From 3d32993c37812a293d61b8cb746ac8a4f246bed0 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 25 Jul 2006 09:38:52 +0000
Subject: [PATCH] FileLoader replaces paste when Dropping files

---
 src/jalview/gui/AlignFrame.java |   27 ++++++++++++++-------------
 1 file changed, 14 insertions(+), 13 deletions(-)

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 2ce8f06..5036a0b 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -37,7 +37,6 @@ import jalview.ws.*;
 import java.awt.dnd.*;
 import org.biojava.dasobert.eventmodel.*;
 
-
 /**
  * DOCUMENT ME!
  *
@@ -479,6 +478,7 @@ public class AlignFrame
     new AnnotationExporter().exportFeatures(alignPanel);
   }
 
+
   public void exportAnnotations_actionPerformed(ActionEvent e)
   {
     new AnnotationExporter().exportAnnotations(
@@ -767,6 +767,7 @@ public class AlignFrame
       String format = new IdentifyFile().Identify(str, "Paste");
       SequenceI[] sequences;
 
+
      if(Desktop.jalviewClipboard!=null)
      {
        // The clipboard was filled from within Jalview, we must use the sequences
@@ -782,32 +783,40 @@ public class AlignFrame
 
       if (newAlignment)
       {
+        System.out.println(format +" 2");
         alignment = new Alignment(sequences);
 
         if(Desktop.jalviewClipboard!=null)
            alignment.setDataset( (Alignment)Desktop.jalviewClipboard[1] );
         else
            alignment.setDataset( null );
+
       }
       else
       {
+        System.out.println(format +" 24");
         alignment = viewport.getAlignment();
 
         //!newAlignment
         for (int i = 0; i < sequences.length; i++)
         {
-
           Sequence newseq = new Sequence(sequences[i].getName(),
               sequences[i].getSequence(), sequences[i].getStart(),
               sequences[i].getEnd());
 
           alignment.addSequence(newseq);
         }
+
+
         viewport.setEndSeq(alignment.getHeight());
         alignment.getWidth();
         viewport.firePropertyChange("alignment", null, alignment.getSequences());
       }
 
+
+
+
+
       // Add any annotations attached to sequences
       for (int i = 0; i < sequences.length; i++)
      {
@@ -1422,7 +1431,7 @@ public class AlignFrame
     {
       viewport.hideSequence(seqs[i]);
     }
-    repaint();
+    alignPanel.repaint();
   }
 
   public void hideSelColumns_actionPerformed(ActionEvent e)
@@ -2842,16 +2851,8 @@ public void drop(DropTargetDropEvent evt)
                                                 AppletFormatAdapter.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)), Desktop.instance);
-
-          this.paste(false);
+          String format = new IdentifyFile().Identify(file, FormatAdapter.FILE);
+          new FileLoader().LoadFile(viewport, file, FormatAdapter.FILE, format);
         }
       }
       else
-- 
1.7.10.2