X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=82ce8359874e9964066a88f7d468c3544eaf4c2c;hb=9a05eeccaf18e0c82cd183f0b84a8be42bf181c7;hp=30feec20004254dd4e2d40a59e956fd6b3f69fde;hpb=ad07946b57c7e3d85d6d2e6dc060fc5af5536cd1;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 30feec2..82ce835 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -69,6 +69,10 @@ public class PopupMenu extends JPopupMenu
   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
 
   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
+  
+  protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
+  
+  //protected JRadioButtonMenuItem covariationColour = new JRadioButtonMenuItem();
 
   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
 
@@ -157,8 +161,8 @@ public class PopupMenu extends JPopupMenu
    * @param links
    * @param groupLinks
    */
-  public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links,
-          Vector groupLinks)
+  public PopupMenu(final AlignmentPanel ap, final Sequence seq, final Vector links,
+          final Vector groupLinks)
   {
     // /////////////////////////////////////////////////////////
     // If this is activated from the sequence panel, the user may want to
@@ -183,6 +187,8 @@ public class PopupMenu extends JPopupMenu
     colours.add(userDefinedColour);
     colours.add(PIDColour);
     colours.add(BLOSUM62Colour);
+    colours.add(purinePyrimidineColour);
+    //colours.add(covariationColour);
 
     for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
     {
@@ -247,10 +253,40 @@ public class PopupMenu extends JPopupMenu
         }
       }
       else
-      {
-        structureMenu.remove(viewStructureMenu);
+      {	
+    	  if(ap.av.alignment.isNucleotide()==false){
+    		  structureMenu.remove(viewStructureMenu);
+    	  }
         // structureMenu.remove(colStructureMenu);
       }
+      
+      if(ap.av.alignment.isNucleotide()==true){
+    	  AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+    	  String rnastruc=new String();
+    	  for(int i=0; i<aa.length;i++){
+    		  if(aa[i]._rnasecstr != null){
+    			  rnastruc=aa[i].getRNAStruc();
+    			  break;
+    		  }
+    	  }
+    	  
+    	  SequenceGroup a = aa[0].groupRef;
+
+    	  //TODO: make rnastrucF a bit more nice
+    	  final String rnastrucF=rnastruc;
+    	  menuItem = new JMenuItem();
+    	  menuItem.setText("RNA structure");
+    	  menuItem.addActionListener(new java.awt.event.ActionListener()
+    	  {
+    		  public void actionPerformed(ActionEvent e)
+    		  {
+    			  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(),ap);
+    		  }
+		  	});	  
+		  	viewStructureMenu.add(menuItem);
+      	}
 
       menuItem = new JMenuItem("Hide Sequences");
       menuItem.addActionListener(new java.awt.event.ActionListener()
@@ -367,6 +403,14 @@ public class PopupMenu extends JPopupMenu
       {
         clustalColour.setSelected(true);
       }
+      else if (sg.cs instanceof PurinePyrimidineColourScheme)
+      {
+    	purinePyrimidineColour.setSelected(true);
+      }
+     /* else if (sg.cs instanceof CovariationColourScheme)
+      {
+    	covariationColour.setSelected(true);
+      }*/
       else
       {
         noColourmenuItem.setSelected(true);
@@ -402,6 +446,7 @@ public class PopupMenu extends JPopupMenu
         final PDBEntry[] pe = pdbe.values().toArray(new PDBEntry[pdbe.size()]);
         final JMenuItem gpdbview;
         structureMenu.add(gpdbview=new JMenuItem("View "+pdbe.size()+" structures."));
+        gpdbview.setToolTipText("Open a new Jmol view with all structures associated with the current selection and superimpose them using the alignment.");
         gpdbview.addActionListener(new ActionListener()
         {
           
@@ -994,6 +1039,8 @@ public class PopupMenu extends JPopupMenu
     colourMenu.add(turnColour);
     colourMenu.add(buriedColour);
     colourMenu.add(nucleotideMenuItem);
+    colourMenu.add(purinePyrimidineColour);
+    //colourMenu.add(covariationColour);
     colourMenu.add(userDefinedColour);
 
     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
@@ -1145,6 +1192,23 @@ public class PopupMenu extends JPopupMenu
         BLOSUM62Colour_actionPerformed();
       }
     });
+    purinePyrimidineColour.setText("Purine/Pyrimidine");
+    purinePyrimidineColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+    	  purinePyrimidineColour_actionPerformed();
+      }
+    });
+   /* 
+    covariationColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+    	  covariationColour_actionPerformed();
+      }
+    });*/
+    
     conservationMenuItem.setText("Conservation");
     conservationMenuItem
             .addActionListener(new java.awt.event.ActionListener()
@@ -1283,7 +1347,19 @@ public class PopupMenu extends JPopupMenu
     getGroup().cs = new NucleotideColourScheme();
     refresh();
   }
-
+  
+  protected void purinePyrimidineColour_actionPerformed()
+  {
+    getGroup().cs = new PurinePyrimidineColourScheme();
+    refresh();
+  }
+  /*
+  protected void covariationColour_actionPerformed()
+  {
+    getGroup().cs = new CovariationColourScheme(sequence.getAnnotation()[0]);
+    refresh();
+  }
+*/
   /**
    * DOCUMENT ME!
    *