X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=ca9903c49c0fbfe2945dbcf2827ffc4e50c2b0c0;hb=2b9c6a8948800edf58dd055631920654729fd675;hp=67995b23cae707bb68f5a360f2ddeba6d41f8ad4;hpb=1fdab090d852d60dfa5e859a1335579d43b5c7f4;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 67995b2..ca9903c 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -16,12 +16,15 @@ import jalview.schemes.*;
 import jalview.datamodel.*;
 import jalview.analysis.*;
 import jalview.io.*;
-import MCview.*;
+import jalview.ws.*;
 import java.awt.*;
 import java.awt.event.*;
 import java.awt.print.*;
 import javax.swing.*;
+import javax.swing.event.*;
 import java.util.*;
+import  java.awt.datatransfer.*;
+
 
 public class AlignFrame extends GAlignFrame
 {
@@ -30,23 +33,60 @@ public class AlignFrame extends GAlignFrame
   public AlignFrame(AlignmentI al)
   {
     super();
-    viewport = new AlignViewport(al,true,true,true,false);
+    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)) );
+
+
+
     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 )  );
@@ -70,10 +110,21 @@ public class AlignFrame extends GAlignFrame
 
   protected void htmlMenuItem_actionPerformed(ActionEvent e)
   {
-    HTMLOutput htmlOutput = new HTMLOutput(viewport.getAlignment(), alignPanel.seqPanel.getColourScheme());
+    HTMLOutput htmlOutput = new HTMLOutput(viewport);
     htmlOutput = null;
   }
 
+  protected void createPNG_actionPerformed(ActionEvent e)
+  {
+    alignPanel.makePNG();
+  }
+
+  protected void epsFile_actionPerformed(ActionEvent e)
+  {
+    alignPanel.makeEPS();
+  }
+
+
   public void printMenuItem_actionPerformed(ActionEvent e)
   {
     //Putting in a thread avoids Swing painting problems
@@ -113,8 +164,9 @@ public class AlignFrame extends GAlignFrame
     }catch(Exception ex){}
   }
 
-  ArrayList  historyList = new ArrayList();
-  ArrayList redoList = new ArrayList();
+  Stack historyList = new Stack();
+  Stack redoList = new Stack();
+  JMenuBar jMenuBar1 = new JMenuBar();
 
   void updateEditMenuBar()
   {
@@ -179,6 +231,167 @@ 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)
   {
@@ -190,7 +403,6 @@ public class AlignFrame extends GAlignFrame
   }
 
 
-
   public void groupsMenuItem_actionPerformed(ActionEvent e)
   {
     GroupEditor geditor = new GroupEditor(viewport, alignPanel);
@@ -200,72 +412,41 @@ public class AlignFrame extends GAlignFrame
     frame.setResizable(false);
   }
 
-  public void groupEditingMenuItem_actionPerformed(ActionEvent e)
+  protected void deleteGroups_actionPerformed(ActionEvent e)
   {
-    viewport.setGroupEdit( groupEditingMenuItem.isSelected() );
+    viewport.alignment.deleteAllGroups();
+    viewport.setSelectionGroup(null);
+
+    alignPanel.RefreshPanels();
   }
 
+
+
   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.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));
-    }
-    PaintRefresher.Refresh(null);
-  }
+      sg.addOrRemove (viewport.getAlignment().getSequenceAt(i));
 
-  public void deleteSelectedMenuItem_actionPerformed(ActionEvent e)
-  {
-    addHistoryItem("delete selection");
-
-    for (int i=0;i < viewport.getSelection().size(); i++)
-            viewport.getAlignment().deleteSequence(viewport.getSelection().sequenceAt(i));
-
-    viewport.getSelection().clear();
-    viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getHeight());
-    alignPanel.RefreshPanels();
-  }
-
-  public void moveSelectedMenuItem_actionPerformed(ActionEvent e)
-  {
-    copySelectedMenuItem_actionPerformed(null);
-    deleteSelectedMenuItem_actionPerformed(null);
-    alignPanel.repaint();
+    PaintRefresher.Refresh(null);
   }
 
