X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=725a702da877fce68aab0c669e68abaa7f32be87;hb=67fe33692d163752fd467468b18ace4a9b4eac7d;hp=3625e45bdec6b0804eecae3b1da5e84a73b01420;hpb=c295dd6ec0487b99ee6b7625fcab12c3d72028f0;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 3625e45..725a702 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -32,37 +32,20 @@ public class AlignFrame extends GAlignFrame
   final AlignViewport viewport;
   public static final int NEW_WINDOW_WIDTH = 700;
   public static final int NEW_WINDOW_HEIGHT = 500;
+  public String currentFileFormat = "Jalview";
 
   public AlignFrame(AlignmentI al)
   {
-    try{
-      String ip = java.net.InetAddress.getLocalHost().getHostAddress();
-      if( !ip.startsWith("10."))
-        alignMenu.setVisible(false);
-    }
-    catch(java.net.UnknownHostException e){}
-    viewport = new AlignViewport(al,true,true,false);
-
-    String fontName = jalview.bin.Cache.getProperty("FONT_NAME");
-    String fontStyle= jalview.bin.Cache.getProperty("FONT_STYLE");
-    String fontSize = jalview.bin.Cache.getProperty("FONT_SIZE");
-    if(fontName!=null && fontStyle!=null && fontSize!=null)
-      viewport.setFont( new Font(fontName,Integer.parseInt(fontStyle),Integer.parseInt(fontSize)) );
-
-    // add conservation graph to alignment
-    viewport.updateConservation();
-    viewport.updateConsensus();
-
+    viewport = new AlignViewport(al);
 
     alignPanel = new AlignmentPanel(this, viewport);
-
     alignPanel.annotationPanel.adjustPanelHeight();
     alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());
     alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());
+    alignPanel.setAnnotationVisible( viewport.getShowAnnotation() );
 
     getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);
 
-
     addInternalFrameListener(new InternalFrameAdapter()
    {
      public void internalFrameActivated(InternalFrameEvent evt)
@@ -78,34 +61,36 @@ public class AlignFrame extends GAlignFrame
 
   }
 
-  protected void saveAs_actionPerformed(ActionEvent e)
+  public void saveAlignmentMenu_actionPerformed(ActionEvent e)
   {
-    String suffix [] = null;
-    if(e.getActionCommand().equals("FASTA"))
-      suffix = new String[]{"fa", "fasta"};
-    else if(e.getActionCommand().equals("MSF"))
-      suffix = new String[]{"msf"};
-    else if(e.getActionCommand().equals("CLUSTAL"))
-      suffix = new String[]{"aln"};
-    else if(e.getActionCommand().equals("BLC"))
-      suffix = new String[]{"blc"};
-    else if(e.getActionCommand().equals("PIR"))
-      suffix = new String[]{"pir"};
-    else if(e.getActionCommand().equals("PFAM"))
-      suffix = new String[]{"pfam"};
-
-
     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY")
-        , suffix, e.getActionCommand()+" file");
+        ,  new String[]{"fa, fasta, fastq", "aln",  "pfam", "msf", "pir","blc","jar"},
+          new String[]{"Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"},
+          currentFileFormat);
+
+    chooser.setAcceptAllFileFilterUsed(false);
     chooser.setFileView(new JalviewFileView());
-    chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format.");
+    chooser.setDialogTitle("Save Alignment to file");
     chooser.setToolTipText("Save");
     int value = chooser.showSaveDialog(this);
     if(value == JalviewFileChooser.APPROVE_OPTION)
     {
+      currentFileFormat  = chooser.getSelectedFormat();
+
+      if (currentFileFormat.equals("Jalview"))
+      {
+        String shortName = title.replace('/', '_');
+        title = title.replace('\\', '_');
+        String choice = chooser.getSelectedFile().getPath();
+        Jalview2XML.SaveState(this, System.currentTimeMillis(), shortName,
+                              choice);
+        // USE Jalview2XML to save this file
+        return;
+      }
+
       String choice =  chooser.getSelectedFile().getPath();
       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
-      String output = FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences());
+      String output = FormatAdapter.formatSequences(currentFileFormat, viewport.getAlignment().getSequences());
       try{
         java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice )  );
         out.println(output);
@@ -123,7 +108,7 @@ public class AlignFrame extends GAlignFrame
      cap.formatForOutput();
      frame.setContentPane(cap);
      Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);
-     cap.setText( FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences()));
+     cap.setText( FormatAdapter.formatSequences(e.getActionCommand(), viewport.getAlignment().getSequences()));
   }
 
   protected void htmlMenuItem_actionPerformed(ActionEvent e)
@@ -184,7 +169,6 @@ public class AlignFrame extends GAlignFrame
 
