X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FSliderPanel.java;h=f98139b75d952d767e1837ae8b1bde50ece70cf2;hb=8dadf27423ca69874dc6a3c9d416974ba5ae767f;hp=ec53e93e1e96e0db1b879ff24b694a46a8674ac6;hpb=163ed5b997bbda48e4cdd950e87a8fe01baae7fb;p=jalview.git

diff --git a/src/jalview/gui/SliderPanel.java b/src/jalview/gui/SliderPanel.java
index ec53e93..f98139b 100755
--- a/src/jalview/gui/SliderPanel.java
+++ b/src/jalview/gui/SliderPanel.java
@@ -26,6 +26,7 @@ import jalview.jbgui.GSliderPanel;
 import jalview.renderer.ResidueShaderI;
 import jalview.util.MessageManager;
 
+import java.awt.event.ActionEvent;
 import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
 import java.beans.PropertyVetoException;
@@ -99,15 +100,15 @@ 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);
     }
@@ -127,7 +128,7 @@ public class SliderPanel extends GSliderPanel
       @Override
       public void mouseReleased(MouseEvent evt)
       {
-        ap.paintAlignment(true);
+        ap.paintAlignment(true, true);
       }
     });
 
@@ -162,15 +163,16 @@ public class SliderPanel extends GSliderPanel
     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())
@@ -230,15 +232,14 @@ public class SliderPanel extends GSliderPanel
     {
       Desktop.addInternalFrame(conservationSlider,
               conservationSlider.getTitle(), 420, 90, false);
-      conservationSlider
-              .addInternalFrameListener(new InternalFrameAdapter()
-              {
-                @Override
-                public void internalFrameClosed(InternalFrameEvent e)
-                {
-                  conservationSlider = null;
-                }
-              });
+      conservationSlider.addInternalFrameListener(new InternalFrameAdapter()
+      {
+        @Override
+        public void internalFrameClosed(InternalFrameEvent e)
+        {
+          conservationSlider = null;
+        }
+      });
       conservationSlider.setLayer(JLayeredPane.PALETTE_LAYER);
     }
   }
@@ -255,8 +256,8 @@ 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();
 
@@ -279,8 +280,8 @@ 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)
     {
@@ -365,7 +366,7 @@ 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 +397,6 @@ public class SliderPanel extends GSliderPanel
   public void setAllGroupsCheckEnabled(boolean b)
   {
     allGroupsCheck.setEnabled(b);
-    allGroupsCheck.setSelected(ap.av.getColourAppliesToAllGroups());
   }
 
   /**
@@ -455,8 +455,8 @@ public class SliderPanel extends GSliderPanel
 
   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()
@@ -497,4 +497,13 @@ public class SliderPanel extends GSliderPanel
     }
     return title;
   }
+
+  @Override
+  protected void allGroupsCheck_actionPerformed(ActionEvent e)
+  {
+    if (allGroupsCheck.isSelected())
+    {
+      valueChanged(slider.getValue());
+    }
+  }
 }