JAL-1517 source formatting

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

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index a8bd6fd..cc1703c 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -100,6 +100,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
         ItemListener, KeyListener, AlignViewControllerGuiI
 {
   public AlignViewControllerI avc;
+
   public AlignmentPanel alignPanel;
 
   public AlignViewport viewport;
@@ -149,7 +150,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     }
     viewport = new AlignViewport(al, applet);
     alignPanel = new AlignmentPanel(this, viewport);
-    avc = new jalview.controller.AlignViewController(this, viewport, alignPanel);
+    avc = new jalview.controller.AlignViewController(this, viewport,
+            alignPanel);
     viewport.updateConservation(alignPanel);
     viewport.updateConsensus(alignPanel);
 
@@ -162,7 +164,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     showSequenceLogo.setState(viewport.isShowSequenceLogo());
     normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
     applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
-    
+
     seqLimits.setState(viewport.showJVSuffix);
 
     if (applet != null)
@@ -308,7 +310,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
         viewport.featureSettings.refreshTable();
       }
       alignPanel.paintAlignment(true);
-      statusBar.setText(MessageManager.getString("label.successfully_added_features_alignment"));
+      statusBar.setText(MessageManager
+              .getString("label.successfully_added_features_alignment"));
     }
     return featuresFile;
   }
@@ -452,7 +455,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
     case KeyEvent.VK_F2:
       viewport.cursorMode = !viewport.cursorMode;
-      statusBar.setText(MessageManager.formatMessage("label.keyboard_editing_mode", new String[]{(viewport.cursorMode ? "on" : "off")}));
+      statusBar.setText(MessageManager.formatMessage(
+              "label.keyboard_editing_mode", new String[]
+              { (viewport.cursorMode ? "on" : "off") }));
       if (viewport.cursorMode)
       {
         alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
@@ -567,7 +572,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
         }
       }
       break;
-      
+
     case KeyEvent.VK_U:
       if (evt.isControlDown())
       {
@@ -996,8 +1001,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       cap.setText(contents.toString());
       Frame frame = new Frame();
       frame.add(cap);
-      jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage("label.alignment_properties", new String[]{getTitle()}),
-                 400, 250);
+      jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
+              "label.alignment_properties", new String[]
+              { getTitle() }), 400, 250);
     }
     else if (source == overviewMenuItem)
     {
@@ -1144,7 +1150,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
     Frame frame = new Frame();
     frame.add(cap);
-    jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.input_cut_paste"), 500, 500);
+    jalview.bin.JalviewLite.addFrame(frame,
+            MessageManager.getString("label.input_cut_paste"), 500, 500);
   }
 
   protected void outputText_actionPerformed(ActionEvent e)
@@ -1152,8 +1159,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
     Frame frame = new Frame();
     frame.add(cap);
-    jalview.bin.JalviewLite.addFrame(frame,
-               MessageManager.formatMessage("label.alignment_output_command", new String[]{e.getActionCommand()}),600, 500);
+    jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
+            "label.alignment_output_command", new String[]
+            { e.getActionCommand() }), 600, 500);
     cap.setText(new AppletFormatAdapter().formatSequences(
             e.getActionCommand(), viewport.getAlignment(),
             viewport.showJVSuffix));
@@ -1162,11 +1170,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   public void loadAnnotations()
   {
     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
-    cap.setText(MessageManager.getString("label.paste_features_annotations_Tcoffee_here"));
+    cap.setText(MessageManager
+            .getString("label.paste_features_annotations_Tcoffee_here"));
     cap.setAnnotationImport();
     Frame frame = new Frame();
     frame.add(cap);
-    jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("action.paste_annotations"), 400, 300);
+    jalview.bin.JalviewLite.addFrame(frame,
+            MessageManager.getString("action.paste_annotations"), 400, 300);
 
   }
 
@@ -1183,7 +1193,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
       Frame frame = new Frame();
       frame.add(cap);
-      jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.annotations"), 600, 500);
+      jalview.bin.JalviewLite.addFrame(frame,
+              MessageManager.getString("label.annotations"), 600, 500);
       cap.setText(annotation);
     }
 
