From ceb4fd3a8909862e45ac79b242ed112a15998d84 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 14 Sep 2005 15:42:08 +0000
Subject: [PATCH] Copy and paste uses FASTA format

---
 src/jalview/gui/AlignFrame.java |   47 +++++++++++++++------------------------
 src/jalview/jbgui/GFinder.java  |   20 ++++++++++++-----
 2 files changed, 32 insertions(+), 35 deletions(-)

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 7984991..9762258 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -560,15 +560,16 @@ public class AlignFrame
   {
     if (viewport.getSelectionGroup() == null)
     {
+      System.out.println("null here");
       return;
     }
 
     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++)
     {
@@ -598,6 +599,8 @@ public class AlignFrame
           index++;
         }
       }
+
+
       //FIND START RES
       //Returns residue following index if gap
       startRes = seq.findPosition(sg.getStartRes());
@@ -620,14 +623,15 @@ 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);
     }
 
-    c.setContents(new StringSelection(buffer.toString()), null);
+    System.out.println("BLOBL"+FastaFile.print(seqs));
+
+    c.setContents(new StringSelection(FastaFile.print(seqs)), null);
   }
 
   /**
@@ -670,33 +674,14 @@ public class AlignFrame
       }
 
       String str = (String) contents.getTransferData(DataFlavor.stringFlavor);
-      StringTokenizer st = new StringTokenizer(str);
-      ArrayList seqs = new ArrayList();
 
-      while (st.hasMoreElements())
-      {
-        String name = st.nextToken();
-        int start = Integer.parseInt(st.nextToken());
-        int end = Integer.parseInt(st.nextToken());
-        Sequence sequence = new Sequence(name, st.nextToken(), start,
-                                         end);
+      String format = IdentifyFile.Identify(str, "Paste");
+      SequenceI[] sequences = FormatAdapter.readFile(str, "Paste", format);
 
-        if (!newAlignment)
-        {
-          viewport.alignment.addSequence(sequence);
-        }
-        else
-        {
-          seqs.add(sequence);
-        }
-      }
 
       if (newAlignment)
       {
-        SequenceI[] newSeqs = new SequenceI[seqs.size()];
-        seqs.toArray(newSeqs);
-
-        AlignFrame af = new AlignFrame(new Alignment(newSeqs));
+        AlignFrame af = new AlignFrame(new Alignment(sequences));
         String newtitle = new String("Copied sequences");
 
         if (title.startsWith("Copied sequences"))
@@ -713,6 +698,10 @@ public class AlignFrame
       }
       else
       {
+        //!newAlignment
+        for (int i = 0; i < sequences.length; i++)
+          viewport.alignment.addSequence(sequences[i]);
+
         viewport.setEndSeq(viewport.alignment.getHeight());
         viewport.alignment.getWidth();
         viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
diff --git a/src/jalview/jbgui/GFinder.java b/src/jalview/jbgui/GFinder.java
index 32d2f24..8ece84d 100755
--- a/src/jalview/jbgui/GFinder.java
+++ b/src/jalview/jbgui/GFinder.java
@@ -22,6 +22,10 @@ import java.awt.*;
 import java.awt.event.*;
 import javax.swing.*;
 import javax.swing.event.*;
+import jalview.io.FormatAdapter;
+import jalview.datamodel.SequenceI;
+import java.awt.datatransfer.DataFlavor;
+import jalview.io.IdentifyFile;
 
 public class GFinder
     extends JPanel
@@ -155,17 +159,21 @@ public class GFinder
 
   public void textfield_caretUpdate(CaretEvent e)
   {
-    if (textfield.getText().indexOf("\t") > -1)
+    if (textfield.getText().indexOf(">") > -1)
     {
       SwingUtilities.invokeLater(new Runnable()
       {
         public void run()
         {
-          String text = textfield.getText();
-          text = text.substring(text.lastIndexOf("\t") + 1).trim();
-          text = jalview.analysis.AlignSeq.extractGaps(
-              jalview.util.Comparison.GapChars, text);
-          textfield.setText(text);
+          String str = textfield.getText();
+          SequenceI[] sequences = FormatAdapter.readFile(str, "Paste", "FASTA");
+          if(sequences!=null && sequences.length>0)
+          {
+            str = jalview.analysis.AlignSeq.extractGaps(
+                jalview.util.Comparison.GapChars, sequences[0].getSequence());
+
+            textfield.setText(str);
+          }
         }
       });
     }
-- 
1.7.10.2