-  public void copySelectedMenuItem_actionPerformed(ActionEvent e)
-  {
-    if(viewport.getSelection().size()==0)
-      return;
-
-   SequenceI[] s = new Sequence[viewport.getSelection().size()];
-   for (int i=0; i < viewport.getSelection().size(); i++) {
-     s[i] = new Sequence(viewport.getSelection().sequenceAt(i));
-    }
-    AlignFrame af = new AlignFrame(new Alignment(s));
-    int newHeight = s.length * af.viewport.getCharHeight() + 200;
-    if(newHeight>500)
-      newHeight=500;
-    Desktop.addInternalFrame(af, "Copied sequences", 700,newHeight);
-  }
 
   public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
   {
@@ -318,7 +499,7 @@ public class AlignFrame extends GAlignFrame
       current = viewport.getAlignment().getSequenceAt(i);
       jSize = current.getLength();
       for (int j=0; j < jSize; j++)
-        if (current.getCharAt(j)=='-' || current.getCharAt(j)=='.' || current.getCharAt(j)==' ')
+        if(jalview.util.Comparison.isGap(current.getCharAt(j)))
         {
           current.deleteCharAt(j);
           j--;
@@ -345,64 +526,29 @@ 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.setContentPane(finder);
-    frame.setSize(300,110);
-    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)
@@ -411,25 +557,10 @@ 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() );
-    alignPanel.RefreshPanels();
+    alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );
   }
 
 
@@ -452,43 +583,16 @@ public class AlignFrame extends GAlignFrame
     alignPanel.RefreshPanels();
   }
 
-
- /* void updateResidueView()
+  public void sequenceFeatures_actionPerformed(ActionEvent evt)
   {
-    if (viewport.getSelection().size() == 0)
-     {
-       for (int i = 0; i < viewport.alignment.getGroups().size(); i++)
-       {
-         SequenceGroup sg = (SequenceGroup) viewport.alignment.getGroups().elementAt(i);
-         sg.setDisplayBoxes( viewBoxesMenuItem.isSelected() );
-         sg.setDisplayText( viewTextMenuItem.isSelected() );
-         sg.setColourText( colourTextMenuItem.isSelected() );
-       }
-     }
-     else
-     {
-       SequenceGroup sg = viewport.alignment.findGroup( (Sequence) viewport.sel.sequenceAt(0));
-       if (alignPanel.seqPanel.isNewSelection(sg))
-       {
-         sg = viewport.getAlignment().addGroup();
-         for (int i = 0; i < viewport.getSelection().size(); i++)
-         {
-           viewport.alignment.removeFromGroup(viewport.alignment.findGroup( (
-               Sequence) viewport.sel.sequenceAt(i)),
-                                              (Sequence) viewport.sel.sequenceAt(
-               i));
-           viewport.alignment.addToGroup(sg,
-                                         (Sequence) viewport.sel.sequenceAt(i));
-         }
-       }
-
-       sg.setDisplayBoxes(viewBoxesMenuItem.isSelected());
-       sg.setDisplayText(viewTextMenuItem.isSelected());
-       sg.setColourText(colourTextMenuItem.isSelected());
-     }
+    viewport.showSequenceFeatures(sequenceFeatures.isSelected());
+    if(viewport.showSequenceFeatures && !((Alignment)viewport.alignment).featuresAdded)
+    {
+         AlignmentUtil.fetchSequenceFeatures( viewport.alignment , alignPanel);
+         ((Alignment)viewport.alignment).featuresAdded = true;
+    }
     alignPanel.RefreshPanels();
-  }*/
-
+  }
 
   public void consensusGraphMenuItem_actionPerformed(ActionEvent e)
   {
@@ -497,6 +601,8 @@ public class AlignFrame extends GAlignFrame
 
   public void overviewMenuItem_actionPerformed(ActionEvent e)
   {
+    if (alignPanel.overviewPanel != null)
+      return;
 
     JInternalFrame frame = new JInternalFrame();
     OverviewPanel overview = alignPanel.getOverviewPanel();
@@ -526,83 +632,195 @@ public class AlignFrame extends GAlignFrame
 
   protected void noColourmenuItem_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme(null, false);
+    changeColour( null );
   }
 
 
   public void clustalColour_actionPerformed(ActionEvent e)
   {
-   // alignPanel.setColourScheme( new ClustalxColourScheme() );
+    abovePIDThreshold.setSelected(false);
+    changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));
   }
 
   public void zappoColour_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme( new ZappoColourScheme(), conservationMenuItem.isSelected() );
+    changeColour(new ZappoColourScheme());
   }
 
   public void taylorColour_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme( new TaylorColourScheme(),conservationMenuItem.isSelected() );
+    changeColour(new TaylorColourScheme());
   }
 