@@ -1239,7 +1250,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       }
       Frame frame = new Frame();
       frame.add(cap);
-      jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.features"), 600, 500);
+      jalview.bin.JalviewLite.addFrame(frame,
+              MessageManager.getString("label.features"), 600, 500);
       cap.setText(features);
     }
     else
@@ -1377,7 +1389,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       undoMenuItem.setEnabled(true);
       CommandI command = (CommandI) viewport.historyList.peek();
-      undoMenuItem.setLabel(MessageManager.formatMessage("label.undo_command", new String[]{command.getDescription()}));
+      undoMenuItem.setLabel(MessageManager.formatMessage(
+              "label.undo_command", new String[]
+              { command.getDescription() }));
     }
     else
     {
@@ -1390,7 +1404,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       redoMenuItem.setEnabled(true);
 
       CommandI command = (CommandI) viewport.redoList.peek();
-      redoMenuItem.setLabel(MessageManager.formatMessage("label.redo_command", new String[]{command.getDescription()}));
+      redoMenuItem.setLabel(MessageManager.formatMessage(
+              "label.redo_command", new String[]
+              { command.getDescription() }));
     }
     else
     {
@@ -1917,7 +1933,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   protected void makeGrpsFromSelection_actionPerformed()
   {
-    if (avc.makeGroupsFromSelection()) {
+    if (avc.makeGroupsFromSelection())
+    {
       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
       alignPanel.updateAnnotation();
       alignPanel.paintAlignment(true);
@@ -1928,6 +1945,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   {
     avc.createGroup();
   }
+
   protected void unGroup_actionPerformed()
   {
     if (avc.unGroup())
@@ -1935,6 +1953,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       alignPanel.alignmentChanged();
     }
   }
+
   protected void deleteGroups_actionPerformed()
   {
     if (avc.deleteGroups())
@@ -2038,7 +2057,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
                 viewport.getSelectionGroup());
       }
 
-      statusBar.setText(MessageManager.formatMessage("label.removed_columns", new String[]{Integer.valueOf(trimRegion.getSize()).toString()}));
+      statusBar.setText(MessageManager.formatMessage(
+              "label.removed_columns", new String[]
+              { Integer.valueOf(trimRegion.getSize()).toString() }));
       addHistoryItem(trimRegion);
 
       for (SequenceGroup sg : viewport.getAlignment().getGroups())
@@ -2078,7 +2099,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
     addHistoryItem(removeGapCols);
 
-    statusBar.setText(MessageManager.formatMessage("label.removed_empty_columns", new String[]{Integer.valueOf(removeGapCols.getSize()).toString()}));
+    statusBar.setText(MessageManager.formatMessage(
+            "label.removed_empty_columns", new String[]
+            { Integer.valueOf(removeGapCols.getSize()).toString() }));
 
     // This is to maintain viewport position on first residue
     // of first sequence
@@ -2305,8 +2328,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     OverviewPanel overview = new OverviewPanel(alignPanel);
     frame.add(overview);
     // +50 must allow for applet frame window
-    jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage("label.overview_params", new String[]{this.getTitle()}),
-            overview.getPreferredSize().width,
+    jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
+            "label.overview_params", new String[]
+            { this.getTitle() }), overview.getPreferredSize().width,
             overview.getPreferredSize().height + 50);
 
     frame.pack();
@@ -2335,9 +2359,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       if (viewport.getAbovePIDThreshold())
       {
-        viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel, cs,
-                "Background"));
-      } 
+        viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
+                cs, "Background"));
+      }
 
       if (viewport.getConservationSelected())
       {
@@ -2461,7 +2485,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       Frame frame = new Frame();
       frame.add(new PairwiseAlignPanel(alignPanel));
-      jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("action.pairwise_alignment"), 600,
+      jalview.bin.JalviewLite.addFrame(frame,
+              MessageManager.getString("action.pairwise_alignment"), 600,
               500);
     }
   }
@@ -2563,12 +2588,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     cap.setTreeImport();
     Frame frame = new Frame();
     frame.add(cap);
-    jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.paste_newick_file"), 400, 300);
+    jalview.bin.JalviewLite.addFrame(frame,
+            MessageManager.getString("label.paste_newick_file"), 400, 300);
   }
 
