Sort by added to preferences

[jalview.git] / src / jalview / gui / Preferences.java

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