update author list in license for (JAL-826)

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

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index ca6b199..e812530 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, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -70,6 +70,11 @@ public class PopupMenu extends JPopupMenu
 
   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
 
+  protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
+
+  // protected JRadioButtonMenuItem covariationColour = new
+  // JRadioButtonMenuItem();
+
   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
 
   protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
@@ -80,7 +85,7 @@ public class PopupMenu extends JPopupMenu
 
   JMenuItem sequenceName = new JMenuItem();
 
-  Sequence sequence;
+  SequenceI sequence;
 
   JMenuItem unGroupMenuItem = new JMenuItem();
 
@@ -157,7 +162,7 @@ public class PopupMenu extends JPopupMenu
    * @param links
    * @param groupLinks
    */
-  public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links,
+  public PopupMenu(final AlignmentPanel ap, final SequenceI seq, Vector links,
           Vector groupLinks)
   {
     // /////////////////////////////////////////////////////////
@@ -183,6 +188,8 @@ 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++)
     {
@@ -248,10 +255,67 @@ public class PopupMenu extends JPopupMenu
       }
       else
       {
+        if (ap.av.alignment.isNucleotide() == false)
+        {
         structureMenu.remove(viewStructureMenu);
+        }
         // structureMenu.remove(colStructureMenu);
       }
 
+      if (ap.av.alignment.isNucleotide() == true)
+      {
+        AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+        for (int i = 0; i < aa.length; i++)
+        {
+          if (aa[i].getRNAStruc() != null)
+          {
+            final String rnastruc = aa[i].getRNAStruc();
+            
+            menuItem = new JMenuItem();
+            menuItem.setText("RNA structure - consensus");
+            menuItem.addActionListener(new java.awt.event.ActionListener()
+            {
+              public void actionPerformed(ActionEvent e)
+              {
+                new AppVarna(seq.getSequenceAsString(), rnastruc, seq
+                        .getName(), ap);
+              }
+            });
+            viewStructureMenu.add(menuItem);
+          }
+        }
+
+        // SequenceFeatures[] test = seq.getSequenceFeatures();
+
+        if (seq.getAnnotation() != null)
+        {
+          AlignmentAnnotation seqAnno[] = seq.getAnnotation();
+          for (int i = 0; i < seqAnno.length; i++)
+          {
+            if (seqAnno[i].getRNAStruc() != null)
+            {
+              final String rnastruc = seqAnno[i].getRNAStruc();
+              
+           // TODO: make rnastrucF a bit more nice
+              menuItem = new JMenuItem();
+              menuItem.setText("RNA structure - "+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);
+                }
+              });
+              viewStructureMenu.add(menuItem);
+            }
+          }
+        }
+
+        
+      }
+
       menuItem = new JMenuItem("Hide Sequences");
       menuItem.addActionListener(new java.awt.event.ActionListener()
       {
@@ -371,6 +435,14 @@ 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);
@@ -391,6 +463,7 @@ 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();
@@ -398,6 +471,10 @@ public class PopupMenu extends JPopupMenu
           for (PDBEntry pe: pes)
           {
             pdbe.put(pe.getId(),  pe);
+            if (sqass==null)
+            {
+              sqass = sq;
+            }
           }
         }
       }
@@ -405,7 +482,12 @@ 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()
         {
@@ -435,7 +517,7 @@ public class PopupMenu extends JPopupMenu
       structureMenu.setVisible(false);
     }
 
-    if (seq !=null && links != null && links.size() > 0)
+    if (links != null && links.size() > 0)
     {
 
       JMenu linkMenu = new JMenu("Link");
@@ -460,7 +542,7 @@ public class PopupMenu extends JPopupMenu
           continue;
         }
         final String label = urlLink.getLabel();
-        if (urlLink.isDynamic())
+        if (seq!=null && urlLink.isDynamic())
         {
 
           // collect matching db-refs
@@ -999,6 +1081,10 @@ public class PopupMenu extends JPopupMenu
     colourMenu.add(turnColour);
     colourMenu.add(buriedColour);
     colourMenu.add(nucleotideMenuItem);
+    if (ap.getAlignment().isNucleotide()) {
+       colourMenu.add(purinePyrimidineColour);
+    }
+    // colourMenu.add(covariationColour);
     colourMenu.add(userDefinedColour);
 
     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
@@ -1150,6 +1236,21 @@ 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()
@@ -1289,6 +1390,16 @@ public class PopupMenu extends JPopupMenu
     refresh();
   }
 
+  protected void purinePyrimidineColour_actionPerformed()
+  {
+    getGroup().cs = new PurinePyrimidineColourScheme();
+    refresh();
+  }
+
+  /*
+   * protected void covariationColour_actionPerformed() { getGroup().cs = new
+   * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
+   */
   /**
    * DOCUMENT ME!
    * 
@@ -1772,7 +1883,7 @@ public class PopupMenu extends JPopupMenu
   public void discoverPDB_actionPerformed()
   {
 
-    final SequenceI[] sequences = ((ap.av.selectionGroup == null) ? new Sequence[]
+    final SequenceI[] sequences = ((ap.av.selectionGroup == null) ? new SequenceI[]
     { sequence }
             : ap.av.selectionGroup.getSequencesInOrder(ap.av.alignment));
     Thread discpdb = new Thread(new Runnable()