X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=5ee6c6264e8e46bc5a6529f367f2bf779623098a;hb=7535505ef73485ad43881cb72a6c52cfb0033c63;hp=8af52d0e4dcc028acb9f6b9c9cd602aa6463400f;hpb=a9770d55354408173fddcf91fb90059c73497448;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 8af52d0..5ee6c62 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -16,34 +16,84 @@ import jalview.schemes.*;
 import jalview.datamodel.*;
 import jalview.analysis.*;
 import jalview.io.*;
-import java.awt.event.*;
+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
 {
-  AlignmentPanel alignPanel;
-  AlignViewport viewport;
+  final AlignmentPanel alignPanel;
+  final AlignViewport viewport;
   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()+"");
+
+    // add conservation graph to alignment
+    viewport.updateConservation();
+    viewport.updateConsensus();
+
+    alignPanel.annotationPanel.adjustPanelHeight();
+    alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());
+    alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());
+
+
+    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 [] = null;
+    if(e.getActionCommand().equals("FASTA"))
+      suffix = new String[]{"fa", "fasta"};
+    else if(e.getActionCommand().equals("MSF"))
+      suffix = new String[]{"msf"};
+    else if(e.getActionCommand().equals("CLUSTAL"))
+      suffix = new String[]{"aln"};
+    else if(e.getActionCommand().equals("BLC"))
+      suffix = new String[]{"blc"};
+    else if(e.getActionCommand().equals("PIR"))
+      suffix = new String[]{"pir"};
+    else if(e.getActionCommand().equals("PFAM"))
+      suffix = new String[]{"pfam"};
+
+    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY")
+        , suffix, e.getActionCommand()+" file");
+    chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format.");
     chooser.setToolTipText("Save");
     int value = chooser.showSaveDialog(this);
-    if(value == JFileChooser.APPROVE_OPTION)
+    if(value == JalviewFileChooser.APPROVE_OPTION)
     {
       String choice =  chooser.getSelectedFile().getPath();
-      jalview.bin.Cache.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 )  );
@@ -67,15 +117,53 @@ 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;
   }
 
-  public void saveAsPostscriptMenuItem_actionPerformed(ActionEvent e)
+  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
+    PrintThread thread = new PrintThread();
+    thread.start();
+  }
+
+  class PrintThread extends Thread
+  {
+    public void run()
+    {
+      PrinterJob printJob = PrinterJob.getPrinterJob();
+      PageFormat pf = printJob.pageDialog(printJob.defaultPage());
+      printJob.setPrintable(alignPanel, pf);
+      if (printJob.printDialog())
+      {
+        try
+        {
+          printJob.print();
+        }
+        catch (Exception PrintException)
+        {
+          PrintException.printStackTrace();
+        }
+      }
+    }
 
   }
 
+
+
+
   public void closeMenuItem_actionPerformed(ActionEvent e)
   {
     try{
@@ -83,77 +171,298 @@ public class AlignFrame extends GAlignFrame
     }catch(Exception ex){}
   }
 
-  public void groupsMenuItem_actionPerformed(ActionEvent e)
+  Stack historyList = new Stack();
+  Stack redoList = new Stack();
+  JMenuBar jMenuBar1 = new JMenuBar();
+
+  void updateEditMenuBar()
   {
+    if(historyList.size()>0)
+     {
+       undoMenuItem.setEnabled(true);
+       Object [] history = (Object[])historyList.get(0);
+       undoMenuItem.setText("Undo "+history[0]);
+     }
+    else
+    {
+      undoMenuItem.setEnabled(false);
+      undoMenuItem.setText("Undo");
+    }
 
+    if(redoList.size()>0)
+     {
+       redoMenuItem.setEnabled(true);
+       Object [] history = (Object[])redoList.get(0);
+       redoMenuItem.setText("Redo "+history[0]);
+     }
+    else
+    {
+      redoMenuItem.setEnabled(false);
+      redoMenuItem.setText("Redo");
+    }
   }
 
-  public void groupEditingMenuItem_actionPerformed(ActionEvent e)
+  public void addHistoryItem(String type)
   {
+    // 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++)
+    {
+      seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),
+                             viewport.getAlignment().getSequenceAt(i).getSequence());
+    }
 
+    historyList.add(0, new Object[]{type,  seq} );
+    updateEditMenuBar();
   }
 
