X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPreferences.java;h=80a42a9470e95dc746656512d32ca4a428a547aa;hb=6403068c0c328cfb63af451f7fa1bd568fa0fdd3;hp=b92f9da7cfc52446f8e163303fa856af255a508f;hpb=aaf78c2f304b237a9c800137126967ace9437c99;p=jalview.git

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index b92f9da..80a42a9 100755
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -137,7 +137,7 @@ public class Preferences extends GPreferences
             .getDefault("SHOW_NPFEATS_TOOLTIP", true));
     showDbRefTooltip.setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP",
             true));
-
+    sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
     for (int i = ColourSchemeProperty.FIRST_COLOUR; i <= ColourSchemeProperty.LAST_COLOUR; i++)
     {
       colour.addItem(ColourSchemeProperty.getColourName(i));
@@ -189,7 +189,7 @@ public class Preferences extends GPreferences
     startupCheckbox
             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
-            "http://www.jalview.org/examples/exampleFile_2_3.jar"));
+            Cache.getDefault("www.jalview.org","http://www.jalview.org")+"/examples/exampleFile_2_3.jar"));
 
     sortby.addItem("No sort");
     sortby.addItem("Id");
@@ -335,8 +335,8 @@ public class Preferences extends GPreferences
     Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby
             .getSelectedItem().toString());
 
-    Cache.applicationProperties.setProperty("ANNOTATIONCOLOUR_MIN", minColour.getBackground().toString());
-    Cache.applicationProperties.setProperty("ANNOTATIONCOLOUR_MAX", maxColour.getBackground().toString());
+    Cache.setColourProperty("ANNOTATIONCOLOUR_MIN", minColour.getBackground());
+    Cache.setColourProperty("ANNOTATIONCOLOUR_MAX", maxColour.getBackground());
     
     if (epsRendering.getSelectedItem().equals("Prompt each time"))
     {
@@ -452,6 +452,8 @@ public class Preferences extends GPreferences
 
     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
             Boolean.toString(autoCalculateConsCheck.isSelected()));
+    Cache.applicationProperties.setProperty("SORT_BY_TREE",
+            Boolean.toString(sortByTree.isSelected()));
     Cache.applicationProperties.setProperty("PAD_GAPS",
             Boolean.toString(padGaps.isSelected()));
 
@@ -503,6 +505,7 @@ public class Preferences extends GPreferences
     try
     {
       wsPrefs.updateWsMenuConfig(true);
+      wsPrefs.refreshWs_actionPerformed(e);
       frame.setClosed(true);
     } catch (Exception ex)
     {