X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=c1a710508c5e432e088c227d37101a6206167db7;hb=ac07859006686a2c62bcf57b24742eb610bc46f0;hp=42094550da539211cfc9eaf91002ff01d5cb9977;hpb=798a8f1eda50a57b71e21df22e015da1364ffd1c;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 4209455..c1a7105 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -23,17 +23,25 @@ import java.awt.print.*;
 import javax.swing.*;
 import javax.swing.event.*;
 import java.util.*;
-import  java.awt.datatransfer.*;
+import java.awt.datatransfer.*;
 
 
 public class AlignFrame extends GAlignFrame
 {
   final AlignmentPanel alignPanel;
   final AlignViewport viewport;
+  public static final int NEW_WINDOW_WIDTH = 700;
+  public static final int NEW_WINDOW_HEIGHT = 500;
+
   public AlignFrame(AlignmentI al)
   {
-    super();
-    viewport = new AlignViewport(al,true,true,true,false);
+    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");
@@ -41,11 +49,20 @@ public class AlignFrame extends GAlignFrame
     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();
 
 
     alignPanel = new AlignmentPanel(this, viewport);
+
+    alignPanel.annotationPanel.adjustPanelHeight();
+    alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());
+    alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());
+
     getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);
 
+
     addInternalFrameListener(new InternalFrameAdapter()
    {
      public void internalFrameActivated(InternalFrameEvent evt)
@@ -63,11 +80,28 @@ public class AlignFrame extends GAlignFrame
 
   protected void saveAs_actionPerformed(ActionEvent e)
   {
-    JFileChooser chooser = new JFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+    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");
+    chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format.");
     chooser.setToolTipText("Save");
     int value = chooser.showSaveDialog(this);
-    if(value == JFileChooser.APPROVE_OPTION)
+    if(value == JalviewFileChooser.APPROVE_OPTION)
     {
       String choice =  chooser.getSelectedFile().getPath();
       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
@@ -98,20 +132,14 @@ public class AlignFrame extends GAlignFrame
     htmlOutput = null;
   }
 
-  protected void createJPG_actionPerformed(ActionEvent e)
+  protected void createPNG_actionPerformed(ActionEvent e)
   {
+    alignPanel.makePNG();
+  }
 
-    int height = (viewport.alignment.getWidth() / viewport.getChunkWidth() +1) * viewport.chunkHeight;
-    int width = alignPanel.seqPanel.getWidth() + alignPanel.idPanel.getWidth();
-
-
-    if(!viewport.getWrapAlignment())
-    {
-      height = viewport.alignment.getHeight() * viewport.charHeight;
-      width = alignPanel.idPanel.getWidth() + viewport.alignment.getWidth() * viewport.charWidth;
-    }
-
-    alignPanel.makeJPG( width, height);
+  protected void epsFile_actionPerformed(ActionEvent e)
+  {
+    alignPanel.makeEPS();
   }
 
 
@@ -156,6 +184,7 @@ public class AlignFrame extends GAlignFrame
 
   Stack historyList = new Stack();
   Stack redoList = new Stack();
+  JMenuBar jMenuBar1 = new JMenuBar();
 
   void updateEditMenuBar()
   {
@@ -217,12 +246,14 @@ public class AlignFrame extends GAlignFrame
       seq = (SequenceI[]) history[1];
       viewport.setAlignment( new Alignment(seq) );
       updateEditMenuBar();
+      viewport.updateConsensus();
+      alignPanel.RefreshPanels();
       alignPanel.RefreshPanels();
   }
 
   public void moveSelectedSequences(boolean up)
   {
-    SequenceGroup sg = viewport.getRubberbandGroup();
+    SequenceGroup sg = viewport.getSelectionGroup();
     if (sg == null)
       return;
 
@@ -266,10 +297,10 @@ public class AlignFrame extends GAlignFrame
 
   protected void copy_actionPerformed(ActionEvent e)
   {
-   if(viewport.getRubberbandGroup()==null)
+   if(viewport.getSelectionGroup()==null)
      return;
 
-   SequenceGroup sg = viewport.getRubberbandGroup();
+   SequenceGroup sg = viewport.getSelectionGroup();
 
      Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
      StringBuffer buffer= new StringBuffer();
@@ -326,15 +357,14 @@ public class AlignFrame extends GAlignFrame
         SequenceI[] newSeqs = new SequenceI[seqs.size()];
         seqs.toArray(newSeqs);
         AlignFrame af = new AlignFrame(new Alignment(newSeqs));
-        int newHeight = newSeqs.length * af.viewport.getCharHeight() + 200;
-        if (newHeight > 500)
-          newHeight = 500;
-        Desktop.addInternalFrame(af, "Copied sequences", 700, newHeight);
+        Desktop.addInternalFrame(af, "Copied sequences", NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);
       }
       else
       {
         viewport.setEndSeq(viewport.alignment.getHeight());
         viewport.alignment.getWidth();
+        viewport.updateConservation();
+        viewport.updateConsensus();
         alignPanel.RefreshPanels();
       }
 
@@ -352,10 +382,10 @@ public class AlignFrame extends GAlignFrame
   protected void delete_actionPerformed(ActionEvent e)
   {
     addHistoryItem("Delete");
-    if (viewport.getRubberbandGroup() == null)
+    if (viewport.getSelectionGroup() == null)
       return;
 
-     SequenceGroup sg = viewport.getRubberbandGroup();
+     SequenceGroup sg = viewport.getSelectionGroup();
      for (int i=0;i < sg.sequences.size(); i++)
      {
        SequenceI seq = sg.getSequenceAt(i);
@@ -368,7 +398,7 @@ public class AlignFrame extends GAlignFrame
           viewport.getAlignment().getSequences().setElementAt(seq, index);
      }
 
-     viewport.setRubberbandGroup(null);
+     viewport.setSelectionGroup(null);
      viewport.alignment.deleteGroup(sg);
      viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getHeight());
      if(viewport.getAlignment().getHeight()<1)
@@ -376,6 +406,8 @@ public class AlignFrame extends GAlignFrame
      {
        this.setClosed(true);
      }catch(Exception ex){}
+   viewport.updateConservation();
+   viewport.updateConsensus();
      alignPanel.RefreshPanels();
 
   }
@@ -388,23 +420,16 @@ public class AlignFrame extends GAlignFrame
      SequenceI[] seq = (SequenceI[]) history[1];
      viewport.setAlignment( new Alignment(seq) );
      updateEditMenuBar();
+     viewport.updateConsensus();
+     alignPanel.RefreshPanels();
      alignPanel.RefreshPanels();
   }
 
 
-  public void groupsMenuItem_actionPerformed(ActionEvent e)
-  {
-    GroupEditor geditor = new GroupEditor(viewport, alignPanel);
-    JInternalFrame frame = new JInternalFrame();
-    frame.setContentPane(geditor);
-    Desktop.addInternalFrame(frame, "Group editor", 710, 410);
-    frame.setResizable(false);
-  }
-
   protected void deleteGroups_actionPerformed(ActionEvent e)
   {
     viewport.alignment.deleteAllGroups();
-    viewport.getSelection().clear();
+    viewport.setSelectionGroup(null);
 
     alignPanel.RefreshPanels();
   }
@@ -413,29 +438,26 @@ public class AlignFrame extends GAlignFrame
 
   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
   {
-    Selection sel = viewport.getSelection();
+    SequenceGroup sg = new SequenceGroup();
     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
-      sel.addElement( viewport.getAlignment().getSequenceAt(i));
+      sg.addSequence( viewport.getAlignment().getSequenceAt(i));
+    sg.setEndRes(viewport.alignment.getWidth());
+    viewport.setSelectionGroup(sg);
     PaintRefresher.Refresh(null);
   }
 
   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
   {
-    viewport.setRubberbandGroup(null);
-    viewport.getSelection().clear();
+    viewport.setSelectionGroup(null);
     PaintRefresher.Refresh(null);
   }
 
   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
   {
-    Selection sel = viewport.getSelection();
+    SequenceGroup sg = viewport.getSelectionGroup();
     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
-    {
-      if (sel.contains(viewport.getAlignment().getSequenceAt(i)))
-        sel.removeElement(viewport.getAlignment().getSequenceAt(i));
-      else
-        sel.addElement(viewport.getAlignment().getSequenceAt(i));
-    }
+      sg.addOrRemove (viewport.getAlignment().getSequenceAt(i));
+
     PaintRefresher.Refresh(null);
   }
 
