X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FCutAndPasteTransfer.java;h=8e758e6696f9a21e6be6417d3931d7024790f3b3;hb=3b4eda86f1f240a932cc778658dc1fbe56e9630d;hp=4a29568676ee176c63d982474b05324734a6cc91;hpb=c5f31d5aa4d907274169f576327785f69aa85e76;p=jalview.git

diff --git a/src/jalview/appletgui/CutAndPasteTransfer.java b/src/jalview/appletgui/CutAndPasteTransfer.java
old mode 100755
new mode 100644
index 4a29568..8e758e6
--- a/src/jalview/appletgui/CutAndPasteTransfer.java
+++ b/src/jalview/appletgui/CutAndPasteTransfer.java
@@ -1,13 +1,13 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
@@ -22,6 +22,8 @@ import java.awt.event.*;
 
 import jalview.datamodel.*;
 import jalview.io.*;
+import jalview.schemes.TCoffeeColourScheme;
+import jalview.util.MessageManager;
 
 public class CutAndPasteTransfer extends Panel implements ActionListener,
         MouseListener
@@ -67,7 +69,7 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
   public void setPDBImport(Sequence seq)
   {
     this.seq = seq;
-    accept.setLabel("Accept");
+    accept.setLabel(MessageManager.getString("action.accept"));
     addSequences.setVisible(false);
     pdbImport = true;
   }
@@ -75,14 +77,14 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
   public void setTreeImport()
   {
     treeImport = true;
-    accept.setLabel("Accept");
+    accept.setLabel(MessageManager.getString("action.accept"));
     addSequences.setVisible(false);
   }
 
   public void setAnnotationImport()
   {
     annotationImport = true;
-    accept.setLabel("Accept");
+    accept.setLabel(MessageManager.getString("action.accept"));
     addSequences.setVisible(false);
   }
 
@@ -150,25 +152,66 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
 
       } catch (Exception ex)
       {
-        // TODO: JAL-1102 - should have a warning message in dialog, not simply overwrite the broken input data with the exception
-        textarea.setText("Could not parse Newick file!\n" + ex);
+        // TODO: JAL-1102 - should have a warning message in dialog, not simply
+        // overwrite the broken input data with the exception
+        textarea.setText(MessageManager.formatMessage("label.could_not_parse_newick_file", new String[]{ex.getMessage()}));
         return;
       }
     }
     else if (annotationImport)
     {
-      if (new AnnotationFile().readAnnotationFile(
-              alignFrame.viewport.getAlignment(), textarea.getText(),
-              jalview.io.AppletFormatAdapter.PASTE))
+      TCoffeeScoreFile tcf = null;
+      try
       {
-        alignFrame.alignPanel.fontChanged();
-        alignFrame.alignPanel.setScrollValues(0, 0);
-
+        tcf = new TCoffeeScoreFile(textarea.getText(),
+                jalview.io.AppletFormatAdapter.PASTE);
+        if (tcf.isValid())
+        {
+          if (tcf.annotateAlignment(alignFrame.viewport.getAlignment(),
+                  true))
+          {
+            alignFrame.tcoffeeColour.setEnabled(true);
+            alignFrame.alignPanel.fontChanged();
+            alignFrame.changeColour(new TCoffeeColourScheme(
+                    alignFrame.viewport.getAlignment()));
+            alignFrame.statusBar
+                    .setText(MessageManager.getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
+          }
+          else
+          {
+            // file valid but didn't get added to alignment for some reason
+            alignFrame.statusBar.setText(MessageManager.formatMessage("label.failed_add_tcoffee_scores", new String[]{(tcf.getWarningMessage() != null ? tcf.getWarningMessage() : "")}));
+          }
+        }
+        else
+        {
+          tcf = null;
+        }
+      } catch (Exception x)
+      {
+        tcf = null;
       }
-      else
+      if (tcf == null)
       {
-        alignFrame.parseFeaturesFile(textarea.getText(),
-                jalview.io.AppletFormatAdapter.PASTE);
+        if (new AnnotationFile().readAnnotationFile(
+                alignFrame.viewport.getAlignment(), textarea.getText(),
+                jalview.io.AppletFormatAdapter.PASTE))
+        {
+          alignFrame.alignPanel.fontChanged();
+          alignFrame.alignPanel.setScrollValues(0, 0);
+          alignFrame.statusBar
+                  .setText("Successfully pasted annotation to alignment.");
+
+        }
+        else
+        {
+          if (!alignFrame.parseFeaturesFile(textarea.getText(),
+                  jalview.io.AppletFormatAdapter.PASTE))
+          {
+            alignFrame.statusBar
+                    .setText("Couldn't parse pasted text as a valid annotation, feature, GFF, or T-Coffee score file.");
+          }
+        }
       }
     }
     else if (alignFrame != null)
@@ -192,13 +235,13 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
         {
           AlignFrame af = new AlignFrame(al, alignFrame.viewport.applet,
                   "Cut & Paste input - " + format, false);
-          af.statusBar.setText("Successfully pasted alignment file");
+          af.statusBar.setText(MessageManager.getString("label.successfully_pasted_annotation_to_alignment"));
         }
         else
         {
           alignFrame.addSequences(al.getSequencesArray());
           alignFrame.statusBar
-                  .setText("Successfully pasted alignment file");
+                  .setText(MessageManager.getString("label.successfully_pasted_alignment_file"));
         }
       }
     }
@@ -242,7 +285,7 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
   private void jbInit() throws Exception
   {
     textarea.setFont(new java.awt.Font("Monospaced", Font.PLAIN, 10));
-    textarea.setText("Paste your alignment file here");
+    textarea.setText(MessageManager.getString("label.paste_your_alignment_file"));
     textarea.addMouseListener(this);
     this.setLayout(borderLayout1);
     accept.addActionListener(this);
@@ -257,7 +300,7 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
 
   public void mousePressed(MouseEvent evt)
   {
-    if (textarea.getText().startsWith("Paste your"))
+    if (textarea.getText().startsWith(MessageManager.getString("label.paste_your")))
     {
       textarea.setText("");
     }