X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FCutAndPasteTransfer.java;h=ce2a3acfd8855629b7e92e683ecb080b53e51d30;hb=770bcd6eedfcb6329d0e1310502a0a03c7279b18;hp=8e758e6696f9a21e6be6417d3931d7024790f3b3;hpb=87ea83af3e209a8c3a4b19f9530a9c05b4541148;p=jalview.git

diff --git a/src/jalview/appletgui/CutAndPasteTransfer.java b/src/jalview/appletgui/CutAndPasteTransfer.java
index 8e758e6..ce2a3ac 100644
--- a/src/jalview/appletgui/CutAndPasteTransfer.java
+++ b/src/jalview/appletgui/CutAndPasteTransfer.java
@@ -1,19 +1,22 @@
 /*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * 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.
+ * 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 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.appletgui;
 
@@ -154,7 +157,9 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
       {
         // 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()}));
+        textarea.setText(MessageManager.formatMessage(
+                "label.could_not_parse_newick_file", new String[]
+                { ex.getMessage() }));
         return;
       }
     }
@@ -175,12 +180,17 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
             alignFrame.changeColour(new TCoffeeColourScheme(
                     alignFrame.viewport.getAlignment()));
             alignFrame.statusBar
-                    .setText(MessageManager.getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
+                    .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() : "")}));
+            alignFrame.statusBar.setText(MessageManager.formatMessage(
+                    "label.failed_add_tcoffee_scores",
+                    new String[]
+                    { (tcf.getWarningMessage() != null ? tcf
+                            .getWarningMessage() : "") }));
           }
         }
         else
@@ -193,14 +203,15 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
       }
       if (tcf == null)
       {
-        if (new AnnotationFile().readAnnotationFile(
-                alignFrame.viewport.getAlignment(), textarea.getText(),
+        if (new AnnotationFile().annotateAlignmentView(alignFrame.viewport,
+                textarea.getText(),
                 jalview.io.AppletFormatAdapter.PASTE))
         {
           alignFrame.alignPanel.fontChanged();
           alignFrame.alignPanel.setScrollValues(0, 0);
           alignFrame.statusBar
-                  .setText("Successfully pasted annotation to alignment.");
+                  .setText(MessageManager
+                          .getString("label.successfully_pasted_annotation_to_alignment"));
 
         }
         else
@@ -209,7 +220,8 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
                   jalview.io.AppletFormatAdapter.PASTE))
           {
             alignFrame.statusBar
-                    .setText("Couldn't parse pasted text as a valid annotation, feature, GFF, or T-Coffee score file.");
+                    .setText(MessageManager
+                            .getString("label.couldnt_parse_pasted_text_as_valid_annotation_feature_GFF_tcoffee_file"));
           }
         }
       }
@@ -235,13 +247,15 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
         {
           AlignFrame af = new AlignFrame(al, alignFrame.viewport.applet,
                   "Cut & Paste input - " + format, false);
-          af.statusBar.setText(MessageManager.getString("label.successfully_pasted_annotation_to_alignment"));
+          af.statusBar
+                  .setText(MessageManager
+                          .getString("label.successfully_pasted_annotation_to_alignment"));
         }
         else
         {
           alignFrame.addSequences(al.getSequencesArray());
-          alignFrame.statusBar
-                  .setText(MessageManager.getString("label.successfully_pasted_alignment_file"));
+          alignFrame.statusBar.setText(MessageManager
+                  .getString("label.successfully_pasted_alignment_file"));
         }
       }
     }
@@ -285,7 +299,8 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
   private void jbInit() throws Exception
   {
     textarea.setFont(new java.awt.Font("Monospaced", Font.PLAIN, 10));
-    textarea.setText(MessageManager.getString("label.paste_your_alignment_file"));
+    textarea.setText(MessageManager
+            .getString("label.paste_your_alignment_file"));
     textarea.addMouseListener(this);
     this.setLayout(borderLayout1);
     accept.addActionListener(this);
@@ -300,7 +315,8 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
 
   public void mousePressed(MouseEvent evt)
   {
-    if (textarea.getText().startsWith(MessageManager.getString("label.paste_your")))
+    if (textarea.getText().startsWith(
+            MessageManager.getString("label.paste_your")))
     {
       textarea.setText("");
     }