X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=a73958d51307c7dfccdd5c0fbc516839b48e5769;hb=52fd681e0f239e20df19fd7560d4b999104ba222;hp=d2b5fc8f96d1d7e7adde0218d30740e22795fc9c;hpb=9ef055c3ca6a391e0a3fe3f42464f69fe6eb404e;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index d2b5fc8..a73958d 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -34,6 +34,7 @@ import jalview.io.*;
 import jalview.jbgui.*;
 import jalview.schemes.*;
 import jalview.ws.*;
+import java.awt.dnd.*;
 
 
 /**
@@ -43,7 +44,7 @@ import jalview.ws.*;
  * @version $Revision$
  */
 public class AlignFrame
-    extends GAlignFrame implements ClipboardOwner
+    extends GAlignFrame implements ClipboardOwner, DropTargetListener
 {
   /** DOCUMENT ME!! */
   public static final int NEW_WINDOW_WIDTH = 700;
@@ -53,9 +54,6 @@ public class AlignFrame
   AlignmentPanel alignPanel;
   AlignViewport viewport;
 
-  Vector viewports = new Vector();
-  Vector alignPanels = new Vector();
-
   /** DOCUMENT ME!! */
   public String currentFileFormat = null;
   Stack historyList = new Stack();
@@ -71,8 +69,8 @@ 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)
     {
@@ -86,7 +84,6 @@ public class AlignFrame
     }
 
     alignPanel = new AlignmentPanel(this, viewport);
-    alignPanels.add(alignPanel);
 
     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", "No sort");
 
@@ -172,18 +169,13 @@ public class AlignFrame
   public void setGUINucleotide(boolean nucleotide)
   {
     showTranslation.setVisible( nucleotide );
-    sequenceFeatures.setVisible(!nucleotide );
-    featureSettings.setVisible( !nucleotide );
+    //sequenceFeatures.setVisible(!nucleotide );
+    //featureSettings.setVisible( !nucleotide );
     conservationMenuItem.setVisible( !nucleotide );
     modifyConservation.setVisible(   !nucleotide );
 
-    //Deal with separators
     //Remember AlignFrame always starts as protein
-    if(nucleotide)
-    {
-      viewMenu.remove(viewMenu.getItemCount()-2);
-    }
-    else
+    if(!nucleotide)
     {
       calculateMenu.remove(calculateMenu.getItemCount()-2);
     }
@@ -198,100 +190,16 @@ public class AlignFrame
     return  jalview.bin.Cache.getProperty("VERSION");
   }
 
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param String DOCUMENT ME!
-   */
-
-  public void parseGroupsFile(String file)
+  public FeatureRenderer getFeatureRenderer()
   {
-    try
-    {
-      BufferedReader in = new BufferedReader(new FileReader(file));
-      SequenceI seq = null;
-      String line, type, desc, token;
-
-      int index, start, end;
-      StringTokenizer st;
-      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() == 2)
-        {
-          type = st.nextToken();
-          UserColourScheme ucs = new UserColourScheme(st.nextToken());
-          fr.setColour(type, ucs.findColour("A"));
-          continue;
-        }
-
-        while (st.hasMoreElements())
-        {
-          desc = 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());
-          }
-
-          start = Integer.parseInt(st.nextToken());
-          end = Integer.parseInt(st.nextToken());
-
-          seq = viewport.alignment.getSequenceAt(index);
-          start = seq.findIndex(start) - 1;
-          end = seq.findIndex(end) - 1;
-
-          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.getDatasetSequence().addSequenceFeature(sf);
-
-
-         // sg = new SequenceGroup(text, ucs, true, true, false, start, end);
-         // sg.addSequence(seq, false);
-
-         // viewport.alignment.addGroup(sg);
-
-        }
-      }
-
-      viewport.showSequenceFeatures = true;
-
-      alignPanel.repaint();
-
-    }
-    catch (Exception ex)
-    {
-      System.out.println("Error parsing groups file: " + ex);
-    }
+    return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
   }
 
+
   public void fetchSequence_actionPerformed(ActionEvent e)
   {
     new SequenceFetcher(this);
   }
-
-
   /**
    * DOCUMENT ME!
    *
@@ -355,7 +263,7 @@ public class AlignFrame
             java.io.File.separatorChar) + 1);
       }
 
-      Jalview2XML.SaveAlignment(this, file, shortName);
+      new Jalview2XML().SaveAlignment(this, file, shortName);
 
