X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=4fbdb7224e15b862d04942d42b1d28e3b61492ba;hb=24ad8bbb87343e317452c0dcb22efd800e7986d6;hp=5ee6c6264e8e46bc5a6529f367f2bf779623098a;hpb=7535505ef73485ad43881cb72a6c52cfb0033c63;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 5ee6c62..4fbdb72 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -23,35 +23,34 @@ 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)
   {
-    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)) );
+    try{
+      String ip = java.net.InetAddress.getLocalHost().getHostAddress();
+      if( !ip.startsWith("10."))
+        webService.setVisible(false);
+    }
+    catch(java.net.UnknownHostException e){}
+    viewport = new AlignViewport(al);
 
 
     alignPanel = new AlignmentPanel(this, viewport);
-    getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);
-
-    // add conservation graph to alignment
-    viewport.updateConservation();
-    viewport.updateConsensus();
-
     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()
    {
@@ -84,6 +83,7 @@ public class AlignFrame extends GAlignFrame
     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());
@@ -94,7 +94,7 @@ public class AlignFrame extends GAlignFrame
     {
       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(e.getActionCommand(), viewport.getAlignment().getSequences());
       try{
         java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice )  );
         out.println(output);
@@ -112,7 +112,7 @@ 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)
@@ -173,7 +173,6 @@ public class AlignFrame extends GAlignFrame
 
   Stack historyList = new Stack();
   Stack redoList = new Stack();
-  JMenuBar jMenuBar1 = new JMenuBar();
 
   void updateEditMenuBar()
   {
@@ -233,11 +232,14 @@ 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) );
       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)
@@ -279,7 +281,7 @@ public class AlignFrame extends GAlignFrame
       }
     }
 
-    alignPanel.RefreshPanels();
+    alignPanel.repaint();
   }
 
 
@@ -346,10 +348,7 @@ 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, 500);
+        Desktop.addInternalFrame(af, "Copied sequences", NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);
       }
       else
       {
@@ -357,7 +356,7 @@ 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
@@ -400,7 +399,7 @@ public class AlignFrame extends GAlignFrame
      }catch(Exception ex){}
    viewport.updateConservation();
    viewport.updateConsensus();
-     alignPanel.RefreshPanels();
+     alignPanel.repaint();
 
   }
 
@@ -413,26 +412,17 @@ public class AlignFrame extends GAlignFrame
      viewport.setAlignment( new Alignment(seq) );
      updateEditMenuBar();
      viewport.updateConsensus();
-     alignPanel.RefreshPanels();
-     alignPanel.RefreshPanels();
+     alignPanel.repaint();
+     alignPanel.repaint();
   }
 
 
-  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.setSelectionGroup(null);
 
-    alignPanel.RefreshPanels();
+    alignPanel.repaint();
   }
 
 
@@ -450,6 +440,8 @@ public class AlignFrame extends GAlignFrame
   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setSelectionGroup(null);
+    viewport.getColumnSelection().clear();
+    viewport.setSelectionGroup(null);
     PaintRefresher.Refresh(null);
   }
 
@@ -462,13 +454,6 @@ 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");
@@ -490,7 +475,7 @@ public class AlignFrame extends GAlignFrame
           viewport.alignment.deleteGroup(sg);
       }
 
-      alignPanel.RefreshPanels();
+      alignPanel.repaint();
     }
   }
 
@@ -515,7 +500,7 @@ public class AlignFrame extends GAlignFrame
 
 
 
-      alignPanel.RefreshPanels();
+      alignPanel.repaint();
     }
 
   }
@@ -526,7 +511,7 @@ public class AlignFrame extends GAlignFrame
     viewport.getAlignment().removeGaps();
     viewport.updateConservation();
     viewport.updateConsensus();
-    alignPanel.RefreshPanels();
+    alignPanel.repaint();
   }
 
   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
@@ -548,40 +533,24 @@ 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);
+    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);
+    FontChooser fc = new FontChooser( alignPanel );
   }
 
   protected void fullSeqId_actionPerformed(ActionEvent e)
@@ -589,39 +558,62 @@ 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)
   {
     viewport.setWrapAlignment( wrapMenuItem.isSelected() );
     alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );
+    scaleAbove.setVisible( wrapMenuItem.isSelected() );
+    scaleLeft.setVisible( wrapMenuItem.isSelected() );
+    scaleRight.setVisible( wrapMenuItem.isSelected() );
+    alignPanel.repaint();
+  }
+
+  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)
   {
     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)
@@ -629,14 +621,20 @@ 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)
   {
+    if(annotationPanelMenuItem.isSelected() && viewport.getWrapAlignment())
+    {
+      annotationPanelMenuItem.setSelected(false);
+      return;
+    }
+    viewport.setShowAnnotation( annotationPanelMenuItem.isSelected() );
     alignPanel.setAnnotationVisible( annotationPanelMenuItem.isSelected() );
   }
 
