X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=cfbd1863b34d8728153dcb1cf772e9e3376115af;hb=0c3e6a10ea83dc9d3591e14b1e55bc98a33dede9;hp=e4ed302efb3e345694029be10ffc855d8be8b12b;hpb=97173a9190084b142021b3822e383de600a2e8a2;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index e4ed302..cfbd186 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -13,7 +13,7 @@
  * GNU General Public License for more details.
  *
  * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
+ * along with this program; if not, write to the Free Softwarechang
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
 package jalview.gui;
@@ -27,7 +27,6 @@ import java.awt.datatransfer.*;
 import java.awt.event.*;
 import java.awt.print.*;
 import javax.swing.*;
-import javax.swing.event.*;
 
 import jalview.analysis.*;
 import jalview.datamodel.*;
@@ -43,15 +42,18 @@ import jalview.ws.*;
  * @version $Revision$
  */
 public class AlignFrame
-    extends GAlignFrame
+    extends GAlignFrame implements ClipboardOwner
 {
   /** DOCUMENT ME!! */
   public static final int NEW_WINDOW_WIDTH = 700;
 
   /** DOCUMENT ME!! */
   public static final int NEW_WINDOW_HEIGHT = 500;
-  final AlignmentPanel alignPanel;
-  final AlignViewport viewport;
+  AlignmentPanel alignPanel;
+  AlignViewport viewport;
+
+  Vector viewports = new Vector();
+  Vector alignPanels = new Vector();
 
   /** DOCUMENT ME!! */
   public String currentFileFormat = null;
@@ -59,6 +61,7 @@ public class AlignFrame
   Stack redoList = new Stack();
   private int treeCount = 0;
 
+
   /**
    * Creates a new AlignFrame object.
    *
@@ -67,41 +70,70 @@ public class AlignFrame
   public AlignFrame(AlignmentI al)
   {
     viewport = new AlignViewport(al);
+    viewports.add(viewport);
+
+
+    if(viewport.vconsensus==null)
+    {
+      //Out of memory calculating consensus.
+      BLOSUM62Colour.setEnabled(false);
+      PIDColour.setEnabled(false);
+      conservationMenuItem.setEnabled(false);
+      modifyConservation.setEnabled(false);
+      abovePIDThreshold.setEnabled(false);
+      modifyPID.setEnabled(false);
+    }
 
     alignPanel = new AlignmentPanel(this, viewport);
-    alignPanel.annotationPanel.adjustPanelHeight();
-    alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.
-        annotationPanel.getPreferredSize());
-    alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.
-        getPreferredSize());
-    alignPanel.setAnnotationVisible(viewport.getShowAnnotation());
+    alignPanels.add(alignPanel);
+
+    String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", "No sort");
+
+    if(sortby.equals("Id"))
+      sortIDMenuItem_actionPerformed(null);
+    else if(sortby.equals("Pairwise Identity"))
+      sortPairwiseMenuItem_actionPerformed(null);
+
+    tabbedPane.add(al.isNucleotide() ? "DNA":"Protein", alignPanel);
 
-    getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);
+    ///Dataset tab
+    /////////////////////////
 
-    addInternalFrameListener(new InternalFrameAdapter()
+    if(al.getDataset()==null)
     {
-      public void internalFrameActivated(InternalFrameEvent evt)
-      {
-        javax.swing.SwingUtilities.invokeLater(new Runnable()
-        {
-          public void run()
-          {
-            alignPanel.requestFocus();
-          }
-        });
-      }
-    });
+      al.setDataset(null);
+    }
+
+    AlignViewport ds = new AlignViewport(al.getDataset(), true);
+    AlignmentPanel dap = new AlignmentPanel(this, ds);
+    tabbedPane.add("Dataset", dap);
+    viewports.add(ds);
+    alignPanels.add(dap);
+    /////////////////////////
+
+
+    viewport.addPropertyChangeListener(new PropertyChangeListener()
+    {
+     public void propertyChange(PropertyChangeEvent evt)
+     {
+       if (evt.getPropertyName().equals("alignment"))
+       {
+         alignmentChanged();
+       }
+     }
+   });
+
+
+	if(Desktop.desktop!=null)
     addServiceListeners();
   }
 
   /* Set up intrinsic listeners for dynamically generated GUI bits. */
   private void addServiceListeners()
   {
-
-    final AlignFrame thisFrame = this;
     final java.beans.PropertyChangeListener thisListener;
     // Do this once to get current state
-    thisFrame.BuildWebServiceMenu();
+    BuildWebServiceMenu();
     Desktop.discoverer.addPropertyChangeListener(
         thisListener = new java.beans.PropertyChangeListener()
     {
@@ -111,7 +143,7 @@ public class AlignFrame
         if (evt.getPropertyName().equals("services"))
         {
           // System.out.println("Rebuilding web service menu");
-          thisFrame.BuildWebServiceMenu();
+          BuildWebServiceMenu();
         }
       }
     });
@@ -123,12 +155,23 @@ public class AlignFrame
       {
         // System.out.println("deregistering discoverer listener");
         Desktop.discoverer.removePropertyChangeListener(thisListener);
+        closeMenuItem_actionPerformed(null);
       }
       ;
     });
 
