JAL-1152 annotation sorting preferences and help documentation

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

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index dba77dd..a7852b4 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -1139,15 +1139,20 @@ public class GAlignFrame extends JInternalFrame
         hideAllAnnotations_actionPerformed(true, false);
       }
     });
+    SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder
+            .valueOf(Cache.getDefault(Cache.SORT_ANNOTATIONS,
+                    SequenceAnnotationOrder.NONE.name()));
     sortAnnBySequence.setText(MessageManager
             .getString("label.sort_annotations_by_sequence"));
+    sortAnnBySequence
+            .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
     sortAnnBySequence.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
       {
         boolean newState = sortAnnBySequence.getState();
-        sortAnnByLabel.setState(false);
+        sortAnnByLabel.setSelected(false);
         setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
                 : SequenceAnnotationOrder.NONE);
         sortAnnotations_actionPerformed();
@@ -1155,13 +1160,15 @@ public class GAlignFrame extends JInternalFrame
     });
     sortAnnByLabel.setText(MessageManager
             .getString("label.sort_annotations_by_label"));
+    sortAnnByLabel
+            .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
     sortAnnByLabel.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
       {
         boolean newState = sortAnnByLabel.getState();
-        sortAnnBySequence.setState(false);
+        sortAnnBySequence.setSelected(false);
         setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
                 : SequenceAnnotationOrder.NONE);
         sortAnnotations_actionPerformed();
@@ -1415,7 +1422,8 @@ public class GAlignFrame extends JInternalFrame
     });
 
     showAutoFirst.setText(MessageManager.getString("label.show_first"));
-    showAutoFirst.setState(Cache.getDefault("SHOW_AUTOCALC_ABOVE", false));
+    showAutoFirst.setState(Cache.getDefault(Cache.SHOW_AUTOCALC_ABOVE,
+            false));
     showAutoFirst.addActionListener(new ActionListener()
     {
       @Override