X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=079f31515fc7c43e013036c8b6e33dca64731f5c;hb=3e63bb86ad0e6f4bc86197053f921cb67b341567;hp=1f6fabd8e2a7f0dc506a055931c722f8ae79b52e;hpb=22be3f466cd70cb03d5eae619ede8589ae69716a;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 1f6fabd..079f315 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -23,7 +23,8 @@ import java.awt.print.*;
 import javax.swing.*;
 import javax.swing.event.*;
 import java.util.*;
-import jalview.datamodel.SequenceI;
+import  java.awt.datatransfer.*;
+
 
 public class AlignFrame extends GAlignFrame
 {
@@ -32,26 +33,60 @@ public class AlignFrame extends GAlignFrame
   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)) );
+
 
-    AlignmentUtil.addUniprotFeatures(al);
 
-    viewport = new AlignViewport(al,true,true,true,false);
     alignPanel = new AlignmentPanel(this, viewport);
     getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);
-    fontNameMenuItem.setText(viewport.getFont().getName());
-    fontSizeMenuItem.setText(viewport.getFont().getSize()+"");
+
+    addInternalFrameListener(new InternalFrameAdapter()
+   {
+     public void internalFrameActivated(InternalFrameEvent evt)
+     {
+          javax.swing.SwingUtilities.invokeLater(new Runnable()
+          {
+            public void run()
+            {      alignPanel.requestFocus();    }
+          });
+
+     }
+   });
+
   }
 
   protected void saveAs_actionPerformed(ActionEvent e)
   {
-    JFileChooser chooser = new JFileChooser(jalview.bin.Cache.LAST_DIRECTORY);
+    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");
+    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.LAST_DIRECTORY = choice;
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
       String output = FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences());
       try{
         java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice )  );
@@ -79,6 +114,36 @@ public class AlignFrame extends GAlignFrame
     htmlOutput = null;
   }
 
+  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);
+  }
+
+  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);
+
+  }
+
+
   public void printMenuItem_actionPerformed(ActionEvent e)
   {
     //Putting in a thread avoids Swing painting problems
@@ -118,8 +183,8 @@ public class AlignFrame extends GAlignFrame
     }catch(Exception ex){}
   }
 
-  ArrayList  historyList = new ArrayList();
-  ArrayList redoList = new ArrayList();
+  Stack historyList = new Stack();
+  Stack redoList = new Stack();
 
   void updateEditMenuBar()
   {
@@ -184,6 +249,167 @@ public class AlignFrame extends GAlignFrame
       alignPanel.RefreshPanels();
   }
 