   }
 
+
+  /*
+   Added so Castor Mapping file can obtain Jalview Version
+  */
+  public String getVersion()
+  {
+    return  jalview.bin.Cache.getProperty("VERSION");
+  }
+
+
   /**
    * DOCUMENT ME!
    *
@@ -141,24 +184,28 @@ public class AlignFrame
     {
       BufferedReader in = new BufferedReader(new FileReader(file));
       SequenceI seq = null;
-      String line, text, token;
-      UserColourScheme ucs;
+      String line, type, desc, token;
+
       int index, start, end;
       StringTokenizer st;
-      SequenceGroup sg;
+      SequenceFeature sf;
+      FeatureRenderer fr = alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
+      int lineNo = 0;
       while ( (line = in.readLine()) != null)
       {
+        lineNo++;
         st = new StringTokenizer(line, "\t");
-        if (st.countTokens() != 6)
+        if (st.countTokens() == 2)
         {
-          System.out.println("Groups file " + file +
-                             " is invalid. Read help file.");
-          System.exit(1);
+          type = st.nextToken();
+          UserColourScheme ucs = new UserColourScheme(st.nextToken());
+          fr.setColour(type, ucs.findColour("A"));
+          continue;
         }
 
         while (st.hasMoreElements())
         {
-          text = st.nextToken();
+          desc = st.nextToken();
           token = st.nextToken();
           if (!token.equals("ID_NOT_SPECIFIED"))
           {
@@ -173,19 +220,39 @@ public class AlignFrame
 
           start = Integer.parseInt(st.nextToken());
           end = Integer.parseInt(st.nextToken());
-          ucs = new UserColourScheme(st.nextToken());
 
           seq = viewport.alignment.getSequenceAt(index);
           start = seq.findIndex(start) - 1;
           end = seq.findIndex(end) - 1;
 
-          sg = new SequenceGroup(text, ucs, true, true, false, start, end);
-          sg.addSequence(seq, true);
+          type = st.nextToken();
+
+          if (fr.getColour(type) == null)
+          {
+            // Probably the old style groups file
+            UserColourScheme ucs = new UserColourScheme(type);
+            fr.setColour(type, ucs.findColour("A"));
+          }
+
+
+          sf = new SequenceFeature(type, desc, "", start, end);
+
+          seq.addSequenceFeature(sf);
+
+
+         // sg = new SequenceGroup(text, ucs, true, true, false, start, end);
+         // sg.addSequence(seq, false);
+
+         // viewport.alignment.addGroup(sg);
 
-          viewport.alignment.addGroup(sg);
         }
       }
 
+      viewport.showSequenceFeatures = true;
+      ((Alignment)viewport.alignment).featuresAdded = true;
+
+      alignPanel.repaint();
+
     }
     catch (Exception ex)
     {
@@ -193,6 +260,12 @@ public class AlignFrame
     }
   }
 
+  public void fetchSequence_actionPerformed(ActionEvent e)
+  {
+    new SequenceFetcher(this);
+  }
+
+
   /**
    * DOCUMENT ME!
    *
@@ -222,7 +295,18 @@ public class AlignFrame
 
     if (value == JalviewFileChooser.APPROVE_OPTION)
     {
-      currentFileFormat = chooser.getSelectedFormat();
+        currentFileFormat = chooser.getSelectedFormat();
+
+        if (currentFileFormat == null)
+        {
+          JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                                                "You must select a file format before saving!",
+                                                "File format not specified",
+                                                JOptionPane.WARNING_MESSAGE);
+          value = chooser.showSaveDialog(this);
+          return;
+        }
+
       jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
                                     currentFileFormat);
 
@@ -252,7 +336,7 @@ public class AlignFrame
     }
     else
     {
-      String output = FormatAdapter.formatSequences(format,
+      String output = new FormatAdapter().formatSequences(format,
           viewport.getAlignment().
           getSequences());
       if (output == null)
@@ -264,7 +348,8 @@ public class AlignFrame
       {
         java.io.PrintWriter out = new java.io.PrintWriter(
             new java.io.FileWriter(file));
-        out.println(output);
+
+        out.print(output);
         out.close();
         return true;
       }
@@ -287,7 +372,7 @@ public class AlignFrame
     Desktop.addInternalFrame(cap,
                              "Alignment output - " + e.getActionCommand(), 600,
                              500);
-    cap.setText(FormatAdapter.formatSequences(e.getActionCommand(),
+    cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
                                               viewport.getAlignment().
                                               getSequences()));
   }
@@ -348,6 +433,7 @@ public class AlignFrame
   {
     try
     {
+      PaintRefresher.components.remove(viewport.alignment);
       this.setClosed(true);
     }
     catch (Exception ex)
@@ -409,6 +495,7 @@ public class AlignFrame
     redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,
                                   HistoryItem.HIDE));
     restoreHistoryItem(hi);
+    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
   }
 
