JAL-1517 source formatting

[jalview.git] / src / jalview / jbgui / GAlignFrame.java

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 24e3af1..d3154c7 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.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.jbgui;
 
@@ -140,6 +143,8 @@ public class GAlignFrame extends JInternalFrame
 
   protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
 
+  protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
+
   // protected JRadioButtonMenuItem covariationColour = new
   // JRadioButtonMenuItem();
 
@@ -182,8 +187,9 @@ public class GAlignFrame extends JInternalFrame
   public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
 
   JMenuItem deleteGroups = new JMenuItem();
-  
+
   JMenuItem createGroup = new JMenuItem();
+
   JMenuItem unGroup = new JMenuItem();
 
   JMenuItem delete = new JMenuItem();
@@ -242,6 +248,8 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenuItem extractScores = new JMenuItem();
 
+  protected JMenuItem expandAlignment = new JMenuItem();
+
   protected JMenu showProducts = new JMenu();
 
   public JMenuItem openFeatureSettings = new JMenuItem();
@@ -408,8 +416,10 @@ public class GAlignFrame extends JInternalFrame
 
               int option = JOptionPane.showInternalConfirmDialog(
                       jalview.gui.Desktop.desktop,
-                      MessageManager.getString("label.remove_from_default_list"),
-                      MessageManager.getString("label.remove_user_defined_colour"),
+                      MessageManager
+                              .getString("label.remove_from_default_list"),
+                      MessageManager
+                              .getString("label.remove_user_defined_colour"),
                       JOptionPane.YES_NO_OPTION);
               if (option == JOptionPane.YES_OPTION)
               {
@@ -457,7 +467,7 @@ public class GAlignFrame extends JInternalFrame
     colours.add(purinePyrimidineColour);
     // colours.add(covariationColour);
     colours.add(tcoffeeColour);
-
+    colours.add(RNAInteractionColour);
     setColourSelected(jalview.bin.Cache
             .getDefault("DEFAULT_COLOUR", "None"));
 
@@ -535,6 +545,11 @@ public class GAlignFrame extends JInternalFrame
         purinePyrimidineColour.setSelected(true);
 