   Stack historyList = new Stack();
   Stack redoList = new Stack();
-  JMenuBar jMenuBar1 = new JMenuBar();
 
   void updateEditMenuBar()
   {
@@ -217,6 +201,7 @@ public class AlignFrame extends GAlignFrame
   {
     // must make sure we add new sequence objects her, not refs to the existing sequences
     redoList.clear();
+
     SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
     for(int i=0; i<viewport.getAlignment().getHeight(); i++)
     {
@@ -224,6 +209,7 @@ public class AlignFrame extends GAlignFrame
                              viewport.getAlignment().getSequenceAt(i).getSequence());
     }
 
+
     historyList.add(0, new Object[]{type,  seq} );
     updateEditMenuBar();
   }
@@ -244,11 +230,15 @@ public class AlignFrame extends GAlignFrame
     redoList.add(0, new Object[] {history[0], seq});
 
       seq = (SequenceI[]) history[1];
+      AlignmentAnnotation [] old = viewport.alignment.getAlignmentAnnotation();
       viewport.setAlignment( new Alignment(seq) );
+      viewport.alignment.setGapCharacter( Preferences.gapSymbol );
       updateEditMenuBar();
+      for(int i=0; i<old.length; i++)
+        viewport.alignment.addAnnotation(old[i]);
       viewport.updateConsensus();
-      alignPanel.RefreshPanels();
-      alignPanel.RefreshPanels();
+      viewport.updateConservation();
+      alignPanel.repaint();
   }
 
   public void moveSelectedSequences(boolean up)
@@ -290,28 +280,49 @@ public class AlignFrame extends GAlignFrame
       }
     }
 
-    alignPanel.RefreshPanels();
+    alignPanel.repaint();
   }
 
 
 
   protected void copy_actionPerformed(ActionEvent e)
   {
-   if(viewport.getSelectionGroup()==null)
-     return;
+     if(viewport.getSelectionGroup()==null)
+       return;
 
-   SequenceGroup sg = viewport.getSelectionGroup();
+     SequenceGroup sg = viewport.getSelectionGroup();
 
      Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
      StringBuffer buffer= new StringBuffer();
 
-       for(int i=0; i<sg.getSize(); i++)
+     Hashtable orderedSeqs = new Hashtable();
+     for(int i=0; i<sg.getSize(); i++)
+     {
+        SequenceI seq = sg.getSequenceAt(i);
+        int index = viewport.alignment.findIndex(seq);
+        orderedSeqs.put(index+"", seq);
+     }
+
+     int index=0;
+     for(int i=0; i<sg.getSize(); i++)
+     {
+       SequenceI seq = null;
+       while( seq == null )
        {
-         SequenceI seq = sg.getSequenceAt(i);
+         if(orderedSeqs.containsKey(index+""))
+         {
+           seq = (SequenceI) orderedSeqs.get(index + "");
+           index++;
+           break;
+         }
+         else
+           index++;
+       }
+
          buffer.append( seq.getName()+"\t"+seq.findPosition( sg.getStartRes() ) +"\t"
                         +seq.findPosition( sg.getEndRes() )+ "\t"
                         +sg.getSequenceAt(i).getSequence(sg.getStartRes(), sg.getEndRes()+1)+"\n");
-       }
+     }
      c.setContents( new StringSelection( buffer.toString()) , null ) ;
 
   }
@@ -357,7 +368,13 @@ public class AlignFrame extends GAlignFrame
         SequenceI[] newSeqs = new SequenceI[seqs.size()];
         seqs.toArray(newSeqs);
         AlignFrame af = new AlignFrame(new Alignment(newSeqs));
-        Desktop.addInternalFrame(af, "Copied sequences", NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);
+        String newtitle = new String("Copied sequences");
+        if( title.startsWith("Copied sequences"))
+         newtitle = title;
+       else
+         newtitle = newtitle.concat("- from "+title);
+
+        Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);
       }
       else
       {
@@ -365,7 +382,7 @@ public class AlignFrame extends GAlignFrame
         viewport.alignment.getWidth();
         viewport.updateConservation();
         viewport.updateConsensus();
-        alignPanel.RefreshPanels();
+        alignPanel.repaint();
       }
 