   /**
@@ -421,9 +508,7 @@ public class AlignFrame
     HistoryItem hi = (HistoryItem) redoList.pop();
     restoreHistoryItem(hi);
     updateEditMenuBar();
-    viewport.updateConsensus();
-    alignPanel.repaint();
-    alignPanel.repaint();
+    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
   }
 
   // used by undo and redo
@@ -468,9 +553,6 @@ public class AlignFrame
 
     updateEditMenuBar();
 
-    viewport.updateConsensus();
-    viewport.updateConservation();
-    alignPanel.repaint();
     viewport.firePropertyChange("alignment", null,
                                 viewport.getAlignment().getSequences());
   }
@@ -537,6 +619,12 @@ public class AlignFrame
     alignPanel.repaint();
   }
 
+  public void lostOwnership(Clipboard clipboard, Transferable contents)
+  {
+    Desktop.jalviewClipboard = null;
+  }
+
+
   /**
    * DOCUMENT ME!
    *
@@ -552,9 +640,9 @@ public class AlignFrame
     SequenceGroup sg = viewport.getSelectionGroup();
 
     Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
-    StringBuffer buffer = new StringBuffer();
 
     Hashtable orderedSeqs = new Hashtable();
+    SequenceI[] seqs = new SequenceI[sg.getSize()];
 
     for (int i = 0; i < sg.getSize(); i++)
     {
@@ -584,6 +672,7 @@ public class AlignFrame
           index++;
         }
       }
+
       //FIND START RES
       //Returns residue following index if gap
       startRes = seq.findPosition(sg.getStartRes());
@@ -606,14 +695,22 @@ public class AlignFrame
         endRes += seq.getStart() - 1;
       }
 
-      buffer.append(seq.getName() + "\t" +
-                    startRes + "\t" +
-                    endRes + "\t" +
-                    seq.getSequence(sg.getStartRes(),
-                                    sg.getEndRes() + 1) + "\n");
+      seqs[i] = new Sequence(seq.getName(),
+                             seq.getSequence(sg.getStartRes(), sg.getEndRes() + 1),
+                             startRes,
+                             endRes);
+      seqs[i].setDescription(seq.getDescription());
+      seqs[i].setDBRef(seq.getDBRef());
+      seqs[i].setSequenceFeatures(seq.getSequenceFeatures());
+      seqs[i].setDatasetSequence(seq.getDatasetSequence());
+
     }
 
-    c.setContents(new StringSelection(buffer.toString()), null);
+    FastaFile ff = new FastaFile();
+    ff.addDBPrefix( viewport.showDBPrefix );
+    ff.addJVSuffix( viewport.showJVSuffix );
+    c.setContents(new StringSelection( ff.print(seqs)), this);
+    Desktop.jalviewClipboard = new Object[]{seqs,  viewport.alignment.getDataset()};
   }
 
   /**
@@ -656,33 +753,35 @@ public class AlignFrame
       }
 
       String str = (String) contents.getTransferData(DataFlavor.stringFlavor);
-      StringTokenizer st = new StringTokenizer(str);
-      ArrayList seqs = new ArrayList();
+      if(str.length()<1)
+        return;
 
-      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);
+      String format = IdentifyFile.Identify(str, "Paste");
+      SequenceI[] sequences;
 
-        if (!newAlignment)
-        {
-          viewport.alignment.addSequence(sequence);
-        }
-        else
-        {
-          seqs.add(sequence);
-        }
-      }
+     if(Desktop.jalviewClipboard!=null)
+     {
+       // The clipboard was filled from within Jalview, we must use the sequences
+       // And dataset from the copied alignment
+       sequences = (SequenceI[])Desktop.jalviewClipboard[0];
+     }
+     else
+     {
+       sequences = new FormatAdapter().readFile(str, "Paste", format);
+     }
 
       if (newAlignment)
       {
-        SequenceI[] newSeqs = new SequenceI[seqs.size()];
-        seqs.toArray(newSeqs);
 
-        AlignFrame af = new AlignFrame(new Alignment(newSeqs));
+        Alignment alignment = new Alignment(sequences);
+
+        if(Desktop.jalviewClipboard!=null)
+           alignment.setDataset( (Alignment)Desktop.jalviewClipboard[1] );
+        else
+           alignment.setDataset( null );
+
+
+        AlignFrame af = new AlignFrame(alignment);
         String newtitle = new String("Copied sequences");
 
         if (title.startsWith("Copied sequences"))
@@ -699,20 +798,37 @@ public class AlignFrame
       }
       else
       {
-        viewport.firePropertyChange("alignment", null,
-                                    viewport.getAlignment().getSequences());
+        //!newAlignment
+        for (int i = 0; i < sequences.length; i++)
+        {
+          viewport.alignment.addSequence(sequences[i]);
+          if(sequences[i].getDatasetSequence()==null)
+          {
+             ////////////////////////////
+            //Datset needs extension;
+            /////////////////////////////
+            Sequence ds = new Sequence(sequences[i].getName(),
+                                       AlignSeq.extractGaps("-. ", sequences[i].getSequence()),
+                                       sequences[i].getStart(),
+                                       sequences[i].getEnd());
+            sequences[i].setDatasetSequence(ds);
+            viewport.alignment.getDataset().addSequence(ds);
+
+
+          }
+
+        }
         viewport.setEndSeq(viewport.alignment.getHeight());
         viewport.alignment.getWidth();
-        viewport.updateConservation();
-        viewport.updateConsensus();
-        alignPanel.repaint();
+        viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
       }
     }
     catch (Exception ex)
     {
+        // could be anything being pasted in here
     }
 