   public void loadTree(jalview.io.NewickFile tree, String treeFile)
   {
-    TreePanel tp = new TreePanel(alignPanel, treeFile, MessageManager.getString("label.load_tree_from_file"), tree);
+    TreePanel tp = new TreePanel(alignPanel, treeFile,
+            MessageManager.getString("label.load_tree_from_file"), tree);
     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
     addTreeMenuItem(tp, treeFile);
   }
@@ -2588,8 +2615,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
             .sortByTree(viewport.getAlignment(), treePanel.getTree());
     // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
     // HistoryItem.SORT));
-    addHistoryItem(new OrderCommand(MessageManager.formatMessage("label.order_by_params", new String[]{title}), oldOrder,
-            viewport.getAlignment()));
+    addHistoryItem(new OrderCommand(MessageManager.formatMessage(
+            "label.order_by_params", new String[]
+            { title }), oldOrder, viewport.getAlignment()));
     alignPanel.paintAlignment(true);
   }
 
@@ -2685,27 +2713,31 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
         // TODO: update this text for each release or centrally store it for
         // lite and application
         g.setFont(new Font("Helvetica", Font.BOLD, 14));
-        g.drawString(MessageManager.formatMessage("label.jalviewLite_release", new String[]{version}), x, y += fh);
+        g.drawString(MessageManager.formatMessage(
+                "label.jalviewLite_release", new String[]
+                { version }), x, y += fh);
         g.setFont(new Font("Helvetica", Font.BOLD, 12));
-        g.drawString(MessageManager.formatMessage("label.jaview_build_date", new String[]{builddate}), x, y += fh);
+        g.drawString(MessageManager.formatMessage(
+                "label.jaview_build_date", new String[]
+                { builddate }), x, y += fh);
         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
-        g.drawString(
-                MessageManager.getString("label.jalview_authors_1"),
+        g.drawString(MessageManager.getString("label.jalview_authors_1"),
                 x, y += fh * 1.5);
-        g.drawString(MessageManager.getString("label.jalview_authors_2"), x + 50, y += fh+8);
-        g.drawString(
-                MessageManager.getString("label.jalview_dev_managers"),
-                x, y += fh);
+        g.drawString(MessageManager.getString("label.jalview_authors_2"),
+                x + 50, y += fh + 8);
         g.drawString(
-                MessageManager.getString("label.jalview_distribution_lists"),
-                x, y += fh);
-        g.drawString(MessageManager.getString("label.jalview_please_cite"), x, y += fh + 8);
+                MessageManager.getString("label.jalview_dev_managers"), x,
+                y += fh);
+        g.drawString(MessageManager
+                .getString("label.jalview_distribution_lists"), x, y += fh);
+        g.drawString(MessageManager.getString("label.jalview_please_cite"),
+                x, y += fh + 8);
         g.drawString(
                 MessageManager.getString("label.jalview_cite_1_authors"),
                 x, y += fh);
         g.drawString(
-                MessageManager.getString("label.jalview_cite_1_title"),
-                x, y += fh);
+                MessageManager.getString("label.jalview_cite_1_title"), x,
+                y += fh);
         g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
                 x, y += fh);
       }
@@ -2714,7 +2746,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     Frame frame = new Frame();
     frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
             .getBuildDate()));
-    jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.jalview"), 580, 220);
+    jalview.bin.JalviewLite.addFrame(frame,
+            MessageManager.getString("label.jalview"), 580, 220);
 
   }
 
@@ -2737,17 +2770,23 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   Menu fileMenu = new Menu(MessageManager.getString("action.file"));
 
-  MenuItem loadApplication = new MenuItem(MessageManager.getString("label.view_full_application"));
+  MenuItem loadApplication = new MenuItem(
+          MessageManager.getString("label.view_full_application"));
 