       // USE Jalview2XML to save this file
       return true;
@@ -452,6 +360,27 @@ public class AlignFrame
     thread.start();
   }
 
+  public void associatedData_actionPerformed(ActionEvent e)
+  {
+    // Pick the tree file
+    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
+        getProperty(
+            "LAST_DIRECTORY"));
+    chooser.setFileView(new JalviewFileView());
+    chooser.setDialogTitle("Load Jalview Annotations or Features File");
+    chooser.setToolTipText("Load Jalview Annotations / Features file");
+
+    int value = chooser.showOpenDialog(null);
+
+    if (value == JalviewFileChooser.APPROVE_OPTION)
+    {
+      String choice = chooser.getSelectedFile().getPath();
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
+      loadJalviewDataFile(choice);
+    }
+
+  }
+
   /**
    * DOCUMENT ME!
    *
@@ -542,42 +471,8 @@ public class AlignFrame
   // used by undo and redo
   void restoreHistoryItem(HistoryItem hi)
   {
-    if (hi.getType() == HistoryItem.SORT)
-    {
-      for (int i = 0; i < hi.getSequences().size(); i++)
-      {
-        viewport.alignment.getSequences().setElementAt(hi.getSequences()
-            .elementAt(i),
-            i);
-      }
-    }
-    else
-    {
-      for (int i = 0; i < hi.getSequences().size(); i++)
-      {
-        SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);
 
-        if (restore.getLength() == 0)
-        {
-          restore.setSequence(hi.getHidden().elementAt(i).toString());
-          viewport.alignment.getSequences().insertElementAt(restore,
-              hi.getAlignIndex(i));
-        }
-        else
-        {
-          restore.setSequence(hi.getHidden().elementAt(i).toString());
-        }
-      }
-
-      if (hi.getType() == HistoryItem.PASTE)
-      {
-        for (int i = viewport.alignment.getHeight() - 1;
-             i > (hi.getSequences().size() - 1); i--)
-        {
-          viewport.alignment.deleteSequence(i);
-        }
-      }
-    }
+    hi.restore();
 
     updateEditMenuBar();
 
@@ -783,7 +678,7 @@ public class AlignFrame
       if(str.length()<1)
         return;
 
-      String format = IdentifyFile.Identify(str, "Paste");
+      String format = new IdentifyFile().Identify(str, "Paste");
       SequenceI[] sequences;
 
      if(Desktop.jalviewClipboard!=null)
@@ -811,6 +706,11 @@ public class AlignFrame
         AlignFrame af = new AlignFrame(alignment);
         String newtitle = new String("Copied sequences");
 
+        //>>>This is a fix for the moment, until a better solution is found!!<<<
+        af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().transferSettings(
+            alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
+
+
         if (title.startsWith("Copied sequences"))
         {
           newtitle = title;
@@ -845,8 +745,16 @@ public class AlignFrame
             viewport.alignment.getDataset().addSequence(ds);
           }
           else
+          {
             newseq.setDatasetSequence(sequences[i].getDatasetSequence());
-
+            if(sequences[i].getDatasetSequence().getAnnotation()!=null)
+            {
+              for(int aa=0; aa<sequences[i].getDatasetSequence().getAnnotation().length; aa++)
+              {
+                viewport.alignment.addAnnotation(sequences[i].getDatasetSequence().getAnnotation()[aa]);
+              }
+            }
+          }
         }
         viewport.setEndSeq(viewport.alignment.getHeight());
         viewport.alignment.getWidth();
@@ -855,6 +763,8 @@ public class AlignFrame
     }
     catch (Exception ex)
     {
+      ex.printStackTrace();
+        System.out.println("Exception whilst pasting: "+ex);
         // could be anything being pasted in here
     }
 
@@ -885,24 +795,50 @@ public class AlignFrame
       return;
     }
 
-    addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
-                                   HistoryItem.HIDE));
 