-    // could be anything being pasted in here
+
   }
 
   /**
@@ -733,7 +849,6 @@ public class AlignFrame
    */
   protected void delete_actionPerformed(ActionEvent e)
   {
-    boolean seqsdeleted = false;
 
     if (viewport.getSelectionGroup() == null)
     {
@@ -765,7 +880,6 @@ public class AlignFrame
 
       if (seq.getSequence().length() < 1)
       {
-        seqsdeleted = true;
         viewport.getAlignment().deleteSequence(seq);
       }
       else
@@ -777,13 +891,10 @@ public class AlignFrame
     viewport.setSelectionGroup(null);
     viewport.alignment.deleteGroup(sg);
 
-    if (seqsdeleted)
-    {
-      viewport.firePropertyChange("alignment", null,
+    viewport.firePropertyChange("alignment", null,
                                   viewport.getAlignment().getSequences());
-    }
 
-    viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getHeight());
+
 
     if (viewport.getAlignment().getHeight() < 1)
     {
@@ -795,10 +906,6 @@ public class AlignFrame
       {
       }
     }
-
-    viewport.updateConservation();
-    viewport.updateConsensus();
-    alignPanel.repaint();
   }
 
   /**
@@ -907,7 +1014,7 @@ public class AlignFrame
         }
       }
 
-      alignPanel.repaint();
+      viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
     }
   }
 
@@ -945,7 +1052,7 @@ public class AlignFrame
         }
       }
 
-      alignPanel.repaint();
+      viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
     }
   }
 
@@ -959,10 +1066,16 @@ public class AlignFrame
     addHistoryItem(new HistoryItem("Remove Gapped Columns",
                                    viewport.alignment, HistoryItem.HIDE));
 
+    //This is to maintain viewport position on first residue
+    //of first sequence
+    SequenceI seq = viewport.alignment.getSequenceAt(0);
+    int startRes = seq.findPosition(viewport.startRes);
+
     viewport.getAlignment().removeGaps();
-    viewport.updateConservation();
-    viewport.updateConsensus();
-    alignPanel.repaint();
+
+    viewport.setStartRes(seq.findIndex(startRes)-1);
+
+   viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
   }
 
   /**
@@ -975,6 +1088,12 @@ public class AlignFrame
     addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
                                    HistoryItem.HIDE));
 
+    //This is to maintain viewport position on first residue
+    //of first sequence
+    SequenceI seq = viewport.alignment.getSequenceAt(0);
+    int startRes = seq.findPosition(viewport.startRes);
+
+
     SequenceI current;
     int jSize;
 
@@ -989,7 +1108,7 @@ public class AlignFrame
     {
       seqs = viewport.getSelectionGroup().sequences;
       start = viewport.getSelectionGroup().getStartRes();
-      end = viewport.getSelectionGroup().getEndRes();
+      end = viewport.getSelectionGroup().getEndRes()+1;
     }
     else
     {
@@ -1001,24 +1120,113 @@ public class AlignFrame
       current = (SequenceI) seqs.elementAt(i);
       jSize = current.getLength();
 
+      // Removing a range is much quicker than removing gaps
+      // one by one for long sequences
       int j = start;
+      int rangeStart=-1, rangeEnd=-1;
 
       do
       {
         if (jalview.util.Comparison.isGap(current.getCharAt(j)))
         {
-          current.deleteCharAt(j);
-          j--;
-          jSize--;
+          if(rangeStart==-1)
+           {
+             rangeStart = j;
+             rangeEnd = j+1;
+           }
+           else
+           {
+             rangeEnd++;
+           }
+           j++;
+        }
+        else
+        {
+          if(rangeStart>-1)
+          {
+            current.deleteChars(rangeStart, rangeEnd);
+            j-=rangeEnd-rangeStart;
+            jSize-=rangeEnd-rangeStart;
+            rangeStart = -1;
+            rangeEnd = -1;
+          }
+          else
+            j++;
         }
-        j++;
       }
       while (j < end && j < jSize);
+      if(rangeStart>-1)
+      {
+       current.deleteChars(rangeStart, rangeEnd);
+      }
     }
 
