JAL-1645 JAL-1355 UI/i18n: added missing messages, moved ‘…’ into action messages...

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index a4f6497..05d6427 100644 (file)
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -6,7 +6,7 @@ action.save_scheme = Save scheme
 action.save_image = Save Image
 action.paste = Paste
 action.show_html_source = Show HTML Source
-action.print = Print
+action.print = Print...
 action.web_service = Web Service
 action.cancel_job = Cancel Job
 action.start_job = Start Job
@@ -30,7 +30,7 @@ action.save_project = Save Project
 action.quit = Quit
 action.expand_views = Expand Views
 action.gather_views = Gather Views
-action.page_setup = Page Setup
+action.page_setup = Page Setup...
 action.reload = