X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FCutAndPasteTransfer.java;h=ec31b0a7cfe3acee7e9048bdd5d7d22ee1a92db7;hb=aa213924876640ba82e866da5a750d9cdaa816d2;hp=6f5498d19647c6d10682f68c01b86f93e9adeddb;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git

diff --git a/src/jalview/appletgui/CutAndPasteTransfer.java b/src/jalview/appletgui/CutAndPasteTransfer.java
index 6f5498d..ec31b0a 100755
--- a/src/jalview/appletgui/CutAndPasteTransfer.java
+++ b/src/jalview/appletgui/CutAndPasteTransfer.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
  * 
- * This program 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 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
  * 
- * This program 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.
+ * 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.
  * 
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * 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/>.
  */
 package jalview.appletgui;
 
@@ -23,6 +22,7 @@ import java.awt.event.*;
 
 import jalview.datamodel.*;
 import jalview.io.*;
+import jalview.schemes.TCoffeeColourScheme;
 
 public class CutAndPasteTransfer extends Panel implements ActionListener,
         MouseListener
@@ -140,8 +140,8 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
     {
       try
       {
-        jalview.io.NewickFile fin = new jalview.io.NewickFile(textarea
-                .getText(), "Paste");
+        jalview.io.NewickFile fin = new jalview.io.NewickFile(
+                textarea.getText(), "Paste");
 
         fin.parse();
         if (fin.getTree() != null)
@@ -151,24 +151,64 @@ 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);
         return;
       }
     }
     else if (annotationImport)
     {
-      if (new AnnotationFile().readAnnotationFile(
-              alignFrame.viewport.alignment, 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("Successfully pasted T-Coffee 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():""));
+          }
+        }
+        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)
@@ -197,10 +237,13 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
         else
         {
           alignFrame.addSequences(al.getSequencesArray());
+          alignFrame.statusBar
+                  .setText("Successfully pasted alignment file");
         }
       }
     }
-
+    // TODO: dialog should indicate if data was parsed correctly or not - see
+    // JAL-1102
     if (this.getParent() instanceof Frame)
     {
       ((Frame) this.getParent()).setVisible(false);