-    viewport.updateConservation();
-    viewport.updateConsensus();
-    alignPanel.repaint();
+    viewport.setStartRes(seq.findIndex(startRes)-1);
+
+    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+  }
+
+ public void alignmentChanged()
+ {
+   if(viewport.vconsensus!=null)
+   {
+     viewport.updateConsensus();
+     viewport.updateConservation();
+   }
+   resetAllColourSchemes();
+   if(alignPanel.overviewPanel!=null)
+     alignPanel.overviewPanel.updateOverviewImage();
+
+  Provenance prov = viewport.alignment.getProvenance();
+  if(prov == null)
+   {
+     prov = new Provenance();
+     viewport.alignment.setProvenance(prov);
+   }
+
+   prov.addEntry("Me",
+       "Edited in Jalview", new java.util.Date(), "myID");
+
+   alignPanel.repaint();
+ }
+
+  void resetAllColourSchemes()
+  {
+    ColourSchemeI cs = viewport.globalColourScheme;
+    if(cs!=null)
+    {
+      if (cs instanceof ClustalxColourScheme)
+      {
+        ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).
+            resetClustalX(viewport.alignment.getSequences(),
+                          viewport.alignment.getWidth());
+      }
+
+      cs.setConsensus(viewport.vconsensus);
+      if (cs.conservationApplied())
+      {
+        Alignment al = (Alignment) viewport.alignment;
+        Conservation c = new Conservation("All",
+                                          ResidueProperties.propHash, 3,
+                                          al.getSequences(), 0,
+                                          al.getWidth() - 1);
+        c.calculate();
+        c.verdict(false, viewport.ConsPercGaps);
+
+        cs.setConservation(c);
+      }
+    }
+
+    int s, sSize = viewport.alignment.getGroups().size();
+    for(s=0; s<sSize; s++)
+    {
+      SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
+      if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
+      {
+        ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());
+      }
+      sg.recalcConservation();
+    }
   }
 
   /**
@@ -1045,9 +1253,7 @@ public class AlignFrame
       }
     }
 
-    viewport.updateConservation();
-    viewport.updateConsensus();
-    alignPanel.repaint();
+    alignmentChanged();
   }
 
   /**
@@ -1071,7 +1277,7 @@ public class AlignFrame
    */
   public void font_actionPerformed(ActionEvent e)
   {
-    FontChooser fc = new FontChooser(alignPanel);
+    new FontChooser(alignPanel);
   }
 
   /**
@@ -1079,14 +1285,23 @@ public class AlignFrame
    *
    * @param e DOCUMENT ME!
    */
-  protected void fullSeqId_actionPerformed(ActionEvent e)
+  protected void seqLimit_actionPerformed(ActionEvent e)
   {
-    viewport.setShowFullId(fullSeqId.isSelected());
+    viewport.setShowJVSuffix(seqLimits.isSelected());
 
     alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());
     alignPanel.repaint();
   }
 
+  public void seqDBRef_actionPerformed(ActionEvent e)
+  {
+    viewport.setShowDBPrefix(seqDBRef.isSelected());
+
+    alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());
+    alignPanel.repaint();
+  }
+
+
   /**
    * DOCUMENT ME!
    *
@@ -1189,14 +1404,16 @@ public class AlignFrame
     viewport.showSequenceFeatures(sequenceFeatures.isSelected());
 
     if (viewport.showSequenceFeatures &&
-        ! ( (Alignment) viewport.alignment).featuresAdded)
+        ! ( (Alignment) viewport.alignment.getDataset()).featuresAdded)
     {
-      SequenceFeatureFetcher sft = new SequenceFeatureFetcher(viewport.
-          alignment,
+      System.out.println("new fetcher");
+      new SequenceFeatureFetcher(viewport.
+         alignment,
           alignPanel);
-      ( (Alignment) viewport.alignment).featuresAdded = true;
     }
 
+    featureSettings.setEnabled(true);
+
     alignPanel.repaint();
   }
 
@@ -1207,14 +1424,6 @@ public class AlignFrame
    */
   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
   {
-    if (annotationPanelMenuItem.isSelected() &&
-        viewport.getWrapAlignment())
-    {
-      annotationPanelMenuItem.setSelected(false);
-
-      return;
-    }
-
     viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
     alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
   }
@@ -1371,66 +1580,50 @@ public class AlignFrame
   {
     int threshold = 0;
 
-    if (viewport.getAbovePIDThreshold())
+    if(cs!=null)
     {
-      threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
-                                                 "Background");
-
-      if (cs instanceof ResidueColourScheme)
+      if (viewport.getAbovePIDThreshold())
       {
-        ( (ResidueColourScheme) cs).setThreshold(threshold,
-                                                 viewport.
-                                                 getIgnoreGapsConsensus());
+        threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
+                                                   "Background");
+
+        cs.setThreshold(threshold,
+                        viewport.getIgnoreGapsConsensus());
+
+        viewport.setGlobalColourScheme(cs);
       }
-      else if (cs instanceof ScoreColourScheme)
+      else
       {
-        ( (ScoreColourScheme) cs).setThreshold(threshold,
-                                               viewport.getIgnoreGapsConsensus());
+        cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
       }
 
