X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=5685e42a13d28e2fa1db3a7df5b52ee5bdf2aa73;hb=c24071f7b9e6b70c94743214677871ae2dc88499;hp=9762258403bb4d2f6d08efd6937b499f150d52cb;hpb=ceb4fd3a8909862e45ac79b242ed112a15998d84;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 9762258..5685e42 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -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.*;
@@ -35,6 +34,8 @@ import jalview.io.*;
 import jalview.jbgui.*;
 import jalview.schemes.*;
 import jalview.ws.*;
+import java.awt.dnd.*;
+
 
 /**
  * DOCUMENT ME!
@@ -43,15 +44,18 @@ import jalview.ws.*;
  * @version $Revision$
  */
 public class AlignFrame
-    extends GAlignFrame
+    extends GAlignFrame implements ClipboardOwner, DropTargetListener
 {
   /** 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 +63,7 @@ public class AlignFrame
   Stack redoList = new Stack();
   private int treeCount = 0;
 
+
   /**
    * Creates a new AlignFrame object.
    *
@@ -67,10 +72,13 @@ public class AlignFrame
   public AlignFrame(AlignmentI al)
   {
     viewport = new AlignViewport(al);
+    viewports.add(viewport);
+
+    this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 
     if(viewport.vconsensus==null)
     {
-      //Out of memory caluclating consensus.
+      //Out of memory calculating consensus.
       BLOSUM62Colour.setEnabled(false);
       PIDColour.setEnabled(false);
       conservationMenuItem.setEnabled(false);
@@ -80,12 +88,7 @@ public class AlignFrame
     }
 
     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");
 
@@ -94,7 +97,26 @@ public class AlignFrame
     else if(sortby.equals("Pairwise Identity"))
       sortPairwiseMenuItem_actionPerformed(null);
 
-    getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);
+   // remove(tabbedPane);
+    getContentPane().add(alignPanel, BorderLayout.CENTER);
+
+
+
+  //  tabbedPane.add(al.isNucleotide() ? "DNA":"Protein", alignPanel);
+
+    ///Dataset tab
+    /////////////////////////
+    if(al.getDataset()==null)
+    {
+      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()
     {
@@ -108,7 +130,11 @@ public class AlignFrame
    });
 
 
+  if (Desktop.desktop != null)
+  {
     addServiceListeners();
+    setGUINucleotide(al.isNucleotide());
+  }
   }
 
   /* Set up intrinsic listeners for dynamically generated GUI bits. */
@@ -145,70 +171,42 @@ public class AlignFrame
 
   }
 
-  /**
-   * DOCUMENT ME!
-   *
-   * @param String DOCUMENT ME!
-   */
-
-  public void parseGroupsFile(String file)
+  public void setGUINucleotide(boolean nucleotide)
   {
-    try
-    {
-      BufferedReader in = new BufferedReader(new FileReader(file));
-      SequenceI seq = null;
-      String line, text, token;
-      UserColourScheme ucs;
-      int index, start, end;
-      StringTokenizer st;
-      SequenceGroup sg;
-      while ( (line = in.readLine()) != null)
-      {
-        st = new StringTokenizer(line, "\t");
-        if (st.countTokens() != 6)
-        {
-          System.out.println("Groups file " + file +
-                             " is invalid. Read help file.");
-          System.exit(1);
-        }
+    showTranslation.setVisible( nucleotide );
+    sequenceFeatures.setVisible(!nucleotide );
+    featureSettings.setVisible( !nucleotide );
+    conservationMenuItem.setVisible( !nucleotide );
+    modifyConservation.setVisible(   !nucleotide );
 
-        while (st.hasMoreElements())
-        {
-          text = st.nextToken();
-          token = st.nextToken();
-          if (!token.equals("ID_NOT_SPECIFIED"))
-          {
-            index = viewport.alignment.findIndex(viewport.alignment.findName(
-                token));
-            st.nextToken();
-          }
-          else
-          {
-            index = Integer.parseInt(st.nextToken());
-          }
+    //Deal with separators
+    //Remember AlignFrame always starts as protein
+    if(nucleotide)
+    {
+      viewMenu.remove(viewMenu.getItemCount()-2);
+    }
+    else
+    {
+      calculateMenu.remove(calculateMenu.getItemCount()-2);
+    }
+  }
 