         break;
+
+      case ColourSchemeProperty.RNAINTERACTION:
+        RNAInteractionColour.setSelected(true);
+
+        break;
       /*
        * case ColourSchemeProperty.COVARIATION:
        * covariationColour.setSelected(true);
@@ -586,7 +601,8 @@ public class GAlignFrame extends JInternalFrame
     colourMenu.setText(MessageManager.getString("action.colour"));
     calculateMenu.setText(MessageManager.getString("action.calculate"));
     webService.setText(MessageManager.getString("action.web_service"));
-    selectAllSequenceMenuItem.setText(MessageManager.getString("action.select_all"));
+    selectAllSequenceMenuItem.setText(MessageManager
+            .getString("action.select_all"));
     selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
             .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
@@ -598,7 +614,8 @@ public class GAlignFrame extends JInternalFrame
                 selectAllSequenceMenuItem_actionPerformed(e);
               }
             });
-    deselectAllSequenceMenuItem.setText(MessageManager.getString("action.deselect_all"));
+    deselectAllSequenceMenuItem.setText(MessageManager
+            .getString("action.deselect_all"));
     deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
             .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
     deselectAllSequenceMenuItem
@@ -609,7 +626,8 @@ public class GAlignFrame extends JInternalFrame
                 deselectAllSequenceMenuItem_actionPerformed(e);
               }
             });
-    invertSequenceMenuItem.setText(MessageManager.getString("action.invert_sequence_selection"));
+    invertSequenceMenuItem.setText(MessageManager
+            .getString("action.invert_sequence_selection"));
     invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
             .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
@@ -621,7 +639,8 @@ public class GAlignFrame extends JInternalFrame
                 invertSequenceMenuItem_actionPerformed(e);
               }
             });
-    grpsFromSelection.setText(MessageManager.getString("action.make_groups_selection"));
+    grpsFromSelection.setText(MessageManager
+            .getString("action.make_groups_selection"));
     grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -629,8 +648,20 @@ public class GAlignFrame extends JInternalFrame
         makeGrpsFromSelection_actionPerformed(e);
       }
     });
-
-    remove2LeftMenuItem.setText(MessageManager.getString("action.remove_left"));
+    expandAlignment.setText(MessageManager
+            .getString("action.view_flanking_regions"));
+    expandAlignment.setToolTipText(MessageManager
+            .getString("label.view_flanking_regions"));
+    expandAlignment.addActionListener(new java.awt.event.ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        expand_newalign(e);
+      }
+    });
+    remove2LeftMenuItem.setText(MessageManager
+            .getString("action.remove_left"));
     remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
             java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
                     .getMenuShortcutKeyMask(), false));
@@ -642,7 +673,8 @@ public class GAlignFrame extends JInternalFrame
                 remove2LeftMenuItem_actionPerformed(e);
               }
             });
-    remove2RightMenuItem.setText(MessageManager.getString("action.remove_right"));
+    remove2RightMenuItem.setText(MessageManager
+            .getString("action.remove_right"));
     remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
             java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
                     .getMenuShortcutKeyMask(), false));
@@ -654,7 +686,8 @@ public class GAlignFrame extends JInternalFrame
                 remove2RightMenuItem_actionPerformed(e);
               }
             });
-    removeGappedColumnMenuItem.setText(MessageManager.getString("action.remove_empty_columns"));
+    removeGappedColumnMenuItem.setText(MessageManager
+            .getString("action.remove_empty_columns"));
     removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
             .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
@@ -666,7 +699,8 @@ public class GAlignFrame extends JInternalFrame
                 removeGappedColumnMenuItem_actionPerformed(e);
               }
             });
-    removeAllGapsMenuItem.setText(MessageManager.getString("action.remove_all_gaps"));
+    removeAllGapsMenuItem.setText(MessageManager
+            .getString("action.remove_all_gaps"));
     removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
             .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
                     .getDefaultToolkit().getMenuShortcutKeyMask()
@@ -679,7 +713,8 @@ public class GAlignFrame extends JInternalFrame
                 removeAllGapsMenuItem_actionPerformed(e);
               }
             });
-    justifyLeftMenuItem.setText(MessageManager.getString("action.left_justify_alignment"));
+    justifyLeftMenuItem.setText(MessageManager
+            .getString("action.left_justify_alignment"));
     justifyLeftMenuItem
             .addActionListener(new java.awt.event.ActionListener()
             {
@@ -688,7 +723,8 @@ public class GAlignFrame extends JInternalFrame
                 justifyLeftMenuItem_actionPerformed(e);
               }
             });
-    justifyRightMenuItem.setText(MessageManager.getString("action.right_justify_alignment"));
+    justifyRightMenuItem.setText(MessageManager
+            .getString("action.right_justify_alignment"));
     justifyRightMenuItem
             .addActionListener(new java.awt.event.ActionListener()
             {
@@ -715,7 +751,8 @@ public class GAlignFrame extends JInternalFrame
         viewTextMenuItem_actionPerformed(e);
       }
     });
-    showNonconservedMenuItem.setText(MessageManager.getString("label.show_non_conversed"));
+    showNonconservedMenuItem.setText(MessageManager
+            .getString("label.show_non_conversed"));
     showNonconservedMenuItem.setState(false);
     showNonconservedMenuItem
             .addActionListener(new java.awt.event.ActionListener()
@@ -725,7 +762,8 @@ public class GAlignFrame extends JInternalFrame
                 showUnconservedMenuItem_actionPerformed(e);
               }
             });
-    sortPairwiseMenuItem.setText(MessageManager.getString("action.by_pairwise_id"));
+    sortPairwiseMenuItem.setText(MessageManager
+            .getString("action.by_pairwise_id"));
     sortPairwiseMenuItem
             .addActionListener(new java.awt.event.ActionListener()
             {
@@ -742,7 +780,8 @@ public class GAlignFrame extends JInternalFrame
         sortIDMenuItem_actionPerformed(e);
       }
     });
-    sortLengthMenuItem.setText(MessageManager.getString("action.by_length"));
+    sortLengthMenuItem
+            .setText(MessageManager.getString("action.by_length"));
     sortLengthMenuItem
             .addActionListener(new java.awt.event.ActionListener()
             {
@@ -759,7 +798,8 @@ public class GAlignFrame extends JInternalFrame
         sortGroupMenuItem_actionPerformed(e);
       }
     });
-    removeRedundancyMenuItem.setText(MessageManager.getString("action.remove_redundancy"));
+    removeRedundancyMenuItem.setText(MessageManager
+            .getString("action.remove_redundancy"));
     removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
             .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
@@ -771,7 +811,8 @@ public class GAlignFrame extends JInternalFrame
                 removeRedundancyMenuItem_actionPerformed(e);
               }
             });
-    pairwiseAlignmentMenuItem.setText(MessageManager.getString("action.pairwise_alignment"));
+    pairwiseAlignmentMenuItem.setText(MessageManager
+            .getString("action.pairwise_alignment"));
     pairwiseAlignmentMenuItem
             .addActionListener(new java.awt.event.ActionListener()
             {
@@ -780,7 +821,8 @@ public class GAlignFrame extends JInternalFrame
                 pairwiseAlignmentMenuItem_actionPerformed(e);
               }
             });
-    PCAMenuItem.setText(MessageManager.getString("label.principal_component_analysis"));
+    PCAMenuItem.setText(MessageManager
+            .getString("label.principal_component_analysis"));
     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -788,8 +830,8 @@ public class GAlignFrame extends JInternalFrame
         PCAMenuItem_actionPerformed(e);
       }
     });
-    averageDistanceTreeMenuItem
-            .setText(MessageManager.getString("label.average_distance_identity"));
+    averageDistanceTreeMenuItem.setText(MessageManager
+            .getString("label.average_distance_identity"));
     averageDistanceTreeMenuItem
             .addActionListener(new java.awt.event.ActionListener()
             {
@@ -798,7 +840,8 @@ public class GAlignFrame extends JInternalFrame
                 averageDistanceTreeMenuItem_actionPerformed(e);
               }
             });
-    neighbourTreeMenuItem.setText(MessageManager.getString("label.neighbour_joining_identity"));
+    neighbourTreeMenuItem.setText(MessageManager
+            .getString("label.neighbour_joining_identity"));
     neighbourTreeMenuItem
             .addActionListener(new java.awt.event.ActionListener()
             {
@@ -813,7 +856,8 @@ public class GAlignFrame extends JInternalFrame
     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
     statusBar.setText(MessageManager.getString("label.status_bar"));
-    outputTextboxMenu.setText(MessageManager.getString("label.out_to_textbox"));
+    outputTextboxMenu.setText(MessageManager
+            .getString("label.out_to_textbox"));
     clustalColour.setText(MessageManager.getString("label.clustalx"));
 
