X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=c35496433f92978d338d81e03c7b7e80ec3bdf87;hb=27e20b88d0c73ced06e9c20a6e0fa14e27fed179;hp=2ac304bc96e1faa364418bddf198c291d04a628a;hpb=f2469e3ede414575d5e8cd510ed5c916095b55bf;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 2ac304b..c354964 100644
--- 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.
  * 
@@ -23,6 +23,14 @@ 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 fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
 
 import MCview.*;
 import jalview.analysis.*;
@@ -69,10 +77,12 @@ 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();
+  protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
+
+  // protected JRadioButtonMenuItem covariationColour = new
+  // JRadioButtonMenuItem();
 
   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
 
@@ -83,8 +93,11 @@ public class PopupMenu extends JPopupMenu
   JMenu sequenceMenu = new JMenu();
 
   JMenuItem sequenceName = new JMenuItem();
+  
+  JMenuItem sequenceDetails = new JMenuItem();
+  JMenuItem sequenceSelDetails = new JMenuItem();
 
-  Sequence sequence;
+  SequenceI sequence;
 
   JMenuItem unGroupMenuItem = new JMenuItem();
 
@@ -161,8 +174,8 @@ 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, final SequenceI seq, Vector links,
+          Vector groupLinks)
   {
     // /////////////////////////////////////////////////////////
     // If this is activated from the sequence panel, the user may want to
@@ -188,7 +201,8 @@ public class PopupMenu extends JPopupMenu
     colours.add(PIDColour);
     colours.add(BLOSUM62Colour);
     colours.add(purinePyrimidineColour);
-    //colours.add(covariationColour);
+    colours.add(RNAInteractionColour);
+    // colours.add(covariationColour);
 
     for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
     {
@@ -214,11 +228,11 @@ 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 +267,81 @@ public class PopupMenu extends JPopupMenu
         }
       }
       else
-      {	
-    	  if(ap.av.alignment.isNucleotide()==false){
-    		  structureMenu.remove(viewStructureMenu);
-    	  }
+      {
+        if (ap.av.getAlignment().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;
-    		  }
-    	  }
-
-    	  //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);
-      	}
+
+      if (ap.av.getAlignment().isNucleotide() == true)
+      {
+        AlignmentAnnotation[] aa = ap.av.getAlignment().getAlignmentAnnotation();
+        for (int i = 0; i < aa.length; i++)
+        {
+          if (aa[i].getRNAStruc() != null)
+          {
+            final String rnastruc = aa[i].getRNAStruc();
+            final String structureLine=aa[i].label;
+            menuItem = new JMenuItem();
+            menuItem.setText("2D RNA "+structureLine);
+            menuItem.addActionListener(new java.awt.event.ActionListener()
+            
+            {
+              public void actionPerformed(ActionEvent e)
+              {
+            		//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);
+          }
+        }
+
+        // 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("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.getName()+" structure",seq,rnastruc,seq.getRNA(), seq.getName(), ap);
+                  new AppVarna(seq.getName()+" structure",seq,seq.getSequenceAsString(), rnastruc, seq
+                          .getName(), ap);
+                }
+              });
+              viewStructureMenu.add(menuItem);
+            }
+          }
+        }
+
+        
+      }
 
       menuItem = new JMenuItem("Hide Sequences");
       menuItem.addActionListener(new java.awt.event.ActionListener()
@@ -310,9 +367,9 @@ public class PopupMenu extends JPopupMenu
         sequenceMenu.add(menuItem);
       }
 
