X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=c1a710508c5e432e088c227d37101a6206167db7;hb=ac07859006686a2c62bcf57b24742eb610bc46f0;hp=1d6cbf440f737c70e691168cdc20dd9b9431a305;hpb=3ac9a19998fe3b2f4e4583bed327a13ca80c874b;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 1d6cbf4..c1a7105 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -17,39 +17,94 @@ import jalview.datamodel.*;
 import jalview.analysis.*;
 import jalview.io.*;
 import jalview.ws.*;
-import MCview.*;
 import java.awt.*;
 import java.awt.event.*;
 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
 {
   final AlignmentPanel alignPanel;
   final AlignViewport viewport;
+  public static final int NEW_WINDOW_WIDTH = 700;
+  public static final int NEW_WINDOW_HEIGHT = 500;
+
   public AlignFrame(AlignmentI al)
   {
-    super();
-    viewport = new AlignViewport(al,true,true,true,false);
+    try{
+      String ip = java.net.InetAddress.getLocalHost().getHostAddress();
+      if( !ip.startsWith("10."))
+        alignMenu.setVisible(false);
+    }
+    catch(java.net.UnknownHostException e){}
+    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)) );
+
+    // add conservation graph to alignment
+    viewport.updateConservation();
+    viewport.updateConsensus();
+
+
     alignPanel = new AlignmentPanel(this, viewport);
+
+    alignPanel.annotationPanel.adjustPanelHeight();
+    alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());
+    alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());
+
     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 [] = 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 )  );
@@ -77,6 +132,17 @@ public class AlignFrame extends GAlignFrame
     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
@@ -116,8 +182,9 @@ 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()
   {
@@ -179,9 +246,173 @@ public class AlignFrame extends GAlignFrame
       seq = (SequenceI[]) history[1];
       viewport.setAlignment( new Alignment(seq) );
       updateEditMenuBar();
+      viewport.updateConsensus();
+      alignPanel.RefreshPanels();
       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));
+        Desktop.addInternalFrame(af, "Copied sequences", NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);
+      }
+      else
+      {
+        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)
   {
@@ -189,22 +420,17 @@ public class AlignFrame extends GAlignFrame
      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);
-  }
-
   protected void deleteGroups_actionPerformed(ActionEvent e)
   {
     viewport.alignment.deleteAllGroups();
+    viewport.setSelectionGroup(null);
+
     alignPanel.RefreshPanels();
   }
 
@@ -212,28 +438,26 @@ 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.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);
   }
 
@@ -253,6 +477,18 @@ public class AlignFrame extends GAlignFrame
       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();
     }
   }
@@ -264,8 +500,19 @@ public class AlignFrame extends GAlignFrame
     if (colSel.size() > 0)
     {
       int max = colSel.getMax();
-      if(max>1)
-        viewport.getAlignment().trimRight(max);
+      viewport.getAlignment().trimRight(max);
+      if(viewport.getSelectionGroup()!=null)
+        viewport.getSelectionGroup().adjustForRemoveRight(max);
+
+      Vector groups = viewport.alignment.getGroups();
+      for(int i=0; i<groups.size(); i++)
+      {
+        SequenceGroup sg = (SequenceGroup) groups.get(i);
+        if(!sg.adjustForRemoveRight(max))
+          viewport.alignment.deleteGroup(sg);
+      }
+
+
 
       alignPanel.RefreshPanels();
     }
@@ -276,6 +523,8 @@ public class AlignFrame extends GAlignFrame
   {
     addHistoryItem("delete gapped columns");
     viewport.getAlignment().removeGaps();
+    viewport.updateConservation();
+    viewport.updateConsensus();
     alignPanel.RefreshPanels();
   }
 
@@ -296,7 +545,8 @@ public class AlignFrame extends GAlignFrame
           jSize--;
         }
     }
-
+    viewport.updateConservation();
+    viewport.updateConsensus();
     alignPanel.RefreshPanels();
   }
 
