Merge branch 'develop' into dev_from_2_8_1

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

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 29370ac..0216276 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -23,6 +23,14 @@ import java.awt.*;
 import java.awt.event.*;
 
 import javax.swing.*;
+import javax.xml.parsers.ParserConfigurationException;
+
+import org.xml.sax.SAXException;
+
+import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
+import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
+import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
+import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
 
 import jalview.analysis.*;
 import jalview.commands.*;
@@ -70,6 +78,7 @@ public class PopupMenu extends JPopupMenu
   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
 
   protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
+  protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
 
   // protected JRadioButtonMenuItem covariationColour = new
   // JRadioButtonMenuItem();
@@ -192,6 +201,7 @@ public class PopupMenu extends JPopupMenu
     colours.add(PIDColour);
     colours.add(BLOSUM62Colour);
     colours.add(purinePyrimidineColour);
+    colours.add(RNAInteractionColour);
     // colours.add(covariationColour);
 
     for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
@@ -280,11 +290,23 @@ public class PopupMenu extends JPopupMenu
             menuItem = new JMenuItem();
             menuItem.setText("2D RNA " + structureLine);
             menuItem.addActionListener(new java.awt.event.ActionListener()
+            
             {
               public void actionPerformed(ActionEvent e)
               {
-                new AppVarna(structureLine, seq, seq.getSequenceAsString(),
-                        rnastruc, seq.getName(), ap);
+                       //System.out.println("1:"+structureLine);
+                       System.out.println("1:sname"+seq.getName());
+                       System.out.println("2:seq"+seq);
+                
+                       //System.out.println("3:"+seq.getSequenceAsString());
+                       System.out.println("3:strucseq"+rnastruc);
+                       //System.out.println("4:struc"+seq.getRNA());
+                       System.out.println("5:name"+seq.getName());
+                       System.out.println("6:ap"+ap);
+                       new AppVarna(structureLine, seq, seq.getSequenceAsString(), rnastruc, seq
+                            .getName(), ap);
+                       //new AppVarna(seq.getName(),seq,rnastruc,seq.getRNA(), seq.getName(), ap);
+                       System.out.println("end");
               }
             });
             viewStructureMenu.add(menuItem);
@@ -310,6 +332,7 @@ public class PopupMenu extends JPopupMenu
                 public void actionPerformed(ActionEvent e)
                 {
                   // TODO: VARNA does'nt print gaps in the sequence
+                
                   new AppVarna(seq.getName() + " structure", seq, seq
                           .getSequenceAsString(), rnastruc, seq.getName(),
                           ap);
@@ -447,6 +470,11 @@ public class PopupMenu extends JPopupMenu
       {
         purinePyrimidineColour.setSelected(true);
       }
+      
+      else if (sg.cs instanceof RNAInteractionColourScheme)
+      {
+        RNAInteractionColour.setSelected(true);
+      }
       /*
        * else if (sg.cs instanceof CovariationColourScheme) {
        * covariationColour.setSelected(true); }
@@ -1130,9 +1158,9 @@ public class PopupMenu extends JPopupMenu
     colourMenu.add(turnColour);
     colourMenu.add(buriedColour);
     colourMenu.add(nucleotideMenuItem);
-    if (ap.getAlignment().isNucleotide())
-    {
-      colourMenu.add(purinePyrimidineColour);
+    if (ap.getAlignment().isNucleotide()) {
+      colourMenu.add(RNAInteractionColour);
+       colourMenu.add(purinePyrimidineColour);
     }
     // colourMenu.add(covariationColour);
     colourMenu.add(userDefinedColour);
@@ -1294,6 +1322,16 @@ public class PopupMenu extends JPopupMenu
                 purinePyrimidineColour_actionPerformed();
               }
             });
+    
+    RNAInteractionColour.setText("RNA Interaction type");
+    RNAInteractionColour
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              public void actionPerformed(ActionEvent e)
+              {
+                RNAInteractionColour_actionPerformed();
+              }
+            });
     /*
      * covariationColour.addActionListener(new java.awt.event.ActionListener() {
      * public void actionPerformed(ActionEvent e) {
@@ -1481,6 +1519,11 @@ public class PopupMenu extends JPopupMenu
     refresh();
   }
 
+  protected void RNAInteractionColour_actionPerformed()
+  {
+    getGroup().cs = new RNAInteractionColourScheme();
+    refresh();
+  }
   /*
    * protected void covariationColour_actionPerformed() { getGroup().cs = new
    * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }