X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=725a702da877fce68aab0c669e68abaa7f32be87;hb=67fe33692d163752fd467468b18ace4a9b4eac7d;hp=867de618376045e969489a5d8aeff5726fe19134;hpb=a2d2bfc9a2efd08446954c01dc5957560fdec9be;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 867de61..725a702 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -23,27 +23,27 @@ 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 String currentFileFormat = "Jalview";
+
   public AlignFrame(AlignmentI al)
   {
-    super();
-    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)) );
-
-
+    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()
@@ -61,33 +61,36 @@ public class AlignFrame extends GAlignFrame
 
   }
 
-  protected void saveAs_actionPerformed(ActionEvent e)
+  public void saveAlignmentMenu_actionPerformed(ActionEvent e)
   {
-    String suffix = "";
-    if(e.getActionCommand().equals("FASTA"))
-      suffix = "fa";
-    else if(e.getActionCommand().equals("MSF"))
-      suffix = "msf";
-    else if(e.getActionCommand().equals("CLUSTAL"))
-      suffix = "aln";
-    else if(e.getActionCommand().equals("BLC"))
-      suffix = "blc";
-    else if(e.getActionCommand().equals("PIR"))
-      suffix = "pir";
-    else if(e.getActionCommand().equals("PFAM"))
-      suffix = "pfam";
-
     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY")
-        , new String[]{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);
@@ -105,7 +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)
@@ -116,31 +119,12 @@ public class AlignFrame extends GAlignFrame
 
   protected void createPNG_actionPerformed(ActionEvent e)
   {
-    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.makePNG( width, height);
+    alignPanel.makePNG();
   }
 
   protected void epsFile_actionPerformed(ActionEvent e)
   {
-    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.makeEPS( width, height);
-
+    alignPanel.makeEPS();
   }
 
 
@@ -185,7 +169,6 @@ public class AlignFrame extends GAlignFrame
 
   Stack historyList = new Stack();
   Stack redoList = new Stack();
-  JMenuBar jMenuBar1 = new JMenuBar();
 
   void updateEditMenuBar()
   {
@@ -218,6 +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++)
     {
@@ -225,6 +209,7 @@ public class AlignFrame extends GAlignFrame
                              viewport.getAlignment().getSequenceAt(i).getSequence());
     }
 
+
     historyList.add(0, new Object[]{type,  seq} );
     updateEditMenuBar();
   }
@@ -245,9 +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();
-      alignPanel.RefreshPanels();
+      for(int i=0; i<old.length; i++)
+        viewport.alignment.addAnnotation(old[i]);
+      viewport.updateConsensus();
+      viewport.updateConservation();
+      alignPanel.repaint();
   }
 
   public void moveSelectedSequences(boolean up)
@@ -289,28 +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 ) ;
 
   }
@@ -356,16 +368,21 @@ 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);
+        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
       {
         viewport.setEndSeq(viewport.alignment.getHeight());
         viewport.alignment.getWidth();
-        alignPanel.RefreshPanels();
+        viewport.updateConservation();
+        viewport.updateConsensus();
+        alignPanel.repaint();
       }
 
     }catch(Exception ex){}// could be anything being pasted in here
@@ -406,7 +423,9 @@ public class AlignFrame extends GAlignFrame
      {
        this.setClosed(true);
      }catch(Exception ex){}
-     alignPanel.RefreshPanels();
+   viewport.updateConservation();
+   viewport.updateConsensus();
+     alignPanel.repaint();
 
   }
 
@@ -417,26 +436,19 @@ 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();
-     alignPanel.RefreshPanels();
+     viewport.updateConsensus();
+     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();
   }
 
 
@@ -454,6 +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);
   }
 
@@ -466,13 +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");
@@ -482,7 +489,19 @@ public class AlignFrame extends GAlignFrame
       int min = colSel.getMin();
       viewport.getAlignment().trimLeft(min);
       colSel.compensateForEdit(0,min);
-      alignPanel.RefreshPanels();
+
+      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.repaint();
     }
   }
 
@@ -493,10 +512,21 @@ 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();
+      alignPanel.repaint();
     }
 
   }
@@ -505,7 +535,9 @@ public class AlignFrame extends GAlignFrame
   {
     addHistoryItem("delete gapped columns");
     viewport.getAlignment().removeGaps();
-    alignPanel.RefreshPanels();
+    viewport.updateConservation();
+    viewport.updateConsensus();
+    alignPanel.repaint();
   }
 
   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
@@ -525,41 +557,26 @@ public class AlignFrame extends GAlignFrame
           jSize--;
         }
     }
-
-    alignPanel.RefreshPanels();
+    viewport.updateConservation();
+    viewport.updateConsensus();
+    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);
+    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)
@@ -567,39 +584,62 @@ 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)
@@ -607,15 +647,21 @@ 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 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)
@@ -624,27 +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 );
 
 
   }
@@ -715,39 +754,11 @@ public class AlignFrame extends GAlignFrame
 
   void changeColour(ColourSchemeI cs)
   {
+    int threshold = 0;
 
-    if(viewport.getColourAppliesToAllGroups())
+    if ( viewport.getAbovePIDThreshold() )
     {
-      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())
-    {
-      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);
@@ -755,44 +766,118 @@ 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);
 
-if ( viewport.getConservationSelected() )
- {
-   ConservationColourScheme ccs = null;
+      SliderPanel.setConservationSlider(alignPanel, ccs, "Background");
+
+    }
+    else
+    {
+        // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
+        if (cs != null)
+          cs.setConsensus(viewport.vconsensus);
+        viewport.setGlobalColourScheme(cs);
+    }
+
+
+    if(viewport.getColourAppliesToAllGroups())
+    {
+      Vector groups = viewport.alignment.getGroups();
+      for(int i=0; i<groups.size(); i++)
+      {
+        SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
+
+        if (cs instanceof ClustalxColourScheme)
+        {
+          sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
+        }
+        else if(cs!=null)
+        {
+          try{
+            sg.cs = (ColourSchemeI) cs.getClass().newInstance();
+          }catch(Exception ex){ex.printStackTrace();}
+        }
 
-   Alignment al = (Alignment) viewport.alignment;
-   Conservation c = new Conservation("All",
-                                     ResidueProperties.propHash, 3,
-                                     al.getSequences(), 0,
-                                     al.getWidth());
+        if(viewport.getAbovePIDThreshold())
+        {
+          if (sg.cs instanceof ResidueColourScheme)
+            ( (ResidueColourScheme) sg.cs).setThreshold(threshold);
+          else if (sg.cs instanceof ScoreColourScheme)
+            ( (ScoreColourScheme) sg.cs).setThreshold(threshold);
 
-   c.calculate();
-   c.verdict(false, 100);
+           sg.cs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()) );
+        }
 
-   ccs = new ConservationColourScheme(c, cs);
+        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);
 
-   int threshold = Desktop.setConservationSliderSource(alignPanel, ccs,
-       "Background");
+          // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
+          ccs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
+          sg.cs = ccs;
+        }
+        else if(cs!=null)
+        {
+          // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
+          sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
+        }
 
-   ccs.inc = threshold;
+      }
+    }
 
-   viewport.setGlobalColourScheme(ccs);
+    if(alignPanel.getOverviewPanel()!=null)
+      alignPanel.getOverviewPanel().updateOverviewImage();
+    alignPanel.repaint();
+  }
 
+  protected void modifyPID_actionPerformed(ActionEvent e)
+  {
+      if(viewport.getAbovePIDThreshold())
+      {
+        SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
+                                   "Background");
+        SliderPanel.showPIDSlider();
+      }
   }
-  else
-       viewport.setGlobalColourScheme( cs );
 
-    alignPanel.RefreshPanels();
+  protected void modifyConservation_actionPerformed(ActionEvent e)
+  {
+    if(viewport.getConservationSelected())
+    {
+      SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
+                                        "Background");
+      SliderPanel.showConservationSlider();
+    }
   }
 
 
@@ -802,17 +887,15 @@ if ( viewport.getConservationSelected() )
 
     viewport.setAbovePIDThreshold(false);
     abovePIDThreshold.setSelected(false);
-    Desktop.hidePIDSlider();
-    if(!viewport.getConservationSelected())
-      Desktop.hideConservationSlider();
 
    ColourSchemeI cs = viewport.getGlobalColourScheme();
    if(cs instanceof ConservationColourScheme )
      changeColour( ((ConservationColourScheme)cs).cs );
     else
       changeColour( cs );
-  }
 
+    modifyConservation_actionPerformed(null);
+  }
 
   public void abovePIDThreshold_actionPerformed(ActionEvent e)
   {
@@ -820,31 +903,22 @@ if ( viewport.getConservationSelected() )
 
     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 );
 
+    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)
@@ -855,7 +929,7 @@ if ( viewport.getConservationSelected() )
 
   public void BLOSUM62Colour_actionPerformed(ActionEvent e)
   {
-    changeColour(new Blosum62ColourScheme(viewport) );
+    changeColour(new Blosum62ColourScheme() );
   }
 
 
@@ -864,14 +938,14 @@ 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)
@@ -879,17 +953,7 @@ 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)
@@ -897,9 +961,7 @@ 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);
 
   }
 
@@ -973,137 +1035,181 @@ 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);
+        }
+        while (++i < sv.size());
+
+        SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method
+        if (alignment != null)
+        {
+          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");
         }
       }
-      DNATwirler twirler = new DNATwirler();
-      twirler.start();
-      webServiceRunning = true;
     }
 
-    class DNATwirler extends Thread
+  protected void jpred_actionPerformed(ActionEvent e)
+{
+
+    if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>0)
     {
-      public void run()
+      // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
+      SequenceGroup seqs = viewport.getSelectionGroup();
+      if (seqs.getSize() == 1 || !viewport.alignment.isAligned())
       {
-        while(webServiceRunning)
+        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++)
         {
-          try{
-            Thread.sleep(100);
-            imageIndex++;
-            imageIndex %=9;
-            repaint();
-          }
-          catch(Exception ex){}
+          msa[i] = (SequenceI) seqs.getSequenceAt(i);
         }
+
+        JPredClient ct = new JPredClient(msa);
       }
+
     }
+    else
+    {
+      Vector seqs = viewport.getAlignment().getSequences();
 
-    // 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()];
+      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);
+        }
 
-         int i = 0;
-         do
-         {
-           seqs[i] = (SequenceI) sv.elementAt(i);
-         }
-         while (++i < sv.size());
+        JPredClient ct = new JPredClient(msa);
+      }
 
-         SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method
+    }
+  }
+  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);
+        }
 
-         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);
+        MsaWSClient ct = new jalview.ws.MsaWSClient(msa);
+      }
+      else
+      {
+        Vector seqs = viewport.getAlignment().getSequences();
 
-         webServiceRunning = false;
-         try{
-           frame.setClosed(true);
-         }catch(Exception ex){}
-       }
+        if (seqs.size() > 1) {
+          SequenceI[] msa = new SequenceI[seqs.size()];
+          for (int i = 0; i < seqs.size(); i++)
+          {
+            msa[i] = (SequenceI) seqs.elementAt(i);
+          }
 
-       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);
-       }
-  }
-  public void jpredMenuItem_actionPerformed(ActionEvent e)
-    {
-      JInternalFrame frame = new JInternalFrame();
-      JPredClient ct = new JPredClient((SequenceI)
-                                       viewport.getAlignment().getSequences().elementAt(0));
-    }
+          MsaWSClient ct = new MsaWSClient(msa);
+        }
 
+      }
+    }
 
-  protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
+    protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
     // Pick the tree file
     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
         getProperty("LAST_DIRECTORY"));
@@ -1115,19 +1221,10 @@ if ( viewport.getConservationSelected() )
     {
       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);
-        }
+        ShowNewickTree(fin, choice);
       }
       catch (Exception ex)
       {
@@ -1140,4 +1237,21 @@ if ( viewport.getConservationSelected() )
     }
   }
 
+  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();}
+  }
+
+
 }