Merge branch 'feature/JAL-3180colourAnnotationMenu' into merge/JAL-3180

Conflicts:
	resources/lang/Messages.properties
	resources/lang/Messages_es.properties

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index aabda20..c5f2372 100644 (file)
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -1391,3 +1391,4 @@ label.alignment = alignment
 label.pca = PCA
 label.create_image_of = Create {0} image of {1}
 label.click_to_edit = Click to edit, right-click for menu
+label.by_annotation_tooltip = Annotation Colour is configured from the main Colour menu

diff --git a/resources/lang/Messages_es.properties b/resources/lang/Messages_es.properties
index b32842e..7ad1828 100644 (file)
--- a/resources/lang/Messages_es.properties
+++ b/resources/lang/Messages_es.properties
@@ -1392,3 +1392,4 @@ label.alignment = alineamiento
 label.pca = ACP
 label.create_image_of = Crear imagen {0} de {1}
 label.click_to_edit = Haga clic para editar, clic en el botón derecho para ver el menú  
+label.by_annotation_tooltip = El color de anotación se configura desde el menú principal de colores

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index e17b331..8dd6d0c 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -136,6 +136,7 @@ import java.util.Hashtable;
 import java.util.List;
 import java.util.Vector;
 
+import javax.swing.ButtonGroup;
 import javax.swing.JCheckBoxMenuItem;
 import javax.swing.JEditorPane;
 import javax.swing.JInternalFrame;
@@ -5593,15 +5594,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     colourMenu.add(textColour);
     colourMenu.addSeparator();
 
-    ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(),
-            false);
+    ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this,
+            viewport.getAlignment(), false);
 
+    colourMenu.add(annotationColour);
+    bg.add(annotationColour);
     colourMenu.addSeparator();
     colourMenu.add(conservationMenuItem);
     colourMenu.add(modifyConservation);
     colourMenu.add(abovePIDThreshold);
     colourMenu.add(modifyPID);
-    colourMenu.add(annotationColour);
 
     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
     ColourMenuHelper.setColourSelected(colourMenu, colourScheme);

diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java
index 384635b..12693f0 100644 (file)
--- a/src/jalview/gui/AnnotationColourChooser.java
+++ b/src/jalview/gui/AnnotationColourChooser.java
@@ -317,7 +317,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
   @Override
   public void reset()
   {
-    av.setGlobalColourScheme(oldcs);
+    this.ap.alignFrame.changeColour(oldcs);
     if (av.getAlignment().getGroups() != null)
     {
 
@@ -442,7 +442,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
 
     acg.setThresholdIsMinMax(thresholdIsMin.isSelected());
 
-    av.setGlobalColourScheme(acg);
+    this.ap.alignFrame.changeColour(acg);
 
     if (av.getAlignment().getGroups() != null)
     {
@@ -465,5 +465,4 @@ public class AnnotationColourChooser extends AnnotationRowFilter
     super.sliderDragReleased();
     ap.paintAlignment(true, true);
   }
-
 }

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index bc7fb3b..8059935 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -46,6 +46,7 @@ import jalview.schemes.Blosum62ColourScheme;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemes;
 import jalview.schemes.PIDColourScheme;
+import jalview.schemes.ResidueColourScheme;
 import jalview.util.GroupUrlLink;
 import jalview.util.GroupUrlLink.UrlStringTooLongException;
 import jalview.util.MessageManager;
@@ -68,11 +69,13 @@ import java.util.SortedMap;
 import java.util.TreeMap;
 import java.util.Vector;
 
+import javax.swing.ButtonGroup;
 import javax.swing.JCheckBoxMenuItem;
 import javax.swing.JColorChooser;
 import javax.swing.JMenu;
 import javax.swing.JMenuItem;
 import javax.swing.JPopupMenu;
+import javax.swing.JRadioButtonMenuItem;
 
 /**
  * DOCUMENT ME!
@@ -92,6 +95,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
 
   protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
 
+  protected JRadioButtonMenuItem annotationColour;
+
   protected JMenuItem modifyConservation = new JMenuItem();
 
   AlignmentPanel ap;
@@ -1411,6 +1416,13 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       }
     });
 
+    annotationColour = new JRadioButtonMenuItem(
+            MessageManager.getString("action.by_annotation"));
+    annotationColour.setName(ResidueColourScheme.ANNOTATION_COLOUR);
+    annotationColour.setEnabled(false);
+    annotationColour.setToolTipText(
+            MessageManager.getString("label.by_annotation_tooltip"));
+
     modifyConservation.setText(MessageManager
             .getString("label.modify_conservation_threshold"));
     modifyConservation.addActionListener(new ActionListener()
@@ -1441,7 +1453,10 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
     colourMenu.add(textColour);
     colourMenu.addSeparator();
 
-    ColourMenuHelper.addMenuItems(colourMenu, this, sg, false);
+    ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this, sg,
+            false);
+    bg.add(annotationColour);
+    colourMenu.add(annotationColour);
 
     colourMenu.addSeparator();
     colourMenu.add(conservationMenuItem);

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 0ee03bc..9f41c92 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -28,6 +28,7 @@ import jalview.bin.Cache;
 import jalview.gui.JvSwingUtils;
 import jalview.gui.Preferences;
 import jalview.io.FileFormats;
+import jalview.schemes.ResidueColourScheme;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 
@@ -125,7 +126,7 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenuItem modifyPID;
 
-  protected JMenuItem annotationColour;
+  protected JRadioButtonMenuItem annotationColour;
 
   protected JMenu sortByTreeMenu = new JMenu();
 
@@ -1962,8 +1963,9 @@ public class GAlignFrame extends JInternalFrame
       }
     });
 
-    annotationColour = new JMenuItem(
+    annotationColour = new JRadioButtonMenuItem(
             MessageManager.getString("action.by_annotation"));
+    annotationColour.setName(ResidueColourScheme.ANNOTATION_COLOUR);
     annotationColour.addActionListener(new ActionListener()
     {
       @Override

diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index c74fdbc..af30689 100755 (executable)
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -478,7 +478,7 @@ public class AnnotationColourGradient extends FollowerColourScheme
   @Override
   public String getSchemeName()
   {
-    return "Annotation";
+    return ANNOTATION_COLOUR;
   }
 
   @Override

diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index 2f7a5e0..03ab536 100755 (executable)
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -46,6 +46,12 @@ public abstract class ResidueColourScheme implements ColourSchemeI
   public static final String USER_DEFINED_MENU = "*User Defined*";
 
   /*
+   * the canonical name of the annotation colour scheme 
+   * (may be used to identify it in menu items)
+   */
+  public static final String ANNOTATION_COLOUR = "Annotation";
+
+  /*
    * lookup up by character value e.g. 'G' to the colors array index
    * e.g. if symbolIndex['K'] = 11 then colors[11] is the colour for K
    */