JAL-842; Implement transmitting of Jalview Sequence highlights to

Varna

Change-Id: I8e1fbc375cdcec6cf36a46cdac56800740c42180

diff --git a/src/jalview/gui/AppVarna.java b/src/jalview/gui/AppVarna.java
index 81ea76c..7617574 100644 (file)
--- a/src/jalview/gui/AppVarna.java
+++ b/src/jalview/gui/AppVarna.java
@@ -19,6 +19,7 @@ package jalview.gui;
 
 import java.util.*;
 import java.awt.*;
+
 import javax.swing.*;
 import javax.swing.event.*;
 
@@ -38,12 +39,13 @@ import fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength;
 import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
 import fr.orsay.lri.varna.interfaces.InterfaceVARNAListener;
 import fr.orsay.lri.varna.models.VARNAConfig;
+import fr.orsay.lri.varna.models.annotations.HighlightRegionAnnotation;
 import fr.orsay.lri.varna.models.rna.ModeleBaseNucleotide;
 import fr.orsay.lri.varna.models.rna.ModeleStyleBP;
 import fr.orsay.lri.varna.models.rna.RNA;
 
 
-public class AppVarna extends JInternalFrame implements InterfaceVARNAListener// implements Runnable,SequenceStructureBinding, ViewSetProvider
+public class AppVarna extends JInternalFrame implements InterfaceVARNAListener,SecondaryStructureListener// implements Runnable,SequenceStructureBinding, ViewSetProvider
 
 {
   AppVarnaBinding vab;
@@ -52,12 +54,14 @@ public class AppVarna extends JInternalFrame implements InterfaceVARNAListener//
   
   public String name;
   
+  public StructureSelectionManager ssm;
+  
   /*public AppVarna(){
          vab = new AppVarnaBinding(); 
          initVarna();
   }*/
   
-  public AppVarna(String seq,String struc,String name){
+  public AppVarna(String seq,String struc,String name,AlignmentPanel ap){
          ArrayList<RNA> rnaList = new ArrayList<RNA>();
          RNA rna1 = new RNA(name);
          try {
@@ -76,7 +80,9 @@ public class AppVarna extends JInternalFrame implements InterfaceVARNAListener//
          //vab = new AppVarnaBinding(seq,struc);
          //System.out.println("Hallo: "+name);
          this.name=name;
-         initVarna();    
+         initVarna();
+      ssm = ap.getStructureSelectionManager();
+         ssm.addStructureViewerListener(this);
   }
   
   public void initVarna(){
@@ -167,7 +173,6 @@ public void onLayoutChanged() {
 
 @Override
 public void onUINewStructure(VARNAConfig v, RNA r) {
-       //TODO _rnaList.add(v, r,"",true);
        // TODO Auto-generated method stub
        
 }
@@ -177,6 +182,30 @@ public void onWarningEmitted(String s) {
        // TODO Auto-generated method stub
        
 }
-  
+/**
+ * If a mouseOver event from the AlignmentPanel 
+ * is noticed the currently selected RNA in the 
+ * VARNA window is highlighted at the specific position. 
+ * To be able to remove it before the next highlight
+ * it is saved in _lastHighlight
+ */
+private  HighlightRegionAnnotation _lastHighlight;
+@Override
+public void mouseOverSequence(SequenceI sequence, int index) {
+       // TODO Auto-generated method stub
+       RNA rna=vab.getSelectedRNA();
+       rna.removeHighlightRegion(_lastHighlight);
+       
+       HighlightRegionAnnotation highlight = new HighlightRegionAnnotation(rna.getBasesBetween(index,index));
+       rna.addHighlightRegion(highlight);
+       _lastHighlight=highlight;
+       vab.updateSelectedRNA(rna);
+}
+
+@Override
+public void mouseOverStructure(int atomIndex, String strInfo) {
+       // TODO Auto-generated method stub
+       
+}
 
 }

diff --git a/src/jalview/gui/AppVarnaBinding.java b/src/jalview/gui/AppVarnaBinding.java
index c235fc1..51819fa 100644 (file)
--- a/src/jalview/gui/AppVarnaBinding.java
+++ b/src/jalview/gui/AppVarnaBinding.java
@@ -221,7 +221,6 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding imple
                                }
                        }
            });
-           
            _rnaList = new BackupHolder(dlm,_sideList);
                        
                try {
@@ -334,6 +333,23 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding imple
        public JPanel getListPanel(){
                return _listPanel;
        }
+       
+       /**
+        * TODO: Is it effective to transfer the whole RNA?
+        * @return Currently selected RNA
+        */
+       public RNA getSelectedRNA(){
+               return _rnaList.getElementAt(_sideList.getSelectedIndex()).rna;
+       }
+       
+       /**
+        * Substitute currently selected RNA with the edited one
+        * @param rnaEdit
+        */
+       public void updateSelectedRNA(RNA rnaEdit){
+               vp.repaint();
+               vp.showRNA(rnaEdit);
+       }
 
        /*
        private void RNAPanelDemoInit() 

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index a4808cf..82ce835 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -282,7 +282,7 @@ public class PopupMenu extends JPopupMenu
                  {
                          System.out.println("Call Varna "+seq.getSequenceAsString()+" "+seq.getName());
                          //TODO: VARNA does'nt print gaps in the sequence
-                         new AppVarna(seq.getSequenceAsString(),rnastrucF,seq.getName());
+                         new AppVarna(seq.getSequenceAsString(),rnastrucF,seq.getName(),ap);
                  }
                        });       
                        viewStructureMenu.add(menuItem);

diff --git a/src/jalview/structure/SecondaryStructureListener.java b/src/jalview/structure/SecondaryStructureListener.java
new file mode 100644 (file)
index 0000000..fe546e4
--- /dev/null
+++ b/src/jalview/structure/SecondaryStructureListener.java
@@ -0,0 +1,27 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * 
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ */
+package jalview.structure;
+
+import jalview.datamodel.*;
+
+public interface SecondaryStructureListener
+{
+  public void mouseOverSequence(SequenceI sequence, int index);
+  public void mouseOverStructure(int atomIndex, String strInfo);
+
+}

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index c4dda8b..880f72a 100644 (file)
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -509,6 +509,9 @@ public class StructureSelectionManager
           ((VamsasListener) listeners.elementAt(i)).mouseOver(seq,
                   indexpos, source);
         }
+        else if(listeners.elementAt(i) instanceof SecondaryStructureListener){
+               ((SecondaryStructureListener) listeners.elementAt(i)).mouseOverSequence(seq,indexpos);
+        }
       }
     }
   }