     clustalColour.addActionListener(new java.awt.event.ActionListener()
@@ -839,7 +883,8 @@ public class GAlignFrame extends JInternalFrame
         taylorColour_actionPerformed(e);
       }
     });
-    hydrophobicityColour.setText(MessageManager.getString("label.hydrophobicity"));
+    hydrophobicityColour.setText(MessageManager
+            .getString("label.hydrophobicity"));
     hydrophobicityColour
             .addActionListener(new java.awt.event.ActionListener()
             {
@@ -856,7 +901,8 @@ public class GAlignFrame extends JInternalFrame
         helixColour_actionPerformed(e);
       }
     });
-    strandColour.setText(MessageManager.getString("label.strand_propensity"));
+    strandColour.setText(MessageManager
+            .getString("label.strand_propensity"));
     strandColour.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -864,7 +910,7 @@ public class GAlignFrame extends JInternalFrame
         strandColour_actionPerformed(e);
       }
     });
-    turnColour.setText(MessageManager.getString("Turn Propensity"));
+    turnColour.setText(MessageManager.getString("label.turn_propensity"));
     turnColour.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -872,7 +918,7 @@ public class GAlignFrame extends JInternalFrame
         turnColour_actionPerformed(e);
       }
     });
-    buriedColour.setText(MessageManager.getString("Buried Index"));
+    buriedColour.setText(MessageManager.getString("label.buried_index"));
     buriedColour.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -880,7 +926,8 @@ public class GAlignFrame extends JInternalFrame
         buriedColour_actionPerformed(e);
       }
     });
-    userDefinedColour.setText(MessageManager.getString("action.user_defined"));
+    userDefinedColour.setText(MessageManager
+            .getString("action.user_defined"));
     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -888,7 +935,8 @@ public class GAlignFrame extends JInternalFrame
         userDefinedColour_actionPerformed(e);
       }
     });
-    PIDColour.setText(MessageManager.getString("label.percentage_identity"));
+    PIDColour
+            .setText(MessageManager.getString("label.percentage_identity"));
     PIDColour.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -896,7 +944,8 @@ public class GAlignFrame extends JInternalFrame
         PIDColour_actionPerformed(e);
       }
     });
-    BLOSUM62Colour.setText(MessageManager.getString("label.blosum62_score"));
+    BLOSUM62Colour
+            .setText(MessageManager.getString("label.blosum62_score"));
     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -913,7 +962,8 @@ public class GAlignFrame extends JInternalFrame
       }
     });
 
-    purinePyrimidineColour.setText(MessageManager.getString("label.purine_pyrimidine"));
+    purinePyrimidineColour.setText(MessageManager
+            .getString("label.purine_pyrimidine"));
     purinePyrimidineColour
             .addActionListener(new java.awt.event.ActionListener()
             {
@@ -922,6 +972,16 @@ public class GAlignFrame extends JInternalFrame
                 purinePyrimidineColour_actionPerformed(e);
               }
             });
+
+    RNAInteractionColour.setText("RNA Interaction type");
+    RNAInteractionColour
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              public void actionPerformed(ActionEvent e)
+              {
+                RNAInteractionColour_actionPerformed(e);
+              }
+            });
     /*
      * covariationColour.setText("Covariation");
      * covariationColour.addActionListener(new java.awt.event.ActionListener() {
@@ -929,7 +989,8 @@ public class GAlignFrame extends JInternalFrame
      * covariationColour_actionPerformed(e); } });
      */
 