-          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;
+  /*
+   Added so Castor Mapping file can obtain Jalview Version
+  */
+  public String getVersion()
+  {
+    return  jalview.bin.Cache.getProperty("VERSION");
+  }
 
-          sg = new SequenceGroup(text, ucs, true, true, false, start, end);
-          sg.addSequence(seq, true);
 
-          viewport.alignment.addGroup(sg);
-        }
-      }
-
-    }
-    catch (Exception ex)
-    {
-      System.out.println("Error parsing groups file: " + ex);
-    }
+  public void fetchSequence_actionPerformed(ActionEvent e)
+  {
+    new SequenceFetcher(this);
   }
 
+
   /**
    * DOCUMENT ME!
    *
@@ -238,7 +236,18 @@ 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);
 
@@ -268,7 +277,7 @@ public class AlignFrame
     }
     else
     {
-      String output = FormatAdapter.formatSequences(format,
+      String output = new FormatAdapter().formatSequences(format,
           viewport.getAlignment().
           getSequences());
       if (output == null)
@@ -304,7 +313,7 @@ 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()));
   }
@@ -316,7 +325,9 @@ public class AlignFrame
    */
   protected void htmlMenuItem_actionPerformed(ActionEvent e)
   {
-    new HTMLOutput(viewport);
+    new HTMLOutput(viewport,
+                   alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
+        alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
   }
 
   public void createImageMap(File file, String image)
@@ -551,6 +562,12 @@ public class AlignFrame
     alignPanel.repaint();
   }
 
+  public void lostOwnership(Clipboard clipboard, Transferable contents)
+  {
+    Desktop.jalviewClipboard = null;
+  }
+
+
   /**
    * DOCUMENT ME!
    *
@@ -560,7 +577,6 @@ public class AlignFrame
   {
     if (viewport.getSelectionGroup() == null)
     {
-      System.out.println("null here");
       return;
     }
 
@@ -569,7 +585,7 @@ public class AlignFrame
     Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
 
     Hashtable orderedSeqs = new Hashtable();
-    SequenceI [] seqs = new SequenceI[sg.getSize()];
+    SequenceI[] seqs = new SequenceI[sg.getSize()];
 
     for (int i = 0; i < sg.getSize(); i++)
     {
@@ -600,7 +616,6 @@ public class AlignFrame
         }
       }
 
-
       //FIND START RES
       //Returns residue following index if gap
       startRes = seq.findPosition(sg.getStartRes());
@@ -624,14 +639,20 @@ public class AlignFrame
       }
 
       seqs[i] = new Sequence(seq.getName(),
-                             seq.getSequence(sg.getStartRes(), sg.getEndRes()+1),
+                             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());
 
-    System.out.println("BLOBL"+FastaFile.print(seqs));
+    }
 
-    c.setContents(new StringSelection(FastaFile.print(seqs)), null);
+    FastaFile ff = new FastaFile();
+    ff.addJVSuffix( viewport.showJVSuffix );
+    c.setContents(new StringSelection( ff.print(seqs)), this);
+    Desktop.jalviewClipboard = new Object[]{seqs,  viewport.alignment.getDataset()};
   }
 
   /**
@@ -674,14 +695,35 @@ public class AlignFrame
       }
 
       String str = (String) contents.getTransferData(DataFlavor.stringFlavor);
+      if(str.length()<1)
+        return;
 
       String format = IdentifyFile.Identify(str, "Paste");
-      SequenceI[] sequences = FormatAdapter.readFile(str, "Paste", format);
+      SequenceI[] sequences;
 