     }catch(Exception ex){}// could be anything being pasted in here
@@ -408,7 +425,7 @@ public class AlignFrame extends GAlignFrame
      }catch(Exception ex){}
    viewport.updateConservation();
    viewport.updateConsensus();
-     alignPanel.RefreshPanels();
+     alignPanel.repaint();
 
   }
 
@@ -419,10 +436,11 @@ public class AlignFrame extends GAlignFrame
      Object [] history = (Object[])redoList.remove(0);
      SequenceI[] seq = (SequenceI[]) history[1];
      viewport.setAlignment( new Alignment(seq) );
+     viewport.alignment.setGapCharacter( Preferences.gapSymbol );
      updateEditMenuBar();
      viewport.updateConsensus();
-     alignPanel.RefreshPanels();
-     alignPanel.RefreshPanels();
+     alignPanel.repaint();
+     alignPanel.repaint();
   }
 
 
@@ -430,8 +448,7 @@ public class AlignFrame extends GAlignFrame
   {
     viewport.alignment.deleteAllGroups();
     viewport.setSelectionGroup(null);
-
-    alignPanel.RefreshPanels();
+    alignPanel.repaint();
   }
 
 
@@ -449,6 +466,8 @@ public class AlignFrame extends GAlignFrame
   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setSelectionGroup(null);
+    viewport.getColumnSelection().clear();
+    viewport.setSelectionGroup(null);
     PaintRefresher.Refresh(null);
   }
 
@@ -461,13 +480,6 @@ public class AlignFrame extends GAlignFrame
     PaintRefresher.Refresh(null);
   }
 
-
-  public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
-  {
-    viewport.getColumnSelection().clear();
-    repaint();
-  }
-
   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
   {
     addHistoryItem("delete columns");
@@ -489,7 +501,7 @@ public class AlignFrame extends GAlignFrame
           viewport.alignment.deleteGroup(sg);
       }
 
-      alignPanel.RefreshPanels();
+      alignPanel.repaint();
     }
   }
 
@@ -514,7 +526,7 @@ public class AlignFrame extends GAlignFrame
 
 
 
-      alignPanel.RefreshPanels();
+      alignPanel.repaint();
     }
 
   }
@@ -525,7 +537,7 @@ public class AlignFrame extends GAlignFrame
     viewport.getAlignment().removeGaps();
     viewport.updateConservation();
     viewport.updateConsensus();
-    alignPanel.RefreshPanels();
+    alignPanel.repaint();
   }
 
   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
@@ -547,29 +559,16 @@ public class AlignFrame extends GAlignFrame
     }
     viewport.updateConservation();
     viewport.updateConsensus();
-    alignPanel.RefreshPanels();
+    alignPanel.repaint();
   }
 
-  public void setGapCharMenuItem_actionPerformed(ActionEvent e)
-  {
-    char thisChar = '-';
-    char nextChar = '.';
-    if(viewport.getGapCharacter()=='-')
-    {
-      thisChar = '.';
-      nextChar = '-';
-    }
-    setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");
-    viewport.setGapCharacter(thisChar);
-    alignPanel.RefreshPanels();
-  }
 
   public void findMenuItem_actionPerformed(ActionEvent e)
   {
     JInternalFrame frame = new JInternalFrame();
     Finder finder = new Finder(viewport, alignPanel, frame);
     frame.setContentPane(finder);
-    Desktop.addInternalFrame(frame, "Find", 340,110, false);
+    Desktop.addInternalFrame(frame, "Find", 340,110);
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
 
   }
@@ -577,11 +576,7 @@ public class AlignFrame extends GAlignFrame
 
   public void font_actionPerformed(ActionEvent e)
   {
-    JInternalFrame frame = new JInternalFrame();
-    FontChooser fc = new FontChooser( alignPanel, frame );
-    frame.setContentPane(fc);
-    Desktop.addInternalFrame(frame, "Change Font", 480,100);
-    frame.setLayer(JLayeredPane.PALETTE_LAYER);
+    FontChooser fc = new FontChooser( alignPanel );
   }
 
   protected void fullSeqId_actionPerformed(ActionEvent e)
@@ -589,13 +584,13 @@ public class AlignFrame extends GAlignFrame
     viewport.setShowFullId( fullSeqId.isSelected() );
 
     alignPanel.idPanel.idCanvas.setPreferredSize( alignPanel.calculateIdWidth() );
-    alignPanel.RefreshPanels();
+    alignPanel.repaint();
   }
 