-  MenuItem loadTree = new MenuItem(MessageManager.getString("label.load_associated_tree"));
+  MenuItem loadTree = new MenuItem(
+          MessageManager.getString("label.load_associated_tree"));
 
-  MenuItem loadAnnotations = new MenuItem(MessageManager.getString("label.load_features_annotations"));
+  MenuItem loadAnnotations = new MenuItem(
+          MessageManager.getString("label.load_features_annotations"));
 
-  MenuItem outputFeatures = new MenuItem(MessageManager.getString("label.export_features"));
+  MenuItem outputFeatures = new MenuItem(
+          MessageManager.getString("label.export_features"));
 
-  MenuItem outputAnnotations = new MenuItem(MessageManager.getString("label.export_annotations"));
+  MenuItem outputAnnotations = new MenuItem(
+          MessageManager.getString("label.export_annotations"));
 
-  MenuItem closeMenuItem = new MenuItem(MessageManager.getString("action.close"));
+  MenuItem closeMenuItem = new MenuItem(
+          MessageManager.getString("action.close"));
 
   Menu editMenu = new Menu(MessageManager.getString("action.edit"));
 
@@ -2755,13 +2794,17 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
 
-  Menu calculateMenu = new Menu(MessageManager.getString("action.calculate"));
+  Menu calculateMenu = new Menu(
+          MessageManager.getString("action.calculate"));
 
-  MenuItem selectAllSequenceMenuItem = new MenuItem(MessageManager.getString("action.select_all"));
+  MenuItem selectAllSequenceMenuItem = new MenuItem(
+          MessageManager.getString("action.select_all"));
 
-  MenuItem deselectAllSequenceMenuItem = new MenuItem(MessageManager.getString("action.deselect_all"));
+  MenuItem deselectAllSequenceMenuItem = new MenuItem(
+          MessageManager.getString("action.deselect_all"));
 
-  MenuItem invertSequenceMenuItem = new MenuItem(MessageManager.getString("action.invert_selection"));
+  MenuItem invertSequenceMenuItem = new MenuItem(
+          MessageManager.getString("action.invert_selection"));
 
   MenuItem remove2LeftMenuItem = new MenuItem();
 
@@ -2839,7 +2882,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
 
-  MenuItem alProperties = new MenuItem(MessageManager.getString("label.alignment_props"));
+  MenuItem alProperties = new MenuItem(
+          MessageManager.getString("label.alignment_props"));
 
   MenuItem overviewMenuItem = new MenuItem();
 