@@ -316,65 +566,29 @@ public class AlignFrame extends GAlignFrame
 
   public void findMenuItem_actionPerformed(ActionEvent e)
   {
-    JOptionPane op = new JOptionPane();
-    JInternalFrame frame =  op.createInternalFrame(this, "Find");
+    JInternalFrame frame = new JInternalFrame();
     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();
-     }
+    Desktop.addInternalFrame(frame, "Find", 340,110, false);
+    frame.setLayer(JLayeredPane.PALETTE_LAYER);
 
   }
 
-  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();
-     }
+    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)
@@ -383,28 +597,36 @@ public class AlignFrame extends GAlignFrame
       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.setWrapAlignment( wrapMenuItem.isSelected() );
+    alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );
+    scaleAbove.setVisible( wrapMenuItem.isSelected() );
+    scaleLeft.setVisible( wrapMenuItem.isSelected() );
+    scaleRight.setVisible( wrapMenuItem.isSelected() );
+    alignPanel.RefreshPanels();
+  }
 
-      viewport.setFont(new java.awt.Font(fontNameMenuItem.getText(),
-                                           style,
-                                           Integer.parseInt(fontSizeMenuItem.getText())));
-      alignPanel.RefreshPanels();
+  protected void scaleAbove_actionPerformed(ActionEvent e)
+  {
+    viewport.setScaleAboveWrapped(scaleAbove.isSelected());
+    alignPanel.repaint();
+  }
 
+  protected void scaleLeft_actionPerformed(ActionEvent e)
+  {
+    viewport.setScaleLeftWrapped(scaleLeft.isSelected());
+    alignPanel.repaint();
   }
 
-  protected void wrapMenuItem_actionPerformed(ActionEvent e)
+  protected void scaleRight_actionPerformed(ActionEvent e)
   {
-    viewport.setWrapAlignment( wrapMenuItem.isSelected() );
-    alignPanel.RefreshPanels();
+    viewport.setScaleRightWrapped(scaleRight.isSelected());
+    alignPanel.repaint();
   }
 
 
+
   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );
@@ -424,14 +646,26 @@ public class AlignFrame extends GAlignFrame
     alignPanel.RefreshPanels();
   }
 
-  public void secondaryStructure_actionPerformed(ActionEvent evt)
+  public void sequenceFeatures_actionPerformed(ActionEvent evt)
   {
-    alignPanel.setSecondaryStructureVisible(secondaryStructure.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)
+  public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
   {
-    alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );
+    if(annotationPanelMenuItem.isSelected() && viewport.getWrapAlignment())
+    {
+      annotationPanelMenuItem.setSelected(false);
+      return;
+    }
+    viewport.setShowAnnotation( annotationPanelMenuItem.isSelected() );
+    alignPanel.setAnnotationVisible( annotationPanelMenuItem.isSelected() );
   }
 
   public void overviewMenuItem_actionPerformed(ActionEvent e)
@@ -467,192 +701,207 @@ public class AlignFrame extends GAlignFrame
 
   protected void noColourmenuItem_actionPerformed(ActionEvent e)
   {
-    viewport.setGlobalColourScheme( null );
-    changeColour();
+    changeColour( null );
   }
 
 
-  public void Colour_actionPerformed(ActionEvent e)
+  public void clustalColour_actionPerformed(ActionEvent e)
   {
-    viewport.setGlobalColourScheme(new ClustalxColourScheme( ));
-    conservationMenuItem.setSelected(false);
     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);
+    viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
+  }
 
 
-     alignPanel.RefreshPanels();
-  }
 
-  void addConservationOrPIDColour()
+  void changeColour(ColourSchemeI cs)
   {
-    int x=0, y=0, threshold = 70;
 
-    if(sliderFrame!=null)
-       try
-       {
-         x = sliderFrame.getX();
-         y = sliderFrame.getY();
-         SliderPanel sp = (SliderPanel) sliderFrame.getContentPane();
-         threshold = sp.getValue();
-         sliderFrame.setClosed(true);
-       }
-       catch (Exception ex)
-       {    ex.printStackTrace();   }
+    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, viewport.ConsPercGaps);
+          ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
+
+          sg.cs = ccs;
+        }
+
+      }
+    }
 
-     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() );
+    if ( viewport.getAbovePIDThreshold() )
+    {
+ //     int threshold = 0;
+   //   threshold = Desktop.setPIDSliderSource(alignPanel, cs, "Background");
+      Desktop.hideConservationSlider();
 