@@ -455,6 +477,18 @@ public class AlignFrame extends GAlignFrame
       int min = colSel.getMin();
       viewport.getAlignment().trimLeft(min);
       colSel.compensateForEdit(0,min);
+
+      if(viewport.getSelectionGroup()!=null)
+        viewport.getSelectionGroup().adjustForRemoveLeft(min);
+
+      Vector groups = viewport.alignment.getGroups();
+      for(int i=0; i<groups.size(); i++)
+      {
+        SequenceGroup sg = (SequenceGroup) groups.get(i);
+        if(!sg.adjustForRemoveLeft(min))
+          viewport.alignment.deleteGroup(sg);
+      }
+
       alignPanel.RefreshPanels();
     }
   }
@@ -466,8 +500,19 @@ public class AlignFrame extends GAlignFrame
     if (colSel.size() > 0)
     {
       int max = colSel.getMax();
-      if(max>1)
-        viewport.getAlignment().trimRight(max);
+      viewport.getAlignment().trimRight(max);
+      if(viewport.getSelectionGroup()!=null)
+        viewport.getSelectionGroup().adjustForRemoveRight(max);
+
+      Vector groups = viewport.alignment.getGroups();
+      for(int i=0; i<groups.size(); i++)
+      {
+        SequenceGroup sg = (SequenceGroup) groups.get(i);
+        if(!sg.adjustForRemoveRight(max))
+          viewport.alignment.deleteGroup(sg);
+      }
+
+
 
       alignPanel.RefreshPanels();
     }
@@ -478,6 +523,8 @@ public class AlignFrame extends GAlignFrame
   {
     addHistoryItem("delete gapped columns");
     viewport.getAlignment().removeGaps();
+    viewport.updateConservation();
+    viewport.updateConsensus();
     alignPanel.RefreshPanels();
   }
 
@@ -498,7 +545,8 @@ public class AlignFrame extends GAlignFrame
           jSize--;
         }
     }
-
+    viewport.updateConservation();
+    viewport.updateConsensus();
     alignPanel.RefreshPanels();
   }
 
@@ -518,23 +566,31 @@ public class AlignFrame extends GAlignFrame
 
   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);
+    JInternalFrame frame = new JInternalFrame();
+    Finder finder = new Finder(viewport, alignPanel, frame);
+    frame.setContentPane(finder);
+    Desktop.addInternalFrame(frame, "Find", 340,110, false);
+    frame.setLayer(JLayeredPane.PALETTE_LAYER);
 
   }
 
 
   public void font_actionPerformed(ActionEvent e)
   {
-   // JOptionPane op = new JOptionPane();
     JInternalFrame frame = new JInternalFrame();
     FontChooser fc = new FontChooser( alignPanel, frame );
     frame.setContentPane(fc);
     Desktop.addInternalFrame(frame, "Change Font", 480,100);
   }
 
+  protected void fullSeqId_actionPerformed(ActionEvent e)
+  {
+    viewport.setShowFullId( fullSeqId.isSelected() );
+
+    alignPanel.idPanel.idCanvas.setPreferredSize( alignPanel.calculateIdWidth() );
+    alignPanel.RefreshPanels();
+  }
+
   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
   {
       viewport.setColourText( colourTextMenuItem.isSelected() );
@@ -545,8 +601,31 @@ public class AlignFrame extends GAlignFrame
   {
     viewport.setWrapAlignment( wrapMenuItem.isSelected() );
     alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );
+    scaleAbove.setVisible( wrapMenuItem.isSelected() );
+    scaleLeft.setVisible( wrapMenuItem.isSelected() );
+    scaleRight.setVisible( wrapMenuItem.isSelected() );
+    alignPanel.RefreshPanels();
   }
 
+  protected void scaleAbove_actionPerformed(ActionEvent e)
+  {
+    viewport.setScaleAboveWrapped(scaleAbove.isSelected());
+    alignPanel.repaint();
+  }
+
+  protected void scaleLeft_actionPerformed(ActionEvent e)
+  {
+    viewport.setScaleLeftWrapped(scaleLeft.isSelected());
+    alignPanel.repaint();
+  }
+
+  protected void scaleRight_actionPerformed(ActionEvent e)
+  {
+    viewport.setScaleRightWrapped(scaleRight.isSelected());
+    alignPanel.repaint();
+  }
+
+
 
   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
   {
@@ -578,9 +657,15 @@ public class AlignFrame extends GAlignFrame
     alignPanel.RefreshPanels();
   }
 