 
   public void hydrophobicityColour_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme( new HydrophobicColourScheme(),conservationMenuItem.isSelected() );
+    changeColour( new HydrophobicColourScheme() );
   }
 
   public void helixColour_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme( new HelixColourScheme(),conservationMenuItem.isSelected() );
+    changeColour(new HelixColourScheme() );
   }
 
 
   public void strandColour_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme( new StrandColourScheme() ,conservationMenuItem.isSelected() );
+    changeColour(new StrandColourScheme());
   }
 
 
   public void turnColour_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme( new TurnColourScheme() ,conservationMenuItem.isSelected() );
+    changeColour(new TurnColourScheme());
   }
 
 
   public void buriedColour_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme( new BuriedColourScheme() ,conservationMenuItem.isSelected() );
+    changeColour(new BuriedColourScheme() );
   }
 
+  public void nucleotideColour_actionPerformed(ActionEvent e)
+  {
+    changeColour(new NucleotideColourScheme());
+  }
 
-  protected  void conservationMenuItem_actionPerformed(ActionEvent e)
+
+  protected void applyToAllGroups_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme ( alignPanel.seqPanel.getColourScheme(),conservationMenuItem.isSelected() );
-    conservationColourIncMenuItem.setEnabled( conservationMenuItem.isSelected() );
+    viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
   }
 
 
 
-  public void conservationColourIncMenuItem_actionPerformed(ActionEvent e)
+  void changeColour(ColourSchemeI cs)
+  {
+
+    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())
+    {
+      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() )
  {
-   ConservationIncrementPanel cip = new ConservationIncrementPanel(viewport, alignPanel);
-   JInternalFrame frame = new JInternalFrame();
-   frame.setContentPane(cip);
-   Desktop.addInternalFrame(frame, "Conservation Colour Increment", 400,90);
-   frame.setMaximizable(false);
- }
+   ConservationColourScheme ccs = null;
+
+   Alignment al = (Alignment) viewport.alignment;
+   Conservation c = new Conservation("All",
+                                     ResidueProperties.propHash, 3,
+                                     al.getSequences(), 0,
+                                     al.getWidth());
+
+   c.calculate();
+   c.verdict(false, 100);
+
+   ccs = new ConservationColourScheme(c, cs);
 
+   int threshold = Desktop.setConservationSliderSource(alignPanel, ccs,
+       "Background");
 
-  public void abovePIDColour_actionPerformed(ActionEvent e)
+   ccs.inc = threshold;
+
+   viewport.setGlobalColourScheme(ccs);
+
+  }
+  else
+       viewport.setGlobalColourScheme( cs );
+
+    alignPanel.RefreshPanels();
+  }
+
+
+  protected  void conservationMenuItem_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme( new PIDColourScheme() ,conservationMenuItem.isSelected() );
+    viewport.setConservationSelected(conservationMenuItem.isSelected());
+
+    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)
+  {
+    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 );
+
+  }
+
+
+
   public void userDefinedColour_actionPerformed(ActionEvent e)
   {
     JInternalFrame frame = new JInternalFrame();
-    UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel.seqPanel );
+    UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);
     frame.setContentPane(chooser);
     Desktop.addInternalFrame(frame,"User defined colours", 450,540 );
     frame.setResizable(false);
@@ -612,24 +830,17 @@ public class AlignFrame extends GAlignFrame
 
   public void PIDColour_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme( new PIDColourScheme(),conservationMenuItem.isSelected() );
+    changeColour( new PIDColourScheme() );
   }
 
 
   public void BLOSUM62Colour_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme( new Blosum62ColourScheme(viewport) ,conservationMenuItem.isSelected() );
+    changeColour(new Blosum62ColourScheme(viewport) );
   }
 
 
 
-  protected void schemeKeyMenuItem_actionPerformed(ActionEvent e)
-  {
-    ColourKey colourKey = new ColourKey( alignPanel.seqPanel.getColourScheme() );
-    Desktop.addInternalFrame(colourKey, "Colour scheme key", 400, 320);
-  }
-
-
   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
   {
     addHistoryItem("sort");
@@ -664,12 +875,18 @@ public class AlignFrame extends GAlignFrame
 
   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
   {
+    RedundancyPanel sp = new RedundancyPanel(alignPanel);
+    JInternalFrame frame = new JInternalFrame();
+    frame.setContentPane(sp);
+    Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100);
+    frame.setMaximizable(false);
+    frame.setResizable(false);
 