-    avDistanceTreeBlosumMenuItem.setText(MessageManager.getString("label.average_distance_bloslum62"));
+    avDistanceTreeBlosumMenuItem.setText(MessageManager
+            .getString("label.average_distance_bloslum62"));
     avDistanceTreeBlosumMenuItem
             .addActionListener(new java.awt.event.ActionListener()
             {
@@ -938,7 +999,8 @@ public class GAlignFrame extends JInternalFrame
                 avTreeBlosumMenuItem_actionPerformed(e);
               }
             });
-    njTreeBlosumMenuItem.setText(MessageManager.getString("label.neighbour_blosum62"));
+    njTreeBlosumMenuItem.setText(MessageManager
+            .getString("label.neighbour_blosum62"));
     njTreeBlosumMenuItem
             .addActionListener(new java.awt.event.ActionListener()
             {
@@ -948,7 +1010,8 @@ public class GAlignFrame extends JInternalFrame
               }
             });
     annotationPanelMenuItem.setActionCommand("");
-    annotationPanelMenuItem.setText(MessageManager.getString("label.show_annotations"));
+    annotationPanelMenuItem.setText(MessageManager
+            .getString("label.show_annotations"));
     annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
             "SHOW_ANNOTATIONS", true));
     annotationPanelMenuItem
@@ -959,7 +1022,8 @@ public class GAlignFrame extends JInternalFrame
                 annotationPanelMenuItem_actionPerformed(e);
               }
             });
-    colourTextMenuItem.setText(MessageManager.getString("label.colour_text"));
+    colourTextMenuItem.setText(MessageManager
+            .getString("label.colour_text"));
     colourTextMenuItem
             .addActionListener(new java.awt.event.ActionListener()
             {
@@ -976,7 +1040,8 @@ public class GAlignFrame extends JInternalFrame
         htmlMenuItem_actionPerformed(e);
       }
     });
-    overviewMenuItem.setText(MessageManager.getString("label.overview_window"));
+    overviewMenuItem.setText(MessageManager
+            .getString("label.overview_window"));
     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -1008,7 +1073,8 @@ public class GAlignFrame extends JInternalFrame
         redoMenuItem_actionPerformed(e);
       }
     });
-    conservationMenuItem.setText(MessageManager.getString("action.by_conservation"));
+    conservationMenuItem.setText(MessageManager
+            .getString("action.by_conservation"));
     conservationMenuItem
             .addActionListener(new java.awt.event.ActionListener()
             {
@@ -1025,7 +1091,7 @@ public class GAlignFrame extends JInternalFrame
         noColourmenuItem_actionPerformed(e);
       }
     });
-    wrapMenuItem.setText(MessageManager.getString("labe.wrap"));
+    wrapMenuItem.setText(MessageManager.getString("label.wrap"));
     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -1044,7 +1110,8 @@ public class GAlignFrame extends JInternalFrame
         printMenuItem_actionPerformed(e);
       }
     });
-    renderGapsMenuItem.setText(MessageManager.getString("action.show_gaps"));
+    renderGapsMenuItem
+            .setText(MessageManager.getString("action.show_gaps"));
     renderGapsMenuItem.setState(true);
     renderGapsMenuItem
             .addActionListener(new java.awt.event.ActionListener()
@@ -1065,7 +1132,8 @@ public class GAlignFrame extends JInternalFrame
         findMenuItem_actionPerformed(e);
       }
     });
-    abovePIDThreshold.setText(MessageManager.getString("label.above_identity_threshold"));
+    abovePIDThreshold.setText(MessageManager
+            .getString("label.above_identity_threshold"));
     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -1073,7 +1141,8 @@ public class GAlignFrame extends JInternalFrame
         abovePIDThreshold_actionPerformed(e);
       }
     });
-    showSeqFeatures.setText(MessageManager.getString("label.show_sequence_features"));
+    showSeqFeatures.setText(MessageManager
+            .getString("label.show_sequence_features"));
     showSeqFeatures.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent actionEvent)
@@ -1087,7 +1156,8 @@ public class GAlignFrame extends JInternalFrame
      * void actionPerformed(ActionEvent actionEvent) {
      * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
      */
-    showDbRefsMenuitem.setText(MessageManager.getString("label.show_database_refs"));
+    showDbRefsMenuitem.setText(MessageManager
+            .getString("label.show_database_refs"));
     showDbRefsMenuitem.addActionListener(new ActionListener()
     {
 
@@ -1097,7 +1167,8 @@ public class GAlignFrame extends JInternalFrame
       }
 
     });
-    showNpFeatsMenuitem.setText(MessageManager.getString("label.show_non_positional_features"));
+    showNpFeatsMenuitem.setText(MessageManager
+            .getString("label.show_non_positional_features"));
     showNpFeatsMenuitem.addActionListener(new ActionListener()
     {
 
@@ -1107,7 +1178,8 @@ public class GAlignFrame extends JInternalFrame
       }
 
     });
-    showGroupConservation.setText(MessageManager.getString("label.group_conservation"));
+    showGroupConservation.setText(MessageManager
+            .getString("label.group_conservation"));
     showGroupConservation.addActionListener(new ActionListener()
     {
 
@@ -1118,7 +1190,8 @@ public class GAlignFrame extends JInternalFrame
 
     });
 
-    showGroupConsensus.setText(MessageManager.getString("label.group_consensus"));
+    showGroupConsensus.setText(MessageManager
+            .getString("label.group_consensus"));
     showGroupConsensus.addActionListener(new ActionListener()
     {
 
@@ -1128,7 +1201,8 @@ public class GAlignFrame extends JInternalFrame
       }
 
     });
-    showConsensusHistogram.setText(MessageManager.getString("label.show_consensus_histogram"));
+    showConsensusHistogram.setText(MessageManager
+            .getString("label.show_consensus_histogram"));
     showConsensusHistogram.addActionListener(new ActionListener()
     {
 
@@ -1138,7 +1212,8 @@ public class GAlignFrame extends JInternalFrame
       }
 
     });
-    showSequenceLogo.setText(MessageManager.getString("label.show_consensus_logo"));
+    showSequenceLogo.setText(MessageManager
+            .getString("label.show_consensus_logo"));
     showSequenceLogo.addActionListener(new ActionListener()
     {
 