@@ -2970,13 +3014,17 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     selectAllSequenceMenuItem.addActionListener(this);
     deselectAllSequenceMenuItem.addActionListener(this);
     invertSequenceMenuItem.addActionListener(this);
-    remove2LeftMenuItem.setLabel(MessageManager.getString("action.remove_left"));
+    remove2LeftMenuItem.setLabel(MessageManager
+            .getString("action.remove_left"));
     remove2LeftMenuItem.addActionListener(this);
-    remove2RightMenuItem.setLabel(MessageManager.getString("action.remove_right"));
+    remove2RightMenuItem.setLabel(MessageManager
+            .getString("action.remove_right"));
     remove2RightMenuItem.addActionListener(this);
-    removeGappedColumnMenuItem.setLabel(MessageManager.getString("action.remove_empty_columns"));
+    removeGappedColumnMenuItem.setLabel(MessageManager
+            .getString("action.remove_empty_columns"));
     removeGappedColumnMenuItem.addActionListener(this);
-    removeAllGapsMenuItem.setLabel(MessageManager.getString("action.remove_all_gaps"));
+    removeAllGapsMenuItem.setLabel(MessageManager
+            .getString("action.remove_all_gaps"));
     removeAllGapsMenuItem.addActionListener(this);
     viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
     viewBoxesMenuItem.setState(true);
@@ -2984,29 +3032,36 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
     viewTextMenuItem.setState(true);
     viewTextMenuItem.addItemListener(this);
-    sortPairwiseMenuItem.setLabel(MessageManager.getString("action.by_pairwise_id"));
+    sortPairwiseMenuItem.setLabel(MessageManager
+            .getString("action.by_pairwise_id"));
     sortPairwiseMenuItem.addActionListener(this);
     sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
     sortIDMenuItem.addActionListener(this);
-    sortLengthMenuItem.setLabel(MessageManager.getString("action.by_length"));
+    sortLengthMenuItem.setLabel(MessageManager
+            .getString("action.by_length"));
     sortLengthMenuItem.addActionListener(this);
     sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
     sortGroupMenuItem.addActionListener(this);
-    removeRedundancyMenuItem.setLabel(MessageManager.getString("action.remove_redundancy"));
+    removeRedundancyMenuItem.setLabel(MessageManager
+            .getString("action.remove_redundancy"));
     removeRedundancyMenuItem.addActionListener(this);
-    pairwiseAlignmentMenuItem.setLabel(MessageManager.getString("action.pairwise_alignment"));
+    pairwiseAlignmentMenuItem.setLabel(MessageManager
+            .getString("action.pairwise_alignment"));
     pairwiseAlignmentMenuItem.addActionListener(this);
-    PCAMenuItem.setLabel(MessageManager.getString("label.principal_component_analysis"));
+    PCAMenuItem.setLabel(MessageManager
+            .getString("label.principal_component_analysis"));
     PCAMenuItem.addActionListener(this);
-    averageDistanceTreeMenuItem
-            .setLabel(MessageManager.getString("label.average_distance_identity"));
+    averageDistanceTreeMenuItem.setLabel(MessageManager
+            .getString("label.average_distance_identity"));
     averageDistanceTreeMenuItem.addActionListener(this);
-    neighbourTreeMenuItem.setLabel(MessageManager.getString("label.neighbour_joining_identity"));
+    neighbourTreeMenuItem.setLabel(MessageManager
+            .getString("label.neighbour_joining_identity"));
     neighbourTreeMenuItem.addActionListener(this);
     statusBar.setBackground(Color.white);
     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
     statusBar.setText(MessageManager.getString("label.status_bar"));
-    outputTextboxMenu.setLabel(MessageManager.getString("label.out_to_textbox"));
+    outputTextboxMenu.setLabel(MessageManager
+            .getString("label.out_to_textbox"));
     clustalColour.setLabel(MessageManager.getString("label.clustalx"));
 
