X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationColourChooser.java;h=f6352d7be728d628c9c636f1a5b6790a0fea7432;hb=7c19c72efd3433b14f845c265747010d9dc596cc;hp=c8dd889c94d51df951d87fb573c2386edd46ce04;hpb=ad15cff29620f960119f80176f1fd443da9f6763;p=jalview.git

diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java
index c8dd889..f6352d7 100644
--- a/src/jalview/gui/AnnotationColourChooser.java
+++ b/src/jalview/gui/AnnotationColourChooser.java
@@ -63,7 +63,6 @@ public class AnnotationColourChooser extends AnnotationRowFilter
 
   JButton defColours = new JButton();
 
-
   JPanel jPanel1 = new JPanel();
 
   JPanel jPanel2 = new JPanel();
@@ -81,9 +80,9 @@ public class AnnotationColourChooser extends AnnotationRowFilter
       oldgroupColours = new Hashtable<SequenceGroup, ColourSchemeI>();
       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
       {
-        if (sg.cs != null)
+        if (sg.getColourScheme() != null)
         {
-          oldgroupColours.put(sg, sg.cs);
+          oldgroupColours.put(sg, sg.getColourScheme());
         }
       }
     }
@@ -140,7 +139,9 @@ public class AnnotationColourChooser extends AnnotationRowFilter
         getThreshold().setSelectedIndex(2);
         break;
       default:
-        throw new Error(MessageManager.getString("error.implementation_error_dont_know_about_thereshold_setting"));
+        throw new Error(
+                MessageManager
+                        .getString("error.implementation_error_dont_know_about_threshold_setting"));
       }
       thresholdIsMin.setSelected(acg.thresholdIsMinMax);
       thresholdValue.setText("" + acg.getAnnotationThreshold());
@@ -209,7 +210,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        ok_actionPerformed(e);
+        ok_actionPerformed();
       }
     });
     cancel.setOpaque(false);
@@ -219,7 +220,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        cancel_actionPerformed(e);
+        cancel_actionPerformed();
       }
     });
     defColours.setOpaque(false);
@@ -232,7 +233,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
       @Override
       public void actionPerformed(ActionEvent arg0)
       {
-        resetColours_actionPerformed(arg0);
+        resetColours_actionPerformed();
       }
     });
 
@@ -241,7 +242,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        annotations_actionPerformed(e);
+        annotations_actionPerformed();
       }
     });
     getThreshold().addActionListener(new ActionListener()
@@ -249,7 +250,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        threshold_actionPerformed(e);
+        threshold_actionPerformed();
       }
     });
     thresholdValue.addActionListener(new ActionListener()
@@ -257,7 +258,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        thresholdValue_actionPerformed(e);
+        thresholdValue_actionPerformed();
       }
     });
     slider.setPaintLabels(false);
@@ -277,7 +278,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        currentColours_actionPerformed(e);
+        currentColours_actionPerformed();
       }
     });
     thresholdIsMin.setBackground(Color.white);
@@ -289,7 +290,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
       @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
-        thresholdIsMin_actionPerformed(actionEvent);
+        thresholdIsMin_actionPerformed();
       }
     });
     seqAssociated.setBackground(Color.white);
@@ -302,7 +303,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
       @Override
       public void actionPerformed(ActionEvent arg0)
       {
-        seqAssociated_actionPerformed(arg0, annotations, seqAssociated);
+        seqAssociated_actionPerformed(annotations);
       }
     });
 
@@ -331,7 +332,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
     this.validate();
   }
 
-  protected void resetColours_actionPerformed(ActionEvent arg0)
+  protected void resetColours_actionPerformed()
   {
     setDefaultMinMax();
     updateView();
@@ -348,7 +349,8 @@ public class AnnotationColourChooser extends AnnotationRowFilter
   public void minColour_actionPerformed()
   {
     Color col = JColorChooser.showDialog(this,
-            MessageManager.getString("label.select_colour_minimum_value"), minColour.getBackground());
+            MessageManager.getString("label.select_colour_minimum_value"),
+            minColour.getBackground());
     if (col != null)
     {
       minColour.setBackground(col);
@@ -360,7 +362,8 @@ public class AnnotationColourChooser extends AnnotationRowFilter
   public void maxColour_actionPerformed()
   {
     Color col = JColorChooser.showDialog(this,
-            MessageManager.getString("label.select_colour_maximum_value"), maxColour.getBackground());
+            MessageManager.getString("label.select_colour_maximum_value"),
+            maxColour.getBackground());
     if (col != null)
     {
       maxColour.setBackground(col);
@@ -369,6 +372,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
     updateView();
   }
 
+  @Override
   public void reset()
   {
     av.setGlobalColourScheme(oldcs);
@@ -377,11 +381,12 @@ public class AnnotationColourChooser extends AnnotationRowFilter
 
       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
       {
-        sg.cs = oldgroupColours.get(sg);
+        sg.setColourScheme(oldgroupColours.get(sg));
       }
     }
   }
 
+  @Override
   public void valueChanged(boolean updateAllAnnotation)
   {
     if (slider.isEnabled())
@@ -408,7 +413,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
     this.threshold = threshold;
   }
 
-  public void currentColours_actionPerformed(ActionEvent e)
+  public void currentColours_actionPerformed()
   {
     if (currentColours.isSelected())
     {
@@ -449,9 +454,10 @@ public class AnnotationColourChooser extends AnnotationRowFilter
             && getCurrentAnnotation().threshold == null)
     {
       getCurrentAnnotation()
-              .setThreshold(new jalview.datamodel.GraphLine(
-                      (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
-                      "Threshold", Color.black));
+              .setThreshold(
+                      new jalview.datamodel.GraphLine(
+                              (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
+                              "Threshold", Color.black));
     }
 
     if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)