JAL-1264 adding show/hide annotation options to applet

[jalview.git] / src / jalview / appletgui / CutAndPasteTransfer.java

diff --git a/src/jalview/appletgui/CutAndPasteTransfer.java b/src/jalview/appletgui/CutAndPasteTransfer.java
index 963961d..036bbe3 100644 (file)
--- a/src/jalview/appletgui/CutAndPasteTransfer.java
+++ b/src/jalview/appletgui/CutAndPasteTransfer.java
@@ -20,20 +20,6 @@
  */
 package jalview.appletgui;
 
-import jalview.analysis.AlignmentUtils;
-import jalview.bin.JalviewLite;
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.Sequence;
-import jalview.io.AnnotationFile;
-import jalview.io.AppletFormatAdapter;
-import jalview.io.IdentifyFile;
-import jalview.io.NewickFile;
-import jalview.io.TCoffeeScoreFile;
-import jalview.schemes.TCoffeeColourScheme;
-import jalview.util.MessageManager;
-
 import java.awt.BorderLayout;
 import java.awt.Button;
 import java.awt.Dialog;
@@ -47,6 +33,20 @@ import java.awt.event.ActionListener;
 import java.awt.event.MouseEvent;
 import java.awt.event.MouseListener;
 
+import jalview.analysis.AlignmentUtils;
+import jalview.bin.JalviewLite;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.io.AnnotationFile;
+import jalview.io.AppletFormatAdapter;
+import jalview.io.IdentifyFile;
+import jalview.io.NewickFile;
+import jalview.io.TCoffeeScoreFile;
+import jalview.schemes.TCoffeeColourScheme;
+import jalview.util.MessageManager;
+
 public class CutAndPasteTransfer extends Panel implements ActionListener,
         MouseListener
 {
@@ -56,7 +56,7 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
 
   boolean annotationImport = false;
 
-  Sequence seq;
+  SequenceI seq;
 
   AlignFrame alignFrame;
 
@@ -88,7 +88,7 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
     textarea.setText(text);
   }
 
-  public void setPDBImport(Sequence seq)
+  public void setPDBImport(SequenceI seq)
   {
     this.seq = seq;
     accept.setLabel(MessageManager.getString("action.accept"));
@@ -395,12 +395,12 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
 
     if (alignFrame.alignPanel.av.applet.jmolAvailable)
     {
-      new jalview.appletgui.AppletJmol(pdb, new Sequence[]
+      new jalview.appletgui.AppletJmol(pdb, new SequenceI[]
       { seq }, null, alignFrame.alignPanel, AppletFormatAdapter.PASTE);
     }
     else
     {
-      new MCview.AppletPDBViewer(pdb, new Sequence[]
+      new MCview.AppletPDBViewer(pdb, new SequenceI[]
       { seq }, null, alignFrame.alignPanel, AppletFormatAdapter.PASTE);
     }
   }