@@ -1148,7 +1223,8 @@ public class GAlignFrame extends JInternalFrame
       }
 
     });
-    normaliseSequenceLogo.setText(MessageManager.getString("label.norm_consensus_logo"));
+    normaliseSequenceLogo.setText(MessageManager
+            .getString("label.norm_consensus_logo"));
     normaliseSequenceLogo.addActionListener(new ActionListener()
     {
 
@@ -1158,7 +1234,8 @@ public class GAlignFrame extends JInternalFrame
       }
 
     });
-    applyAutoAnnotationSettings.setText(MessageManager.getString("label.apply_all_groups"));
+    applyAutoAnnotationSettings.setText(MessageManager
+            .getString("label.apply_all_groups"));
     applyAutoAnnotationSettings.setState(false);
     applyAutoAnnotationSettings.setVisible(true);
     applyAutoAnnotationSettings.addActionListener(new ActionListener()
@@ -1192,7 +1269,8 @@ public class GAlignFrame extends JInternalFrame
       }
     });
 
-    deleteGroups.setText(MessageManager.getString("action.undefine_groups"));
+    deleteGroups
+            .setText(MessageManager.getString("action.undefine_groups"));
     deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
             java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
                     .getMenuShortcutKeyMask(), false));
@@ -1216,8 +1294,9 @@ public class GAlignFrame extends JInternalFrame
     });
     unGroup.setText(MessageManager.getString("action.remove_group"));
     unGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
-            java.awt.event.KeyEvent.VK_G,Toolkit.getDefaultToolkit()
-                    .getMenuShortcutKeyMask() | java.awt.event.KeyEvent.SHIFT_MASK, false));
+            java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
+                    .getMenuShortcutKeyMask()
+                    | java.awt.event.KeyEvent.SHIFT_MASK, false));
     unGroup.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -1282,7 +1361,8 @@ public class GAlignFrame extends JInternalFrame
         pasteThis_actionPerformed(e);
       }
     });
-    applyToAllGroups.setText(MessageManager.getString("label.apply_colour_to_all_groups"));
+    applyToAllGroups.setText(MessageManager
+            .getString("label.apply_colour_to_all_groups"));
     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -1297,7 +1377,8 @@ public class GAlignFrame extends JInternalFrame
         createPNG(null);
       }
     });
-    createPNG.setActionCommand(MessageManager.getString("label.save_png_image"));
+    createPNG.setActionCommand(MessageManager
+            .getString("label.save_png_image"));
     createPNG.setText("PNG");
     font.setText(MessageManager.getString("action.font"));
     font.addActionListener(new java.awt.event.ActionListener()
@@ -1308,7 +1389,8 @@ public class GAlignFrame extends JInternalFrame
       }
     });
 
-    seqLimits.setText(MessageManager.getString("label.show_sequence_limits"));
+    seqLimits.setText(MessageManager
+            .getString("label.show_sequence_limits"));
     seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
     seqLimits.addActionListener(new java.awt.event.ActionListener()
     {
@@ -1325,8 +1407,10 @@ public class GAlignFrame extends JInternalFrame
         createEPS(null);
       }
     });
-    LoadtreeMenuItem.setActionCommand(MessageManager.getString("label.load_tree_for_sequence_set"));
-    LoadtreeMenuItem.setText(MessageManager.getString("label.load_associated_tree"));
+    LoadtreeMenuItem.setActionCommand(MessageManager
+            .getString("label.load_tree_for_sequence_set"));
+    LoadtreeMenuItem.setText(MessageManager
+            .getString("label.load_associated_tree"));
     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -1366,7 +1450,8 @@ public class GAlignFrame extends JInternalFrame
     });
     centreColumnLabelsMenuItem.setVisible(true);
     centreColumnLabelsMenuItem.setState(false);
-    centreColumnLabelsMenuItem.setText(MessageManager.getString("label.centre_column_labels"));
+    centreColumnLabelsMenuItem.setText(MessageManager
+            .getString("label.centre_column_labels"));
     centreColumnLabelsMenuItem
             .addActionListener(new java.awt.event.ActionListener()
             {
@@ -1377,7 +1462,8 @@ public class GAlignFrame extends JInternalFrame
             });
     followHighlightMenuItem.setVisible(true);
     followHighlightMenuItem.setState(true);
-    followHighlightMenuItem.setText(MessageManager.getString("label.automatic_scrolling"));
+    followHighlightMenuItem.setText(MessageManager
+            .getString("label.automatic_scrolling"));
     followHighlightMenuItem.addActionListener(new ActionListener()
     {
 
@@ -1388,7 +1474,8 @@ public class GAlignFrame extends JInternalFrame
 
     });
 