+  public void moveSelectedSequences(boolean up)
+  {
+    SequenceGroup sg = viewport.getSelectionGroup();
+    if (sg == null)
+      return;
+
+    if (up)
+    {
+      for (int i = 1; i < viewport.alignment.getHeight(); i++)
+      {
+        SequenceI seq = viewport.alignment.getSequenceAt(i);
+        if (!sg.sequences.contains(seq))
+          continue;
+
+        SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
+        if (sg.sequences.contains(temp))
+          continue;
+
+        viewport.alignment.getSequences().setElementAt(temp, i);
+        viewport.alignment.getSequences().setElementAt(seq, i - 1);
+      }
+    }
+    else
+    {
+      for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
+      {
+        SequenceI seq = viewport.alignment.getSequenceAt(i);
+        if (!sg.sequences.contains(seq))
+          continue;
+
+        SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
+        if (sg.sequences.contains(temp))
+          continue;
+
+        viewport.alignment.getSequences().setElementAt(temp, i);
+        viewport.alignment.getSequences().setElementAt(seq, i + 1);
+      }
+    }
+
+    alignPanel.RefreshPanels();
+  }
+
+
+
+  protected void copy_actionPerformed(ActionEvent e)
+  {
+   if(viewport.getSelectionGroup()==null)
+     return;
+
+   SequenceGroup sg = viewport.getSelectionGroup();
+
+     Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
+     StringBuffer buffer= new StringBuffer();
+
+       for(int i=0; i<sg.getSize(); i++)
+       {
+         SequenceI seq = sg.getSequenceAt(i);
+         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 ) ;
+
+  }
+
+
+  protected void pasteNew_actionPerformed(ActionEvent e)
+  {
+    paste(true);
+  }
+
+  protected void pasteThis_actionPerformed(ActionEvent e)
+  {
+    addHistoryItem("Paste");
+    paste(false);
+  }
+
+  void paste(boolean newAlignment)
+  {
+    try{
+      Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
+      Transferable contents = c.getContents(this);
+      if (contents == null)
+        return;
+
+      String str = (String) contents.getTransferData(DataFlavor.stringFlavor);
+      StringTokenizer st = new StringTokenizer(str);
+      ArrayList seqs = new ArrayList();
+      while (st.hasMoreElements())
+      {
+        String name = st.nextToken();
+        int start = Integer.parseInt(st.nextToken());
+        int end = Integer.parseInt(st.nextToken());
+        Sequence sequence = new Sequence(name,st.nextToken(), start, end);
+
+        if(!newAlignment)
+          viewport.alignment.addSequence(sequence);
+        else
+          seqs.add(sequence);
+      }
+
+      if(newAlignment)
+      {
+        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);
+      }
+      else
+      {
+        viewport.setEndSeq(viewport.alignment.getHeight());
+        viewport.alignment.getWidth();
+        alignPanel.RefreshPanels();
+      }
+
+    }catch(Exception ex){}// could be anything being pasted in here
+
+  }
+
+
+  protected void cut_actionPerformed(ActionEvent e)
+  {
+    copy_actionPerformed(null);
+    delete_actionPerformed(null);
+  }
+
+  protected void delete_actionPerformed(ActionEvent e)
+  {
+    addHistoryItem("Delete");
+    if (viewport.getSelectionGroup() == null)
+      return;
+
+     SequenceGroup sg = viewport.getSelectionGroup();
+     for (int i=0;i < sg.sequences.size(); i++)
+     {
+       SequenceI seq = sg.getSequenceAt(i);
+       int index = viewport.getAlignment().findIndex(seq);
+       seq.deleteChars(sg.getStartRes(), sg.getEndRes()+1);
+
+       if(seq.getSequence().length()<1)
+          viewport.getAlignment().deleteSequence(seq);
+      else
+          viewport.getAlignment().getSequences().setElementAt(seq, index);
+     }
+
+     viewport.setSelectionGroup(null);
+     viewport.alignment.deleteGroup(sg);
+     viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getHeight());
+     if(viewport.getAlignment().getHeight()<1)
+     try
+     {
+       this.setClosed(true);
+     }catch(Exception ex){}
+     alignPanel.RefreshPanels();
+
+  }
+
+
 
   protected void redoMenuItem_actionPerformed(ActionEvent e)
   {
@@ -207,7 +433,7 @@ public class AlignFrame extends GAlignFrame
   protected void deleteGroups_actionPerformed(ActionEvent e)
   {
     viewport.alignment.deleteAllGroups();
-    viewport.getSelection().clear();
+    viewport.setSelectionGroup(null);
 
     alignPanel.RefreshPanels();
   }
@@ -216,29 +442,26 @@ 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);
   }
 
@@ -321,65 +544,29 @@ public class AlignFrame extends GAlignFrame
 
   public void findMenuItem_actionPerformed(ActionEvent e)
   {
-    JOptionPane op = new JOptionPane();
-    JInternalFrame frame =  op.createInternalFrame(this, "Find");
-    Finder finder = new Finder(viewport, alignPanel, frame);
-    frame.setClosable(true);
-    frame.setContentPane(finder);
-    frame.setSize(340,110);
-    frame.setVisible(true);
-  }
-
-
-
-  public void fontNameMenuItem_actionPerformed(ActionEvent e)
-  {
-    String fonts[] = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
-
-
-    String selection = JOptionPane.showInternalInputDialog(this,
-                                "Select font",
-                                "Font selection",
-                                JOptionPane.QUESTION_MESSAGE,
-                                null,fonts
-                                ,fontNameMenuItem.getText()).toString();
-    if(selection!=null)
-    {
-       fontNameMenuItem.setText(selection);
-       SetFont();
-     }
+      JInternalFrame frame = new JInternalFrame();
+      Finder finder = new Finder(viewport, alignPanel, frame);
+      frame.setContentPane(finder);
+     Desktop.addInternalFrame(frame, "Find", 340,110);
 