-  public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
+  protected void undoMenuItem_actionPerformed(ActionEvent e)
   {
-    Selection sel = viewport.getSelection();
-    for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
-      sel.addElement( viewport.getAlignment().getSequenceAt(i));
-    PaintRefresher.Refresh(null);
+    Object [] history = (Object[])historyList.remove(0);
+    // add the redo state before continuing!!
+    SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
+    for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
+    {
+      seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),
+                            viewport.getAlignment().getSequenceAt(i).
+                            getSequence());
+    }
+    /////////
+
+    redoList.add(0, new Object[] {history[0], seq});
+
+      seq = (SequenceI[]) history[1];
+      viewport.setAlignment( new Alignment(seq) );
+      updateEditMenuBar();
+      viewport.updateConsensus();
+      alignPanel.RefreshPanels();
+      alignPanel.RefreshPanels();
   }
 
-  public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
+  public void moveSelectedSequences(boolean up)
   {
-    viewport.getSelection().clear();
-    PaintRefresher.Refresh(null);
+    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();
   }
 
-  public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
+
+
+  protected void copy_actionPerformed(ActionEvent e)
   {
-    Selection sel = viewport.getSelection();
-    for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
-    {
-      if (sel.contains(viewport.getAlignment().getSequenceAt(i)))
-        sel.removeElement(viewport.getAlignment().getSequenceAt(i));
+   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, 500);
+      }
       else
-        sel.addElement(viewport.getAlignment().getSequenceAt(i));
-    }
-    PaintRefresher.Refresh(null);
+      {
+        viewport.setEndSeq(viewport.alignment.getHeight());
+        viewport.alignment.getWidth();
+        viewport.updateConservation();
+        viewport.updateConsensus();
+        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){}
+   viewport.updateConservation();
+   viewport.updateConsensus();
+     alignPanel.RefreshPanels();
+
+  }
+
+
+
+  protected void redoMenuItem_actionPerformed(ActionEvent e)
+  {
+     Object [] history = (Object[])redoList.remove(0);
+     SequenceI[] seq = (SequenceI[]) history[1];
+     viewport.setAlignment( new Alignment(seq) );
+     updateEditMenuBar();
+     viewport.updateConsensus();
+     alignPanel.RefreshPanels();
+     alignPanel.RefreshPanels();
+  }
+
+
+  public void groupsMenuItem_actionPerformed(ActionEvent e)
+  {
+    GroupEditor geditor = new GroupEditor(viewport, alignPanel);
+    JInternalFrame frame = new JInternalFrame();
+    frame.setContentPane(geditor);
+    Desktop.addInternalFrame(frame, "Group editor", 710, 410);
+    frame.setResizable(false);
   }
 
-  public void deleteSelectedMenuItem_actionPerformed(ActionEvent e)
+  protected void deleteGroups_actionPerformed(ActionEvent e)
   {
-    for (int i=0;i < viewport.getSelection().size(); i++)
-            viewport.getAlignment().deleteSequence(viewport.getSelection().sequenceAt(i));
+    viewport.alignment.deleteAllGroups();
+    viewport.setSelectionGroup(null);
 
-    viewport.getSelection().clear();
-    viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getHeight());
     alignPanel.RefreshPanels();
   }
 
-  public void moveSelectedMenuItem_actionPerformed(ActionEvent e)
+
+
+  public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
   {
-    copySelectedMenuItem_actionPerformed(null);
-    deleteSelectedMenuItem_actionPerformed(null);
-    alignPanel.repaint();
+    SequenceGroup sg = new SequenceGroup();
+    for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
+      sg.addSequence( viewport.getAlignment().getSequenceAt(i));
+    sg.setEndRes(viewport.alignment.getWidth());
+    viewport.setSelectionGroup(sg);
+    PaintRefresher.Refresh(null);
   }
 
-  public void copySelectedMenuItem_actionPerformed(ActionEvent e)
+  public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
   {
-    if(viewport.getSelection().size()==0)
-      return;
+    viewport.setSelectionGroup(null);
+    PaintRefresher.Refresh(null);
+  }
 
-   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));
+  public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
+  {
+    SequenceGroup sg = viewport.getSelectionGroup();
+    for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
+      sg.addOrRemove (viewport.getAlignment().getSequenceAt(i));
 
-    int newHeight = s.length * af.viewport.getCharHeight() + 200;
-    if(newHeight>500)
-      newHeight=500;
-    Desktop.addInternalFrame(af, "Copied sequences", 700,newHeight);
+    PaintRefresher.Refresh(null);
   }
 