-      if (ap.av.hasHiddenRows)
+      if (ap.av.hasHiddenRows())
       {
-        final int index = ap.av.alignment.findIndex(seq);
+        final int index = ap.av.getAlignment().findIndex(seq);
 
         if (ap.av.adjustForHiddenSeqs(index)
                 - ap.av.adjustForHiddenSeqs(index - 1) > 1)
@@ -331,7 +388,11 @@ 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 +413,7 @@ 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.");
@@ -403,12 +464,17 @@ public class PopupMenu extends JPopupMenu
       }
       else if (sg.cs instanceof PurinePyrimidineColourScheme)
       {
-    	purinePyrimidineColour.setSelected(true);
+        purinePyrimidineColour.setSelected(true);
       }
-     /* else if (sg.cs instanceof CovariationColourScheme)
+      
+      else if (sg.cs instanceof RNAInteractionColourScheme)
       {
-    	covariationColour.setSelected(true);
-      }*/
+        RNAInteractionColour.setSelected(true);
+      }
+      /*
+       * else if (sg.cs instanceof CovariationColourScheme) {
+       * covariationColour.setSelected(true); }
+       */
       else
       {
         noColourmenuItem.setSelected(true);
@@ -429,6 +495,7 @@ 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 +503,10 @@ public class PopupMenu extends JPopupMenu
           for (PDBEntry pe: pes)
           {
             pdbe.put(pe.getId(),  pe);
+            if (sqass==null)
+            {
+              sqass = sq;
+            }
           }
         }
       }
@@ -443,7 +514,12 @@ 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()
         {
@@ -462,7 +538,7 @@ public class PopupMenu extends JPopupMenu
       editMenu.setVisible(false);
     }
 
-    if (!ap.av.alignment.getGroups().contains(sg))
+    if (!ap.av.getAlignment().getGroups().contains(sg))
     {
       unGroupMenuItem.setVisible(false);
     }
@@ -498,7 +574,7 @@ public class PopupMenu extends JPopupMenu
           continue;
         }
         final String label = urlLink.getLabel();
-        if (urlLink.isDynamic())
+        if (seq!=null && urlLink.isDynamic())
         {
 
           // collect matching db-refs
@@ -851,6 +927,20 @@ public class PopupMenu extends JPopupMenu
         sequenceName_actionPerformed();
       }
     });
+    sequenceDetails.setText("Sequence Details ...");
+    sequenceDetails.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        sequenceDetails_actionPerformed();
+     }});
+    sequenceSelDetails.setText("Sequence Details ...");
+    sequenceSelDetails.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        sequenceSelectionDetails_actionPerformed();
+     }});    
     PIDColour.setFocusPainted(false);
     unGroupMenuItem.setText("Remove Group");
     unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
@@ -960,7 +1050,30 @@ 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();
+		} catch (ExceptionUnmatchedClosingParentheses e1) {
+			// TODO Auto-generated catch block
+			e1.printStackTrace();
+		}
       }
     });
     enterPDB.setText("Enter PDB Id");
@@ -1008,15 +1121,15 @@ public class PopupMenu extends JPopupMenu
         editSequence_actionPerformed(actionEvent);
       }
     });
+    
     /*
      * annotationMenuItem.setText("By Annotation");
      * annotationMenuItem.addActionListener(new ActionListener() { public void
      * actionPerformed(ActionEvent actionEvent) {
      * annotationMenuItem_actionPerformed(actionEvent); } });
      */
-
+    groupMenu.add(sequenceSelDetails);
     add(groupMenu);
-
     add(sequenceMenu);
     this.add(structureMenu);
     groupMenu.add(editMenu);
@@ -1024,6 +1137,7 @@ public class PopupMenu extends JPopupMenu
     groupMenu.add(sequenceFeature);
     groupMenu.add(jMenu1);
     sequenceMenu.add(sequenceName);
+    sequenceMenu.add(sequenceDetails);
     colourMenu.add(textColour);
     colourMenu.add(noColourmenuItem);
     colourMenu.add(clustalColour);
@@ -1037,8 +1151,11 @@ public class PopupMenu extends JPopupMenu
     colourMenu.add(turnColour);
     colourMenu.add(buriedColour);
     colourMenu.add(nucleotideMenuItem);
-    colourMenu.add(purinePyrimidineColour);
-    //colourMenu.add(covariationColour);
+    colourMenu.add(RNAInteractionColour);
+    if (ap.getAlignment().isNucleotide()) {
+    	colourMenu.add(purinePyrimidineColour);
+    }
+    // colourMenu.add(covariationColour);
     colourMenu.add(userDefinedColour);
 
