JAL-3210 Barebones gradle/buildship/eclipse. See README

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

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 1ebf584..7d01222 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -383,8 +383,9 @@ public class AlignViewport extends AlignmentViewport
      */
     if (align != null)
     {
-      Desktop.getInstance().getStructureSelectionManager()
-              .registerMappings(align.getCodonFrames());
+      StructureSelectionManager ssm = StructureSelectionManager
+              .getStructureSelectionManager(Desktop.instance);
+      ssm.registerMappings(align.getCodonFrames());
     }
 
     /*
@@ -404,8 +405,8 @@ public class AlignViewport extends AlignmentViewport
       List<AlignedCodonFrame> mappings = al.getCodonFrames();
       if (mappings != null)
       {
-        StructureSelectionManager ssm = Desktop.getInstance()
-                .getStructureSelectionManager();
+        StructureSelectionManager ssm = StructureSelectionManager
+                .getStructureSelectionManager(Desktop.instance);
         for (AlignedCodonFrame acf : mappings)
         {
           if (noReferencesTo(acf))
@@ -530,10 +531,12 @@ public class AlignViewport extends AlignmentViewport
   @Override
   public void sendSelection()
   {
-    Desktop.getInstance().getStructureSelectionManager().sendSelection(
-            new SequenceGroup(getSelectionGroup()),
-            new ColumnSelection(getColumnSelection()),
-            new HiddenColumns(getAlignment().getHiddenColumns()), this);
+    jalview.structure.StructureSelectionManager
+            .getStructureSelectionManager(Desktop.instance)
+            .sendSelection(new SequenceGroup(getSelectionGroup()),
+                    new ColumnSelection(getColumnSelection()),
+                    new HiddenColumns(getAlignment().getHiddenColumns()),
+                    this);
   }
 
   /**
@@ -574,7 +577,8 @@ public class AlignViewport extends AlignmentViewport
   @Override
   public StructureSelectionManager getStructureSelectionManager()
   {
-    return Desktop.getInstance().getStructureSelectionManager();
+    return StructureSelectionManager
+            .getStructureSelectionManager(Desktop.instance);
   }
 
   @Override
@@ -766,7 +770,7 @@ public class AlignViewport extends AlignmentViewport
      * dialog responses 0, 1, 2 (even though JOptionPane shows them
      * in reverse order)
      */
-    JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.getDesktopPane())
+    JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop)
             .setResponseHandler(0, new Runnable()
             {
               @Override