     clustalColour.addActionListener(this);
@@ -3014,45 +3069,60 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     zappoColour.addActionListener(this);
     taylorColour.setLabel(MessageManager.getString("label.taylor"));
     taylorColour.addActionListener(this);
-    hydrophobicityColour.setLabel(MessageManager.getString("label.hydrophobicity"));
+    hydrophobicityColour.setLabel(MessageManager
+            .getString("label.hydrophobicity"));
     hydrophobicityColour.addActionListener(this);
-    helixColour.setLabel(MessageManager.getString("label.helix_propensity"));
+    helixColour
+            .setLabel(MessageManager.getString("label.helix_propensity"));
     helixColour.addActionListener(this);
-    strandColour.setLabel(MessageManager.getString("label.strand_propensity"));
+    strandColour.setLabel(MessageManager
+            .getString("label.strand_propensity"));
     strandColour.addActionListener(this);
     turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
     turnColour.addActionListener(this);
     buriedColour.setLabel(MessageManager.getString("label.buried_index"));
     buriedColour.addActionListener(this);
-    purinePyrimidineColour.setLabel(MessageManager.getString("label.purine_pyrimidine"));
+    purinePyrimidineColour.setLabel(MessageManager
+            .getString("label.purine_pyrimidine"));
     purinePyrimidineColour.addActionListener(this);
-    RNAInteractionColour.setLabel(MessageManager.getString("label.rna_interaction"));
+    RNAInteractionColour.setLabel(MessageManager
+            .getString("label.rna_interaction"));
     RNAInteractionColour.addActionListener(this);
-    RNAHelixColour.setLabel(MessageManager.getString("action.by_rna_helixes"));
+    RNAHelixColour.setLabel(MessageManager
+            .getString("action.by_rna_helixes"));
     RNAHelixColour.addActionListener(this);
-    userDefinedColour.setLabel(MessageManager.getString("action.user_defined"));
+    userDefinedColour.setLabel(MessageManager
+            .getString("action.user_defined"));
     userDefinedColour.addActionListener(this);
-    PIDColour.setLabel(MessageManager.getString("label.percentage_identity"));
+    PIDColour.setLabel(MessageManager
+            .getString("label.percentage_identity"));
     PIDColour.addActionListener(this);
-    BLOSUM62Colour.setLabel(MessageManager.getString("label.blosum62_score"));
+    BLOSUM62Colour.setLabel(MessageManager
+            .getString("label.blosum62_score"));
     BLOSUM62Colour.addActionListener(this);
-    tcoffeeColour.setLabel(MessageManager.getString("label.tcoffee_scores"));
+    tcoffeeColour
+            .setLabel(MessageManager.getString("label.tcoffee_scores"));
     tcoffeeColour.setEnabled(false); // it will enabled only if a score file is
                                      // provided
     tcoffeeColour.addActionListener(this);
-    avDistanceTreeBlosumMenuItem
-            .setLabel(MessageManager.getString("label.average_distance_bloslum62"));
+    avDistanceTreeBlosumMenuItem.setLabel(MessageManager
+            .getString("label.average_distance_bloslum62"));
     avDistanceTreeBlosumMenuItem.addActionListener(this);
-    njTreeBlosumMenuItem.setLabel(MessageManager.getString("label.neighbour_blosum62"));
+    njTreeBlosumMenuItem.setLabel(MessageManager
+            .getString("label.neighbour_blosum62"));
     njTreeBlosumMenuItem.addActionListener(this);
-    annotationPanelMenuItem.setLabel(MessageManager.getString("label.show_annotations"));
+    annotationPanelMenuItem.setLabel(MessageManager
+            .getString("label.show_annotations"));
     annotationPanelMenuItem.addItemListener(this);
-    colourTextMenuItem.setLabel(MessageManager.getString("label.colour_text"));
+    colourTextMenuItem.setLabel(MessageManager
+            .getString("label.colour_text"));
     colourTextMenuItem.addItemListener(this);
-    displayNonconservedMenuItem.setLabel(MessageManager.getString("label.show_non_conversed"));
+    displayNonconservedMenuItem.setLabel(MessageManager
+            .getString("label.show_non_conversed"));
     displayNonconservedMenuItem.addItemListener(this);
     alProperties.addActionListener(this);
-    overviewMenuItem.setLabel(MessageManager.getString("label.overview_window"));
+    overviewMenuItem.setLabel(MessageManager
+            .getString("label.overview_window"));
     overviewMenuItem.addActionListener(this);
     undoMenuItem.setEnabled(false);
     undoMenuItem.setLabel(MessageManager.getString("action.undo"));
@@ -3060,24 +3130,29 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     redoMenuItem.setEnabled(false);
