JAL-3253-applet headless branch - just experimenting.

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

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 7c3dca0..779b48e 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -214,7 +214,7 @@ public class AlignViewport extends AlignmentViewport
 
     setRightAlignIds(Cache.getDefault(Preferences.RIGHT_ALIGN_IDS, false));
     setCentreColumnLabels(Cache.getDefault(Preferences.CENTRE_COLUMN_LABELS, false));
-    autoCalculateConsensus = Cache.getDefault(Preferences.AUTO_CALC_CONSENSUS, true);
+    autoCalculateConsensusAndConservation = Cache.getDefault(Preferences.AUTO_CALC_CONSENSUS, true);
 
     setPadGaps(Cache.getDefault(Preferences.PAD_GAPS, true));
     setShowNPFeats(Cache.getDefault(Preferences.SHOW_NPFEATS_TOOLTIP, true));
@@ -391,7 +391,7 @@ public class AlignViewport extends AlignmentViewport
      */
     if (align != null)
     {
-      Desktop.getInstance().getStructureSelectionManager()
+      getStructureSelectionManager()
               .registerMappings(align.getCodonFrames());
     }
 
@@ -410,10 +410,13 @@ public class AlignViewport extends AlignmentViewport
     if (al != null)
     {
       List<AlignedCodonFrame> mappings = al.getCodonFrames();
-      if (mappings != null)
+      if (mappings != null && Desktop.getInstance() != null)
       {
-        StructureSelectionManager ssm = Desktop.getInstance()
-                .getStructureSelectionManager();
+        // StructureSelectionManager ssm = Desktop.getInstance()
+        // .getStructureSelectionManager();
+
+        // BH 2019.08.27 allows for null Desktop instance
+        StructureSelectionManager ssm = getStructureSelectionManager();
         for (AlignedCodonFrame acf : mappings)
         {
           if (noReferencesTo(acf))
@@ -538,7 +541,7 @@ public class AlignViewport extends AlignmentViewport
   @Override
   public void sendSelection()
   {
-    Desktop.getInstance().getStructureSelectionManager().sendSelection(
+    getStructureSelectionManager().sendSelection(
             new SequenceGroup(getSelectionGroup()),
             new ColumnSelection(getColumnSelection()),
             new HiddenColumns(getAlignment().getHiddenColumns()), this);
@@ -582,7 +585,9 @@ public class AlignViewport extends AlignmentViewport
   @Override
   public StructureSelectionManager getStructureSelectionManager()
   {
-    return Desktop.getInstance().getStructureSelectionManager();
+    // BH allows for null Desktop instance
+    return StructureSelectionManager
+            .getStructureSelectionManager(Desktop.getInstance());
   }
 
   @Override