-       c.calculate();
-       c.verdict(false, 100);
+ //     if (cs instanceof ResidueColourScheme)
+ //       ( (ResidueColourScheme) cs).setThreshold(threshold);
+  //    else if (cs instanceof ScoreColourScheme)
+   //     ( (ScoreColourScheme) cs).setThreshold(threshold);
 
-       if(ccs!=null)
-         ccs = new ConservationColourScheme(c, ccs.cs);
-       else
-         ccs = new ConservationColourScheme(c, oldCs);
+      viewport.setGlobalColourScheme(cs);
 
-        viewport.setGlobalColourScheme( ccs );
+    }
+    else
+    if (cs instanceof ResidueColourScheme)
+      ( (ResidueColourScheme) cs).setThreshold(0);
+    else if (cs instanceof ScoreColourScheme)
+      ( (ScoreColourScheme) cs).setThreshold(0);
 
-     }
-     else if(oldCs instanceof ConservationColourScheme)
-     {
-       oldCs = ccs.cs;
-       viewport.setGlobalColourScheme( oldCs );
-     }
 
 
-     if( conservationMenuItem.isSelected() || abovePIDThreshold.isSelected() )
-     {
-       sliderFrame = new JInternalFrame();
-       sliderFrame.setMaximizable(false);
-       sliderFrame.setResizable(false);
 
-       SliderPanel sp = null;
-       if (conservationMenuItem.isSelected())
-       {
-        if(threshold > 50)
-          threshold = 30;
-        sp = new SliderPanel(alignPanel, threshold, true,ccs);
-        Desktop.addInternalFrame(sliderFrame, "Conservation Colour Increment  (Global colour)", 400, 90);
-        threshold = 0;
-       }
-       else if (abovePIDThreshold.isSelected())
-       {
-         sp = new SliderPanel(alignPanel, threshold, false, oldCs);
-         sp.cs = oldCs;
-         Desktop.addInternalFrame(sliderFrame, "Percentage Identity Threshold (Global colour)", 400, 90);
-       }
+if ( viewport.getConservationSelected() )
+ {
+   ConservationColourScheme ccs = null;
 
-       sliderFrame.setContentPane(sp);
-       if(x!=0 && y!=0)
-               sliderFrame.setLocation(x,y);
+   Alignment al = (Alignment) viewport.alignment;
+   Conservation c = new Conservation("All",
+                                     ResidueProperties.propHash, 3,
+                                     al.getSequences(), 0,
+                                     al.getWidth());
 
-     }
-     else
-       threshold = 0;
+   c.calculate();
+   c.verdict(false, viewport.ConsPercGaps);
 
+   ccs = new ConservationColourScheme(c, cs);
 
-     if (oldCs instanceof ResidueColourScheme)
-     {
-       ResidueColourScheme rcs = (ResidueColourScheme) oldCs;
-       rcs.setThreshold(threshold);
-     }
-     else if (oldCs instanceof ScoreColourScheme)
-     {
-       ScoreColourScheme scs = (ScoreColourScheme) oldCs;
-       scs.setThreshold(threshold);
-     }
+ //  int threshold = Desktop.setConservationSliderSource(alignPanel, ccs,    "Background");
 
+ //  ccs.inc = threshold;
 
+   viewport.setGlobalColourScheme(ccs);
+
+  }
+  else
+       viewport.setGlobalColourScheme( cs );
+
+    alignPanel.RefreshPanels();
+  }
+
+  protected void modifyPID_actionPerformed(ActionEvent e)
+  {
+    Desktop.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(), "Background");
+  }
+
+  protected void modifyConservation_actionPerformed(ActionEvent e)
+  {
+    Desktop.setConservationSliderSource(alignPanel, viewport.globalColourScheme,    "Background");
   }
 
+
   protected  void conservationMenuItem_actionPerformed(ActionEvent e)
   {
-   if(abovePIDThreshold.isSelected())
+    viewport.setConservationSelected(conservationMenuItem.isSelected());
+    if(coloursChanging)
+      return;
+
+    coloursChanging = true;
+
+    viewport.setAbovePIDThreshold(false);
     abovePIDThreshold.setSelected(false);
+    Desktop.hidePIDSlider();
+    if(!viewport.getConservationSelected())
+      Desktop.hideConservationSlider();
 
