selects default colour

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 22671fb..e83a074 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -12,6 +12,9 @@ import javax.swing.*;
 import java.awt.event.*;\r
 import java.awt.*;\r
 \r
+import jalview.gui.Preferences;\r
+import jalview.schemes.ColourSchemeProperty;\r
+\r
 public class GAlignFrame extends JInternalFrame\r
 {\r
   protected JMenuBar alignFrameMenuBar = new JMenuBar();\r
@@ -99,6 +102,41 @@ public class GAlignFrame extends JInternalFrame
   JMenuItem msaAlignMenuItem = new JMenuItem();\r
   public GAlignFrame()\r
   {\r
+    ButtonGroup colours = new ButtonGroup();\r
+    colours.add(noColourmenuItem);\r
+    colours.add(clustalColour);\r
+    colours.add(zappoColour);\r
+    colours.add(taylorColour);\r
+    colours.add(hydrophobicityColour);\r
+    colours.add(helixColour);\r
+    colours.add(strandColour);\r
+    colours.add(turnColour);\r
+    colours.add(buriedColour);\r
+    colours.add(userDefinedColour);\r
+    colours.add(PIDColour);\r
+    colours.add(BLOSUM62Colour);\r
+    colours.add(nucleotideColour);\r
+\r
+   noColourmenuItem.setSelected(true);\r
+   String defaultColour = Preferences.defaultColour;\r
+   if(defaultColour!=null)\r
+   {\r
+   int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);\r
+   switch(index)\r
+   {\r
+     case ColourSchemeProperty.CLUSTAL : clustalColour.setSelected(true); break;\r
+     case ColourSchemeProperty.BLOSUM : BLOSUM62Colour.setSelected(true); break;\r
+     case ColourSchemeProperty.PID : PIDColour.setSelected(true); break;\r
+     case ColourSchemeProperty.ZAPPO : zappoColour.setSelected(true); break;\r
+     case ColourSchemeProperty.HYDROPHOBIC: hydrophobicityColour.setSelected(true); break;\r
+     case ColourSchemeProperty.HELIX: helixColour.setSelected(true); break;\r
+     case ColourSchemeProperty.STRAND: strandColour.setSelected(true); break;\r
+     case ColourSchemeProperty.TURN : turnColour.setSelected(true); break;\r
+     case ColourSchemeProperty.BURIED: buriedColour.setSelected(true); break;\r
+     case ColourSchemeProperty.NUCLEOTIDE: nucleotideColour.setSelected(true); break;\r
+     case ColourSchemeProperty.USER_DEFINED : userDefinedColour.setSelected(true); break;\r
+   }\r
+   }\r
 \r
 \r
     try\r
@@ -137,20 +175,6 @@ public class GAlignFrame extends JInternalFrame
       e.printStackTrace();\r
     }\r
 \r
-    ButtonGroup colours = new ButtonGroup();\r
-    colours.add(noColourmenuItem);\r
-    colours.add(clustalColour);\r
-    colours.add(zappoColour);\r
-    colours.add(taylorColour);\r
-    colours.add(hydrophobicityColour);\r
-    colours.add(helixColour);\r
-    colours.add(strandColour);\r
-    colours.add(turnColour);\r
-    colours.add(buriedColour);\r
-    colours.add(userDefinedColour);\r
-    colours.add(PIDColour);\r
-    colours.add(BLOSUM62Colour);\r
-    colours.add(nucleotideColour);\r
   }\r
   private void jbInit() throws Exception\r
   {\r
@@ -331,8 +355,8 @@ public class GAlignFrame extends JInternalFrame
     statusBar.setText("Status bar");\r
     outputTextboxMenu.setMnemonic('T');\r
     outputTextboxMenu.setText("Output to Textbox");\r
-    clustalColour.setSelected(false);\r
     clustalColour.setText("Clustalx");\r
+\r
     clustalColour.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -438,7 +462,7 @@ public class GAlignFrame extends JInternalFrame
     });\r
     annotationPanelMenuItem.setActionCommand("");\r
     annotationPanelMenuItem.setText("Show Annotations");\r
-    annotationPanelMenuItem.setState(true);\r
+    annotationPanelMenuItem.setState( jalview.gui.Preferences.showAnnotation );\r
     annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -501,7 +525,6 @@ public class GAlignFrame extends JInternalFrame
       }\r
     });\r
     noColourmenuItem.setText("None");\r
-    noColourmenuItem.setSelected(true);\r
     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -568,7 +591,6 @@ public class GAlignFrame extends JInternalFrame
         nucleotideColour_actionPerformed(e);\r
       }\r
     });\r
-    deleteGroups.setSelected(false);\r
     deleteGroups.setText("Undefine groups");\r
     deleteGroups.addActionListener(new java.awt.event.ActionListener()\r
     {\r