-      viewport.setGlobalColourScheme(cs);
-    }
-    else if (cs instanceof ResidueColourScheme)
-    {
-      ( (ResidueColourScheme) cs).setThreshold(0,
-                                               viewport.getIgnoreGapsConsensus());
-    }
-    else if (cs instanceof ScoreColourScheme)
-    {
-      ( (ScoreColourScheme) cs).setThreshold(0, viewport.getIgnoreGapsConsensus());
-    }
-
-    if (viewport.getConservationSelected())
-    {
-      ConservationColourScheme ccs = null;
-
-      Alignment al = (Alignment) viewport.alignment;
-      Conservation c = new Conservation("All",
-                                        ResidueProperties.propHash, 3,
-                                        al.getSequences(), 0,
-                                        al.getWidth() - 1);
+      if (viewport.getConservationSelected())
+      {
 
-      c.calculate();
-      c.verdict(false, viewport.ConsPercGaps);
+        Alignment al = (Alignment) viewport.alignment;
+        Conservation c = new Conservation("All",
+                                          ResidueProperties.propHash, 3,
+                                          al.getSequences(), 0,
+                                          al.getWidth() - 1);
 
-      ccs = new ConservationColourScheme(c, cs);
+        c.calculate();
+        c.verdict(false, viewport.ConsPercGaps);
 
-      viewport.setGlobalColourScheme(ccs);
+        cs.setConservation(c);
 
-      ccs.inc = SliderPanel.setConservationSlider(alignPanel, ccs,
-                                                  "Background");
-    }
-    else
-    {
-      // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
-      if (cs != null)
+        cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
+            "Background"));
+      }
+      else
       {
-        cs.setConsensus(viewport.vconsensus);
+        cs.setConservation(null);
       }
 
-      viewport.setGlobalColourScheme(cs);
+      cs.setConsensus(viewport.vconsensus);
     }
 
+    viewport.setGlobalColourScheme(cs);
+
     if (viewport.getColourAppliesToAllGroups())
     {
       Vector groups = viewport.alignment.getGroups();
@@ -1442,8 +1635,10 @@ public class AlignFrame
         if (cs == null)
         {
           sg.cs = null;
+          continue;
         }
-        else if (cs instanceof ClustalxColourScheme)
+
+        if (cs instanceof ClustalxColourScheme)
         {
           sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
         }
@@ -1462,22 +1657,19 @@ public class AlignFrame
           }
         }
 
-        if (viewport.getAbovePIDThreshold())
+        if (viewport.getAbovePIDThreshold()
+            || cs instanceof PIDColourScheme
+            || cs instanceof Blosum62ColourScheme)
         {
-          if (sg.cs instanceof ResidueColourScheme)
-          {
-            ( (ResidueColourScheme) sg.cs).setThreshold(threshold,
+         sg.cs.setThreshold(threshold,
                 viewport.getIgnoreGapsConsensus());
-          }
-          else if (sg.cs instanceof ScoreColourScheme)
-          {
-            ( (ScoreColourScheme) sg.cs).setThreshold(threshold,
-                viewport.getIgnoreGapsConsensus());
-          }
 
           sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
               sg.getWidth()));
         }
+        else
+          sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
+
 
         if (viewport.getConservationSelected())
         {
@@ -1487,21 +1679,10 @@ public class AlignFrame
                                             viewport.alignment.getWidth() - 1);
           c.calculate();
           c.verdict(false, viewport.ConsPercGaps);
-
-          ConservationColourScheme ccs = new ConservationColourScheme(c,
-              sg.cs);
-
-          // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
-          ccs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
-                                                 sg.getWidth()));
-          sg.cs = ccs;
-        }
-        else if (cs != null)
-        {
-          // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
-          sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
-              sg.getWidth()));
+          sg.cs.setConservation(c);
         }
+        else
+          sg.cs.setConservation(null);
       }
     }
 
@@ -1520,7 +1701,7 @@ public class AlignFrame
    */
   protected void modifyPID_actionPerformed(ActionEvent e)
   {
-    if (viewport.getAbovePIDThreshold())
+    if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
     {
       SliderPanel.setPIDSliderSource(alignPanel,
                                      viewport.getGlobalColourScheme(),
@@ -1536,7 +1717,7 @@ public class AlignFrame
    */
   protected void modifyConservation_actionPerformed(ActionEvent e)
   {
-    if (viewport.getConservationSelected())
+    if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
     {
       SliderPanel.setConservationSlider(alignPanel,
                                         viewport.globalColourScheme,
@@ -1557,16 +1738,7 @@ public class AlignFrame
     viewport.setAbovePIDThreshold(false);
     abovePIDThreshold.setSelected(false);
 
-    ColourSchemeI cs = viewport.getGlobalColourScheme();
-
-    if (cs instanceof ConservationColourScheme)
-    {
-      changeColour( ( (ConservationColourScheme) cs).cs);
-    }
-    else
-    {
-      changeColour(cs);
-    }
+    changeColour(viewport.getGlobalColourScheme());
 
     modifyConservation_actionPerformed(null);
   }
@@ -1583,16 +1755,7 @@ public class AlignFrame
     conservationMenuItem.setSelected(false);
     viewport.setConservationSelected(false);
 