     SequenceGroup sg = viewport.getSelectionGroup();
-    boolean allSequences = false;
-    if (sg.sequences.size() == viewport.alignment.getHeight())
+
+
+
+    //Jalview no longer allows deletion of residues.
+    //Check here whether any residues are in selection area
+   /* if( sg.getEndRes()-sg.getStartRes() < viewport.alignment.getWidth()-1)
     {
-      allSequences = true;
-    }
+      for (int i = 0; i < sg.sequences.size(); i++)
+      {
+        SequenceI seq = sg.getSequenceAt(i);
+        int j = sg.getStartRes();
+        do
+        {
+          if (!jalview.util.Comparison.isGap(seq.getCharAt(j)))
+          {
+            JOptionPane.showInternalMessageDialog(
+                Desktop.desktop, "Cannot delete residues from alignment!\n"
+                + "Try hiding columns instead.",
+                "Deletion of residues not permitted",
+                JOptionPane.WARNING_MESSAGE);
+
+            return;
+          }
+          j++;
+        }while(j<=sg.getEndRes());
+      }
+    }*/
+
+
+    addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
+                                   HistoryItem.HIDE));
+
 
     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 the cut affects all sequences, remove highlighted columns
-      if (allSequences)
+      if (sg.sequences.size() == viewport.alignment.getHeight())
       {
         viewport.getColumnSelection().removeElements(sg.getStartRes(),
             sg.getEndRes() + 1);
@@ -977,11 +913,16 @@ public class AlignFrame
    */
   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
   {
+    if(viewport.cursorMode)
+    {
+      alignPanel.seqPanel.keyboardNo1 = null;
+      alignPanel.seqPanel.keyboardNo2 = null;
+    }
     viewport.setSelectionGroup(null);
     viewport.getColumnSelection().clear();
     viewport.setSelectionGroup(null);
     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
-    alignPanel.annotationPanel.activeRes = null;
+    alignPanel.idPanel.idCanvas.searchResults = null;
     PaintRefresher.Refresh(null, viewport.alignment);
   }
 
@@ -1199,7 +1140,10 @@ public class AlignFrame
 
  public void alignmentChanged()
  {
-   if(viewport.vconsensus!=null)
+   if(viewport.padGaps)
+     viewport.getAlignment().padGaps();
+
+   if(viewport.vconsensus!=null && viewport.autoCalculateConsensus)
    {
      viewport.updateConsensus();
      viewport.updateConservation();
@@ -1208,6 +1152,8 @@ public class AlignFrame
    if(alignPanel.overviewPanel!=null)
      alignPanel.overviewPanel.updateOverviewImage();
 
+   viewport.alignment.adjustSequenceAnnotations();
+
    alignPanel.repaint();
  }
 
@@ -1260,20 +1206,9 @@ 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());
-      }
-    }
+    viewport.padGaps = padGapsMenuitem.isSelected();
 
+   // if (viewport.padGaps)
     alignmentChanged();
   }
 
@@ -1287,8 +1222,8 @@ public class AlignFrame
     JInternalFrame frame = new JInternalFrame();
     Finder finder = new Finder(viewport, alignPanel, frame);
     frame.setContentPane(finder);
-    Desktop.addInternalFrame(frame, "Find", 340, 110);
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
+    Desktop.addInternalFrame(frame, "Find", 340, 110);
   }
 
   /**
@@ -1301,6 +1236,14 @@ public class AlignFrame
     new FontChooser(alignPanel);
   }
 
+  public void smoothFont_actionPerformed(ActionEvent e)
+  {
+    viewport.antiAlias = smoothFont.isSelected();
+    alignPanel.annotationPanel.image = null;
+    alignPanel.repaint();
+  }
+
+
   /**
    * DOCUMENT ME!
    *
@@ -1407,25 +1350,37 @@ public class AlignFrame
     alignPanel.repaint();
   }
 
+  public void fetchSeqFeatures_actionPerformed(ActionEvent e)
+  {
+    if (!viewport.alignment.isNucleotide())
+    {
+      new SequenceFeatureFetcher(viewport.
+                                 alignment,
+                                 alignPanel);
+      viewport.setShowSequenceFeatures(true);
+      showSeqFeatures.setSelected(true);
+    }
+  }
+
+
+  public void featureSettings_actionPerformed(ActionEvent e)
+  {
+    new FeatureSettings(viewport, alignPanel);
+  }
+
   /**
    * DOCUMENT ME!
    *
    * @param evt DOCUMENT ME!
    */
-  public void sequenceFeatures_actionPerformed(ActionEvent evt)
+  public void showSeqFeatures_actionPerformed(ActionEvent evt)
   {
-    viewport.showSequenceFeatures(sequenceFeatures.isSelected());
-
-    if (viewport.showSequenceFeatures)
+    viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
+    alignPanel.repaint();
+    if (alignPanel.getOverviewPanel() != null)
     {
-      new SequenceFeatureFetcher(viewport.
-         alignment,
-          alignPanel);
+      alignPanel.getOverviewPanel().updateOverviewImage();
     }
-
-    featureSettings.setEnabled(true);
-
-    alignPanel.repaint();
   }
 
