X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSliderPanel.java;h=31ad0836f03accf1c9ceac9c7334cbfad043835d;hb=47806656477f02076cac0467c7374e231a59ab7e;hp=ec53e93e1e96e0db1b879ff24b694a46a8674ac6;hpb=163ed5b997bbda48e4cdd950e87a8fe01baae7fb;p=jalview.git

diff --git a/src/jalview/gui/SliderPanel.java b/src/jalview/gui/SliderPanel.java
index ec53e93..31ad083 100755
--- a/src/jalview/gui/SliderPanel.java
+++ b/src/jalview/gui/SliderPanel.java
@@ -44,14 +44,11 @@ import javax.swing.event.InternalFrameEvent;
  * @author $author$
  * @version $Revision$
  */
+@SuppressWarnings("serial")
 public class SliderPanel extends GSliderPanel
 {
   private static final String BACKGROUND = "Background";
 
-  static JInternalFrame conservationSlider;
-
-  static JInternalFrame PIDSlider;
-
   AlignmentPanel ap;
 
   boolean forConservation = true;
@@ -65,6 +62,12 @@ public class SliderPanel extends GSliderPanel
    */
   public static SliderPanel getSliderPanel()
   {
+
+    JInternalFrame conservationSlider = Desktop
+            .getInstance().conservationSlider;
+
+    JInternalFrame PIDSlider = Desktop.getInstance().PIDSlider;
+
     if (conservationSlider != null && conservationSlider.isVisible())
     {
       return (SliderPanel) conservationSlider.getContentPane();
@@ -99,15 +102,15 @@ public class SliderPanel extends GSliderPanel
 
     if (forConservation)
     {
-      label.setText(MessageManager
-              .getString("label.enter_value_increase_conservation_visibility"));
+      label.setText(MessageManager.getString(
+              "label.enter_value_increase_conservation_visibility"));
       slider.setMinimum(0);
       slider.setMaximum(100);
     }
     else
     {
-      label.setText(MessageManager
-              .getString("label.enter_percentage_identity_above_which_colour_residues"));
+      label.setText(MessageManager.getString(
+              "label.enter_percentage_identity_above_which_colour_residues"));
       slider.setMinimum(0);
       slider.setMaximum(100);
     }
@@ -117,7 +120,7 @@ public class SliderPanel extends GSliderPanel
       @Override
       public void stateChanged(ChangeEvent evt)
       {
-        valueField.setText(slider.getValue() + "");
+        valueField.setText(String.valueOf(slider.getValue()));
         valueChanged(slider.getValue());
       }
     });
@@ -127,12 +130,12 @@ public class SliderPanel extends GSliderPanel
       @Override
       public void mouseReleased(MouseEvent evt)
       {
-        ap.paintAlignment(true);
+        ap.paintAlignment(true, true);
       }
     });
 
     slider.setValue(value);
-    valueField.setText(value + "");
+    valueField.setText(String.valueOf(value));
   }
 
   /**
@@ -152,25 +155,30 @@ public class SliderPanel extends GSliderPanel
   {
     SliderPanel sliderPanel = null;
 
+    JInternalFrame conservationSlider = Desktop
+            .getInstance().conservationSlider;
+
     if (conservationSlider == null)
     {
       sliderPanel = new SliderPanel(ap, rs.getConservationInc(), true, rs);
-      conservationSlider = new JInternalFrame();
+      conservationSlider = Desktop
+              .getInstance().conservationSlider = new JInternalFrame();
       conservationSlider.setContentPane(sliderPanel);
       conservationSlider.setLayer(JLayeredPane.PALETTE_LAYER);
     }
     else
     {
       sliderPanel = (SliderPanel) conservationSlider.getContentPane();
-      sliderPanel.valueField.setText(String.valueOf(rs.getConservationInc()));
+      sliderPanel.valueField
+              .setText(String.valueOf(rs.getConservationInc()));
       sliderPanel.cs = rs;
       sliderPanel.ap = ap;
       sliderPanel.slider.setValue(rs.getConservationInc());
     }
 
     conservationSlider.setTitle(MessageManager.formatMessage(
-            "label.conservation_colour_increment",
-            new String[] { source == null ? BACKGROUND : source }));
+            "label.conservation_colour_increment", new String[]
+            { source == null ? BACKGROUND : source }));
 
     List<SequenceGroup> groups = ap.av.getAlignment().getGroups();
     if (groups != null && !groups.isEmpty())
@@ -190,12 +198,14 @@ public class SliderPanel extends GSliderPanel
    */
   public static void hidePIDSlider()
   {
+    JInternalFrame PIDSlider = Desktop.getInstance().PIDSlider;
+
     if (PIDSlider != null)
     {
       try
       {
         PIDSlider.setClosed(true);
-        PIDSlider = null;
+        Desktop.getInstance().PIDSlider = null;
       } catch (PropertyVetoException ex)
       {
       }
@@ -207,12 +217,15 @@ public class SliderPanel extends GSliderPanel
    */
   public static void hideConservationSlider()
   {
+    JInternalFrame conservationSlider = Desktop
+            .getInstance().conservationSlider;
+
     if (conservationSlider != null)
     {
       try
       {
         conservationSlider.setClosed(true);
-        conservationSlider = null;
+        Desktop.getInstance().conservationSlider = null;
       } catch (PropertyVetoException ex)
       {
       }
@@ -226,19 +239,22 @@ public class SliderPanel extends GSliderPanel
   {
     hidePIDSlider();
 
