X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=037f0070997b302d4913198437b53744c3d9a477;hb=6fb502e4a8749d1d98f5442c3b8156ab47996b77;hp=3bc7c5c574b30cd6535dad2e64b96e84713d6ca9;hpb=e5ecde79316259cf913da454373e9f5ee7488798;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 3bc7c5c..037f007 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -70,6 +70,7 @@ 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();
@@ -121,7 +122,11 @@ public class PopupMenu extends JPopupMenu
   JMenu pdbMenu = new JMenu();
 
   JMenuItem pdbFromFile = new JMenuItem();
-
+    // JBPNote: Commented these out - Should add these services via the web services menu system.
+    // JMenuItem ContraFold = new JMenuItem();
+  
+    // JMenuItem RNAFold = new JMenuItem();
+  
   JMenuItem enterPDB = new JMenuItem();
 
   JMenuItem discoverPDB = new JMenuItem();
@@ -192,6 +197,7 @@ 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 +286,23 @@ 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 +328,7 @@ 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 +466,8 @@ public class PopupMenu extends JPopupMenu
       {
         purinePyrimidineColour.setSelected(true);
       }
+      
+   
       /*
        * else if (sg.cs instanceof CovariationColourScheme) {
        * covariationColour.setSelected(true); }
@@ -1053,6 +1074,32 @@ public class PopupMenu extends JPopupMenu
         pdbFromFile_actionPerformed();
       }
     });
+//    RNAFold.setText("From RNA Fold with predict2D");
+//    RNAFold.addActionListener(new ActionListener()
+//    {
+//      public void actionPerformed(ActionEvent e)
+//      {
+//    	  try {
+//			RNAFold_actionPerformed();
+//		} catch (Exception e1) {
+//			// TODO Auto-generated catch block
+//			e1.printStackTrace();
+//		}
+//      }   
+//    });
+//    ContraFold.setText("From Contra Fold with predict2D");
+//    ContraFold.addActionListener(new ActionListener()
+//    {
+//      public void actionPerformed(ActionEvent e)
+//      {
+//    	  try {
+//			ContraFold_actionPerformed();
+//		} catch (Exception e1) {
+//			// TODO Auto-generated catch block
+//			e1.printStackTrace();
+//		}
+//      }   
+//    });
     enterPDB.setText("Enter PDB Id");
     enterPDB.addActionListener(new ActionListener()
     {
@@ -1130,9 +1177,10 @@ 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()) {
+	// JBPNote - commented since the colourscheme isn't functional
+	//  colourMenu.add(RNAInteractionColour);
+    	colourMenu.add(purinePyrimidineColour);
     }
     // colourMenu.add(covariationColour);
     colourMenu.add(userDefinedColour);
@@ -1167,6 +1215,9 @@ public class PopupMenu extends JPopupMenu
     editMenu.add(lowerCase);
     editMenu.add(toggle);
     pdbMenu.add(pdbFromFile);
+    // JBPNote: These shouldn't be added here - should appear in a generic 'apply web service to this sequence menu'
+    //    pdbMenu.add(RNAFold);
+    //    pdbMenu.add(ContraFold);
     pdbMenu.add(enterPDB);
     pdbMenu.add(discoverPDB);
     jMenu1.add(groupName);
@@ -1294,6 +1345,8 @@ public class PopupMenu extends JPopupMenu
                 purinePyrimidineColour_actionPerformed();
               }
             });
+    
+   
     /*
      * covariationColour.addActionListener(new java.awt.event.ActionListener() {
      * public void actionPerformed(ActionEvent e) {
@@ -1481,6 +1534,7 @@ public class PopupMenu extends JPopupMenu
     refresh();
   }
 
+
   /*
    * protected void covariationColour_actionPerformed() { getGroup().cs = new
    * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
@@ -1960,7 +2014,18 @@ public class PopupMenu extends JPopupMenu
     }
 
   }
-
+    // JBNote: commented out - these won't be instantiated here...!  
+//  public void RNAFold_actionPerformed() throws Exception
+//  {
+//	  Predict2D P2D = new Predict2D();
+//	  P2D.getStructure2DFromRNAFold("toto");
+//  }
+//  
+//  public void ContraFold_actionPerformed() throws Exception
+//  {
+//	  Predict2D P2D = new Predict2D();
+//	  P2D.getStructure2DFromContraFold("toto");
+//  }
   public void enterPDB_actionPerformed()
   {
     String id = JOptionPane.showInternalInputDialog(Desktop.desktop,