalview.util.MessageManager;
+import javax.swing.JInternalFrame;
+import javax.swing.JLayeredPane;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
 
 /**
  * DOCUMENT ME!
@@ -87,6 +91,7 @@ public class SliderPanel extends GSliderPanel
 
     slider.addChangeListener(new ChangeListener()
     {
+      @Override
       public void stateChanged(ChangeEvent evt)
       {
         valueField.setText(slider.getValue() + "");
@@ -96,6 +101,7 @@ public class SliderPanel extends GSliderPanel
 
     slider.addMouseListener(new MouseAdapter()
     {
+      @Override
       public void mouseReleased(MouseEvent evt)
       {
         ap.paintAlignment(true);
@@ -136,7 +142,10 @@ public class SliderPanel extends GSliderPanel
       sp.cs = cs;
     }
 
-    conservationSlider.setTitle(MessageManager.formatMessage("label.conservation_colour_increment", new String[]{source}));
+    conservationSlider
+            .setTitle(MessageManager.formatMessage(
+                    "label.conservation_colour_increment",
+                    new String[] { source }));
 
     if (ap.av.getAlignment().getGroups() != null)
     {
@@ -150,6 +159,28 @@ public class SliderPanel extends GSliderPanel
     return sp.getValue();
   }
 
+  public static void hidePIDSlider()
+  {
+    try
+    {
+      PIDSlider.setClosed(true);
+      PIDSlider = null;
+    } catch (PropertyVetoException ex)
+    {
+    }
+  }
+
+  public static void hideConservationSlider()
+  {
+    try
+    {
+      conservationSlider.setClosed(true);
+      conservationSlider = null;
+    } catch (PropertyVetoException ex)
+    {
+    }
+  }
+
   /**
    * DOCUMENT ME!
    */
@@ -170,6 +201,7 @@ public class SliderPanel extends GSliderPanel
       conservationSlider
               .addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
               {
+                @Override
                 public void internalFrameClosed(
                         javax.swing.event.InternalFrameEvent e)
                 {
@@ -212,7 +244,10 @@ public class SliderPanel extends GSliderPanel
       pid.cs = cs;
     }
 
-    PIDSlider.setTitle(MessageManager.formatMessage("label.percentage_identity_thereshold", new String[]{source}));
+    PIDSlider
+            .setTitle(MessageManager.formatMessage(
+                    "label.percentage_identity_threshold",
+                    new String[] { source }));
 
     if (ap.av.getAlignment().getGroups() != null)
     {
@@ -247,6 +282,7 @@ public class SliderPanel extends GSliderPanel
       PIDSlider
               .addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
               {
+                @Override
                 public void internalFrameClosed(
                         javax.swing.event.InternalFrameEvent e)
                 {
@@ -286,13 +322,15 @@ public class SliderPanel extends GSliderPanel
       }
       else
       {
-        toChange.setThreshold(i, ap.av.getIgnoreGapsConsensus());
+        toChange.setThreshold(i, ap.av.isIgnoreGapsConsensus());
       }
       if (allGroups != null && allGroups.hasNext())
       {
         while ((toChange = allGroups.next().cs) == null
                 && allGroups.hasNext())
+        {
           ;
+        }
       }
       else
       {
@@ -300,7 +338,7 @@ public class SliderPanel extends GSliderPanel
       }
     }
 
-    ap.seqPanel.seqCanvas.repaint();
+    ap.getSeqPanel().seqCanvas.repaint();
   }
 
   /**
@@ -317,24 +355,6 @@ public class SliderPanel extends GSliderPanel
   /**
    * DOCUMENT ME!
    * 
-   * @param e
-   *          DOCUMENT ME!
-   */
-  public void valueField_actionPerformed(ActionEvent e)
-  {
-    try
-    {
-      int i = Integer.parseInt(valueField.getText());
-      slider.setValue(i);
-    } catch (NumberFormatException ex)
-    {
-      valueField.setText(slider.getValue() + "");
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
    * @param value
    *          DOCUMENT ME!
    */
@@ -353,6 +373,7 @@ public class SliderPanel extends GSliderPanel
     return Integer.parseInt(valueField.getText());
   }
 
+  @Override
   public void slider_mouseReleased(MouseEvent e)
   {
     if (ap.overviewPanel != null)