+
   public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.getColumnSelection().clear();
@@ -162,24 +471,49 @@ public class AlignFrame extends GAlignFrame
 
   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
   {
+    addHistoryItem("delete columns");
     ColumnSelection colSel = viewport.getColumnSelection();
     if (colSel.size() > 0)
     {
       int min = colSel.getMin();
       viewport.getAlignment().trimLeft(min);
       colSel.compensateForEdit(0,min);
+
+      if(viewport.getSelectionGroup()!=null)
+        viewport.getSelectionGroup().adjustForRemoveLeft(min);
+
+      Vector groups = viewport.alignment.getGroups();
+      for(int i=0; i<groups.size(); i++)
+      {
+        SequenceGroup sg = (SequenceGroup) groups.get(i);
+        if(!sg.adjustForRemoveLeft(min))
+          viewport.alignment.deleteGroup(sg);
+      }
+
       alignPanel.RefreshPanels();
     }
   }
 
   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
   {
+    addHistoryItem("delete columns");
     ColumnSelection colSel = viewport.getColumnSelection();
     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();
     }
@@ -188,12 +522,16 @@ public class AlignFrame extends GAlignFrame
 
   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
   {
+    addHistoryItem("delete gapped columns");
     viewport.getAlignment().removeGaps();
+    viewport.updateConservation();
+    viewport.updateConsensus();
     alignPanel.RefreshPanels();
   }
 
   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
   {
+    addHistoryItem("delete all gaps");
     SequenceI current;
     int jSize;
     for (int i=0; i < viewport.getAlignment().getSequences().size();i++)
@@ -201,102 +539,72 @@ 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--;
           jSize--;
         }
     }
-
+    viewport.updateConservation();
+    viewport.updateConsensus();
     alignPanel.RefreshPanels();
   }
 
   public void setGapCharMenuItem_actionPerformed(ActionEvent e)
   {
-    String thisChar = "-";
-    String nextChar = ".";
-    if(viewport.getGapCharacter().equals("-"))
+    char thisChar = '-';
+    char nextChar = '.';
+    if(viewport.getGapCharacter()=='-')
     {
-      thisChar = ".";
-      nextChar = "-";
+      thisChar = '.';
+      nextChar = '-';
     }
     setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");
     viewport.setGapCharacter(thisChar);
+    alignPanel.RefreshPanels();
   }
 
-
-  public void fontNameMenuItem_actionPerformed(ActionEvent e)
+  public void findMenuItem_actionPerformed(ActionEvent e)
   {
-    String fonts[] = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
-
-
-    String selection = JOptionPane.showInputDialog(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.showInputDialog(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.showInputDialog(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)
   {
-    viewport.setColourText( colourTextMenuItem.isSelected() );
-    alignPanel.RefreshPanels();
+      viewport.setColourText( colourTextMenuItem.isSelected() );
+      alignPanel.RefreshPanels();
   }
 
-  void SetFont()
+  protected void wrapMenuItem_actionPerformed(ActionEvent e)
   {
-      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();
-
+    viewport.setWrapAlignment( wrapMenuItem.isSelected() );
+    alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );
   }
 
+
   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );
@@ -310,13 +618,32 @@ public class AlignFrame extends GAlignFrame
   }
 
 
-  public void consensusGraphMenuItem_actionPerformed(ActionEvent e)
+  protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
+  {
+    viewport.setRenderGaps(renderGapsMenuItem.isSelected());
+    alignPanel.RefreshPanels();
+  }
+
+  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();
+  }
+
+  public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
   {
-    alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );
+    alignPanel.setAnnotationVisible( annotationPanelMenuItem.isSelected() );
   }
 
   public void overviewMenuItem_actionPerformed(ActionEvent e)
   {
+    if (alignPanel.overviewPanel != null)
+      return;
 
     JInternalFrame frame = new JInternalFrame();
     OverviewPanel overview = alignPanel.getOverviewPanel();
@@ -336,76 +663,216 @@ public class AlignFrame extends GAlignFrame
 
   }catch(java.lang.OutOfMemoryError ex)
    {
-     JOptionPane.showMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!",
+     JOptionPane.showInternalMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!"
+                                   +"\nTry reducing the font size.",
                                    "Out of memory", JOptionPane.WARNING_MESSAGE);
    }
 