   /**
@@ -1572,6 +1527,12 @@ public class AlignFrame
     changeColour(new NucleotideColourScheme());
   }
 
+  public void annotationColour_actionPerformed(ActionEvent e)
+  {
+    new AnnotationColourChooser(viewport, alignPanel);
+  }
+
+
   /**
    * DOCUMENT ME!
    *
@@ -1979,6 +1940,17 @@ public class AlignFrame
      new PCAPanel(viewport);
   }
 
+
+  public void autoCalculate_actionPerformed(ActionEvent e)
+  {
+    viewport.autoCalculateConsensus = autoCalculate.isSelected();
+    if(viewport.autoCalculateConsensus)
+    {
+      alignmentChanged();
+    }
+  }
+
+
   /**
    * DOCUMENT ME!
    *
@@ -2028,7 +2000,7 @@ public class AlignFrame
    */
   void NewTreePanel(String type, String pwType, String title)
   {
-    final TreePanel tp;
+    TreePanel tp;
 
     if ( (viewport.getSelectionGroup() != null) &&
         (viewport.getSelectionGroup().getSize() > 3))
@@ -2080,7 +2052,6 @@ public class AlignFrame
     }
 
     addTreeMenuItem(tp, title);
-    viewport.setCurrentTree(tp.getTree());
 
     Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);
   }
@@ -2389,6 +2360,7 @@ public class AlignFrame
       {
         // Add any Multiple Sequence Alignment Services
         final JMenu msawsmenu = new JMenu("Alignment");
+        final AlignFrame af = this;
         for (int i = 0, j = msaws.size(); i < j; i++)
         {
           final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws.
@@ -2400,7 +2372,7 @@ public class AlignFrame
             {
               SequenceI[] msa = gatherSequencesForAlignment();
               new jalview.ws.MsaWSClient(sh, title, msa,
-                  false, true, viewport.getAlignment().getDataset());
+                  false, true, viewport.getAlignment().getDataset(), af);
 
             }
 
@@ -2417,7 +2389,7 @@ public class AlignFrame
               {
                 SequenceI[] msa = gatherSequencesForAlignment();
                 new jalview.ws.MsaWSClient(sh, title, msa,
-                    true, true, viewport.getAlignment().getDataset());
+                    true, true, viewport.getAlignment().getDataset(), af);
 
               }
 
@@ -2497,10 +2469,7 @@ public class AlignFrame
     }
   }*/
 
-  public void featureSettings_actionPerformed(ActionEvent e)
-  {
-    new FeatureSettings(viewport, alignPanel);
-  }
+
 
 
 
@@ -2517,6 +2486,8 @@ public void showTranslation_actionPerformed(ActionEvent e)
     protein = new StringBuffer();
     seq = AlignSeq.extractGaps("-. ", viewport.alignment.getSequenceAt(s).getSequence());
     resSize = seq.length();
+    resSize -= resSize%3;
+
     for(res = 0; res < resSize; res+=3)
     {
       String codon = seq.substring(res, res+3);
@@ -2542,42 +2513,42 @@ public void showTranslation_actionPerformed(ActionEvent e)
   jalview.datamodel.AlignmentAnnotation[] annotations
       = viewport.alignment.getAlignmentAnnotation();
   int a, aSize;
-  for (int i = 0; i < annotations.length; i++)
+  if(annotations!=null)
   {
-
-    if (annotations[i].label.equals("Quality") ||
-        annotations[i].label.equals("Conservation") ||
-        annotations[i].label.equals("Consensus"))
+    for (int i = 0; i < annotations.length; i++)
     {
-      continue;
-    }
-
+      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];
+      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;
+      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);
-    }
+        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
+      jalview.datamodel.AlignmentAnnotation aa
           = new jalview.datamodel.AlignmentAnnotation(annotations[i].label,
-       annotations[i].description, anots );
-     al.addAnnotation(aa);
+          annotations[i].description, anots);
+      al.addAnnotation(aa);
+    }
   }
 