@@ -646,27 +644,20 @@ 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 );
 
 
   }
@@ -737,39 +728,11 @@ public class AlignFrame extends GAlignFrame
 
   void changeColour(ColourSchemeI cs)
   {
+    int threshold = 0;
 
-    if(viewport.getColourAppliesToAllGroups())
-    {
-      Vector groups = viewport.alignment.getGroups();
-      for(int i=0; i<groups.size(); i++)
-      {
-        SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
-        sg.cs = cs;
-
-        if(abovePIDThreshold.isSelected())
-          abovePIDThreshold_actionPerformed(null);
-        else if( viewport.getConservationSelected() )
-        {
-          Conservation c = new Conservation("Group",
-                                            ResidueProperties.propHash, 3,
-                                            sg.sequences, sg.getStartRes(),
-                                            sg.getEndRes());
-          c.calculate();
-          c.verdict(false, 100);
-          ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
-
-          sg.cs = ccs;
-        }
-
-      }
-    }
-
-
-    if ( viewport.getAbovePIDThreshold())
+    if ( viewport.getAbovePIDThreshold() )
     {
-      int threshold = 0;
-      threshold = Desktop.setPIDSliderSource(alignPanel, cs, "Background");
-      Desktop.hideConservationSlider();
+      threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
 
       if (cs instanceof ResidueColourScheme)
         ( (ResidueColourScheme) cs).setThreshold(threshold);
@@ -777,60 +740,131 @@ public class AlignFrame extends GAlignFrame
         ( (ScoreColourScheme) cs).setThreshold(threshold);
 
       viewport.setGlobalColourScheme(cs);
-
     }
-    else
-    if (cs instanceof ResidueColourScheme)
+    else if (cs instanceof ResidueColourScheme)
       ( (ResidueColourScheme) cs).setThreshold(0);
     else if (cs instanceof ScoreColourScheme)
       ( (ScoreColourScheme) cs).setThreshold(0);
 
 
 
+    if (viewport.getConservationSelected())
+    {
+      ConservationColourScheme ccs = null;
+
+      Alignment al = (Alignment) viewport.alignment;
+      Conservation c = new Conservation("All",
+                                        ResidueProperties.propHash, 3,
+                                        al.getSequences(), 0,
+                                        al.getWidth() - 1);
+
+      c.calculate();
+      c.verdict(false, viewport.ConsPercGaps);
+
+      ccs = new ConservationColourScheme(c, cs);
+
+      // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
+      ccs.setConsensus( viewport.vconsensus );
+      viewport.setGlobalColourScheme(ccs);
+
+      SliderPanel.setConservationSlider(alignPanel, ccs, "Background");
 
-if ( viewport.getConservationSelected() )
- {
-   ConservationColourScheme ccs = null;
+    }
+    else
+    {
+        // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
+        if (cs != null)
+          cs.setConsensus(viewport.vconsensus);
+        viewport.setGlobalColourScheme(cs);
+    }
 
-   Alignment al = (Alignment) viewport.alignment;
-   Conservation c = new Conservation("All",
-                                     ResidueProperties.propHash, 3,
-                                     al.getSequences(), 0,
-                                     al.getWidth());
 
-   c.calculate();
-   c.verdict(false, 100);
+    if(viewport.getColourAppliesToAllGroups())
+    {
+      Vector groups = viewport.alignment.getGroups();
+      for(int i=0; i<groups.size(); i++)
+      {
+        SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
 
-   ccs = new ConservationColourScheme(c, cs);
+        if (cs instanceof ClustalxColourScheme)
+        {
+          sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
+        }
+        else
+          try
+          {
+            sg.cs = (ColourSchemeI) cs.getClass().newInstance();
+          }
+          catch (Exception ex)
+          {
+            ex.printStackTrace();
+            sg.cs = cs;
+          }
 
-   int threshold = Desktop.setConservationSliderSource(alignPanel, ccs,
-       "Background");
+        if(viewport.getAbovePIDThreshold())
+        {
+          if (sg.cs instanceof ResidueColourScheme)
+            ( (ResidueColourScheme) sg.cs).setThreshold(threshold);
+          else if (sg.cs instanceof ScoreColourScheme)
+            ( (ScoreColourScheme) sg.cs).setThreshold(threshold);
 
-   ccs.inc = threshold;
+           sg.cs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()) );
+        }
 
-   viewport.setGlobalColourScheme(ccs);
+        if( viewport.getConservationSelected() )
+        {
+          Conservation c = new Conservation("Group",
+                                            ResidueProperties.propHash, 3,
+                                            sg.sequences, 0, viewport.alignment.getWidth()-1);
+          c.calculate();
+          c.verdict(false, viewport.ConsPercGaps);
+          ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
 
+          // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
+          ccs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
+          sg.cs = ccs;
+        }
+        else
+        {
+          // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
+          sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
+        }
+
+      }
+    }
+
+    if(alignPanel.getOverviewPanel()!=null)
+      alignPanel.getOverviewPanel().updateOverviewImage();
+    alignPanel.repaint();
   }
-  else
-       viewport.setGlobalColourScheme( cs );
 
-    alignPanel.RefreshPanels();
+  protected void modifyPID_actionPerformed(ActionEvent e)
+  {
+      if(viewport.getAbovePIDThreshold())
+      {
+        SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
+                                   "Background");
+        SliderPanel.showPIDSlider();
+      }
+  }
+
+  protected void modifyConservation_actionPerformed(ActionEvent e)
+  {
+    if(viewport.getConservationSelected())
+    {
+      SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
+                                        "Background");
+      SliderPanel.showConservationSlider();
+    }
   }
 
 
   protected  void conservationMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setConservationSelected(conservationMenuItem.isSelected());
-    if(coloursChanging)
-      return;
-
-    coloursChanging = true;
 
     viewport.setAbovePIDThreshold(false);
     abovePIDThreshold.setSelected(false);
-    Desktop.hidePIDSlider();
-    if(!viewport.getConservationSelected())
-      Desktop.hideConservationSlider();
 
    ColourSchemeI cs = viewport.getGlobalColourScheme();
    if(cs instanceof ConservationColourScheme )
@@ -838,46 +872,31 @@ if ( viewport.getConservationSelected() )
     else
       changeColour( cs );
 
-    coloursChanging = false;
+    modifyConservation_actionPerformed(null);
   }
 
-  boolean coloursChanging = false;
   public void abovePIDThreshold_actionPerformed(ActionEvent e)
   {
-    if(coloursChanging)
-      return;
-
-    coloursChanging = true;
     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
 
     conservationMenuItem.setSelected(false);
     viewport.setConservationSelected(false);
-    Desktop.hideConservationSlider();
-
-    if(!viewport.getAbovePIDThreshold())
-      Desktop.hidePIDSlider();
-
 
     ColourSchemeI cs = viewport.getGlobalColourScheme();
+
     if(cs instanceof ConservationColourScheme )
         changeColour( ((ConservationColourScheme)cs).cs );
     else
         changeColour( cs );
 
-    coloursChanging = false;
+    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 );
-    frame.setResizable(false);
-    frame.setIconifiable(false);
-    frame.setMaximizable(false);
+    UserDefinedColours chooser = new UserDefinedColours( alignPanel, null);
   }
 
   public void PIDColour_actionPerformed(ActionEvent e)
@@ -888,7 +907,7 @@ if ( viewport.getConservationSelected() )
 
   public void BLOSUM62Colour_actionPerformed(ActionEvent e)
   {
-    changeColour(new Blosum62ColourScheme(viewport) );
+    changeColour(new Blosum62ColourScheme() );
   }
 
 
@@ -897,14 +916,14 @@ if ( viewport.getConservationSelected() )
   {
     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)
@@ -912,17 +931,7 @@ if ( viewport.getConservationSelected() )
     addHistoryItem("sort");
     AlignmentSorter.sortByGroup(viewport.getAlignment());
     AlignmentSorter.sortGroups(viewport.getAlignment());
-    alignPanel.RefreshPanels();
-  }
-
-  public void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)
-  {
-    addHistoryItem("sort");
-    if(viewport.getCurrentTree()==null)
-      return;
-
-    AlignmentSorter.sortByTree(viewport.getAlignment(), viewport.getCurrentTree());
-    alignPanel.RefreshPanels();
+    alignPanel.repaint();
   }
 
   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
@@ -930,9 +939,7 @@ if ( viewport.getConservationSelected() )
     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);
 
   }
 
@@ -1006,140 +1013,110 @@ if ( viewport.getConservationSelected() )
       return;
     }
 
-    TreePanel tp=null;
-   if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize() > 3)
-   {
-     tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences,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.repaint();
+      }
+    });
 
