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

[jalview.git] / src / jalview / jbgui / GPreferences.java

diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java
index 9eb6cf1..2b71c03 100755 (executable)
--- a/src/jalview/jbgui/GPreferences.java
+++ b/src/jalview/jbgui/GPreferences.java
@@ -241,6 +241,8 @@ public class GPreferences extends JPanel
 
   protected JCheckBox followHighlight = new JCheckBox();
 
+  protected JCheckBox sortByTree= new JCheckBox();
+
   /**
    * Creates a new GPreferences object.
    */
@@ -447,6 +449,7 @@ public class GPreferences extends JPanel
           maxColour_actionPerformed();
       }
     });
+    
     startupCheckbox.setText("Open file");
     startupCheckbox.setFont(verdana11);
     startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
@@ -626,8 +629,12 @@ public class GPreferences extends JPanel
     autoCalculateConsCheck.setText("AutoCalculate Consensus");
     autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
     padGaps.setFont(JvSwingUtils.getLabelFont());
-    padGaps.setText("Pad gaps when editing");
+    padGaps.setText("Pad Gaps When Editing");
     padGaps.setBounds(new Rectangle(22, 94, 168, 23));
+    sortByTree.setFont(JvSwingUtils.getLabelFont());
+    sortByTree.setText("Sort Alignment With New Tree");
+    sortByTree.setToolTipText("When selected, any trees calculated or laoded onto the alignment will automatically sort the alignment.");
+    sortByTree.setBounds(new Rectangle(22, 136, 168, 23));
     modellerOutput.setFont(JvSwingUtils.getLabelFont());
     modellerOutput.setText("Use Modeller Output");
     modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
@@ -790,6 +797,8 @@ public class GPreferences extends JPanel
     tabbedPane.add(calcTab, "Editing");
     calcTab.add(autoCalculateConsCheck);
     calcTab.add(padGaps);
+    calcTab.add(sortByTree);
+    
     tabbedPane.add(dasPanel, "DAS Settings");
     tabbedPane.add(wsPanel, "Web Services");