-    modifyPID.setText(MessageManager.getString("label.modify_identity_thereshold"));
+    modifyPID.setText(MessageManager
+            .getString("label.modify_identity_thereshold"));
     modifyPID.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -1396,7 +1483,8 @@ public class GAlignFrame extends JInternalFrame
         modifyPID_actionPerformed(e);
       }
     });
-    modifyConservation.setText(MessageManager.getString("label.modify_conservation_thereshold"));
+    modifyConservation.setText(MessageManager
+            .getString("label.modify_conservation_thereshold"));
     modifyConservation
             .addActionListener(new java.awt.event.ActionListener()
             {
@@ -1405,7 +1493,8 @@ public class GAlignFrame extends JInternalFrame
                 modifyConservation_actionPerformed(e);
               }
             });
-    sortByTreeMenu.setText(MessageManager.getString("action.by_tree_order"));
+    sortByTreeMenu
+            .setText(MessageManager.getString("action.by_tree_order"));
     sort.setText(MessageManager.getString("action.sort"));
     sort.addMenuListener(new MenuListener()
     {
@@ -1422,7 +1511,8 @@ public class GAlignFrame extends JInternalFrame
       {
       }
     });
-    sortByAnnotScore.setText(MessageManager.getString("label.sort_by_score"));
+    sortByAnnotScore.setText(MessageManager
+            .getString("label.sort_by_score"));
     sort.add(sortByAnnotScore);
     sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
     {
@@ -1442,7 +1532,8 @@ public class GAlignFrame extends JInternalFrame
     });
     sortByAnnotScore.setVisible(false);
 
-    calculateTree.setText(MessageManager.getString("action.calculate_tree"));
+    calculateTree
+            .setText(MessageManager.getString("action.calculate_tree"));
 
     jMenu2.setText(MessageManager.getString("label.export_image"));
     padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
@@ -1464,7 +1555,8 @@ public class GAlignFrame extends JInternalFrame
         vamsasStore_actionPerformed(e);
       }
     });
-    showTranslation.setText(MessageManager.getString("label.translate_cDNA"));
+    showTranslation.setText(MessageManager
+            .getString("label.translate_cDNA"));
     showTranslation.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -1472,7 +1564,8 @@ public class GAlignFrame extends JInternalFrame
         showTranslation_actionPerformed(e);
       }
     });
-    extractScores.setText(MessageManager.getString("label.extract_scores") + "...");
+    extractScores.setText(MessageManager.getString("label.extract_scores")
+            + "...");
     extractScores.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -1489,7 +1582,8 @@ public class GAlignFrame extends JInternalFrame
      * public void actionPerformed(ActionEvent e) {
      * showProducts_actionPerformed(e); } });
      */
-    openFeatureSettings.setText(MessageManager.getString("label.feature_settings"));
+    openFeatureSettings.setText(MessageManager
+            .getString("label.feature_settings"));
     openFeatureSettings.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -1497,7 +1591,8 @@ public class GAlignFrame extends JInternalFrame
         featureSettings_actionPerformed(e);
       }
     });
-    fetchSequence.setText(MessageManager.getString("label.fetch_sequences"));
+    fetchSequence
+            .setText(MessageManager.getString("label.fetch_sequences"));
     fetchSequence.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -1506,7 +1601,8 @@ public class GAlignFrame extends JInternalFrame
       }
     });
 
-    annotationColour.setText(MessageManager.getString("action.by_annotation"));
+    annotationColour.setText(MessageManager
+            .getString("action.by_annotation"));
     annotationColour.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -1515,7 +1611,8 @@ public class GAlignFrame extends JInternalFrame
       }
     });
 
-    rnahelicesColour.setText(MessageManager.getString("action.by_rna_helixes"));
+    rnahelicesColour.setText(MessageManager
+            .getString("action.by_rna_helixes"));
     rnahelicesColour.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -1524,7 +1621,8 @@ public class GAlignFrame extends JInternalFrame
       }
     });
 
-    associatedData.setText(MessageManager.getString("label.load_features_annotations"));
+    associatedData.setText(MessageManager
+            .getString("label.load_features_annotations"));
     associatedData.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -1532,7 +1630,8 @@ public class GAlignFrame extends JInternalFrame
         associatedData_actionPerformed(e);
       }
     });
-    autoCalculate.setText(MessageManager.getString("label.autocalculate_consensus"));
+    autoCalculate.setText(MessageManager
+            .getString("label.autocalculate_consensus"));
     autoCalculate.setState(jalview.bin.Cache.getDefault(
             "AUTO_CALC_CONSENSUS", true));
     autoCalculate.addActionListener(new ActionListener()
@@ -1542,9 +1641,12 @@ public class GAlignFrame extends JInternalFrame
         autoCalculate_actionPerformed(e);
       }
     });
-    sortByTree.setText(MessageManager.getString("label.sort_alignment_new_tree"));
+    sortByTree.setText(MessageManager
+            .getString("label.sort_alignment_new_tree"));
     sortByTree
-            .setToolTipText("<html>" + MessageManager.getString("label.enable_automatically_sort_alignment_when_open_new_tree"));
+            .setToolTipText("<html>"
+                    + MessageManager
+                            .getString("label.enable_automatically_sort_alignment_when_open_new_tree"));
     sortByTree
             .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
     sortByTree.addActionListener(new ActionListener()
@@ -1555,9 +1657,12 @@ public class GAlignFrame extends JInternalFrame
       }
     });
 
-    listenToViewSelections.setText(MessageManager.getString("label.listen_for_selections"));
+    listenToViewSelections.setText(MessageManager
+            .getString("label.listen_for_selections"));
     listenToViewSelections
-            .setToolTipText("<html>" + MessageManager.getString("label.selections_mirror_selections_made_same_sequences_other_views"));
+            .setToolTipText("<html>"
+                    + MessageManager
+                            .getString("label.selections_mirror_selections_made_same_sequences_other_views"));
     listenToViewSelections.setState(false);
     listenToViewSelections.addActionListener(new ActionListener()
     {
@@ -1567,7 +1672,8 @@ public class GAlignFrame extends JInternalFrame
       }
     });
 
