JAL-1752 structure highlight scoped to only its mapped sequences

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

diff --git a/src/jalview/gui/AppVarnaBinding.java b/src/jalview/gui/AppVarnaBinding.java
index a738a2c..38385f0 100644 (file)
--- a/src/jalview/gui/AppVarnaBinding.java
+++ b/src/jalview/gui/AppVarnaBinding.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,8 +20,6 @@
  */
 package jalview.gui;
 
-import jalview.util.MessageManager;
-
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.Component;
@@ -71,6 +69,10 @@ import fr.orsay.lri.varna.models.VARNAConfig;
 import fr.orsay.lri.varna.models.rna.Mapping;
 import fr.orsay.lri.varna.models.rna.RNA;
 
+import jalview.datamodel.SequenceI;
+import jalview.structure.AtomSpec;
+import jalview.util.MessageManager;
+
 public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding
         implements DropTargetListener, InterfaceVARNAListener,
         MouseListener
@@ -827,8 +829,6 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding
 
   public void onWarningEmitted(String s)
   {
-    // TODO Auto-generated method stub
-
   }
 
   public void mouseClicked(MouseEvent e)
@@ -852,127 +852,79 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding
 
   public void mouseEntered(MouseEvent arg0)
   {
-    // TODO Auto-generated method stub
-
   }
 
   public void mouseExited(MouseEvent arg0)
   {
-    // TODO Auto-generated method stub
-
   }
 
   public void mousePressed(MouseEvent arg0)
   {
-    // TODO Auto-generated method stub
-
   }
 
   public void mouseReleased(MouseEvent arg0)
   {
-    // TODO Auto-generated method stub
-
-  }
-
-  @Override
-  public Color getColour(int atomIndex, int pdbResNum, String chain,
-          String pdbId)
-  {
-    // TODO Auto-generated method stub
-    return null;
   }
 
   @Override
   public String[] getPdbFile()
   {
-    // TODO Auto-generated method stub
     return null;
   }
 
   @Override
-  public void highlightAtom(int atomIndex, int pdbResNum, String chain,
-          String pdbId)
-  {
-    // TODO Auto-generated method stub
-
-  }
-
-  @Override
-  public void mouseOverStructure(int atomIndex, String strInfo)
-  {
-    // TODO Auto-generated method stub
-
-  }
-
-  @Override
   public void releaseReferences(Object svl)
   {
-    // TODO Auto-generated method stub
-
   }
 
   @Override
   public void updateColours(Object source)
   {
-    // TODO Auto-generated method stub
-
   }
 
   @Override
   public void componentHidden(ComponentEvent e)
   {
-    // TODO Auto-generated method stub
-
   }
 
   @Override
   public void componentMoved(ComponentEvent e)
   {
-    // TODO Auto-generated method stub
-
   }
 
   @Override
   public void componentResized(ComponentEvent e)
   {
-    // TODO Auto-generated method stub
-
   }
 
   @Override
   public void componentShown(ComponentEvent e)
   {
-    // TODO Auto-generated method stub
-
   }
 
   @Override
   public void onStructureRedrawn()
   {
-    // TODO Auto-generated method stub
-
   }
 
   @Override
   public void onZoomLevelChanged()
   {
-    // TODO Auto-generated method stub
-
   }
 
   @Override
   public void onTranslationChanged()
   {
-    // TODO Auto-generated method stub
+  }
 
+  @Override
+  public void highlightAtoms(List<AtomSpec> atoms)
+  {
   }
-}
 
-/*
- * public static void main(String[] args) { JTextField str = new
- * JTextField("ATGC");
- * 
- * AppVarnaBinding vab = new AppVarnaBinding(); vab.varnagui.set_seq(str);
- * vab.varnagui.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
- * vab.varnagui.pack(); vab.varnagui.setVisible(true); } }
- */
+  @Override
+  public boolean isListeningFor(SequenceI seq)
+  {
+    return true;
+  }
+}