X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPreferences.java;h=ff44fe4e8c5f4811d69ff911f4a47d231d2d9739;hb=65310fba3ddf0942d5f868130bca9e093888ce7a;hp=bec82a538c0a74bf01ae6288de938022ccac8b51;hpb=b06fdb4903a91fd56543db123d491f494c42501c;p=jalview.git

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index bec82a5..ff44fe4 100755
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -93,21 +93,14 @@ public class Preferences extends GPreferences
         quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
         identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 
-        for (int i = 0; i < 12; i++)
+        for (int i = 0; i < 13; i++)
         {
             colour.addItem(ColourSchemeProperty.getColourName(i));
         }
 
-        String string = Cache.getProperty("DEFAULT_COLOUR");
+        String string = Cache.getDefault("DEFAULT_COLOUR", "None");
 
-        if (string != null)
-        {
-            colour.setSelectedItem(string);
-        }
-        else
-        {
-            colour.setSelectedIndex(11);
-        }
+        colour.setSelectedItem(string);
 
         String[] fonts = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment()
                                                      .getAvailableFontFamilyNames();
@@ -139,6 +132,11 @@ public class Preferences extends GPreferences
         startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
          "http://www.jalview.org/examples/exampleFile.jar"));
 
+        sortby.addItem("No sort");
+        sortby.addItem("Id");
+        sortby.addItem("Pairwise Identity");
+        sortby.setSelectedItem( Cache.getDefault("SORT_ALIGNMENT", "No sort") );
+
   /****************************************************
    * Set up Connections
    */
@@ -198,6 +196,8 @@ public class Preferences extends GPreferences
       Cache.applicationProperties.setProperty("STARTUP_FILE", startupFileTextfield.getText());
       Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",  Boolean.toString(startupCheckbox.isSelected()));
 
+      Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby.getSelectedItem().toString() );
+
       if(defaultBrowser.getText().trim().length()<1)
         Cache.applicationProperties.remove("DEFAULT_BROWSER");
       else