   }
 
-  public void fontSizeMenuItem_actionPerformed(ActionEvent e)
+
+  public void font_actionPerformed(ActionEvent e)
   {
-    String selection = JOptionPane.showInternalInputDialog(this,
-                                "Select font size",
-                                "Font size",
-                                JOptionPane.QUESTION_MESSAGE,
-                                null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"}
-                                ,fontSizeMenuItem.getText()).toString();
-    if(selection!=null)
-     {
-       fontSizeMenuItem.setText(selection);
-       SetFont();
-     }
+   // JOptionPane op = new JOptionPane();
+    JInternalFrame frame = new JInternalFrame();
+    FontChooser fc = new FontChooser( alignPanel, frame );
+    frame.setContentPane(fc);
+    Desktop.addInternalFrame(frame, "Change Font", 480,100);
   }
 
-  public void fontStyleMenuItem_actionPerformed(ActionEvent e)
+  protected void fullSeqId_actionPerformed(ActionEvent e)
   {
-    String selection = JOptionPane.showInternalInputDialog(this,
-                                "Select font style",
-                                "Font style",
-                                JOptionPane.QUESTION_MESSAGE,
-                                null, new String[]{"plain", "bold", "italic"}
-                                ,fontStyleMenuItem.getText()).toString();
-    if(selection!=null)
-    {
-      fontStyleMenuItem.setText(selection);
-      SetFont();
-    }
+    viewport.setShowFullId( fullSeqId.isSelected() );
 
+    alignPanel.idPanel.idCanvas.setPreferredSize( alignPanel.calculateIdWidth() );
+    alignPanel.RefreshPanels();
   }
 
   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
@@ -388,21 +575,6 @@ public class AlignFrame extends GAlignFrame
       alignPanel.RefreshPanels();
   }
 
-  void SetFont()
-  {
-      int style = java.awt.Font.PLAIN;
-      if(fontStyleMenuItem.getText().equals("bold"))
-        style = java.awt.Font.BOLD;
-      else if(fontStyleMenuItem.getText().equals("italic"))
-        style = java.awt.Font.ITALIC;
-
-      viewport.setFont(new java.awt.Font(fontNameMenuItem.getText(),
-                                           style,
-                                           Integer.parseInt(fontSizeMenuItem.getText())));
-      alignPanel.RefreshPanels();
-
-  }
-
   protected void wrapMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setWrapAlignment( wrapMenuItem.isSelected() );
@@ -432,6 +604,11 @@ public class AlignFrame extends GAlignFrame
   public void sequenceFeatures_actionPerformed(ActionEvent evt)
   {
     viewport.showSequenceFeatures(sequenceFeatures.isSelected());
+    if(viewport.showSequenceFeatures && !((Alignment)viewport.alignment).featuresAdded)
+    {
+         AlignmentUtil.fetchSequenceFeatures( viewport.alignment , alignPanel);
+         ((Alignment)viewport.alignment).featuresAdded = true;
+    }
     alignPanel.RefreshPanels();
   }
 
@@ -473,171 +650,187 @@ public class AlignFrame extends GAlignFrame
 
   protected void noColourmenuItem_actionPerformed(ActionEvent e)
   {
-    viewport.setGlobalColourScheme( null );
-    changeColour();
+    changeColour( null );
   }
 
 
   public void clustalColour_actionPerformed(ActionEvent e)
   {
-    viewport.setGlobalColourScheme(
-      new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));
     abovePIDThreshold.setSelected(false);
-    changeColour();
+    changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));
   }
 
   public void zappoColour_actionPerformed(ActionEvent e)
   {
-    viewport.setGlobalColourScheme(new ZappoColourScheme() );
-    changeColour();
+    changeColour(new ZappoColourScheme());
   }
 
   public void taylorColour_actionPerformed(ActionEvent e)
   {
-    viewport.setGlobalColourScheme(new TaylorColourScheme() );
-    changeColour();
+    changeColour(new TaylorColourScheme());
   }
 
 
   public void hydrophobicityColour_actionPerformed(ActionEvent e)
   {
-    viewport.setGlobalColourScheme( new HydrophobicColourScheme() );
-    changeColour();
+    changeColour( new HydrophobicColourScheme() );
   }
 
   public void helixColour_actionPerformed(ActionEvent e)
   {
-    viewport.setGlobalColourScheme( new HelixColourScheme()  );
-    changeColour();
+    changeColour(new HelixColourScheme() );
   }
 
 
   public void strandColour_actionPerformed(ActionEvent e)
   {
-    viewport.setGlobalColourScheme(new StrandColourScheme() );
-    changeColour();
+    changeColour(new StrandColourScheme());
   }
 