     redoMenuItem.setLabel(MessageManager.getString("action.redo"));
     redoMenuItem.addActionListener(this);
-    conservationMenuItem.setLabel(MessageManager.getString("action.by_conservation"));
+    conservationMenuItem.setLabel(MessageManager
+            .getString("action.by_conservation"));
     conservationMenuItem.addItemListener(this);
     noColourmenuItem.setLabel(MessageManager.getString("label.none"));
     noColourmenuItem.addActionListener(this);
     wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
     wrapMenuItem.addItemListener(this);
-    renderGapsMenuItem.setLabel(MessageManager.getString("action.show_gaps"));
+    renderGapsMenuItem.setLabel(MessageManager
+            .getString("action.show_gaps"));
     renderGapsMenuItem.setState(true);
     renderGapsMenuItem.addItemListener(this);
     findMenuItem.setLabel(MessageManager.getString("action.find"));
     findMenuItem.addActionListener(this);
-    abovePIDThreshold.setLabel(MessageManager.getString("label.above_identity_threshold"));
+    abovePIDThreshold.setLabel(MessageManager
+            .getString("label.above_identity_threshold"));
     abovePIDThreshold.addItemListener(this);
     nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
     nucleotideColour.addActionListener(this);
-    deleteGroups.setLabel(MessageManager.getString("action.undefine_groups"));
+    deleteGroups.setLabel(MessageManager
+            .getString("action.undefine_groups"));
     deleteGroups.addActionListener(this);
-    grpsFromSelection.setLabel(MessageManager.getString("action.make_groups_selection"));
+    grpsFromSelection.setLabel(MessageManager
+            .getString("action.make_groups_selection"));
     grpsFromSelection.addActionListener(this);
     createGroup.setLabel(MessageManager.getString("action.create_group"));
     unGroup.setLabel(MessageManager.getString("action.remove_group"));
@@ -3092,7 +3167,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     pasteNew.addActionListener(this);
     pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
     pasteThis.addActionListener(this);
-    applyToAllGroups.setLabel(MessageManager.getString("label.apply_colour_to_all_groups"));
+    applyToAllGroups.setLabel(MessageManager
+            .getString("label.apply_colour_to_all_groups"));
     applyToAllGroups.setState(true);
     applyToAllGroups.addItemListener(this);
     font.setLabel(MessageManager.getString("action.font"));
@@ -3109,20 +3185,26 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     scaleRight.setState(true);
     scaleRight.setLabel(MessageManager.getString("action.scale_right"));
     scaleRight.addItemListener(this);
-    modifyPID.setLabel(MessageManager.getString("label.modify_identity_thereshold"));
+    modifyPID.setLabel(MessageManager
+            .getString("label.modify_identity_thereshold"));
     modifyPID.addActionListener(this);
-    modifyConservation.setLabel(MessageManager.getString("label.modify_conservation_thereshold"));
+    modifyConservation.setLabel(MessageManager
+            .getString("label.modify_conservation_thereshold"));
     modifyConservation.addActionListener(this);
-    sortByTreeMenu.setLabel(MessageManager.getString("action.by_tree_order"));
+    sortByTreeMenu.setLabel(MessageManager
+            .getString("action.by_tree_order"));
     sort.setLabel(MessageManager.getString("action.sort"));
     calculate.setLabel(MessageManager.getString("action.calculate_tree"));
     autoCalculate.addItemListener(this);
     sortByTree.addItemListener(this);
-    inputText.setLabel(MessageManager.getString("label.input_from_textbox"));
+    inputText
+            .setLabel(MessageManager.getString("label.input_from_textbox"));
     inputText.addActionListener(this);
-    centreColumnLabelFlag.setLabel(MessageManager.getString("label.centre_column_labels"));
+    centreColumnLabelFlag.setLabel(MessageManager
+            .getString("label.centre_column_labels"));
     centreColumnLabelFlag.addItemListener(this);
-    followMouseOverFlag.setLabel(MessageManager.getString("label.automatic_scrolling"));
+    followMouseOverFlag.setLabel(MessageManager
+            .getString("label.automatic_scrolling"));
     followMouseOverFlag.addItemListener(this);
     helpMenu.setLabel(MessageManager.getString("action.help"));
     documentation.setLabel(MessageManager.getString("label.documentation"));
@@ -3131,34 +3213,52 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     about.setLabel(MessageManager.getString("label.about"));
     about.addActionListener(this);
     seqLimits.setState(true);