-
     AlignFrame af = new AlignFrame(al);
     Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),
                              NEW_WINDOW_WIDTH,
@@ -2610,4 +2581,217 @@ public void showTranslation_actionPerformed(ActionEvent e)
   viewport = (AlignViewport)viewports.elementAt(index);
   alignPanel = (AlignmentPanel)alignPanels.elementAt(index);
  }*/
+
+/**
+ * DOCUMENT ME!
+ *
+ * @param String DOCUMENT ME!
+ */
+public boolean parseGroupsFile(String file)
+{
+    String line = null;
+    try
+    {
+      BufferedReader in = new BufferedReader(new FileReader(file));
+      SequenceI seq = null;
+      String type, desc, token;
+
+      int index, start, end;
+      StringTokenizer st;
+      SequenceFeature sf;
+      int lineNo = 0;
+      String featureGroup = null;
+      while ( (line = in.readLine()) != null)
+      {
+        lineNo++;
+        st = new StringTokenizer(line, "\t");
+        if (st.countTokens() == 2)
+        {
+          type = st.nextToken();
+          if (type.equalsIgnoreCase("startgroup"))
+          {
+            featureGroup = st.nextToken();
+          }
+          else if (type.equalsIgnoreCase("endgroup"))
+          {
+            //We should check whether this is the current group,
+            //but at present theres no way of showing more than 1 group
+            st.nextToken();
+            featureGroup = null;
+          }
+          else
+          {
+            UserColourScheme ucs = new UserColourScheme(st.nextToken());
+            alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(type,
+                ucs.findColour("A"));
+          }
+          continue;
+        }
+
+        while (st.hasMoreElements())
+        {
+          desc = 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());
+          }
+
+          start = Integer.parseInt(st.nextToken());
+          end = Integer.parseInt(st.nextToken());
+
+          seq = viewport.alignment.getSequenceAt(index);
+
+          type = st.nextToken();
+
+          if (alignPanel.seqPanel.seqCanvas.getFeatureRenderer().getColour(type) == null)
+          {
+            // Probably the old style groups file
+            UserColourScheme ucs = new UserColourScheme(type);
+            alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(type, ucs.findColour("A"));
+          }
+
+          sf = new SequenceFeature(type, desc, "", start, end, featureGroup);
+
+          seq.getDatasetSequence().addSequenceFeature(sf);
+        }
+      }
+    }
+    catch (Exception ex)
+    {
+      System.out.println(line);
+      ex.printStackTrace();
+      System.out.println("Error parsing groups file: " + ex +"\n"+line);
+      return false;
+    }
+
+    viewport.showSequenceFeatures = true;
+    showSeqFeatures.setSelected(true);
+    alignPanel.repaint();
+    return true;
+}
+
+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)
+    {
+      try
+      {
+
+        for (int i = 0; i < files.size(); i++)
+        {
+          loadJalviewDataFile(files.get(i).toString());
+        }
+      }
+      catch (Exception ex)
+      {
+        ex.printStackTrace();
+      }
+    }
+}
+
+  // This method will attempt to load a "dropped" file first by testing
+  // whether its and Annotation file, then features file. If both are
+  // false then the user may have dropped an alignment file onto this
+  // AlignFrame
+   public void loadJalviewDataFile(String file)
+  {
+    try{
+      boolean isAnnotation = new AnnotationReader().readAnnotationFile(viewport.
+          alignment, file);
+
+      if (!isAnnotation)
+      {
+        boolean isGroupsFile = parseGroupsFile(file);
+        if (!isGroupsFile)
+        {
+          String protocol = "File";
+          String format = new IdentifyFile().Identify(file, protocol);
+          SequenceI[] sequences = new FormatAdapter().readFile(file, protocol,
+              format);
+
+          FastaFile ff = new FastaFile();
+          Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
+          c.setContents(new StringSelection(ff.print(sequences)), this);
+
+          this.paste(false);
+        }
+      }
+
+      if (isAnnotation)
+      {
+        int height = alignPanel.annotationPanel.adjustPanelHeight();
+        alignPanel.annotationScroller.setPreferredSize(
+            new Dimension(alignPanel.annotationScroller.getWidth(),
+                          height));
+
+        alignPanel.annotationSpaceFillerHolder.setPreferredSize(new Dimension(
+            alignPanel.annotationSpaceFillerHolder.getWidth(),
+            height));
+
+        alignPanel.addNotify();
+      }
+
+    }catch(Exception ex)
+    {
+      ex.printStackTrace();
+    }
+  }
 }