     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
@@ -1191,22 +1308,30 @@ public class PopupMenu extends JPopupMenu
       }
     });
     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();
-      }
-    });*/
+    purinePyrimidineColour
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              public void actionPerformed(ActionEvent e)
+              {
+                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) {
+     * covariationColour_actionPerformed(); } });
+     */
+
     conservationMenuItem.setText("Conservation");
     conservationMenuItem
             .addActionListener(new java.awt.event.ActionListener()
@@ -1218,6 +1343,40 @@ public class PopupMenu extends JPopupMenu
             });
   }
 
+  protected void sequenceSelectionDetails_actionPerformed()
+  {
+    createSequenceDetailsReport(ap.av.getSequenceSelection());
+  }
+
+  protected void sequenceDetails_actionPerformed()
+  {
+    createSequenceDetailsReport(new SequenceI[]{sequence});
+  }
+  public void createSequenceDetailsReport(SequenceI[] sequences)
+  {
+    CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
+    StringBuffer contents = new StringBuffer();
+    for (SequenceI seq:sequences)
+    {
+    contents.append("<p><h2>Annotation for "+seq.getDisplayId(true)+"</h2></p><p>");
+    new SequenceAnnotationReport(null)
+            .createSequenceAnnotationReport(
+                    contents,
+                    seq,
+                    true,
+                    true,false, 
+                    (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.minmax
+                            : null);
+    contents.append("</p>");
+    }
+    cap.setText("<html>" + contents.toString() + "</html>");
+    
+    Desktop.instance.addInternalFrame(cap, 
+            "Sequence Details for " + (sequences.length==1 ? sequences[0].getDisplayId(true) : "Selection") 
+, 500, 400);
+    
+  }
+
   protected void showNonconserved_actionPerformed()
   {
     getGroup().setShowNonconserved(displayNonconserved.isSelected());
@@ -1245,8 +1404,7 @@ public class PopupMenu extends JPopupMenu
   {
     SequenceGroup sg = getGroup();
     sg.cs = new ClustalxColourScheme(
-            sg.getSequences(ap.av.hiddenRepSequences),
-            ap.av.alignment.getWidth());
+            sg,ap.av.getHiddenRepSequences());
     refresh();
   }
 
@@ -1345,19 +1503,22 @@ public class PopupMenu extends JPopupMenu
     getGroup().cs = new NucleotideColourScheme();
     refresh();
   }
-  
+
   protected void purinePyrimidineColour_actionPerformed()
   {
     getGroup().cs = new PurinePyrimidineColourScheme();
     refresh();
   }
-  /*
-  protected void covariationColour_actionPerformed()
+
+  protected void RNAInteractionColour_actionPerformed()
   {
-    getGroup().cs = new CovariationColourScheme(sequence.getAnnotation()[0]);
+    getGroup().cs = new RNAInteractionColourScheme();
     refresh();
   }
-*/
+  /*
+   * protected void covariationColour_actionPerformed() { getGroup().cs = new
+   * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
+   */
   /**
    * DOCUMENT ME!
    * 
@@ -1375,7 +1536,7 @@ public class PopupMenu extends JPopupMenu
     if (abovePIDColour.isSelected())
     {
       sg.cs.setConsensus(AAFrequency.calculate(
-              sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),
+              sg.getSequences(ap.av.getHiddenRepSequences()), sg.getStartRes(),
               sg.getEndRes() + 1));
 
       int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
@@ -1429,7 +1590,7 @@ public class PopupMenu extends JPopupMenu
     SequenceGroup sg = getGroup();
     sg.cs = new PIDColourScheme();
     sg.cs.setConsensus(AAFrequency.calculate(
-            sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),
+            sg.getSequences(ap.av.getHiddenRepSequences()), sg.getStartRes(),
             sg.getEndRes() + 1));
     refresh();
   }
@@ -1447,7 +1608,7 @@ public class PopupMenu extends JPopupMenu
     sg.cs = new Blosum62ColourScheme();
 
     sg.cs.setConsensus(AAFrequency.calculate(
-            sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),
+            sg.getSequences(ap.av.getHiddenRepSequences()), sg.getStartRes(),
             sg.getEndRes() + 1));
 
     refresh();
@@ -1483,11 +1644,11 @@ public class PopupMenu extends JPopupMenu
     {
       Conservation c = new Conservation("Group",
               ResidueProperties.propHash, 3,
-              sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),
+              sg.getSequences(ap.av.getHiddenRepSequences()), sg.getStartRes(),
               sg.getEndRes() + 1);
 
       c.calculate();
-      c.verdict(false, ap.av.ConsPercGaps);
+      c.verdict(false, ap.av.getConsPercGaps());
 
       sg.cs.setConservation(c);
 