-    seqLimits.setLabel(MessageManager.getString("label.show_sequence_limits"));
+    seqLimits.setLabel(MessageManager
+            .getString("label.show_sequence_limits"));
     seqLimits.addItemListener(this);
-    featureSettings.setLabel(MessageManager.getString("label.feature_settings"));
+    featureSettings.setLabel(MessageManager
+            .getString("label.feature_settings"));
     featureSettings.addActionListener(this);
-    sequenceFeatures.setLabel(MessageManager.getString("label.sequence_features"));
+    sequenceFeatures.setLabel(MessageManager
+            .getString("label.sequence_features"));
     sequenceFeatures.addItemListener(this);
     sequenceFeatures.setState(false);
-    annotationColour.setLabel(MessageManager.getString("action.by_annotation"));
+    annotationColour.setLabel(MessageManager
+            .getString("action.by_annotation"));
     annotationColour.addActionListener(this);
-    invertSequenceMenuItem.setLabel(MessageManager.getString("action.invert_sequence_selection"));
-    invertColSel.setLabel(MessageManager.getString("action.invert_column_selection"));
+    invertSequenceMenuItem.setLabel(MessageManager
+            .getString("action.invert_sequence_selection"));
+    invertColSel.setLabel(MessageManager
+            .getString("action.invert_column_selection"));
     menu1.setLabel(MessageManager.getString("action.show"));
     showColumns.setLabel(MessageManager.getString("label.all_columns"));
     showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
     menu2.setLabel(MessageManager.getString("action.hide"));
-    hideColumns.setLabel(MessageManager.getString("label.selected_columns"));
-    hideSequences.setLabel(MessageManager.getString("label.selected_sequences"));
-    hideAllButSelection.setLabel(MessageManager.getString("label.all_but_selected_region"));
-    hideAllSelection.setLabel(MessageManager.getString("label.selected_region"));
-    showAllHidden.setLabel(MessageManager.getString("label.all_sequences_columns"));
-    showGroupConsensus.setLabel(MessageManager.getString("label.group_consensus"));
-    showGroupConservation.setLabel(MessageManager.getString("label.group_conservation"));
-    showConsensusHistogram.setLabel(MessageManager.getString("label.show_consensus_histogram"));
-    showSequenceLogo.setLabel(MessageManager.getString("label.show_consensus_logo"));
-    normSequenceLogo.setLabel(MessageManager.getString("label.norm_consensus_logo"));
-    applyAutoAnnotationSettings.setLabel(MessageManager.getString("label.apply_all_groups"));
+    hideColumns
+            .setLabel(MessageManager.getString("label.selected_columns"));
+    hideSequences.setLabel(MessageManager
+            .getString("label.selected_sequences"));
+    hideAllButSelection.setLabel(MessageManager
+            .getString("label.all_but_selected_region"));
+    hideAllSelection.setLabel(MessageManager
+            .getString("label.selected_region"));
+    showAllHidden.setLabel(MessageManager
+            .getString("label.all_sequences_columns"));
+    showGroupConsensus.setLabel(MessageManager
+            .getString("label.group_consensus"));
+    showGroupConservation.setLabel(MessageManager
+            .getString("label.group_conservation"));
+    showConsensusHistogram.setLabel(MessageManager
+            .getString("label.show_consensus_histogram"));
+    showSequenceLogo.setLabel(MessageManager
+            .getString("label.show_consensus_logo"));
+    normSequenceLogo.setLabel(MessageManager
+            .getString("label.norm_consensus_logo"));
+    applyAutoAnnotationSettings.setLabel(MessageManager
+            .getString("label.apply_all_groups"));
     applyAutoAnnotationSettings.setState(true);
-    autoAnnMenu.setLabel(MessageManager.getString("label.autocalculated_annotation"));
+    autoAnnMenu.setLabel(MessageManager
+            .getString("label.autocalculated_annotation"));
 
     invertColSel.addActionListener(this);
     showColumns.addActionListener(this);
@@ -3254,7 +3354,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     colourMenu.add(buriedColour);
     colourMenu.add(nucleotideColour);
     colourMenu.add(purinePyrimidineColour);
-    //    colourMenu.add(RNAInteractionColour);
+    // colourMenu.add(RNAInteractionColour);
     colourMenu.add(tcoffeeColour);
     colourMenu.add(userDefinedColour);
     colourMenu.addSeparator();
@@ -3317,8 +3417,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   }
 
-  
-  public void setStatus(String string) {
+  public void setStatus(String string)
+  {
     statusBar.setText(string);
   };