+     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)
       {
-        AlignFrame af = new AlignFrame(new Alignment(sequences));
+
+        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"))
@@ -700,8 +742,27 @@ public class AlignFrame
       {
         //!newAlignment
         for (int i = 0; i < sequences.length; i++)
-          viewport.alignment.addSequence(sequences[i]);
+        {
+          Sequence newseq = new Sequence(sequences[i].getName(),
+              sequences[i].getSequence(), sequences[i].getStart(),
+              sequences[i].getEnd());
+          viewport.alignment.addSequence(newseq);
+          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());
+            newseq.setDatasetSequence(ds);
+            viewport.alignment.getDataset().addSequence(ds);
+          }
+          else
+            newseq.setDatasetSequence(sequences[i].getDatasetSequence());
 
+        }
         viewport.setEndSeq(viewport.alignment.getHeight());
         viewport.alignment.getWidth();
         viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
@@ -834,6 +895,7 @@ public class AlignFrame
     viewport.setSelectionGroup(null);
     viewport.getColumnSelection().clear();
     viewport.setSelectionGroup(null);
+    alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
     alignPanel.annotationPanel.activeRes = null;
     PaintRefresher.Refresh(null, viewport.alignment);
   }
@@ -1112,22 +1174,8 @@ public class AlignFrame
   {
     addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment,
                                    HistoryItem.HIDE));
-
-    SequenceI current;
-    int Width = viewport.getAlignment().getWidth();
-
-    for (int i = 0; i < viewport.getAlignment().getSequences().size();
-         i++)
-    {
-      current = viewport.getAlignment().getSequenceAt(i);
-
-      if (current.getLength() < Width)
-      {
-        current.insertCharAt(Width - 1, viewport.getGapCharacter());
-      }
-    }
-
-    alignmentChanged();
+    if (viewport.getAlignment().padGaps())
+      alignmentChanged();
   }
 
   /**
@@ -1151,22 +1199,31 @@ public class AlignFrame
    */
   public void font_actionPerformed(ActionEvent e)
   {
-    FontChooser fc = new FontChooser(alignPanel);
+    new FontChooser(alignPanel);
+  }
+
+  public void smoothFont_actionPerformed(ActionEvent e)
+  {
+    viewport.antiAlias = smoothFont.isSelected();
+    alignPanel.annotationPanel.image = null;
+    alignPanel.repaint();
   }
 
+
   /**
    * DOCUMENT ME!
    *
    * @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();
   }
 
+
   /**
    * DOCUMENT ME!
    *
@@ -1268,15 +1325,15 @@ public class AlignFrame
   {
     viewport.showSequenceFeatures(sequenceFeatures.isSelected());
 
-    if (viewport.showSequenceFeatures &&
-        ! ( (Alignment) viewport.alignment).featuresAdded)
+    if (viewport.showSequenceFeatures)
     {
-      SequenceFeatureFetcher sft = new SequenceFeatureFetcher(viewport.
-          alignment,
+      new SequenceFeatureFetcher(viewport.
+         alignment,
           alignPanel);
-      ( (Alignment) viewport.alignment).featuresAdded = true;
     }
 
+    featureSettings.setEnabled(true);
+
     alignPanel.repaint();
   }
 
@@ -1287,14 +1344,6 @@ 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());
   }
@@ -1432,6 +1481,12 @@ public class AlignFrame
     changeColour(new NucleotideColourScheme());
   }
 
+  public void annotationColour_actionPerformed(ActionEvent e)
+  {
+    new AnnotationColourChooser(viewport, alignPanel);
+  }
+
+
   /**
    * DOCUMENT ME!
    *
@@ -1626,8 +1681,6 @@ public class AlignFrame
     conservationMenuItem.setSelected(false);
     viewport.setConservationSelected(false);
 
-    ColourSchemeI cs = viewport.getGlobalColourScheme();
-
     changeColour(viewport.getGlobalColourScheme());
 
     modifyPID_actionPerformed(null);
@@ -1838,11 +1891,7 @@ public class AlignFrame
       return;
     }
 