-   viewport.setConservationSelected(conservationMenuItem.isSelected());
+   ColourSchemeI cs = viewport.getGlobalColourScheme();
+   if(cs instanceof ConservationColourScheme )
+     changeColour( ((ConservationColourScheme)cs).cs );
+    else
+      changeColour( cs );
 
-   addConservationOrPIDColour();
+    coloursChanging = false;
   }
 
-  JInternalFrame sliderFrame;
+  boolean coloursChanging = false;
   public void abovePIDThreshold_actionPerformed(ActionEvent e)
   {
-      if(conservationMenuItem.isSelected())
-        conservationMenuItem.setSelected(false);
+    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 );
 
-      addConservationOrPIDColour();
+    coloursChanging = false;
   }
 
 
@@ -662,34 +911,22 @@ public class AlignFrame extends GAlignFrame
     JInternalFrame frame = new JInternalFrame();
     UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);
     frame.setContentPane(chooser);
-    Desktop.addInternalFrame(frame,"User defined colours", 450,540 );
-    frame.setResizable(false);
-    frame.setIconifiable(false);
-    frame.setMaximizable(false);
+    Desktop.addInternalFrame(frame,"User defined colours", 450,540, false );
   }
 
   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)  );
-    alignPanel.setColourScheme();
+    changeColour(new Blosum62ColourScheme(viewport) );
   }
 
 
 
-  protected void schemeKeyMenuItem_actionPerformed(ActionEvent e)
-  {
-    ColourKey colourKey = new ColourKey( viewport.getGlobalColourScheme() );
-    Desktop.addInternalFrame(colourKey, "Colour scheme key", 400, 320);
-  }
-
-
   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
   {
     addHistoryItem("sort");
@@ -712,30 +949,18 @@ public class AlignFrame extends GAlignFrame
     alignPanel.RefreshPanels();
   }
 
-  public void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)
-  {
-    addHistoryItem("sort");
-    if(viewport.getCurrentTree()==null)
-      return;
-
-    AlignmentSorter.sortByTree(viewport.getAlignment(), viewport.getCurrentTree());
-    alignPanel.RefreshPanels();
-  }
-
   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);
+    Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100, 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
     {
@@ -747,7 +972,8 @@ 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"
@@ -794,25 +1020,56 @@ public class AlignFrame extends GAlignFrame
 
   void NewTreePanel(String type, String pwType, String title)
   {
-    JInternalFrame frame = new javax.swing.JInternalFrame();
-    TreePanel tp=null;
-   if (viewport.getSelection() != null && viewport.getSelection().size() > 3)
-   {
-     tp = new TreePanel(viewport, viewport.getSelection().asVector(),type, pwType,
-                         viewport.getStartRes(), viewport.getEndRes());
-   }
-   else
-   {
-     tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
-                         type, pwType, viewport.getStartRes(),
-                         viewport.getEndRes());
-   }
+    //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;
+    }
+
+    final TreePanel tp;
+    if (viewport.getSelectionGroup() != null &&
+        viewport.getSelectionGroup().getSize() > 3)
+    {
+      tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,
+                         pwType,
+                         0, viewport.alignment.getWidth());
+    }
+    else
+    {
+      tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
+                         type, pwType, 0, viewport.alignment.getWidth());
+    }
 
-   frame.setContentPane(tp);
-   Desktop.addInternalFrame(frame, title, 600, 500);
+   addTreeMenuItem(tp, title);
+
+   Desktop.addInternalFrame(tp, title, 600, 500);
   }
 
+  void addTreeMenuItem(final TreePanel treePanel, String title)
+  {
+    final JMenuItem item = new JMenuItem(title);
+    sortByTreeMenu.add(item);
+    item.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        addHistoryItem("sort");
+        AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
+        alignPanel.RefreshPanels();
+      }
+    });
+
+    treePanel.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+    {
+      public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
+      {
+        sortByTreeMenu.remove(item);
+      };
+    });
 