-    addSequenceMenu.setText(MessageManager.getString("label.add_sequences"));
+    addSequenceMenu
+            .setText(MessageManager.getString("label.add_sequences"));
     addFromFile.setText(MessageManager.getString("label.from_file"));
     addFromFile.addActionListener(new ActionListener()
     {
@@ -1592,7 +1698,8 @@ public class GAlignFrame extends JInternalFrame
         addFromURL_actionPerformed(e);
       }
     });
-    exportFeatures.setText(MessageManager.getString("label.export_features"));
+    exportFeatures.setText(MessageManager
+            .getString("label.export_features"));
     exportFeatures.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -1600,7 +1707,8 @@ public class GAlignFrame extends JInternalFrame
         exportFeatures_actionPerformed(e);
       }
     });
-    exportAnnotations.setText(MessageManager.getString("label.export_annotations"));
+    exportAnnotations.setText(MessageManager
+            .getString("label.export_annotations"));
     exportAnnotations.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -1611,7 +1719,8 @@ public class GAlignFrame extends JInternalFrame
     statusPanel.setLayout(gridLayout1);
     jMenu3.setText(MessageManager.getString("action.show"));
     showAllSeqs.setText(MessageManager.getString("label.all_sequences"));
-    showAllSeqs.setToolTipText(MessageManager.getString("label.toggle_sequence_visibility"));
+    showAllSeqs.setToolTipText(MessageManager
+            .getString("label.toggle_sequence_visibility"));
     showAllSeqs.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -1620,7 +1729,8 @@ public class GAlignFrame extends JInternalFrame
       }
     });
     showAllColumns.setText(MessageManager.getString("label.all_columns"));
-    showAllColumns.setToolTipText(MessageManager.getString("label.toggle_columns_visibility"));
+    showAllColumns.setToolTipText(MessageManager
+            .getString("label.toggle_columns_visibility"));
     showAllColumns.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -1629,8 +1739,10 @@ public class GAlignFrame extends JInternalFrame
       }
     });
     hideMenu.setText(MessageManager.getString("action.hide"));
-    hideSelSequences.setText(MessageManager.getString("label.selected_sequences"));
-    hideSelSequences.setToolTipText(MessageManager.getString("label.toggle_sequence_visibility"));
+    hideSelSequences.setText(MessageManager
+            .getString("label.selected_sequences"));
+    hideSelSequences.setToolTipText(MessageManager
+            .getString("label.toggle_sequence_visibility"));
     hideSelSequences.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -1638,8 +1750,10 @@ public class GAlignFrame extends JInternalFrame
         hideSelSequences_actionPerformed(e);
       }
     });
-    hideSelColumns.setText(MessageManager.getString("label.selected_columns"));
-    hideSelColumns.setToolTipText(MessageManager.getString("label.toggle_columns_visibility"));
+    hideSelColumns.setText(MessageManager
+            .getString("label.selected_columns"));
+    hideSelColumns.setToolTipText(MessageManager
+            .getString("label.toggle_columns_visibility"));
     hideSelColumns.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -1647,7 +1761,8 @@ public class GAlignFrame extends JInternalFrame
         hideSelColumns_actionPerformed(e);
       }
     });
-    hideAllSelection.setText(MessageManager.getString("label.selected_region"));
+    hideAllSelection.setText(MessageManager
+            .getString("label.selected_region"));
     hideAllSelection.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -1656,7 +1771,8 @@ public class GAlignFrame extends JInternalFrame
       }
     });
     // TODO: should be hidden if no selection exists.
-    hideAllButSelection.setText(MessageManager.getString("label.all_but_selected_region"));
+    hideAllButSelection.setText(MessageManager
+            .getString("label.all_but_selected_region"));
     hideAllButSelection.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -1664,9 +1780,10 @@ public class GAlignFrame extends JInternalFrame
         hideAllButSelection_actionPerformed(e);
       }
     });
-    showAllhidden.setText(MessageManager.getString("label.all_sequences_columns"));
-    showAllhidden
-            .setToolTipText(MessageManager.getString("label.toggles_visibility_hidden_selected_regions"));
+    showAllhidden.setText(MessageManager
+            .getString("label.all_sequences_columns"));
+    showAllhidden.setToolTipText(MessageManager
+            .getString("label.toggles_visibility_hidden_selected_regions"));
     showAllhidden.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -1675,7 +1792,8 @@ public class GAlignFrame extends JInternalFrame
       }
     });
 