-    ColourSchemeI cs = viewport.getGlobalColourScheme();
-
-    if (cs instanceof ConservationColourScheme)
-    {
-      changeColour( ( (ConservationColourScheme) cs).cs);
-    }
-    else
-    {
-      changeColour(cs);
-    }
+    changeColour(viewport.getGlobalColourScheme());
 
     modifyPID_actionPerformed(null);
   }
@@ -1638,8 +1801,37 @@ public class AlignFrame
 
       while (userColours.hasMoreElements())
       {
-        JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
+        final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
             nextElement().toString());
+        radioItem.setName("USER_DEFINED");
+        radioItem.addMouseListener(new MouseAdapter()
+            {
+              public void mousePressed(MouseEvent evt)
+              {
+                if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
+                {
+                  radioItem.removeActionListener(radioItem.getActionListeners()[0]);
+
+                  int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
+                      "Remove from default list?",
+                      "Remove user defined colour",
+                      JOptionPane.YES_NO_OPTION);
+                  if(option == JOptionPane.YES_OPTION)
+                  {
+                    jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
+                    colourMenu.remove(radioItem);
+                  }
+                  else
+                    radioItem.addActionListener(new ActionListener()
+                    {
+                      public void actionPerformed(ActionEvent evt)
+                      {
+                        userDefinedColour_actionPerformed(evt);
+                      }
+                    });
+                }
+              }
+            });
         radioItem.addActionListener(new ActionListener()
         {
           public void actionPerformed(ActionEvent evt)
@@ -1647,6 +1839,7 @@ public class AlignFrame
             userDefinedColour_actionPerformed(evt);
           }
         });
+
         colourMenu.insert(radioItem, 15);
         colours.add(radioItem);
       }
@@ -1696,7 +1889,7 @@ public class AlignFrame
   {
     addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
                                    HistoryItem.SORT));
-    AlignmentSorter.sortByID(viewport.getAlignment());
+    AlignmentSorter.sortByID(viewport.getAlignment(), viewport.showDBPrefix);
     alignPanel.repaint();
   }
 
@@ -1772,21 +1965,7 @@ public class AlignFrame
       return;
     }
 
-    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);
-    }
+     new PCAPanel(viewport);
   }
 
   /**
@@ -1968,17 +2147,6 @@ public class AlignFrame
       }
       ;
     });
-    viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()
-    {
-      public void propertyChange(PropertyChangeEvent evt)
-      {
-        if (evt.getPropertyName().equals("alignment"))
-        {
-          treePanel.getTree().UpdatePlaceHolders( (Vector) evt.getNewValue());
-          treePanel.repaint();
-        }
-      }
-    });
   }
 
   /**
@@ -2125,6 +2293,11 @@ public class AlignFrame
     }
   }
 
+
+  public TreePanel ShowNewickTree(NewickFile nf, String title)
+  {
+    return ShowNewickTree(nf,title,600,500,4,5);
+  }
   /**
    * DOCUMENT ME!
    *
@@ -2133,7 +2306,7 @@ public class AlignFrame
    *
    * @return DOCUMENT ME!
    */
-  public TreePanel ShowNewickTree(NewickFile nf, String title)
+  public TreePanel ShowNewickTree(NewickFile nf, String title, int w,int h,int x, int y)
   {
     TreePanel tp = null;
 
@@ -2147,7 +2320,14 @@ public class AlignFrame
                            viewport.getAlignment().getSequences(), nf,
                            "FromFile",
                            title);
-        Desktop.addInternalFrame(tp, title, 600, 500);
+
+        tp.setSize(w,h);
+
+        if(x>0 && y>0)
+          tp.setLocation(x,y);
+
+
+        Desktop.addInternalFrame(tp, title, w, h);
         addTreeMenuItem(tp, title);
       }
     }
@@ -2188,11 +2368,11 @@ public class AlignFrame
    */
   public void BuildWebServiceMenu()
   {
-    if ( (Desktop.discoverer.services != null)
-        && (Desktop.discoverer.services.size() > 0))
+    if ( (Discoverer.services != null)
+        && (Discoverer.services.size() > 0))
     {
-      Vector msaws = (Vector) Desktop.discoverer.services.get("MsaWS");
-      Vector secstrpr = (Vector) Desktop.discoverer.services.get("SecStrPred");
+      Vector msaws = (Vector) Discoverer.services.get("MsaWS");
+      Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred");
       Vector wsmenu = new Vector();
       if (msaws != null)
       {
@@ -2208,8 +2388,8 @@ public class AlignFrame
             public void actionPerformed(ActionEvent e)
             {
               SequenceI[] msa = gatherSequencesForAlignment();
-              MsaWSClient ct = new jalview.ws.MsaWSClient(sh, title, msa,
-                  false, true);
+              new jalview.ws.MsaWSClient(sh, title, msa,
+                  false, true, viewport.getAlignment().getDataset());
 
             }
 
@@ -2225,8 +2405,8 @@ public class AlignFrame
               public void actionPerformed(ActionEvent e)
               {
                 SequenceI[] msa = gatherSequencesForAlignment();
-                MsaWSClient ct = new jalview.ws.MsaWSClient(sh, title, msa,
-                    true, true);
+                new jalview.ws.MsaWSClient(sh, title, msa,
+                    true, true, viewport.getAlignment().getDataset());
 
