From 1db1f53588cf74844c414838eda44015a5bfdf70 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 24 Mar 2006 15:27:21 +0000
Subject: [PATCH] Annotation colour scheme added

---
 src/jalview/appletgui/AlignFrame.java |   17 ++++++++++-------
 1 file changed, 10 insertions(+), 7 deletions(-)

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index aceb508..189a36d 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -229,8 +229,7 @@ public class AlignFrame extends Frame implements ActionListener,
             fr.setColour(type, ucs.findColour("A"));
           }
 
-          sf = new SequenceFeature(type, desc, "", start, end);
-          sf.setFeatureGroup(featureGroup);
+          sf = new SequenceFeature(type, desc, "", start, end, featureGroup);
 
           seq.addSequenceFeature(sf);
         }
@@ -423,6 +422,8 @@ public void itemStateChanged(ItemEvent evt)
             PIDColour_actionPerformed();
     else if(evt.getSource()==BLOSUM62Colour)
             BLOSUM62Colour_actionPerformed();
+    else if(evt.getSource()==annotationColour)
+           new AnnotationColourChooser(viewport, alignPanel);
     else if(evt.getSource()==sortPairwiseMenuItem)
             sortPairwiseMenuItem_actionPerformed();
     else if(evt.getSource()==sortIDMenuItem)
@@ -1689,8 +1690,8 @@ public void itemStateChanged(ItemEvent evt)
     protected Menu colourMenu = new Menu("Colour");
     protected Menu calculateMenu = new Menu("Calculate");
     protected MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
-    protected MenuItem deselectAllSequenceMenuItem = new MenuItem();
-    protected MenuItem invertSequenceMenuItem = new MenuItem();
+    protected MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
+    protected MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
     protected MenuItem remove2LeftMenuItem = new MenuItem();
     protected MenuItem remove2RightMenuItem = new MenuItem();
     protected MenuItem removeGappedColumnMenuItem = new MenuItem();
@@ -1793,9 +1794,7 @@ public void itemStateChanged(ItemEvent evt)
 
         loadTree.addActionListener(this);
         selectAllSequenceMenuItem.addActionListener(this);
-        deselectAllSequenceMenuItem.setLabel("Deselect All");
         deselectAllSequenceMenuItem.addActionListener(this);
-        invertSequenceMenuItem.setLabel("Invert Selection");
         invertSequenceMenuItem.addActionListener(this);
         remove2LeftMenuItem.setLabel("Remove Left");
         remove2LeftMenuItem.addActionListener(this);
@@ -1944,6 +1943,8 @@ public void itemStateChanged(ItemEvent evt)
     sequenceFeatures.setLabel("Sequence Features");
     sequenceFeatures.addItemListener(this);
     sequenceFeatures.setState(false);
+    annotationColour.setLabel("by Annotation...");
+    annotationColour.addActionListener(this);
 
     alignFrameMenuBar.add(fileMenu);
         alignFrameMenuBar.add(editMenu);
@@ -2014,7 +2015,8 @@ public void itemStateChanged(ItemEvent evt)
         colourMenu.add(modifyConservation);
         colourMenu.add(abovePIDThreshold);
         colourMenu.add(modifyPID);
-        calculateMenu.add(sort);
+    colourMenu.add(annotationColour);
+    calculateMenu.add(sort);
         calculateMenu.add(calculate);
         calculateMenu.addSeparator();
         calculateMenu.add(pairwiseAlignmentMenuItem);
@@ -2103,6 +2105,7 @@ public void itemStateChanged(ItemEvent evt)
       viewPopup, colourPopup, calculatePopup, helpPopup;
   MenuItem featureSettings = new MenuItem();
   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
+  MenuItem annotationColour = new MenuItem();
 
   public void mousePressed(MouseEvent evt)
   {
-- 
1.7.10.2