Merge remote-tracking branch 'remotes/origin/2_5_1_rna_merge' into develop (JAL-826)

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

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 2ac304b..1cc4cd7 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -69,10 +69,6 @@ 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();
 
@@ -161,8 +157,8 @@ public class PopupMenu extends JPopupMenu
    * @param links
    * @param groupLinks
    */
-  public PopupMenu(final AlignmentPanel ap, final Sequence seq, final Vector links,
-          final Vector groupLinks)
+  public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links,
+          Vector groupLinks)
   {
     // /////////////////////////////////////////////////////////
     // If this is activated from the sequence panel, the user may want to
@@ -187,8 +183,6 @@ 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++)
     {
@@ -214,11 +208,11 @@ public class PopupMenu extends JPopupMenu
       e.printStackTrace();
     }
 
+    JMenuItem menuItem;
     if (seq != null)
     {
       sequenceMenu.setText(sequence.getName());
 
-      JMenuItem menuItem;
       if (seq.getDatasetSequence().getPDBId() != null
               && seq.getDatasetSequence().getPDBId().size() > 0)
       {
@@ -253,38 +247,10 @@ public class PopupMenu extends JPopupMenu
         }
       }
       else
-      {        
-         if(ap.av.alignment.isNucleotide()==false){
-                 structureMenu.remove(viewStructureMenu);
-         }
+      {
+        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;
-                 }
-         }
-
-         //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());
-                 }
-                       });       
-                       viewStructureMenu.add(menuItem);
-       }
 
       menuItem = new JMenuItem("Hide Sequences");
       menuItem.addActionListener(new java.awt.event.ActionListener()
@@ -331,7 +297,11 @@ public class PopupMenu extends JPopupMenu
           });
           add(menuItem);
         }
-
+      }
+    }
+    // for the case when no sequences are even visible
+    if (ap.av.hasHiddenRows) {
+      {
         menuItem = new JMenuItem("Reveal All");
         menuItem.addActionListener(new ActionListener()
         {
@@ -352,7 +322,7 @@ public class PopupMenu extends JPopupMenu
 
     SequenceGroup sg = ap.av.getSelectionGroup();
 
-    if (sg != null)
+    if (sg != null&& sg.getSize()>0)
     {
       groupName.setText("Name: "+sg.getName());
       groupName.setText("Edit name and description of current group.");
@@ -401,14 +371,6 @@ 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);
@@ -429,6 +391,7 @@ public class PopupMenu extends JPopupMenu
       }
       // Add a 'show all structures' for the current selection
       Hashtable<String, PDBEntry> pdbe=new Hashtable<String,PDBEntry>();
+      SequenceI sqass=null;
       for (SequenceI sq: ap.av.getSequenceSelection())
       {
         Vector<PDBEntry> pes = (Vector<PDBEntry>) sq.getDatasetSequence().getPDBId();
@@ -436,6 +399,10 @@ public class PopupMenu extends JPopupMenu
           for (PDBEntry pe: pes)
           {
             pdbe.put(pe.getId(),  pe);
+            if (sqass==null)
+            {
+              sqass = sq;
+            }
           }
         }
       }
@@ -443,7 +410,12 @@ 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."));
+        if (pdbe.size()==1)
+        {
+          structureMenu.add(gpdbview=new JMenuItem("View structure for "+sqass.getDisplayId(false)));
+        } else {
+          structureMenu.add(gpdbview=new JMenuItem("View all "+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()
         {
@@ -498,7 +470,7 @@ public class PopupMenu extends JPopupMenu
           continue;
         }
         final String label = urlLink.getLabel();
-        if (urlLink.isDynamic())
+        if (seq!=null && urlLink.isDynamic())
         {
 
           // collect matching db-refs
@@ -1037,8 +1009,6 @@ 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)
@@ -1190,23 +1160,6 @@ 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()
@@ -1345,19 +1298,7 @@ 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!
    *