               }
 
@@ -2254,8 +2434,7 @@ public class AlignFrame
               if (msa.length == 1)
               {
                 // Single Sequence prediction
-                jalview.ws.JPredClient ct = new jalview.ws.JPredClient(sh,
-                    title, msa[0]);
+                new jalview.ws.JPredClient(sh,title, msa[0]);
               }
               else
               {
@@ -2288,4 +2467,144 @@ public class AlignFrame
     // TODO: group services by location as well as function.
   }
 
+  public void vamsasStore_actionPerformed(ActionEvent e)
+  {
+    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
+        getProperty("LAST_DIRECTORY"));
+
+    chooser.setFileView(new JalviewFileView());
+    chooser.setDialogTitle("Export to Vamsas file");
+    chooser.setToolTipText("Export");
+
+    int value = chooser.showSaveDialog(this);
+
+    if (value == JalviewFileChooser.APPROVE_OPTION)
+    {
+      jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
+      //vs.store(chooser.getSelectedFile().getAbsolutePath()   );
+      vs.storeJalview( chooser.getSelectedFile().getAbsolutePath(), this);
+    }
+  }
+
+  public void featureSettings_actionPerformed(ActionEvent e)
+  {
+    new FeatureSettings(viewport, alignPanel);
+  }
+
+
+
+public void showTranslation_actionPerformed(ActionEvent e)
+{
+
+  if(!viewport.alignment.isNucleotide())
+    return;
+
+  viewport.showTranslation(showTranslation.isSelected());
+
+  if(!viewport.alignment.isNucleotide())
+    return;
+
+  int s, sSize = viewport.alignment.getHeight();
+  SequenceI [] newSeq = new SequenceI[sSize];
+
+  int res, resSize;
+  StringBuffer protein;
+  SequenceI seq;
+  for(s=0; s<sSize; s++)
+  {
+    protein = new StringBuffer();
+    seq = (SequenceI)viewport.alignment.getSequenceAt(s);
+    resSize = seq.getLength();
+    for(res = 0; res < resSize; res+=3)
+    {
+      String codon = seq.getSequence(res, res+3);
+      codon = codon.replace('U', 'T');
+      String aa = ResidueProperties.codonTranslate(codon);
+      if(aa==null)
+        protein.append(viewport.getGapCharacter());
+      else if(aa.equals("STOP"))
+        protein.append("X");
+      else
+        protein.append( aa );
+    }
+    newSeq[s] = new Sequence(seq.getName(), protein.toString());
+  }
+
+
+  AlignmentI al = new Alignment(newSeq);
+  al.setDataset(null);
+
+
+  ////////////////////////////////
+  // Copy annotations across
+  jalview.datamodel.AlignmentAnnotation[] annotations
+      = viewport.alignment.getAlignmentAnnotation();
+  int a, aSize;
+  for (int i = 0; i < annotations.length; i++)
+  {
+
+    if (annotations[i].label.equals("Quality") ||
+        annotations[i].label.equals("Conservation") ||
+        annotations[i].label.equals("Consensus"))
+    {
+      continue;
+    }
+
+
+    aSize = viewport.alignment.getWidth()/3;
+    jalview.datamodel.Annotation [] anots =
+        new jalview.datamodel.Annotation[aSize];
+
+    for(a=0; a<viewport.alignment.getWidth(); a++)
+    {
+     if( annotations[i].annotations[a]==null
+      || annotations[i].annotations[a]==null)
+       continue;
+
+      anots[a/3] = new Annotation(
+     annotations[i].annotations[a].displayCharacter,
+     annotations[i].annotations[a].description,
+     annotations[i].annotations[a].secondaryStructure,
+     annotations[i].annotations[a].value,
+     annotations[i].annotations[a].colour);
+    }
+
+    jalview.datamodel.AlignmentAnnotation aa
+          = new jalview.datamodel.AlignmentAnnotation(annotations[i].label,
+       annotations[i].description, anots );
+     al.addAnnotation(aa);
+  }
+
+
+   // Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),
+    //                         NEW_WINDOW_WIDTH,
+     //                        NEW_WINDOW_HEIGHT);
+
+    AlignViewport newViewport = new AlignViewport(al);
+    AlignmentPanel ap = new AlignmentPanel(this, newViewport);
+    tabbedPane.add("Protein", ap);
+    viewports.add(newViewport);
+    alignPanels.add(ap);
+
+    ///Dataset tab
+  /////////////////////////
+
+    AlignViewport ds = new AlignViewport(al.getDataset());
+    ds.setDataset(true);
+    AlignmentPanel dap = new AlignmentPanel(this, ds);
+    tabbedPane.add("Dataset", dap);
+    viewports.add(ds);
+    alignPanels.add(dap);
+  /////////////////////////
+
+
+}
+
+public void tabSelected()
+{
+  int index = tabbedPane.getSelectedIndex();
+  viewport = (AlignViewport)viewports.elementAt(index);
+  alignPanel = (AlignmentPanel)alignPanels.elementAt(index);
+}
+
 }