@@ -1557,7 +1718,7 @@ public class PopupMenu extends JPopupMenu
     // this method won't add a new group if it already exists
     if (sg != null)
     {
-      ap.av.alignment.addGroup(sg);
+      ap.av.getAlignment().addGroup(sg);
     }
 
     return sg;
@@ -1611,7 +1772,7 @@ public class PopupMenu extends JPopupMenu
   void unGroupMenuItem_actionPerformed()
   {
     SequenceGroup sg = ap.av.getSelectionGroup();
-    ap.av.alignment.deleteGroup(sg);
+    ap.av.getAlignment().deleteGroup(sg);
     ap.av.setSelectionGroup(null);
     refresh();
   }
@@ -1765,7 +1926,7 @@ public class PopupMenu extends JPopupMenu
       }
 
       ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
-              sg.getSequencesAsArray(ap.av.hiddenRepSequences), startEnd,
+              sg.getSequencesAsArray(ap.av.getHiddenRepSequences()), startEnd,
               caseChange);
 
       ap.alignFrame.addHistoryItem(caseCommand);
@@ -1792,7 +1953,7 @@ public class PopupMenu extends JPopupMenu
     ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection());
     omitHidden = ap.av.getViewAsString(true);
     Alignment oal = new Alignment(ap.av.getSequenceSelection());
-    AlignmentAnnotation[] nala = ap.av.alignment.getAlignmentAnnotation();
+    AlignmentAnnotation[] nala = ap.av.getAlignment().getAlignmentAnnotation();
     if (nala != null)
     {
       for (int i = 0; i < nala.length; i++)
@@ -1806,7 +1967,7 @@ public class PopupMenu extends JPopupMenu
     oal = null;
   }
 
-  public void pdbFromFile_actionPerformed()
+  public void pdbFromFile_actionPerformed() throws ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
   {
     jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
@@ -1841,9 +2002,9 @@ public class PopupMenu extends JPopupMenu
   public void discoverPDB_actionPerformed()
   {
 
-    final SequenceI[] sequences = ((ap.av.selectionGroup == null) ? new Sequence[]
+    final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[]
     { sequence }
-            : ap.av.selectionGroup.getSequencesInOrder(ap.av.alignment));
+            : ap.av.getSequenceSelection());
     Thread discpdb = new Thread(new Runnable()
     {
       public void run()
@@ -1912,10 +2073,10 @@ public class PopupMenu extends JPopupMenu
     AlignmentAnnotation an = new AlignmentAnnotation("Structure",
             "Coloured by " + pdbid, anots);
 
-    ap.av.alignment.addAnnotation(an);
+    ap.av.getAlignment().addAnnotation(an);
     an.createSequenceMapping(sequence, 0, true);
     // an.adjustForAlignment();
-    ap.av.alignment.setAnnotationIndex(an, 0);
+    ap.av.getAlignment().setAnnotationIndex(an, 0);
 
     ap.adjustAnnotationHeight();
 
@@ -1942,8 +2103,8 @@ public class PopupMenu extends JPopupMenu
         EditCommand editCommand = new EditCommand("Edit Sequences",
                 EditCommand.REPLACE, dialog.getName().replace(' ',
                         ap.av.getGapCharacter()),
-                sg.getSequencesAsArray(ap.av.hiddenRepSequences),
-                sg.getStartRes(), sg.getEndRes() + 1, ap.av.alignment);
+                sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
+                sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());
 
         ap.alignFrame.addHistoryItem(editCommand);