 
   public void turnColour_actionPerformed(ActionEvent e)
   {
-    viewport.setGlobalColourScheme(new TurnColourScheme() );
-    changeColour();
+    changeColour(new TurnColourScheme());
   }
 
 
   public void buriedColour_actionPerformed(ActionEvent e)
   {
-    viewport.setGlobalColourScheme( new BuriedColourScheme() );
-    changeColour();
+    changeColour(new BuriedColourScheme() );
   }
 
   public void nucleotideColour_actionPerformed(ActionEvent e)
   {
-    viewport.setGlobalColourScheme( new NucleotideColourScheme() );
-    changeColour();
+    changeColour(new NucleotideColourScheme());
   }
 
 
-  void changeColour()
+  protected void applyToAllGroups_actionPerformed(ActionEvent e)
   {
-    if(abovePIDThreshold.isSelected())
-      abovePIDThreshold_actionPerformed(null);
-    else if(conservationMenuItem.isSelected())
-      conservationMenuItem_actionPerformed(null);
-
-    alignPanel.RefreshPanels();
+    viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
   }
 
 
-  protected  void conservationMenuItem_actionPerformed(ActionEvent e)
+
+  void changeColour(ColourSchemeI cs)
   {
-   if(abovePIDThreshold.isSelected())
-   {
-     abovePIDThreshold.setSelected(false);
-     Desktop.hidePIDSlider();
-   }
 
-   viewport.setConservationSelected(conservationMenuItem.isSelected());
+    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;
 
-   ColourSchemeI oldCs = viewport.getGlobalColourScheme();
+        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();
+
+      if (cs instanceof ResidueColourScheme)
+        ( (ResidueColourScheme) cs).setThreshold(threshold);
+      else if (cs instanceof ScoreColourScheme)
+        ( (ScoreColourScheme) cs).setThreshold(threshold);
+
+      viewport.setGlobalColourScheme(cs);
+
+    }
+    else
+    if (cs instanceof ResidueColourScheme)
+      ( (ResidueColourScheme) cs).setThreshold(0);
+    else if (cs instanceof ScoreColourScheme)
+      ( (ScoreColourScheme) cs).setThreshold(0);
+
+
+
+
+if ( viewport.getConservationSelected() )
+ {
    ConservationColourScheme ccs = null;
-   if (oldCs instanceof ConservationColourScheme)
-         ccs = (ConservationColourScheme) oldCs;
 
-       if (conservationMenuItem.isSelected())
-       {
-         Alignment al = (Alignment) viewport.alignment;
-         Conservation c = new Conservation("All",
-                                           ResidueProperties.propHash, 3,
-                                           al.getSequences(), 0,
-                                           al.getWidth());
+   Alignment al = (Alignment) viewport.alignment;
+   Conservation c = new Conservation("All",
+                                     ResidueProperties.propHash, 3,
+                                     al.getSequences(), 0,
+                                     al.getWidth());
 
-         c.calculate();
-         c.verdict(false, 100);
+   c.calculate();
+   c.verdict(false, 100);
 
-         if (ccs != null)
-           ccs = new ConservationColourScheme(c, ccs.cs);
-         else
-           ccs = new ConservationColourScheme(c, oldCs);
+   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);
 
-         if (ccs.cs instanceof ResidueColourScheme)
-           ((ResidueColourScheme) ccs.cs).setThreshold(0);
-         else if (ccs.cs instanceof ScoreColourScheme)
-           ((ScoreColourScheme)ccs.cs).setThreshold(0);
+  }
+  else
+       viewport.setGlobalColourScheme( cs );
 
-         viewport.setGlobalColourScheme(ccs);
+    alignPanel.RefreshPanels();
+  }
 
 
-       }
-       else if (oldCs instanceof ConservationColourScheme)
-       {
-         /// ie, if we remove ConservationColourScheme from backgroundColour
-         oldCs = ccs.cs;
-         viewport.setGlobalColourScheme(oldCs);
-         Desktop.hideConservationSlider();
-       }
+  protected  void conservationMenuItem_actionPerformed(ActionEvent e)
+  {
+    viewport.setConservationSelected(conservationMenuItem.isSelected());
 
-       if(e!=null)
-         alignPanel.RefreshPanels();
+    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 );
   }
 
 
   public void abovePIDThreshold_actionPerformed(ActionEvent e)
   {
-      if(conservationMenuItem.isSelected())
-        conservationMenuItem.setSelected(false);
+    viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
 
