JAL-2236 code restored (and some compiler warnings addressed)

diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java
index 93c9a6b..39cde03 100644 (file)
--- a/src/jalview/gui/AnnotationColourChooser.java
+++ b/src/jalview/gui/AnnotationColourChooser.java
@@ -210,7 +210,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        ok_actionPerformed(e);
+        ok_actionPerformed();
       }
     });
     cancel.setOpaque(false);
@@ -220,7 +220,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        cancel_actionPerformed(e);
+        cancel_actionPerformed();
       }
     });
     defColours.setOpaque(false);
@@ -233,7 +233,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
       @Override
       public void actionPerformed(ActionEvent arg0)
       {
-        resetColours_actionPerformed(arg0);
+        resetColours_actionPerformed();
       }
     });
 
@@ -242,7 +242,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        annotations_actionPerformed(e);
+        annotations_actionPerformed();
       }
     });
     getThreshold().addActionListener(new ActionListener()
@@ -250,7 +250,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        threshold_actionPerformed(e);
+        threshold_actionPerformed();
       }
     });
     thresholdValue.addActionListener(new ActionListener()
@@ -258,7 +258,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        thresholdValue_actionPerformed(e);
+        thresholdValue_actionPerformed();
       }
     });
     slider.setPaintLabels(false);
@@ -278,7 +278,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        currentColours_actionPerformed(e);
+        currentColours_actionPerformed();
       }
     });
     thresholdIsMin.setBackground(Color.white);
@@ -290,7 +290,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
       @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
-        thresholdIsMin_actionPerformed(actionEvent);
+        thresholdIsMin_actionPerformed();
       }
     });
     seqAssociated.setBackground(Color.white);
@@ -303,7 +303,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
       @Override
       public void actionPerformed(ActionEvent arg0)
       {
-        seqAssociated_actionPerformed(arg0, annotations, seqAssociated);
+        seqAssociated_actionPerformed(annotations);
       }
     });
 
@@ -332,7 +332,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
     this.validate();
   }
 
-  protected void resetColours_actionPerformed(ActionEvent arg0)
+  protected void resetColours_actionPerformed()
   {
     setDefaultMinMax();
     updateView();
@@ -372,6 +372,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
     updateView();
   }
 
+  @Override
   public void reset()
   {
     av.setGlobalColourScheme(oldcs);
@@ -385,6 +386,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
     }
   }
 
+  @Override
   public void valueChanged(boolean updateAllAnnotation)
   {
     if (slider.isEnabled())
@@ -411,7 +413,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
     this.threshold = threshold;
   }
 
-  public void currentColours_actionPerformed(ActionEvent e)
+  public void currentColours_actionPerformed()
   {
     if (currentColours.isSelected())
     {

diff --git a/src/jalview/gui/AnnotationColumnChooser.java b/src/jalview/gui/AnnotationColumnChooser.java
index c0d7084..1290d70 100644 (file)
--- a/src/jalview/gui/AnnotationColumnChooser.java
+++ b/src/jalview/gui/AnnotationColumnChooser.java
@@ -178,7 +178,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        ok_actionPerformed(e);
+        ok_actionPerformed();
       }
     });
 
@@ -189,7 +189,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        cancel_actionPerformed(e);
+        cancel_actionPerformed();
       }
     });
 
@@ -201,7 +201,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        threshold_actionPerformed(e);
+        threshold_actionPerformed();
       }
     });
 
@@ -212,7 +212,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        thresholdValue_actionPerformed(e);
+        thresholdValue_actionPerformed();
       }
     });
 
@@ -288,14 +288,15 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     String defaultTtip = MessageManager
             .getString("info.change_threshold_mode_to_enable");
 
-    String threshold = getThreshold().getSelectedItem().toString();
-    if (threshold.equalsIgnoreCase("No Threshold"))
+    String thresh = getThreshold().getSelectedItem().toString();
+    if (thresh.equalsIgnoreCase("No Threshold"))
     {
       thresholdValue.setToolTipText(defaultTtip);
       slider.setToolTipText(defaultTtip);
     }
   }
 
+  @Override
   public void reset()
   {
     if (this.getOldColumnSelection() != null)
@@ -324,6 +325,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
 
   }
 
+  @Override
   public void valueChanged(boolean updateAllAnnotation)
   {
     if (slider.isEnabled())

diff --git a/src/jalview/gui/AnnotationRowFilter.java b/src/jalview/gui/AnnotationRowFilter.java
index 8335042..37f1e55 100644 (file)
--- a/src/jalview/gui/AnnotationRowFilter.java
+++ b/src/jalview/gui/AnnotationRowFilter.java
@@ -26,7 +26,6 @@ import jalview.datamodel.SequenceGroup;
 import jalview.schemes.AnnotationColourGradient;
 import jalview.util.MessageManager;
 