-      PCAPanel pcaPanel = new PCAPanel(viewport, null);
-      JInternalFrame frame = new JInternalFrame();
-      frame.setContentPane(pcaPanel);
-      Desktop.addInternalFrame(frame, "Principal component analysis",
-                               400, 400);
+     new PCAPanel(viewport);
   }
 
   /**
@@ -2245,11 +2294,11 @@ 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)
       {
@@ -2265,8 +2314,8 @@ 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());
 
             }
 
@@ -2282,8 +2331,8 @@ 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());
 
               }
 
@@ -2311,8 +2360,7 @@ 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
               {
@@ -2345,4 +2393,239 @@ 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)
+{
+  int s, sSize = viewport.alignment.getHeight();
+  SequenceI [] newSeq = new SequenceI[sSize];
+
+  int res, resSize;
+  StringBuffer protein;
+  String seq;
+  for(s=0; s<sSize; s++)
+  {
+    protein = new StringBuffer();
+    seq = AlignSeq.extractGaps("-. ", viewport.alignment.getSequenceAt(s).getSequence());
+    resSize = seq.length();
+    for(res = 0; res < resSize; res+=3)
+    {
+      String codon = seq.substring(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(viewport.alignment.getSequenceAt(s).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);
+  }
+
+
+    AlignFrame af = new AlignFrame(al);
+    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);
+ }*/
+
+/**
+ * DOCUMENT ME!
+ *
+ * @param String DOCUMENT ME!
+ */
+public boolean parseGroupsFile(String file)
+{
+  AnnotationReader ar = new AnnotationReader();
+
+  if (ar.readGroupsFile(alignPanel.seqPanel.seqCanvas.getFeatureRenderer(),
+                        viewport.alignment, file))
+  {
+    viewport.showSequenceFeatures = true;
+    alignPanel.repaint();
+    return true;
+  }
+  else
+    return false;
+}
+
+public void dragEnter(DropTargetDragEvent evt)
+{}
+
+public void dragExit(DropTargetEvent evt)
+{}
+
+public void dragOver(DropTargetDragEvent evt)
+{}
+
+public void dropActionChanged(DropTargetDragEvent evt)
+{}
+
+public void drop(DropTargetDropEvent evt)
+{
+    Transferable t = evt.getTransferable();
+    java.util.List files = null;
+
+    try
+    {
+      DataFlavor uriListFlavor = new DataFlavor("text/uri-list;class=java.lang.String");
+      if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
+      {
+        //Works on Windows and MacOSX
+        evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
+        files = (java.util.List) t.getTransferData(DataFlavor.javaFileListFlavor);
+      }
+      else if (t.isDataFlavorSupported(uriListFlavor))
+      {
+        // This is used by Unix drag system
+        evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
+        String data = (String) t.getTransferData(uriListFlavor);
+        files = new java.util.ArrayList(1);
+        for (java.util.StringTokenizer st = new java.util.StringTokenizer(
+            data,
+            "\r\n");
+             st.hasMoreTokens(); )
+        {
+          String s = st.nextToken();
+          if (s.startsWith("#"))
+          {
+            // the line is a comment (as per the RFC 2483)
+            continue;
+          }
+
+          java.net.URI uri = new java.net.URI(s);
+          java.io.File file = new java.io.File(uri);
+          files.add(file);
+        }
+      }
+    }
+    catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+
+    if (files != null)
+    {
+      AnnotationReader ar = new AnnotationReader();
+      try
+      {
+        for (int i = 0; i < files.size(); i++)
+        {
+          String file = files.get(i).toString();
+          if(! ar.readAnnotationFile(viewport.alignment, file) )
+            parseGroupsFile(file);
+          else
+          {
+
+          }
+        }
+
+        alignPanel.annotationPanel.adjustPanelHeight();
+        alignPanel.annotationScroller.validate();
+        alignPanel.repaint();
+      }
+      catch (Exception ex)
+      {
+        ex.printStackTrace();
+      }
+    }
+}
+
 }