v2

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

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 23a5008..f6c1379 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -23,6 +23,13 @@ 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 MCview.*;
 import jalview.analysis.*;
@@ -71,6 +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();
@@ -189,6 +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++)
@@ -270,15 +279,25 @@ public class PopupMenu extends JPopupMenu
           if (aa[i].getRNAStruc() != null)
           {
             final String rnastruc = aa[i].getRNAStruc();
-            
+            final String structureLine=aa[i].label;
             menuItem = new JMenuItem();
-            menuItem.setText("RNA structure - consensus");
+            menuItem.setText("2D RNA "+structureLine);
             menuItem.addActionListener(new java.awt.event.ActionListener()
+            
             {
               public void actionPerformed(ActionEvent e)
               {
-                new AppVarna(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(seq.getName(),seq,rnastruc,seq.getRNA(), seq.getName(), ap);
+                       System.out.println("end");
               }
             });
             viewStructureMenu.add(menuItem);
@@ -298,14 +317,15 @@ public class PopupMenu extends JPopupMenu
               
            // TODO: make rnastrucF a bit more nice
               menuItem = new JMenuItem();
-              menuItem.setText("RNA structure - "+seq.getName());
+              menuItem.setText("2D RNA - "+seq.getName());
               menuItem.addActionListener(new java.awt.event.ActionListener()
               {
                 public void actionPerformed(ActionEvent e)
                 {
                   // TODO: VARNA does'nt print gaps in the sequence
-                  new AppVarna(seq.getSequenceAsString(), rnastruc, seq
-                          .getName(), ap);
+                
+                  new AppVarna(seq.getName()+" structure",seq,rnastruc,seq.getRNA(), 
+                                 seq.getName(), ap);
                 }
               });
               viewStructureMenu.add(menuItem);
@@ -439,6 +459,11 @@ 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); }
@@ -1004,7 +1029,27 @@ public class PopupMenu extends JPopupMenu
     {
       public void actionPerformed(ActionEvent e)
       {
-        pdbFromFile_actionPerformed();
+        try {
+                       pdbFromFile_actionPerformed();
+               } catch (ExceptionFileFormatOrSyntax e1) {
+                       // TODO Auto-generated catch block
+                       e1.printStackTrace();
+               } catch (ParserConfigurationException e1) {
+                       // TODO Auto-generated catch block
+                       e1.printStackTrace();
+               } catch (SAXException e1) {
+                       // TODO Auto-generated catch block
+                       e1.printStackTrace();
+               } catch (ExceptionPermissionDenied e1) {
+                       // TODO Auto-generated catch block
+                       e1.printStackTrace();
+               } catch (ExceptionLoadingFailed e1) {
+                       // TODO Auto-generated catch block
+                       e1.printStackTrace();
+               } catch (InterruptedException e1) {
+                       // TODO Auto-generated catch block
+                       e1.printStackTrace();
+               }
       }
     });
     enterPDB.setText("Enter PDB Id");
@@ -1081,6 +1126,7 @@ public class PopupMenu extends JPopupMenu
     colourMenu.add(turnColour);
     colourMenu.add(buriedColour);
     colourMenu.add(nucleotideMenuItem);
+    colourMenu.add(RNAInteractionColour);
     if (ap.getAlignment().isNucleotide()) {
        colourMenu.add(purinePyrimidineColour);
     }
@@ -1245,6 +1291,16 @@ 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) {
@@ -1289,8 +1345,7 @@ public class PopupMenu extends JPopupMenu
   {
     SequenceGroup sg = getGroup();
     sg.cs = new ClustalxColourScheme(
-            sg.getSequences(ap.av.getHiddenRepSequences()),
-            ap.av.getAlignment().getWidth());
+            sg,ap.av.getHiddenRepSequences());
     refresh();
   }
 
@@ -1396,6 +1451,11 @@ 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(); }
@@ -1848,7 +1908,7 @@ public class PopupMenu extends JPopupMenu
     oal = null;
   }
 
-  public void pdbFromFile_actionPerformed()
+  public void pdbFromFile_actionPerformed() throws ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
   {
     jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));