JAL-2360 ColourSchemes holds configured schemes, AlignFrame colour menu

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

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 9080cdd..2f5ac3a 100644 (file)
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -45,6 +45,7 @@ import jalview.schemes.HelixColourScheme;
 import jalview.schemes.HydrophobicColourScheme;
 import jalview.schemes.NucleotideColourScheme;
 import jalview.schemes.PIDColourScheme;
+import jalview.schemes.PurinePyrimidineColourScheme;
 import jalview.schemes.StrandColourScheme;
 import jalview.schemes.TaylorColourScheme;
 import jalview.schemes.TurnColourScheme;
@@ -113,6 +114,8 @@ public class APopupMenu extends java.awt.PopupMenu implements
 
   MenuItem nucleotideMenuItem = new MenuItem();
 
+  MenuItem purinePyrimidineMenuItem = new MenuItem();
+
   Menu colourMenu = new Menu();
 
   CheckboxMenuItem showBoxes = new CheckboxMenuItem();
@@ -563,6 +566,10 @@ public class APopupMenu extends java.awt.PopupMenu implements
     {
       nucleotideMenuItem_actionPerformed();
     }
+    else if (source == purinePyrimidineMenuItem)
+    {
+      purinePyrimidineColour_actionPerformed();
+    }
 
     else if (source == userDefinedColour)
     {
@@ -891,11 +898,6 @@ public class APopupMenu extends java.awt.PopupMenu implements
             .getString("action.create_group"));
     createGroupMenuItem.addActionListener(this);
 
-    nucleotideMenuItem.setLabel(MessageManager
-            .getString("label.nucleotide"));
-    nucleotideMenuItem.addActionListener(this);
-    conservationMenuItem.addItemListener(this);
-    abovePIDColour.addItemListener(this);
     colourMenu.setLabel(MessageManager.getString("label.group_colour"));
     showBoxes.setLabel(MessageManager.getString("action.boxes"));
     showBoxes.setState(true);
@@ -904,7 +906,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
     sequenceDetails.addActionListener(this);
     selSeqDetails.addActionListener(this);
     displayNonconserved.setLabel(MessageManager
-            .getString("label.show_non_conversed"));
+            .getString("label.show_non_conserved"));
     displayNonconserved.setState(false);
     displayNonconserved.addItemListener(this);
     showText.setLabel(MessageManager.getString("action.text"));
@@ -948,6 +950,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
     colourMenu.add(turnColour);
     colourMenu.add(buriedColour);
     colourMenu.add(nucleotideMenuItem);
+    colourMenu.add(purinePyrimidineMenuItem);
     colourMenu.add(userDefinedColour);
     colourMenu.addSeparator();
     colourMenu.add(abovePIDColour);
@@ -956,38 +959,52 @@ public class APopupMenu extends java.awt.PopupMenu implements
     noColourmenuItem.setLabel(MessageManager.getString("label.none"));
     noColourmenuItem.addActionListener(this);
 
-    clustalColour.setLabel(MessageManager.getString("label.clustalx"));
+    clustalColour.setLabel(MessageManager
+            .getString("label.colourScheme_clustal"));
     clustalColour.addActionListener(this);
-    zappoColour.setLabel(MessageManager.getString("label.zappo"));
+    zappoColour.setLabel(MessageManager
+            .getString("label.colourScheme_zappo"));
     zappoColour.addActionListener(this);
-    taylorColour.setLabel(MessageManager.getString("label.taylor"));
+    taylorColour.setLabel(MessageManager
+            .getString("label.colourScheme_taylor"));
     taylorColour.addActionListener(this);
     hydrophobicityColour.setLabel(MessageManager
-            .getString("label.hydrophobicity"));
+            .getString("label.colourScheme_hydrophobic"));
     hydrophobicityColour.addActionListener(this);
-    helixColour
-            .setLabel(MessageManager.getString("label.helix_propensity"));
+    helixColour.setLabel(MessageManager
+            .getString("label.colourScheme_helix_propensity"));
     helixColour.addActionListener(this);
     strandColour.setLabel(MessageManager
-            .getString("label.strand_propensity"));
+            .getString("label.colourScheme_strand_propensity"));
     strandColour.addActionListener(this);
-    turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
+    turnColour.setLabel(MessageManager
+            .getString("label.colourScheme_turn_propensity"));
     turnColour.addActionListener(this);
-    buriedColour.setLabel(MessageManager.getString("label.buried_index"));
+    buriedColour.setLabel(MessageManager
+            .getString("label.colourScheme_buried_index"));
     buriedColour.addActionListener(this);
     abovePIDColour.setLabel(MessageManager
-            .getString("label.above_identity_percentage"));
+            .getString("label.above_identity_threshold"));
 
     userDefinedColour.setLabel(MessageManager
             .getString("action.user_defined"));
     userDefinedColour.addActionListener(this);
     PIDColour.setLabel(MessageManager
-            .getString("label.percentage_identity"));
+            .getString("label.colourScheme_%_identity"));
     PIDColour.addActionListener(this);
-    BLOSUM62Colour.setLabel("BLOSUM62");
+    BLOSUM62Colour.setLabel(MessageManager
+            .getString("label.colourScheme_blosum62"));
     BLOSUM62Colour.addActionListener(this);
     conservationMenuItem.setLabel(MessageManager
             .getString("label.conservation"));
+    nucleotideMenuItem.setLabel(MessageManager
+            .getString("label.colourScheme_nucleotide"));
+    nucleotideMenuItem.addActionListener(this);
+    purinePyrimidineMenuItem.setLabel(MessageManager
+            .getString("label.colourScheme_purine/pyrimidine"));
+    purinePyrimidineMenuItem.addActionListener(this);
+    conservationMenuItem.addItemListener(this);
+    abovePIDColour.addItemListener(this);
 
     editMenu.add(copy);
     copy.addActionListener(this);
@@ -1089,6 +1106,12 @@ public class APopupMenu extends java.awt.PopupMenu implements
     refresh();
   }
 
+  public void purinePyrimidineColour_actionPerformed()
+  {
+    getGroup().cs = new PurinePyrimidineColourScheme();
+    refresh();
+  }
+
   protected void abovePIDColour_itemStateChanged()
   {
     SequenceGroup sg = getGroup();