+  }
 
 
   public void clustalAlignMenuItem_actionPerformed(ActionEvent e)
@@ -822,47 +1079,49 @@ public class AlignFrame extends GAlignFrame
     Thread t = new Thread(ct);
     t.start();
     frame.setContentPane(ct);
-     Desktop.addInternalFrame(frame, title, 300, 80);
+     Desktop.addInternalFrame(frame, title, 320, 90);
 
   }
 
   class ClustalThread extends JPanel implements Runnable
   {
-    Image [] image;
-    int imageIndex = 0;
+    Image image;
+    int angle = 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/logo.gif");
+      if (url != null)
       {
-        java.net.URL url = getClass().getResource("/dna" + (i+1) + ".gif");
-        if (url != null)
+        image = java.awt.Toolkit.getDefaultToolkit().createImage(url);
+        MediaTracker mt = new MediaTracker(this);
+        mt.addImage(image, 0);
+        try
         {
-          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){}
+          mt.waitForID(0);
         }
+        catch (Exception ex)
+        {}
       }
-      DNATwirler twirler = new DNATwirler();
-      twirler.start();
+
+      ImageSpinner spinner = new ImageSpinner();
+      spinner.start();
       webServiceRunning = true;
     }
 
-    class DNATwirler extends Thread
+    class ImageSpinner extends Thread
     {
       public void run()
       {
         while(webServiceRunning)
         {
           try{
-            Thread.sleep(100);
-            imageIndex++;
-            imageIndex %=9;
+            Thread.sleep(10);
+            angle+=1;
+            angle %=360;
             repaint();
           }
           catch(Exception ex){}
@@ -891,8 +1150,9 @@ public class AlignFrame extends GAlignFrame
          if (alignment != null)
          {
            AlignFrame af = new AlignFrame(new Alignment(alignment));
-           Desktop.addInternalFrame(af, getTitle().concat(" - ClustalW Alignment"),
-                                    700, 500); // JBPNote - is there a new window geom. property ?
+           Desktop.addInternalFrame(af, getTitle().concat(" - ClustalW Alignment"),NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);
+           af.clustalColour_actionPerformed(null);
+           af.clustalColour.setSelected(true);
          }
          else
            JOptionPane.showMessageDialog(Desktop.desktop, "Problem obtaining clustal alignment", "Web service error",
@@ -904,64 +1164,109 @@ public class AlignFrame extends GAlignFrame
          }catch(Exception ex){}
        }
 
-       public void paintComponent(Graphics g)
+       public void paintComponent(Graphics g1)
        {
+         Graphics2D g = (Graphics2D)g1;
          g.setColor(Color.white);
          g.fillRect(0,0,getWidth(), getHeight());
          if(image!=null)
          {
-           g.drawImage(image[imageIndex],10,10,this);
+
+           g.rotate (Math.toRadians(angle), 28, 28);
+
+           g.drawImage(image,10,10,this);
+           g.rotate (-Math.toRadians(angle), 28, 28 );
          }
          g.setFont(new Font("Arial", Font.BOLD, 12));
          g.setColor(Color.black);
-         g.drawString("Clustal Alignment Web Service running", 30,30);
+         g.drawString("Clustal Alignment Web Service running", 60,30);
        }
-
-
   }
+  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);
+        }
 
-  public void pdbTest_actionPerformed(ActionEvent e)
-  {
-   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;
+        JPredClient ct = new JPredClient(msa);
+      }
 
-   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();
-   }
+    }
+    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);
+      }
 
-  public void doKeyPressed(KeyEvent evt)
-  {
+    }
+  }
 
-    System.out.println(evt.getKeyChar());
-    if(evt.isControlDown() && evt.getKeyChar()=='f')
-      findMenuItem_actionPerformed(null);
+    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);
+          addTreeMenuItem(tp, title);
+        }
+      }
+      catch (Exception ex)
+      {
+        JOptionPane.showMessageDialog(Desktop.desktop,
+                                      "Problem reading tree file",
+                                      ex.getMessage(),
+                                      JOptionPane.WARNING_MESSAGE);
+        ex.printStackTrace();
+      }
+    }
   }
 
-
 }