 
   }
 
+  protected void noColourmenuItem_actionPerformed(ActionEvent e)
+  {
+    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() );
+    changeColour(new ZappoColourScheme());
   }
 
   public void taylorColour_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme( new TaylorColourScheme() );
+    changeColour(new TaylorColourScheme());
   }
 
 
   public void hydrophobicityColour_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme( new HydrophobicColourScheme() );
+    changeColour( new HydrophobicColourScheme() );
   }
 
   public void helixColour_actionPerformed(ActionEvent e)
   {
-    alignPanel.seqPanel.setColourScheme( new HelixColourScheme() );
+    changeColour(new HelixColourScheme() );
   }
 
+
   public void strandColour_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme( new StrandColourScheme() );
+    changeColour(new StrandColourScheme());
   }
 
+
   public void turnColour_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme( new TurnColourScheme() );
+    changeColour(new TurnColourScheme());
   }
 
+
   public void buriedColour_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme( new BuriedColourScheme() );
+    changeColour(new BuriedColourScheme() );
   }
 
-  public void conservationColour_actionPerformed(ActionEvent e)
+  public void nucleotideColour_actionPerformed(ActionEvent e)
   {
+    changeColour(new NucleotideColourScheme());
+  }
+
 
+  protected void applyToAllGroups_actionPerformed(ActionEvent e)
+  {
+    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() )
  {
+   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");
 
- }
+   ccs.inc = threshold;
 
+   viewport.setGlobalColourScheme(ccs);
 
-  public void abovePIDColour_actionPerformed(ActionEvent e)
+  }
+  else
+       viewport.setGlobalColourScheme( cs );
+
+    alignPanel.RefreshPanels();
+  }
+
+
+  protected  void conservationMenuItem_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme( new PIDColourScheme() );
+    viewport.setConservationSelected(conservationMenuItem.isSelected());
+    if(coloursChanging)
+      return;
+
+    coloursChanging = true;
+
+    viewport.setAbovePIDThreshold(false);
+    abovePIDThreshold.setSelected(false);
+    Desktop.hidePIDSlider();
+    if(!viewport.getConservationSelected())
+      Desktop.hideConservationSlider();
+
+   ColourSchemeI cs = viewport.getGlobalColourScheme();
+   if(cs instanceof ConservationColourScheme )
+     changeColour( ((ConservationColourScheme)cs).cs );
+    else
+      changeColour( cs );
+
+    coloursChanging = false;
   }
 
+  boolean coloursChanging = false;
+  public void abovePIDThreshold_actionPerformed(ActionEvent e)
+  {
+    if(coloursChanging)
+      return;
+
+    coloursChanging = true;
+    viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
+
+    conservationMenuItem.setSelected(false);
+    viewport.setConservationSelected(false);
+    Desktop.hideConservationSlider();
+
+    if(!viewport.getAbovePIDThreshold())
+      Desktop.hidePIDSlider();
+
+
+    ColourSchemeI cs = viewport.getGlobalColourScheme();
+    if(cs instanceof ConservationColourScheme )
+        changeColour( ((ConservationColourScheme)cs).cs );
+    else
+        changeColour( cs );
+
+    coloursChanging = false;
+  }
+
+
 
   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);
@@ -415,43 +882,42 @@ public class AlignFrame extends GAlignFrame
 
   public void PIDColour_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme( new PIDColourScheme() );
+    changeColour( new PIDColourScheme() );
   }
 
+
   public void BLOSUM62Colour_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme( new Blosum62ColourScheme(viewport) );
+    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");
     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));
     alignPanel.RefreshPanels();
   }
 
   public void sortIDMenuItem_actionPerformed(ActionEvent e)
   {
+    addHistoryItem("sort");
     AlignmentSorter.sortByID( viewport.getAlignment() );
     alignPanel.RefreshPanels();
   }
 
   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
   {
-    AlignmentSorter.sortGroups(viewport.getAlignment());
+    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;
 
@@ -461,13 +927,19 @@ 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)
-      JOptionPane.showMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);
+    if(viewport.getSelectionGroup().getSize()<2)
+      JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);
     else
     {
       JInternalFrame frame = new JInternalFrame();
@@ -478,20 +950,29 @@ 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.showMessageDialog(this, "Principal component analysis must take\n"
+      JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"
                                     +"at least 4 input sequences.",
                                     "Sequence selection insufficient",
                                     JOptionPane.WARNING_MESSAGE);
       return;
     }
 