   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
   {
       viewport.setColourText( colourTextMenuItem.isSelected() );
-      alignPanel.RefreshPanels();
+      alignPanel.repaint();
   }
 
   protected void wrapMenuItem_actionPerformed(ActionEvent e)
@@ -605,7 +600,7 @@ public class AlignFrame extends GAlignFrame
     scaleAbove.setVisible( wrapMenuItem.isSelected() );
     scaleLeft.setVisible( wrapMenuItem.isSelected() );
     scaleRight.setVisible( wrapMenuItem.isSelected() );
-    alignPanel.RefreshPanels();
+    alignPanel.repaint();
   }
 
   protected void scaleAbove_actionPerformed(ActionEvent e)
@@ -631,20 +626,20 @@ public class AlignFrame extends GAlignFrame
   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );
-    alignPanel.RefreshPanels();
+    alignPanel.repaint();
   }
 
   public void viewTextMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setShowText( viewTextMenuItem.isSelected() );
-    alignPanel.RefreshPanels();
+    alignPanel.repaint();
   }
 
 
   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
-    alignPanel.RefreshPanels();
+    alignPanel.repaint();
   }
 
   public void sequenceFeatures_actionPerformed(ActionEvent evt)
@@ -652,10 +647,10 @@ public class AlignFrame extends GAlignFrame
     viewport.showSequenceFeatures(sequenceFeatures.isSelected());
     if(viewport.showSequenceFeatures && !((Alignment)viewport.alignment).featuresAdded)
     {
-         AlignmentUtil.fetchSequenceFeatures( viewport.alignment , alignPanel);
+         SequenceFeatureFetcher sft = new SequenceFeatureFetcher(viewport.alignment, alignPanel);
          ((Alignment)viewport.alignment).featuresAdded = true;
     }
-    alignPanel.RefreshPanels();
+    alignPanel.repaint();
   }
 
   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
@@ -675,27 +670,20 @@ public class AlignFrame extends GAlignFrame
       return;
 
     JInternalFrame frame = new JInternalFrame();
-    OverviewPanel overview = alignPanel.getOverviewPanel();
-   try{
-     overview = new OverviewPanel(alignPanel, viewport);
+    OverviewPanel overview = new OverviewPanel(alignPanel);
      frame.setContentPane(overview);
     Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
                              frame.getWidth(), frame.getHeight());
     frame.pack();
+    frame.setLayer(JLayeredPane.PALETTE_LAYER);
     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
     { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
       {
             alignPanel.setOverviewPanel(null);
       };
     });
-    alignPanel.setOverviewPanel( overview );
 
-  }catch(java.lang.OutOfMemoryError ex)
-   {
-     JOptionPane.showInternalMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!"
-                                   +"\nTry reducing the font size.",
-                                   "Out of memory", JOptionPane.WARNING_MESSAGE);
-   }
+    alignPanel.setOverviewPanel( overview );
 
 
   }
@@ -805,12 +793,15 @@ public class AlignFrame extends GAlignFrame
       ccs.setConsensus( viewport.vconsensus );
       viewport.setGlobalColourScheme(ccs);
 
+      SliderPanel.setConservationSlider(alignPanel, ccs, "Background");
+
     }
     else
     {
         // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
-      cs.setConsensus( viewport.vconsensus );
-      viewport.setGlobalColourScheme(cs);
+        if (cs != null)
+          cs.setConsensus(viewport.vconsensus);
+        viewport.setGlobalColourScheme(cs);
     }
 
 
@@ -825,16 +816,12 @@ public class AlignFrame extends GAlignFrame
         {
           sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
         }
-        else
-          try
-          {
+        else if(cs!=null)
+        {
+          try{
             sg.cs = (ColourSchemeI) cs.getClass().newInstance();
-          }
-          catch (Exception ex)
-          {
-            ex.printStackTrace();
-            sg.cs = cs;
-          }
+          }catch(Exception ex){ex.printStackTrace();}
+        }
 
         if(viewport.getAbovePIDThreshold())
         {
@@ -859,7 +846,7 @@ public class AlignFrame extends GAlignFrame
           ccs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
           sg.cs = ccs;
         }
-        else
+        else if(cs!=null)
         {
           // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
           sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
@@ -868,9 +855,9 @@ public class AlignFrame extends GAlignFrame
       }
     }
 
-
-
-    alignPanel.RefreshPanels();
+    if(alignPanel.getOverviewPanel()!=null)
+      alignPanel.getOverviewPanel().updateOverviewImage();
+    alignPanel.repaint();
   }
 
   protected void modifyPID_actionPerformed(ActionEvent e)
@@ -907,9 +894,9 @@ public class AlignFrame extends GAlignFrame
     else
       changeColour( cs );
 