-  public void consensusGraphMenuItem_actionPerformed(ActionEvent e)
+  public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
   {
-    alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );
+    if(annotationPanelMenuItem.isSelected() && viewport.getWrapAlignment())
+    {
+      annotationPanelMenuItem.setSelected(false);
+      return;
+    }
+    viewport.setShowAnnotation( annotationPanelMenuItem.isSelected() );
+    alignPanel.setAnnotationVisible( annotationPanelMenuItem.isSelected() );
   }
 
   public void overviewMenuItem_actionPerformed(ActionEvent e)
@@ -698,7 +783,7 @@ public class AlignFrame extends GAlignFrame
                                             sg.sequences, sg.getStartRes(),
                                             sg.getEndRes());
           c.calculate();
-          c.verdict(false, 100);
+          c.verdict(false, viewport.ConsPercGaps);
           ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
 
           sg.cs = ccs;
@@ -708,16 +793,16 @@ public class AlignFrame extends GAlignFrame
     }
 
 
-    if ( viewport.getAbovePIDThreshold())
+    if ( viewport.getAbovePIDThreshold() )
     {
-      int threshold = 0;
-      threshold = Desktop.setPIDSliderSource(alignPanel, cs, "Background");
+ //     int threshold = 0;
+   //   threshold = Desktop.setPIDSliderSource(alignPanel, cs, "Background");
       Desktop.hideConservationSlider();
 
-      if (cs instanceof ResidueColourScheme)
-        ( (ResidueColourScheme) cs).setThreshold(threshold);
-      else if (cs instanceof ScoreColourScheme)
-        ( (ScoreColourScheme) cs).setThreshold(threshold);
+ //     if (cs instanceof ResidueColourScheme)
+ //       ( (ResidueColourScheme) cs).setThreshold(threshold);
+  //    else if (cs instanceof ScoreColourScheme)
+   //     ( (ScoreColourScheme) cs).setThreshold(threshold);
 
       viewport.setGlobalColourScheme(cs);
 
@@ -742,14 +827,13 @@ if ( viewport.getConservationSelected() )
                                      al.getWidth());
 
    c.calculate();
-   c.verdict(false, 100);
+   c.verdict(false, viewport.ConsPercGaps);
 
    ccs = new ConservationColourScheme(c, cs);
 
-   int threshold = Desktop.setConservationSliderSource(alignPanel, ccs,
-       "Background");
+ //  int threshold = Desktop.setConservationSliderSource(alignPanel, ccs,    "Background");
 
-   ccs.inc = threshold;
+ //  ccs.inc = threshold;
 
    viewport.setGlobalColourScheme(ccs);
 
@@ -760,10 +844,24 @@ if ( viewport.getConservationSelected() )
     alignPanel.RefreshPanels();
   }
 
+  protected void modifyPID_actionPerformed(ActionEvent e)
+  {
+    Desktop.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(), "Background");
+  }
+
+  protected void modifyConservation_actionPerformed(ActionEvent e)
+  {
+    Desktop.setConservationSliderSource(alignPanel, viewport.globalColourScheme,    "Background");
+  }
+
 
   protected  void conservationMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setConservationSelected(conservationMenuItem.isSelected());
+    if(coloursChanging)
+      return;
+
+    coloursChanging = true;
 
     viewport.setAbovePIDThreshold(false);
     abovePIDThreshold.setSelected(false);
@@ -776,11 +874,17 @@ if ( viewport.getConservationSelected() )
      changeColour( ((ConservationColourScheme)cs).cs );
     else
       changeColour( cs );
-  }
 
+    coloursChanging = false;
+  }
 
+  boolean coloursChanging = false;
   public void abovePIDThreshold_actionPerformed(ActionEvent e)
   {
+    if(coloursChanging)
+      return;
+
+    coloursChanging = true;
     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
 
     conservationMenuItem.setSelected(false);
@@ -797,6 +901,7 @@ if ( viewport.getConservationSelected() )
     else
         changeColour( cs );
 
+    coloursChanging = false;
   }
 
 
@@ -806,10 +911,7 @@ if ( viewport.getConservationSelected() )
     JInternalFrame frame = new JInternalFrame();
     UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);
     frame.setContentPane(chooser);
-    Desktop.addInternalFrame(frame,"User defined colours", 450,540 );
-    frame.setResizable(false);
-    frame.setIconifiable(false);
-    frame.setMaximizable(false);
+    Desktop.addInternalFrame(frame,"User defined colours", 450,540, false );
   }
 
   public void PIDColour_actionPerformed(ActionEvent e)
@@ -847,30 +949,18 @@ if ( viewport.getConservationSelected() )
     alignPanel.RefreshPanels();
   }
 
