JAL-1628 employ new AnnotationFile reader method to allow the current view's ColumnSe...

[jalview.git] / src / jalview / appletgui / CutAndPasteTransfer.java

diff --git a/src/jalview/appletgui/CutAndPasteTransfer.java b/src/jalview/appletgui/CutAndPasteTransfer.java
old mode 100755 (executable)
new mode 100644 (file)
index 4cc0f44..ce2a3ac
--- a/src/jalview/appletgui/CutAndPasteTransfer.java
+++ b/src/jalview/appletgui/CutAndPasteTransfer.java
@@ -1,19 +1,22 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * 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 2.8.2)
+ * 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;
 
@@ -23,6 +26,7 @@ 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
@@ -68,7 +72,7 @@ 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;
   }
@@ -76,14 +80,14 @@ 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);
   }
 
@@ -153,7 +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("Could not parse Newick file!\n" + ex);
+        textarea.setText(MessageManager.formatMessage(
+                "label.could_not_parse_newick_file", new String[]
+                { ex.getMessage() }));
         return;
       }
     }
@@ -174,14 +180,17 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
             alignFrame.changeColour(new TCoffeeColourScheme(
                     alignFrame.viewport.getAlignment()));
             alignFrame.statusBar
-                    .setText("Successfully pasted T-Coffee 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("Failed to add T-Coffee scores: "
-                    + (tcf.getWarningMessage() != null ? tcf
-                            .getWarningMessage() : ""));
+            alignFrame.statusBar.setText(MessageManager.formatMessage(
+                    "label.failed_add_tcoffee_scores",
+                    new String[]
+                    { (tcf.getWarningMessage() != null ? tcf
+                            .getWarningMessage() : "") }));
           }
         }
         else
@@ -194,14 +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
@@ -210,7 +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"));
           }
         }
       }
@@ -236,13 +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("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");
+          alignFrame.statusBar.setText(MessageManager
+                  .getString("label.successfully_pasted_alignment_file"));
         }
       }
     }
@@ -286,7 +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("Paste your alignment file here");
+    textarea.setText(MessageManager
+            .getString("label.paste_your_alignment_file"));
     textarea.addMouseListener(this);
     this.setLayout(borderLayout1);
     accept.addActionListener(this);
@@ -301,7 +315,8 @@ 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("");
     }