+    modifyConservation_actionPerformed(null);
   }
 
- // boolean coloursChanging = false;
   public void abovePIDThreshold_actionPerformed(ActionEvent e)
   {
     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
@@ -923,16 +910,15 @@ public class AlignFrame extends GAlignFrame
         changeColour( ((ConservationColourScheme)cs).cs );
     else
         changeColour( cs );
+
+    modifyPID_actionPerformed(null);
   }
 
 
 
   public void userDefinedColour_actionPerformed(ActionEvent e)
   {
-    JInternalFrame frame = new JInternalFrame();
-    UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);
-    frame.setContentPane(chooser);
-    Desktop.addInternalFrame(frame,"User defined colours", 450,540, false );
+    UserDefinedColours chooser = new UserDefinedColours( alignPanel, null);
   }
 
   public void PIDColour_actionPerformed(ActionEvent e)
@@ -952,14 +938,14 @@ public class AlignFrame extends GAlignFrame
   {
     addHistoryItem("sort");
     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));
-    alignPanel.RefreshPanels();
+    alignPanel.repaint();
   }
 
   public void sortIDMenuItem_actionPerformed(ActionEvent e)
   {
     addHistoryItem("sort");
     AlignmentSorter.sortByID( viewport.getAlignment() );
-    alignPanel.RefreshPanels();
+    alignPanel.repaint();
   }
 
   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
@@ -967,7 +953,7 @@ public class AlignFrame extends GAlignFrame
     addHistoryItem("sort");
     AlignmentSorter.sortByGroup(viewport.getAlignment());
     AlignmentSorter.sortGroups(viewport.getAlignment());
-    alignPanel.RefreshPanels();
+    alignPanel.repaint();
   }
 
   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
@@ -1078,7 +1064,7 @@ public class AlignFrame extends GAlignFrame
       {
         addHistoryItem("sort");
         AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
-        alignPanel.RefreshPanels();
+        alignPanel.repaint();
       }
     });
 
@@ -1189,6 +1175,39 @@ public class AlignFrame extends GAlignFrame
 
     }
   }
+  protected void msaAlignMenuItem_actionPerformed(ActionEvent e)
+  {
+    // TODO:resolve which menu item was actually selected
+    // Now, check we have enough sequences
+      if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>1)
+      {
+        // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
+        SequenceGroup seqs = viewport.getSelectionGroup();
+        int sz;
+        SequenceI[] msa = new SequenceI[sz=seqs.getSize()];
+        for (int i = 0; i < sz; i++)
+        {
+          msa[i] = (SequenceI) seqs.getSequenceAt(i);
+        }
+
+        MsaWSClient ct = new jalview.ws.MsaWSClient(msa);
+      }
+      else
+      {
+        Vector seqs = viewport.getAlignment().getSequences();
+
+        if (seqs.size() > 1) {
+          SequenceI[] msa = new SequenceI[seqs.size()];
+          for (int i = 0; i < seqs.size(); i++)
+          {
+            msa[i] = (SequenceI) seqs.elementAt(i);
+          }
+
+          MsaWSClient ct = new MsaWSClient(msa);
+        }
+
+      }
+    }
 
     protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
     // Pick the tree file
@@ -1202,20 +1221,10 @@ public class AlignFrame extends GAlignFrame
     {
       String choice = chooser.getSelectedFile().getPath();
       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
-      TreePanel treepanel = null;
       try
       {
         jalview.io.NewickFile fin = new jalview.io.NewickFile(choice, "File");
-        fin.parse();
-
-        if (fin.getTree() != null)
-        {
-          TreePanel tp = null;
-          tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
-                             fin, "FromFile", choice);
-          Desktop.addInternalFrame(tp, title, 600, 500);
-          addTreeMenuItem(tp, title);
-        }
+        ShowNewickTree(fin, choice);
       }
       catch (Exception ex)
       {
@@ -1228,4 +1237,21 @@ public class AlignFrame extends GAlignFrame
     }
   }
 
+  public void ShowNewickTree(NewickFile nf, String title)
+  {
+    try{
+      nf.parse();
+      if (nf.getTree() != null)
+      {
+        TreePanel tp = new TreePanel(viewport,
+                                     viewport.getAlignment().getSequences(),
+                                     nf, "FromFile", title);
+        Desktop.addInternalFrame(tp, title, 600, 500);
+        addTreeMenuItem(tp, title);
+        viewport.setCurrentTree(tp.getTree());
+      }
+     }catch(Exception ex){ex.printStackTrace();}
+  }
+
+
 }