-  public void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)
-  {
-    addHistoryItem("sort");
-    if(viewport.getCurrentTree()==null)
-      return;
-
-    AlignmentSorter.sortByTree(viewport.getAlignment(), viewport.getCurrentTree());
-    alignPanel.RefreshPanels();
-  }
-
   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
   {
     RedundancyPanel sp = new RedundancyPanel(alignPanel);
     JInternalFrame frame = new JInternalFrame();
     frame.setContentPane(sp);
-    Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100);
-    frame.setMaximizable(false);
-    frame.setResizable(false);
+    Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100, false);
 
   }
 
   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
   {
-    if(viewport.getSelection().size()<2)
+    if(viewport.getSelectionGroup().getSize()<2)
       JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);
     else
     {
@@ -882,7 +972,8 @@ if ( viewport.getConservationSelected() )
 
   public void PCAMenuItem_actionPerformed(ActionEvent e)
   {
-    if( (viewport.getSelection().size()<4 && viewport.getSelection().size()>0)
+
+    if( (viewport.getSelectionGroup()!=null && viewport.getSelectionGroup().getSize()<4 && viewport.getSelectionGroup().getSize()>0)
        || viewport.getAlignment().getHeight()<4)
     {
       JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"
@@ -937,22 +1028,48 @@ if ( viewport.getConservationSelected() )
       return;
     }
 
-    TreePanel tp=null;
-   if (viewport.getSelection() != null && viewport.getSelection().size() > 3)
-   {
-     tp = new TreePanel(viewport, viewport.getSelection().asVector(),type, pwType,
+    final TreePanel tp;
+    if (viewport.getSelectionGroup() != null &&
+        viewport.getSelectionGroup().getSize() > 3)
+    {
+      tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,
+                         pwType,
                          0, viewport.alignment.getWidth());
-   }
-   else
-   {
-     tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
-                         type, pwType,  0, viewport.alignment.getWidth());
-   }
+    }
+    else
+    {
+      tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
+                         type, pwType, 0, viewport.alignment.getWidth());
+    }
+
+   addTreeMenuItem(tp, title);
 
    Desktop.addInternalFrame(tp, title, 600, 500);
   }
 
+  void addTreeMenuItem(final TreePanel treePanel, String title)
+  {
+    final JMenuItem item = new JMenuItem(title);
+    sortByTreeMenu.add(item);
+    item.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        addHistoryItem("sort");
+        AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
+        alignPanel.RefreshPanels();
+      }
+    });
 
+    treePanel.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+    {
+      public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
+      {
+        sortByTreeMenu.remove(item);
+      };
+    });
+
+  }
 
 
   public void clustalAlignMenuItem_actionPerformed(ActionEvent e)
@@ -962,47 +1079,49 @@ if ( viewport.getConservationSelected() )
     Thread t = new Thread(ct);
     t.start();
     frame.setContentPane(ct);
-     Desktop.addInternalFrame(frame, title, 300, 80);
+     Desktop.addInternalFrame(frame, title, 320, 90);
 
   }
 
   class ClustalThread extends JPanel implements Runnable
   {
-    Image [] image;
-    int imageIndex = 0;
+    Image image;
+    int angle = 0;
     boolean webServiceRunning = false;
     JInternalFrame frame;
     public ClustalThread(JInternalFrame frame)
     {
       this.frame = frame;
-      image = new Image[9];
-      for(int i=0; i<9; i++)
+
+      java.net.URL url = getClass().getResource("/images/logo.gif");
+      if (url != null)
       {
-        java.net.URL url = getClass().getResource("/images/dna" + (i+1) + ".gif");
-        if (url != null)
+        image = java.awt.Toolkit.getDefaultToolkit().createImage(url);
+        MediaTracker mt = new MediaTracker(this);
+        mt.addImage(image, 0);
+        try
         {
-          image[i] = java.awt.Toolkit.getDefaultToolkit().createImage(url);
-          MediaTracker mt = new MediaTracker(this);
-          mt.addImage(image[i], i);
-          try{mt.waitForID(i);}
-          catch(Exception ex){}
+          mt.waitForID(0);
         }
+        catch (Exception ex)
+        {}
       }
-      DNATwirler twirler = new DNATwirler();
-      twirler.start();
+
+      ImageSpinner spinner = new ImageSpinner();
+      spinner.start();
       webServiceRunning = true;
     }
 
