JAL-1517 fix copyright for 2.8.2

[jalview.git] / src / jalview / gui / AlignFrame.java

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 664f92d..92316b3 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -6,14 +6,16 @@
  * 
  * 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.gui;
@@ -993,7 +995,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle("Save Alignment to file");
-    chooser.setToolTipText(MessageManager.getString("action.save"));\r
+    chooser.setToolTipText(MessageManager.getString("action.save"));
 
     int value = chooser.showSaveDialog(this);
 
@@ -1162,7 +1164,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               viewport.getAlignment(), omitHidden,
               viewport.getColumnSelection()));
       Desktop.addInternalFrame(cap,
-              MessageManager.formatMessage("label.alignment_output_command", new String[]{e.getActionCommand()}), 600, 500);\r
+              MessageManager.formatMessage("label.alignment_output_command", new String[]{e.getActionCommand()}), 600, 500);
     } catch (OutOfMemoryError oom)
     {
       new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
@@ -1258,8 +1260,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     JalviewFileChooser chooser = new JalviewFileChooser(
             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
     chooser.setFileView(new JalviewFileView());
-    chooser.setDialogTitle(MessageManager.getString("label.load_jalview_annotations"));\r
-    chooser.setToolTipText(MessageManager.getString("label.load_jalview_annotations"));\r
+    chooser.setDialogTitle(MessageManager.getString("label.load_jalview_annotations"));
+    chooser.setToolTipText(MessageManager.getString("label.load_jalview_annotations"));
 
     int value = chooser.showOpenDialog(null);
 
@@ -3018,7 +3020,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     JInternalFrame frame = new JInternalFrame();
     frame.getContentPane().add(new JScrollPane(editPane));
 
-    Desktop.instance.addInternalFrame(frame, MessageManager.formatMessage("label.alignment_properties", new String[]{getTitle()}), 500, 400);\r
+    Desktop.instance.addInternalFrame(frame, MessageManager.formatMessage("label.alignment_properties", new String[]{getTitle()}), 500, 400);
   }
 
   /**
@@ -3038,7 +3040,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     JInternalFrame frame = new JInternalFrame();
     OverviewPanel overview = new OverviewPanel(alignPanel);
     frame.setContentPane(overview);
-    Desktop.addInternalFrame(frame, MessageManager.formatMessage("label.overview_params", new String[]{this.getTitle()}),\r
+    Desktop.addInternalFrame(frame, MessageManager.formatMessage("label.overview_params", new String[]{this.getTitle()}),
             frame.getWidth(), frame.getHeight());
     frame.pack();
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
@@ -3421,7 +3423,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void userDefinedColour_actionPerformed(ActionEvent e)
   {
-    if (e.getActionCommand().equals(MessageManager.getString("action.user_defined")))\r
+    if (e.getActionCommand().equals(MessageManager.getString("action.user_defined")))
     {
       new UserDefinedColours(alignPanel, null);
     }
@@ -3630,7 +3632,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       JInternalFrame frame = new JInternalFrame();
       frame.setContentPane(new PairwiseAlignPanel(viewport));
-      Desktop.addInternalFrame(frame, MessageManager.getString("action.pairwise_alignment"), 600, 500);\r
+      Desktop.addInternalFrame(frame, MessageManager.getString("action.pairwise_alignment"), 600, 500);
     }
   }
 
@@ -4113,8 +4115,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     JalviewFileChooser chooser = new JalviewFileChooser(
             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
     chooser.setFileView(new JalviewFileView());
-    chooser.setDialogTitle(MessageManager.getString("label.select_newick_like_tree_file"));\r
-    chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));\r
+    chooser.setDialogTitle(MessageManager.getString("label.select_newick_like_tree_file"));
+    chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
 
     int value = chooser.showOpenDialog(null);
 
@@ -4637,7 +4639,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     else
     {
       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
-      Desktop.addInternalFrame(af, MessageManager.formatMessage("label.translation_of_params", new String[]{this.getTitle()}),\r
+      Desktop.addInternalFrame(af, MessageManager.formatMessage("label.translation_of_params", new String[]{this.getTitle()}),
               DEFAULT_WIDTH, DEFAULT_HEIGHT);
     }
   }
@@ -4680,7 +4682,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     else
     {
       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
-      Desktop.addInternalFrame(af, MessageManager.formatMessage("label.translation_of_params", new String[]{this.getTitle()}),\r
+      Desktop.addInternalFrame(af, MessageManager.formatMessage("label.translation_of_params", new String[]{this.getTitle()}),
               DEFAULT_WIDTH, DEFAULT_HEIGHT);
     }
   }
@@ -5193,8 +5195,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     // TODO We probably want to store a sequence database checklist in
     // preferences and have checkboxes.. rather than individual sources selected
     // here
-    final JMenu rfetch = new JMenu(MessageManager.getString("action.fetch_db_references"));\r
-    rfetch.setToolTipText(MessageManager.getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));\r
+    final JMenu rfetch = new JMenu(MessageManager.getString("action.fetch_db_references"));
+    rfetch.setToolTipText(MessageManager.getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
     webService.add(rfetch);
 
     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(MessageManager.getString("option.trim_retrieved_seqs"));
@@ -5208,8 +5210,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     };
     });
     rfetch.add(trimrs);
-    JMenuItem fetchr = new JMenuItem(MessageManager.getString("label.standard_databases"));\r
-    fetchr.setToolTipText(MessageManager.getString("label.fetch_embl_uniprot"));\r
+    JMenuItem fetchr = new JMenuItem(MessageManager.getString("label.standard_databases"));
+    fetchr.setToolTipText(MessageManager.getString("label.fetch_embl_uniprot"));
     fetchr.addActionListener(new ActionListener()
     {
 
@@ -5313,7 +5315,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                         .toArray(new DbSourceProxy[0]);
                 // fetch all entry
                 DbSourceProxy src = otherdb.get(0);
-                fetchr = new JMenuItem(MessageManager.formatMessage("label.fetch_all_param", new String[]{src.getDbSource()}));\r
+                fetchr = new JMenuItem(MessageManager.formatMessage("label.fetch_all_param", new String[]{src.getDbSource()}));
                 fetchr.addActionListener(new ActionListener()
                 {
                   @Override