JAL-2089 patch broken merge to master for Release 2.10.0b1

[jalview.git] / src / jalview / appletgui / FeatureSettings.java

diff --git a/src/jalview/appletgui/FeatureSettings.java b/src/jalview/appletgui/FeatureSettings.java
index 7ae318c..2c454a4 100755 (executable)
--- a/src/jalview/appletgui/FeatureSettings.java
+++ b/src/jalview/appletgui/FeatureSettings.java
@@ -20,11 +20,10 @@
  */
 package jalview.appletgui;
 
+import jalview.api.FeatureColourI;
 import jalview.api.FeatureSettingsControllerI;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceFeature;
-import jalview.schemes.AnnotationColourGradient;
-import jalview.schemes.GraduatedColor;
 import jalview.util.MessageManager;
 
 import java.awt.BorderLayout;
@@ -186,12 +185,11 @@ public class FeatureSettings extends Panel implements ItemListener,
   }
 
   protected void popupSort(final MyCheckbox check,
-          final Map<String, float[][]> minmax,
-          int x, int y)
+          final Map<String, float[][]> minmax, int x, int y)
   {
     final String type = check.type;
-    final Object typeCol = fr.getFeatureStyle(type);
-    java.awt.PopupMenu men = new PopupMenu(MessageManager.formatMessage(
+    final FeatureColourI typeCol = fr.getFeatureStyle(type);
+    PopupMenu men = new PopupMenu(MessageManager.formatMessage(
             "label.settings_for_type", new String[] { type }));
     java.awt.MenuItem scr = new MenuItem(
             MessageManager.getString("label.sort_by_score"));
@@ -243,7 +241,7 @@ public class FeatureSettings extends Panel implements ItemListener,
         // graduated colourschemes for those where minmax exists for the
         // positional features
         MenuItem mxcol = new MenuItem(
-                (typeCol instanceof Color) ? "Graduated Colour"
+                (typeCol.isSimpleColour()) ? "Graduated Colour"
                         : "Single Colour");
         men.add(mxcol);
         mxcol.addActionListener(new ActionListener()
@@ -252,7 +250,7 @@ public class FeatureSettings extends Panel implements ItemListener,
           @Override
           public void actionPerformed(ActionEvent e)
           {
-            if (typeCol instanceof Color)
+            if (typeCol.isSimpleColour())
             {
               new FeatureColourChooser(me, type);
               // write back the current colour object to update the table
@@ -260,8 +258,7 @@ public class FeatureSettings extends Panel implements ItemListener,
             }
             else
             {
-              new UserDefinedColours(me, check.type,
-                      ((GraduatedColor) typeCol));
+              new UserDefinedColours(me, check.type, typeCol);
             }
           }
 
@@ -637,19 +634,9 @@ public class FeatureSettings extends Panel implements ItemListener,
     }
   }
 
-  public void setUserColour(String feature, Object originalColour)
+  public void setUserColour(String feature, FeatureColourI originalColour)
   {
-    if (originalColour instanceof Color
-            || originalColour instanceof GraduatedColor)
-    {
-      fr.setColour(feature, originalColour);
-    }
-    else
-    {
-      throw new Error(
-              MessageManager
-                      .getString("error.implementation_error_unsupported_feature_colour_object"));
-    }
+    fr.setColour(feature, originalColour);
     refreshTable();
   }
 
@@ -686,10 +673,10 @@ public class FeatureSettings extends Panel implements ItemListener,
 
     if (evt.getClickCount() > 1)
     {
-      Object fcol = fr.getFeatureStyle(check.type);
-      if (fcol instanceof Color)
+      FeatureColourI fcol = fr.getFeatureStyle(check.type);
+      if (fcol.isSimpleColour())
       {
-        new UserDefinedColours(this, check.type, (Color) fcol);
+        new UserDefinedColours(this, check.type, fcol.getColour());
       }
       else
       {
@@ -721,49 +708,34 @@ public class FeatureSettings extends Panel implements ItemListener,
 
     boolean hasLink;
 
-    GraduatedColor gcol;
-
-    Color col;
+    FeatureColourI col;
 
-    public void updateColor(Object newcol)
+    public void updateColor(FeatureColourI newcol)
     {
-      if (newcol instanceof Color)
-      {
-        col = (Color) newcol;
-        gcol = null;
-      }
-      else if (newcol instanceof GraduatedColor)
+      col = newcol;
+      if (col.isSimpleColour())
       {
-        gcol = (GraduatedColor) newcol;
-        col = null;
-      }
-      else
-      {
-        throw new Error(
-                MessageManager
-                        .getString("error.invalid_colour_for_mycheckbox"));
-      }
-      if (col != null)
-      {
-        setBackground(col);
+        setBackground(col.getColour());
       }
       else
       {
         String vlabel = type;
-        if (gcol.getThreshType() != AnnotationColourGradient.NO_THRESHOLD)
+        if (col.isAboveThreshold())
         {
-          vlabel += " "
-                  + ((gcol.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD) ? "(>)"
-                          : "(<)");
+          vlabel += " (>)";
         }
-        if (gcol.isColourByLabel())
+        else if (col.isBelowThreshold())
+        {
+          vlabel += " (<)";
+        }
+        if (col.isColourByLabel())
         {
           setBackground(Color.white);
           vlabel += " (by Label)";
         }
         else
         {
-          setBackground(gcol.getMinColor());
+          setBackground(col.getMinColour());
         }
         this.setLabel(vlabel);
       }
@@ -780,7 +752,7 @@ public class FeatureSettings extends Panel implements ItemListener,
     }
 
     public MyCheckbox(String type, boolean selected, boolean b,
-            Object featureStyle)
+            FeatureColourI featureStyle)
     {
       this(type, selected, b);
       updateColor(featureStyle);
@@ -790,9 +762,9 @@ public class FeatureSettings extends Panel implements ItemListener,
     public void paint(Graphics g)
     {
       Dimension d = getSize();
-      if (gcol != null)
+      if (col != null)
       {
-        if (gcol.isColourByLabel())
+        if (col.isColourByLabel())
         {
           g.setColor(Color.white);
           g.fillRect(d.width / 2, 0, d.width / 2, d.height);
@@ -808,9 +780,9 @@ public class FeatureSettings extends Panel implements ItemListener,
            */
 
         }
-        else
+        else if (col.isGraduatedColour())
         {
-          Color maxCol = gcol.getMaxColor();
+          Color maxCol = col.getMaxColour();
           g.setColor(maxCol);
           g.fillRect(d.width / 2, 0, d.width / 2, d.height);
 
@@ -825,22 +797,16 @@ public class FeatureSettings extends Panel implements ItemListener,
     }
   }
 
-  @Override
-  public void mousePressed(MouseEvent e)
-  {
-  }
-
   /**
    * Hide columns containing (or not containing) a given feature type
    * 
    * @param type
    * @param columnsContaining
    */
-  void hideFeatureColumns(final String type,
-          boolean columnsContaining)
+  void hideFeatureColumns(final String type, boolean columnsContaining)
   {
-    if (ap.alignFrame.avc.markColumnsContainingFeatures(
-            columnsContaining, false, false, type))
+    if (ap.alignFrame.avc.markColumnsContainingFeatures(columnsContaining,
+            false, false, type))
     {
       if (ap.alignFrame.avc.markColumnsContainingFeatures(
               !columnsContaining, false, false, type))
@@ -850,4 +816,11 @@ public class FeatureSettings extends Panel implements ItemListener,
     }
   }
 
+  @Override
+  public void mousePressed(MouseEvent e)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
 }