-    class DNATwirler extends Thread
+    class ImageSpinner extends Thread
     {
       public void run()
       {
         while(webServiceRunning)
         {
           try{
-            Thread.sleep(100);
-            imageIndex++;
-            imageIndex %=9;
+            Thread.sleep(10);
+            angle+=1;
+            angle %=360;
             repaint();
           }
           catch(Exception ex){}
@@ -1031,10 +1150,9 @@ if ( viewport.getConservationSelected() )
          if (alignment != null)
          {
            AlignFrame af = new AlignFrame(new Alignment(alignment));
-          af.clustalColour.setSelected(true);
-          af.clustalColour_actionPerformed(null);
-           Desktop.addInternalFrame(af, getTitle().concat(" - ClustalW Alignment"),
-                                    700, 500); // JBPNote - is there a new window geom. property ?
+           Desktop.addInternalFrame(af, getTitle().concat(" - ClustalW Alignment"),NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);
+           af.clustalColour_actionPerformed(null);
+           af.clustalColour.setSelected(true);
          }
          else
            JOptionPane.showMessageDialog(Desktop.desktop, "Problem obtaining clustal alignment", "Web service error",
@@ -1046,17 +1164,109 @@ if ( viewport.getConservationSelected() )
          }catch(Exception ex){}
        }
 
-       public void paintComponent(Graphics g)
+       public void paintComponent(Graphics g1)
        {
+         Graphics2D g = (Graphics2D)g1;
          g.setColor(Color.white);
          g.fillRect(0,0,getWidth(), getHeight());
          if(image!=null)
          {
-           g.drawImage(image[imageIndex],10,10,this);
+
+           g.rotate (Math.toRadians(angle), 28, 28);
+
+           g.drawImage(image,10,10,this);
+           g.rotate (-Math.toRadians(angle), 28, 28 );
          }
          g.setFont(new Font("Arial", Font.BOLD, 12));
          g.setColor(Color.black);
-         g.drawString("Clustal Alignment Web Service running", 30,30);
+         g.drawString("Clustal Alignment Web Service running", 60,30);
        }
   }
+  protected void jpred_actionPerformed(ActionEvent e)
+{
+
+    JInternalFrame frame = new JInternalFrame();
+    if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>0)
+    {
+      // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
+      SequenceGroup seqs = viewport.getSelectionGroup();
+      if (seqs.getSize() == 1 || !viewport.alignment.isAligned())
+      {
+        JPredClient ct = new JPredClient( (SequenceI)
+                                         seqs.getSequenceAt(0));
+      }
+      else
+      {
+        int sz;
+        SequenceI[] msa = new SequenceI[sz=seqs.getSize()];
+        for (int i = 0; i < sz; i++)
+        {
+          msa[i] = (SequenceI) seqs.getSequenceAt(i);
+        }
+
+        JPredClient ct = new JPredClient(msa);
+      }
+
+    }
+    else
+    {
+      Vector seqs = viewport.getAlignment().getSequences();
+
+      if (seqs.size() == 1 || !viewport.alignment.isAligned())
+      {
+        JPredClient ct = new JPredClient( (SequenceI)
+                                         seqs.elementAt(0));
+      }
+      else
+      {
+        SequenceI[] msa = new SequenceI[seqs.size()];
+        for (int i = 0; i < seqs.size(); i++)
+        {
+          msa[i] = (SequenceI) seqs.elementAt(i);
+        }
+
+        JPredClient ct = new JPredClient(msa);
+      }
+
+    }
+  }
+
+    protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
+    // Pick the tree file
+    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
+        getProperty("LAST_DIRECTORY"));
+    chooser.setFileView(new JalviewFileView());
+    chooser.setDialogTitle("Select a newick-like tree file");
+    chooser.setToolTipText("Load a tree file");
+    int value = chooser.showOpenDialog(null);
+    if (value == JalviewFileChooser.APPROVE_OPTION)
+    {
+      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);
+        }
+      }
+      catch (Exception ex)
+      {
+        JOptionPane.showMessageDialog(Desktop.desktop,
+                                      "Problem reading tree file",
+                                      ex.getMessage(),
+                                      JOptionPane.WARNING_MESSAGE);
+        ex.printStackTrace();
+      }
+    }
+  }
+
 }