   }
 
   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
     {
@@ -681,7 +898,8 @@ 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"
@@ -728,73 +946,179 @@ 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);
   }
 
 
 
+
   public void clustalAlignMenuItem_actionPerformed(ActionEvent e)
   {
-    JOptionPane.showInternalMessageDialog(this, "Jalview is currently being reengineered"
-                                  +"\nwithin the Barton Group, Dundee University."
-                                  +"\nThis will be available as a web service 2005",
-                                  "Web service", JOptionPane.INFORMATION_MESSAGE);
+    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);
+
   }
 
-  public void pdbTest_actionPerformed(ActionEvent e)
+  class ClustalThread extends JPanel implements Runnable
   {
-   String reply = JOptionPane.showInternalInputDialog(this, "Enter pdb code", "PDB test viewer", JOptionPane.QUESTION_MESSAGE);
-
-   String url = "http://www.ebi.ac.uk/cgi-bin/pdbfetch?id=1a4u";
-   if (reply.length()>1)
-     url = "http://www.ebi.ac.uk/cgi-bin/pdbfetch?id="+reply;
+    Image [] image;
+    int imageIndex = 0;
+    boolean webServiceRunning = false;
+    JInternalFrame frame;
+    public ClustalThread(JInternalFrame frame)
+    {
+      this.frame = frame;
+      image = new Image[9];
+      for(int i=0; i<9; i++)
+      {
+        java.net.URL url = getClass().getResource("/images/dna" + (i+1) + ".gif");
+        if (url != null)
+        {
+          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){}
+        }
+      }
+      DNATwirler twirler = new DNATwirler();
+      twirler.start();
+      webServiceRunning = true;
+    }
 
-   try
-   {
-     PDBfile pdb = new PDBfile(url,
-                               "URL");
-    Sequence seq = (Sequence)viewport.getAlignment().getSequenceAt(0);
-    seq.setPDBfile(pdb);
-     ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).isVisible = true;
-     ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).sequence = seq;
-  // ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).colourBySequence();
-
-     rotCanvas rc = new rotCanvas(pdb);
-     JInternalFrame frame = new JInternalFrame();
-     frame.setContentPane(rc);
-     Desktop.addInternalFrame(frame, url, 400,400);
-   }
-   catch (Exception ex)
-   {
-     ex.printStackTrace();
-   }
+    class DNATwirler extends Thread
+    {
+      public void run()
+      {
+        while(webServiceRunning)
+        {
+          try{
+            Thread.sleep(100);
+            imageIndex++;
+            imageIndex %=9;
+            repaint();
+          }
+          catch(Exception ex){}
+        }
+      }
+    }
 
-  }
+    // 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());
 
-  public void doKeyPressed(KeyEvent evt)
-  {
+         SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method
 
-    System.out.println(evt.getKeyChar());
-    if(evt.isControlDown() && evt.getKeyChar()=='f')
-      findMenuItem_actionPerformed(null);
+         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);
+       }
   }
+  public void jpredMenuItem_actionPerformed(ActionEvent e)
+    {
+    //  JInternalFrame frame = new JInternalFrame();
+//      JPredClient ct = new JPredClient((SequenceI)
+    ///                                   viewport.getAlignment().getSequences().elementAt(0));
+    }
+
+*/}}
+  protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
+    // Pick the tree file
+    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
+        getProperty("LAST_DIRECTORY"));
+    chooser.setFileView(new JalviewFileView());
+    chooser.setDialogTitle("Select a newick-like tree file");
+    chooser.setToolTipText("Load a tree file");
+    int value = chooser.showOpenDialog(null);
+    if (value == JalviewFileChooser.APPROVE_OPTION)
+    {
+      String choice = chooser.getSelectedFile().getPath();
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
+      TreePanel treepanel = null;
+      try
+      {
+        jalview.io.NewickFile fin = new jalview.io.NewickFile(choice, "File");
+        fin.parse();
 
+        if (fin.getTree() != null)
+        {
+          TreePanel tp = null;
+          tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
+                             fin, "FromFile", choice);
+          Desktop.addInternalFrame(tp, title, 600, 500);
+        }
+      }
+      catch (Exception ex)
+      {
+        JOptionPane.showMessageDialog(Desktop.desktop,
+                                      "Problem reading tree file",
+                                      ex.getMessage(),
+                                      JOptionPane.WARNING_MESSAGE);
+        ex.printStackTrace();
+      }
+    }
+  }
 
 }