+    JInternalFrame conservationSlider = Desktop
+            .getInstance().conservationSlider;
+
     if (!conservationSlider.isVisible())
     {
       Desktop.addInternalFrame(conservationSlider,
-              conservationSlider.getTitle(), 420, 90, false);
-      conservationSlider
-              .addInternalFrameListener(new InternalFrameAdapter()
-              {
-                @Override
-                public void internalFrameClosed(InternalFrameEvent e)
-                {
-                  conservationSlider = null;
-                }
-              });
+              conservationSlider.getTitle(), true, FRAME_WIDTH,
+              FRAME_HEIGHT, false, true);
+      conservationSlider.addInternalFrameListener(new InternalFrameAdapter()
+      {
+        @Override
+        public void internalFrameClosed(InternalFrameEvent e)
+        {
+          Desktop.getInstance().conservationSlider = null;
+        }
+      });
       conservationSlider.setLayer(JLayeredPane.PALETTE_LAYER);
     }
   }
@@ -255,17 +271,19 @@ public class SliderPanel extends GSliderPanel
    * 
    * @return
    */
-  public static int setPIDSliderSource(AlignmentPanel ap,
-          ResidueShaderI rs, String source)
+  public static int setPIDSliderSource(AlignmentPanel ap, ResidueShaderI rs,
+          String source)
   {
     int threshold = rs.getThreshold();
 
     SliderPanel sliderPanel = null;
 
+    JInternalFrame PIDSlider = Desktop.getInstance().PIDSlider;
+
     if (PIDSlider == null)
     {
       sliderPanel = new SliderPanel(ap, threshold, false, rs);
-      PIDSlider = new JInternalFrame();
+      PIDSlider = Desktop.getInstance().PIDSlider = new JInternalFrame();
       PIDSlider.setContentPane(sliderPanel);
       PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);
     }
@@ -279,8 +297,8 @@ public class SliderPanel extends GSliderPanel
     }
 
     PIDSlider.setTitle(MessageManager.formatMessage(
-            "label.percentage_identity_threshold",
-            new String[] { source == null ? BACKGROUND : source }));
+            "label.percentage_identity_threshold", new String[]
+            { source == null ? BACKGROUND : source }));
 
     if (ap.av.getAlignment().getGroups() != null)
     {
@@ -303,17 +321,19 @@ public class SliderPanel extends GSliderPanel
   {
     hideConservationSlider();
 
+    JInternalFrame PIDSlider = Desktop.getInstance().PIDSlider;
+
     if (!PIDSlider.isVisible())
     {
-      Desktop.addInternalFrame(PIDSlider, PIDSlider.getTitle(), 420, 90,
-              false);
+      Desktop.addInternalFrame(PIDSlider, PIDSlider.getTitle(), true,
+              FRAME_WIDTH, FRAME_HEIGHT, false, true);
       PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);
       PIDSlider.addInternalFrameListener(new InternalFrameAdapter()
       {
         @Override
         public void internalFrameClosed(InternalFrameEvent e)
         {
-          PIDSlider = null;
+          Desktop.getInstance().PIDSlider = null;
         }
       });
       PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);
@@ -365,7 +385,7 @@ public class SliderPanel extends GSliderPanel
     }
     if (forConservation)
     {
-      if (!scheme.conservationApplied())
+      if (!scheme.conservationApplied() && sg != null)
       {
         /*
          * first time the colour scheme has had Conservation shading applied
@@ -396,7 +416,6 @@ public class SliderPanel extends GSliderPanel
   public void setAllGroupsCheckEnabled(boolean b)
   {
     allGroupsCheck.setEnabled(b);
-    allGroupsCheck.setSelected(ap.av.getColourAppliesToAllGroups());
   }
 
   /**
@@ -450,18 +469,18 @@ public class SliderPanel extends GSliderPanel
 
   public static int getConservationValue()
   {
-    return getValue(conservationSlider);
+    return getValue(Desktop.getInstance().conservationSlider);
   }
 
   static int getValue(JInternalFrame slider)
   {
-    return slider == null ? 0 : ((SliderPanel) slider.getContentPane())
-            .getValue();
+    return slider == null ? 0
+            : ((SliderPanel) slider.getContentPane()).getValue();
   }
 
   public static int getPIDValue()
   {
-    return getValue(PIDSlider);
+    return getValue(Desktop.getInstance().PIDSlider);
   }
 
   /**
@@ -484,6 +503,10 @@ public class SliderPanel extends GSliderPanel
   public String getTitle()
   {
     String title = null;
+    JInternalFrame conservationSlider = Desktop
+            .getInstance().conservationSlider;
+    JInternalFrame PIDSlider = Desktop.getInstance().PIDSlider;
+
     if (isForConservation())
     {
       if (conservationSlider != null)