+    treePanel.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+    {
+      public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
+      {
+        sortByTreeMenu.remove(item);
+      };
+    });
+
+  }
 
 
   public void clustalAlignMenuItem_actionPerformed(ActionEvent e)
   {
-    JInternalFrame frame = new JInternalFrame();
-    ClustalThread ct = new ClustalThread(frame);
-    Thread t = new Thread(ct);
-    t.start();
-    frame.setContentPane(ct);
-     Desktop.addInternalFrame(frame, title, 300, 80);
+     WebserviceInfo info = new WebserviceInfo("Clustal web service",
+     "\"Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple"+
+     " sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice."
+    +" Nucleic Acids Research, submitted, June 1994.",
+     450, 150);
 
+    ClustalThread thread = new ClustalThread(info);
+    thread.start();
   }
 
-  class ClustalThread extends JPanel implements Runnable
-  {
-    Image [] image;
-    int imageIndex = 0;
-    boolean webServiceRunning = false;
-    JInternalFrame frame;
-    public ClustalThread(JInternalFrame frame)
+    class ClustalThread extends Thread
     {
-      this.frame = frame;
-      image = new Image[9];
-      for(int i=0; i<9; i++)
+      WebserviceInfo info;
+      public ClustalThread(WebserviceInfo info)
+      {this.info = info; }
+
+      public void run()
       {
-        java.net.URL url = getClass().getResource("/images/dna" + (i+1) + ".gif");
-        if (url != null)
+        info.setStatus(WebserviceInfo.STATE_RUNNING);
+        jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();
+        Vector sv = viewport.getAlignment().getSequences();
+        SequenceI[] seqs = new SequenceI[sv.size()];
+
+        int i = 0;
+        do
         {
-          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){}
+          seqs[i] = (SequenceI) sv.elementAt(i);
         }
-      }
-      DNATwirler twirler = new DNATwirler();
-      twirler.start();
-      webServiceRunning = true;
-    }
+        while (++i < sv.size());
 
-    class DNATwirler extends Thread
-    {
-      public void run()
-      {
-        while(webServiceRunning)
+        SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method
+        if (alignment != null)
         {
-          try{
-            Thread.sleep(100);
-            imageIndex++;
-            imageIndex %=9;
-            repaint();
-          }
-          catch(Exception ex){}
+          AlignFrame af = new AlignFrame(new Alignment(alignment));
+          Desktop.addInternalFrame(af, title.concat(" - ClustalW Alignment"),
+                                   NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);
+          af.clustalColour_actionPerformed(null);
+          af.clustalColour.setSelected(true);
+          info.setStatus(WebserviceInfo.STATE_STOPPED_OK);
+        }
+        else
+        {
+            info.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+            info.appendProgressText("Problem obtaining clustal alignment");
         }
       }
     }
 
-    // JBPNote
-    // Should check to see if the server settings are valid
-    // Need visual-delay indication here.
-    public void run()
-       {
-         jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();
-         Vector sv = viewport.getAlignment().getSequences();
-         SequenceI[] seqs = new SequenceI[sv.size()];
-
-         int i = 0;
-         do
-         {
-           seqs[i] = (SequenceI) sv.elementAt(i);
-         }
-         while (++i < sv.size());
-
-         SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method
-
-         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 ?
-         }
-         else
-           JOptionPane.showMessageDialog(Desktop.desktop, "Problem obtaining clustal alignment", "Web service error",
-                                         JOptionPane.WARNING_MESSAGE);
-
-         webServiceRunning = false;
-         try{
-           frame.setClosed(true);
-         }catch(Exception ex){}
-       }
-
-       public void paintComponent(Graphics g)
-       {
-         g.setColor(Color.white);
-         g.fillRect(0,0,getWidth(), getHeight());
-         if(image!=null)
-         {
-           g.drawImage(image[imageIndex],10,10,this);
-         }
-         g.setFont(new Font("Arial", Font.BOLD, 12));
-         g.setColor(Color.black);
-         g.drawString("Clustal Alignment Web Service running", 30,30);
-       }
-  }
   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));
+        JPredClient ct = new JPredClient( (SequenceI)seqs.getSequenceAt(0));
       }
       else
       {
@@ -1176,6 +1153,39 @@ if ( viewport.getConservationSelected() )
 
     }
   }
+  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
@@ -1201,6 +1211,7 @@ if ( viewport.getConservationSelected() )
           tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
                              fin, "FromFile", choice);
           Desktop.addInternalFrame(tp, title, 600, 500);
+          addTreeMenuItem(tp, title);
         }
       }
       catch (Exception ex)