-    hiddenMarkers.setText(MessageManager.getString("action.show_hidden_markers"));
+    hiddenMarkers.setText(MessageManager
+            .getString("action.show_hidden_markers"));
     hiddenMarkers.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -1683,7 +1801,8 @@ public class GAlignFrame extends JInternalFrame
         hiddenMarkers_actionPerformed(e);
       }
     });
-    invertColSel.setText(MessageManager.getString("action.invert_column_selection"));
+    invertColSel.setText(MessageManager
+            .getString("action.invert_column_selection"));
     invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
             java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
                     .getMenuShortcutKeyMask()
@@ -1749,8 +1868,11 @@ public class GAlignFrame extends JInternalFrame
         newView_actionPerformed(e);
       }
     });
-    tabbedPane.setToolTipText("<html><i>" + MessageManager.getString("label.rename_tab_eXpand_reGroup") + "</i></html>");
-    textColour.setText(MessageManager.getString("label.colour_text") + "...");
+    tabbedPane.setToolTipText("<html><i>"
+            + MessageManager.getString("label.rename_tab_eXpand_reGroup")
+            + "</i></html>");
+    textColour.setText(MessageManager.getString("label.colour_text")
+            + "...");
     textColour.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -1760,7 +1882,8 @@ public class GAlignFrame extends JInternalFrame
     });
     formatMenu.setText(MessageManager.getString("action.format"));
     selectMenu.setText(MessageManager.getString("action.select"));
-    idRightAlign.setText(MessageManager.getString("label.right_align_sequence_id"));
+    idRightAlign.setText(MessageManager
+            .getString("label.right_align_sequence_id"));
     idRightAlign.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -1790,7 +1913,8 @@ public class GAlignFrame extends JInternalFrame
         expandViews_actionPerformed(e);
       }
     });
-    pageSetup.setText(MessageManager.getString("action.page_setup") + "...");
+    pageSetup
+            .setText(MessageManager.getString("action.page_setup") + "...");
     pageSetup.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -1798,7 +1922,8 @@ public class GAlignFrame extends JInternalFrame
         pageSetup_actionPerformed(e);
       }
     });
-    alignmentProperties.setText(MessageManager.getString("label.alignment_props") + "...");
+    alignmentProperties.setText(MessageManager
+            .getString("label.alignment_props") + "...");
     alignmentProperties.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent actionEvent)
@@ -1806,8 +1931,10 @@ public class GAlignFrame extends JInternalFrame
         alignmentProperties();
       }
     });
-    tooltipSettingsMenu.setText(MessageManager.getString("label.sequence_id_tooltip"));
-    autoAnnMenu.setText(MessageManager.getString("label.autocalculated_annotation"));
+    tooltipSettingsMenu.setText(MessageManager
+            .getString("label.sequence_id_tooltip"));
+    autoAnnMenu.setText(MessageManager
+            .getString("label.autocalculated_annotation"));
     alignFrameMenuBar.add(fileMenu);
     alignFrameMenuBar.add(editMenu);
     alignFrameMenuBar.add(selectMenu);
@@ -1898,6 +2025,7 @@ public class GAlignFrame extends JInternalFrame
     colourMenu.add(buriedColour);
     colourMenu.add(nucleotideColour);
     colourMenu.add(purinePyrimidineColour);
+    colourMenu.add(RNAInteractionColour);
     // colourMenu.add(covariationColour);
     colourMenu.add(tcoffeeColour);
     colourMenu.add(userDefinedColour);
@@ -1920,7 +2048,8 @@ public class GAlignFrame extends JInternalFrame
     calculateMenu.add(sortByTree);
     calculateMenu.addSeparator();
     calculateMenu.add(extractScores);
-    webServiceNoServices = new JMenuItem(MessageManager.getString("label.no_services"));
+    webServiceNoServices = new JMenuItem(
+            MessageManager.getString("label.no_services"));
     webService.add(webServiceNoServices);
     pasteMenu.add(pasteNew);
     pasteMenu.add(pasteThis);
@@ -1929,10 +2058,6 @@ public class GAlignFrame extends JInternalFrame
     sort.add(sortGroupMenuItem);
     sort.add(sortPairwiseMenuItem);
     sort.add(sortByTreeMenu);
-    calculateTree.add(averageDistanceTreeMenuItem);
-    calculateTree.add(neighbourTreeMenuItem);
-    calculateTree.add(avDistanceTreeBlosumMenuItem);
-    calculateTree.add(njTreeBlosumMenuItem);
     jMenu2.add(htmlMenuItem);
     jMenu2.add(epsFile);
     jMenu2.add(createPNG);
@@ -1975,6 +2100,7 @@ public class GAlignFrame extends JInternalFrame
     selectMenu.add(unGroup);
     selectMenu.add(grpsFromSelection);
     selectMenu.add(deleteGroups);
+    calculateMenu.add(expandAlignment);
     // TODO - determine if the listenToViewSelections button is needed : see bug
     // JAL-574
     // selectMenu.addSeparator();
@@ -2295,6 +2421,10 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
+  protected void RNAInteractionColour_actionPerformed(ActionEvent e)
+  {
+  }
+
   /*
    * protected void covariationColour_actionPerformed(ActionEvent e) { }
    */
@@ -2334,11 +2464,11 @@ public class GAlignFrame extends JInternalFrame
   protected void deleteGroups_actionPerformed(ActionEvent e)
   {
   }
-  
+
   protected void createGroup_actionPerformed(ActionEvent e)
   {
   }
-  
+
   protected void unGroup_actionPerformed(ActionEvent e)
   {
   }
@@ -2615,4 +2745,10 @@ public class GAlignFrame extends JInternalFrame
   {
 
   }
+
+  protected void expand_newalign(ActionEvent e)
+  {
+    // TODO Auto-generated method stub
+
+  }
 }