JAL-468 JAL-936 sort alignment by tree and autosort for new tree

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

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 9267800..80a42a9 100755 (executable)
--- 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));
@@ -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()));