-    PCAPanel pcaPanel = new PCAPanel(viewport, null);
-    JInternalFrame frame = new JInternalFrame();
-    frame.setContentPane(pcaPanel);
-    Desktop.addInternalFrame(frame, "Principal component analysis", 400,400);
+    try{
+      PCAPanel pcaPanel = new PCAPanel(viewport, null);
+      JInternalFrame frame = new JInternalFrame();
+      frame.setContentPane(pcaPanel);
+      Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);
+   }catch(java.lang.OutOfMemoryError ex)
+   {
+     JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",
+                                   "Out of memory", JOptionPane.WARNING_MESSAGE);
+   }
+
+
   }
 
   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
@@ -517,32 +998,220 @@ 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.showMessageDialog(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);
+
+  }
+
+  class ClustalThread extends JPanel implements Runnable
+  {
+    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;
+    }
+
+    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());
+
+         SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method
+
+         if (alignment != null)
+         {
+           AlignFrame af = new AlignFrame(new Alignment(alignment));
+          af.clustalColour.setSelected(true);
+          af.clustalColour_actionPerformed(null);
+           Desktop.addInternalFrame(af, getTitle().concat(" - ClustalW Alignment"),
+                                    700, 500); // JBPNote - is there a new window geom. property ?
+         }
+         else
+           JOptionPane.showMessageDialog(Desktop.desktop, "Problem obtaining clustal alignment", "Web service error",
+                                         JOptionPane.WARNING_MESSAGE);
+
+         webServiceRunning = false;
+         try{
+           frame.setClosed(true);
+         }catch(Exception ex){}
+       }
+
+       public void paintComponent(Graphics g)
+       {
+         g.setColor(Color.white);
+         g.fillRect(0,0,getWidth(), getHeight());
+         if(image!=null)
+         {
+           g.drawImage(image[imageIndex],10,10,this);
+         }
+         g.setFont(new Font("Arial", Font.BOLD, 12));
+         g.setColor(Color.black);
+         g.drawString("Clustal Alignment Web Service running", 30,30);
+       }
+  }
+  protected void jpred_actionPerformed(ActionEvent e)
+{
+
+    JInternalFrame frame = new JInternalFrame();
+    if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>0)
+    {
+      // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
+      SequenceGroup seqs = viewport.getSelectionGroup();
+      if (seqs.getSize() == 1 || !viewport.alignment.isAligned())
+      {
+        JPredClient ct = new JPredClient( (SequenceI)
+                                         seqs.getSequenceAt(0));
+      }
+      else
+      {
+        int sz;
+        SequenceI[] msa = new SequenceI[sz=seqs.getSize()];
+        for (int i = 0; i < sz; i++)
+        {
+          msa[i] = (SequenceI) seqs.getSequenceAt(i);
+        }
+
+        JPredClient ct = new JPredClient(msa);
+      }
+
+    }
+    else
+    {
+      Vector seqs = viewport.getAlignment().getSequences();
+
+      if (seqs.size() == 1 || !viewport.alignment.isAligned())
+      {
+        JPredClient ct = new JPredClient( (SequenceI)
+                                         seqs.elementAt(0));
+      }
+      else
+      {
+        SequenceI[] msa = new SequenceI[seqs.size()];
+        for (int i = 0; i < seqs.size(); i++)
+        {
+          msa[i] = (SequenceI) seqs.elementAt(i);
+        }
+
+        JPredClient ct = new JPredClient(msa);
+      }
+
+    }
+  }
+
+    protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
+    // Pick the tree file
+    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
+        getProperty("LAST_DIRECTORY"));
+    chooser.setFileView(new JalviewFileView());
+    chooser.setDialogTitle("Select a newick-like tree file");
+    chooser.setToolTipText("Load a tree file");
+    int value = chooser.showOpenDialog(null);
+    if (value == JalviewFileChooser.APPROVE_OPTION)
+    {
+      String choice = chooser.getSelectedFile().getPath();
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
+      TreePanel treepanel = null;
+      try
+      {
+        jalview.io.NewickFile fin = new jalview.io.NewickFile(choice, "File");
+        fin.parse();
+
+        if (fin.getTree() != null)
+        {
+          TreePanel tp = null;
+          tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
+                             fin, "FromFile", choice);
+          Desktop.addInternalFrame(tp, title, 600, 500);
+        }
+      }
+      catch (Exception ex)
+      {
+        JOptionPane.showMessageDialog(Desktop.desktop,
+                                      "Problem reading tree file",
+                                      ex.getMessage(),
+                                      JOptionPane.WARNING_MESSAGE);
+        ex.printStackTrace();
+      }
+    }
   }
 
 }