-import java.awt.event.ActionEvent;
 import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
 import java.util.Vector;
@@ -52,7 +51,7 @@ public abstract class AnnotationRowFilter extends JPanel
 
   protected boolean enableSeqAss = false;
 
-  private jalview.datamodel.AlignmentAnnotation currentAnnotation;
+  private AlignmentAnnotation currentAnnotation;
 
   protected boolean adjusting = false;
 
@@ -162,7 +161,8 @@ public abstract class AnnotationRowFilter extends JPanel
       }
       String label = av.getAlignment().getAlignmentAnnotation()[i].label;
       // add associated sequence ID if available
-      if (av.getAlignment().getAlignmentAnnotation()[i].sequenceRef != null)
+      if (!isSeqAssociated
+              && av.getAlignment().getAlignmentAnnotation()[i].sequenceRef != null)
       {
         label = label
                 + "_"
@@ -208,7 +208,7 @@ public abstract class AnnotationRowFilter extends JPanel
     seqAssociated.setEnabled(enableSeqAss);
   }
 
-  public void ok_actionPerformed(ActionEvent e)
+  public void ok_actionPerformed()
   {
     try
     {
@@ -218,7 +218,7 @@ public abstract class AnnotationRowFilter extends JPanel
     }
   }
 
-  public void cancel_actionPerformed(ActionEvent e)
+  public void cancel_actionPerformed()
   {
     reset();
     ap.paintAlignment(true);
@@ -230,22 +230,22 @@ public abstract class AnnotationRowFilter extends JPanel
     }
   }
 
-  public void thresholdCheck_actionPerformed(ActionEvent e)
+  public void thresholdCheck_actionPerformed()
   {
     updateView();
   }
 
-  public void annotations_actionPerformed(ActionEvent e)
+  public void annotations_actionPerformed()
   {
     updateView();
   }
 
-  public void threshold_actionPerformed(ActionEvent e)
+  public void threshold_actionPerformed()
   {
     updateView();
   }
 
-  public void thresholdValue_actionPerformed(ActionEvent e)
+  public void thresholdValue_actionPerformed()
   {
     try
     {
@@ -257,7 +257,7 @@ public abstract class AnnotationRowFilter extends JPanel
     }
   }
 
-  public void thresholdIsMin_actionPerformed(ActionEvent actionEvent)
+  public void thresholdIsMin_actionPerformed()
   {
     updateView();
   }
@@ -272,8 +272,7 @@ public abstract class AnnotationRowFilter extends JPanel
             .getString("label.threshold_feature_below_threshold"));
   }
 
-  protected void seqAssociated_actionPerformed(ActionEvent arg0,
-          JComboBox<String> annotations, JCheckBox seqAssociated)
+  protected void seqAssociated_actionPerformed(JComboBox<String> annotations)
   {
     adjusting = true;
     String cursel = (String) annotations.getSelectedItem();
@@ -331,25 +330,25 @@ public abstract class AnnotationRowFilter extends JPanel
   }
 
   protected boolean colorAlignmContaining(
-          AlignmentAnnotation currentAnnotation, int selectedThresholdItem)
+          AlignmentAnnotation currentAnn, int selectedThresholdOption)
   {
 
     AnnotationColourGradient acg = null;
     if (currentColours.isSelected())
     {
-      acg = new AnnotationColourGradient(currentAnnotation,
-              av.getGlobalColourScheme(), selectedThresholdItem);
+      acg = new AnnotationColourGradient(currentAnn,
+              av.getGlobalColourScheme(), selectedThresholdOption);
     }
     else
     {
-      acg = new AnnotationColourGradient(currentAnnotation,
+      acg = new AnnotationColourGradient(currentAnn,
               minColour.getBackground(), maxColour.getBackground(),
-              selectedThresholdItem);
+              selectedThresholdOption);
     }
     acg.setSeqAssociated(seqAssociated.isSelected());
 
-    if (currentAnnotation.graphMin == 0f
-            && currentAnnotation.graphMax == 0f)
+    if (currentAnn.graphMin == 0f
+            && currentAnn.graphMax == 0f)
     {
       acg.setPredefinedColours(true);
     }
@@ -370,17 +369,17 @@ public abstract class AnnotationRowFilter extends JPanel
 
         if (currentColours.isSelected())
         {
-          sg.cs = new AnnotationColourGradient(currentAnnotation, sg.cs,
-                  selectedThresholdItem);
+          sg.cs = new AnnotationColourGradient(currentAnn, sg.cs,
+                  selectedThresholdOption);
           ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
                   .isSelected());
 
         }
         else
         {
-          sg.cs = new AnnotationColourGradient(currentAnnotation,
+          sg.cs = new AnnotationColourGradient(currentAnn,
                   minColour.getBackground(), maxColour.getBackground(),
-                  selectedThresholdItem);
+                  selectedThresholdOption);
           ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
                   .isSelected());
         }