-      ColourSchemeI oldCs = viewport.getGlobalColourScheme();
-      int threshold = 0;
-      if (oldCs instanceof ConservationColourScheme)
-     {
-       ConservationColourScheme ccs = (ConservationColourScheme) oldCs;
-       oldCs = ccs.cs;
-     }
+    conservationMenuItem.setSelected(false);
+    viewport.setConservationSelected(false);
+    Desktop.hideConservationSlider();
 
-     if(abovePIDThreshold.isSelected())
-     {
-       threshold = Desktop.setPIDSliderSource(alignPanel, oldCs, "Background");
-       Desktop.hideConservationSlider();
-     }
-     else
-       Desktop.hidePIDSlider();
+    if(!viewport.getAbovePIDThreshold())
+      Desktop.hidePIDSlider();
 
-      if (oldCs instanceof ResidueColourScheme)
-          ((ResidueColourScheme) oldCs).setThreshold(threshold);
-      else if (oldCs instanceof ScoreColourScheme)
-          ((ScoreColourScheme)oldCs).setThreshold(threshold);
 
-    viewport.setGlobalColourScheme(oldCs);
-     if(e!=null)
-        alignPanel.RefreshPanels();
+    ColourSchemeI cs = viewport.getGlobalColourScheme();
+    if(cs instanceof ConservationColourScheme )
+        changeColour( ((ConservationColourScheme)cs).cs );
+    else
+        changeColour( cs );
+
   }
 
 
@@ -655,15 +848,13 @@ public class AlignFrame extends GAlignFrame
 
   public void PIDColour_actionPerformed(ActionEvent e)
   {
-    viewport.setGlobalColourScheme( new PIDColourScheme() );
-    alignPanel.setColourScheme( );
+    changeColour( new PIDColourScheme() );
   }
 
 
   public void BLOSUM62Colour_actionPerformed(ActionEvent e)
   {
-    viewport.setGlobalColourScheme( new Blosum62ColourScheme(viewport)  );
-    changeColour();
+    changeColour(new Blosum62ColourScheme(viewport) );
   }
 
 
@@ -713,7 +904,7 @@ public class AlignFrame extends GAlignFrame
 
   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
     {
@@ -725,7 +916,8 @@ public class AlignFrame extends GAlignFrame
 
   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"
@@ -772,22 +964,27 @@ public class AlignFrame extends GAlignFrame
 
   void NewTreePanel(String type, String pwType, String title)
   {
-    JInternalFrame frame = new javax.swing.JInternalFrame();
+    //are the sequences aligned?
+    if(!viewport.alignment.isAligned())
+    {
+      JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.",
+                                    "Sequences not aligned", JOptionPane.WARNING_MESSAGE);
+      return;
+    }
+
     TreePanel tp=null;
-   if (viewport.getSelection() != null && viewport.getSelection().size() > 3)
+   if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize() > 3)
    {
-     tp = new TreePanel(viewport, viewport.getSelection().asVector(),type, pwType,
-                         viewport.getStartRes(), viewport.getEndRes());
+     tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences,type, pwType,
+                         0, viewport.alignment.getWidth());
    }
    else
    {
      tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
-                         type, pwType, viewport.getStartRes(),
-                         viewport.getEndRes());
+                         type, pwType,  0, viewport.alignment.getWidth());
    }
 
-   frame.setContentPane(tp);
-   Desktop.addInternalFrame(frame, title, 600, 500);
+   Desktop.addInternalFrame(tp, title, 600, 500);
   }
 
 
@@ -816,7 +1013,7 @@ public class AlignFrame extends GAlignFrame
       image = new Image[9];
       for(int i=0; i<9; i++)
       {
-        java.net.URL url = getClass().getResource("/dna" + (i+1) + ".gif");
+        java.net.URL url = getClass().getResource("/images/dna" + (i+1) + ".gif");
         if (url != null)
         {
           image[i] = java.awt.Toolkit.getDefaultToolkit().createImage(url);
@@ -897,13 +1094,4 @@ public class AlignFrame extends GAlignFrame
          g.drawString("Clustal Alignment Web Service running", 30,30);
        }
   }
-
-
-  public void doKeyPressed(KeyEvent evt)
-  {
-    if(evt.isControlDown() && evt.getKeyChar()=='f')
-      findMenuItem_actionPerformed(null);
-  }
-
-
 }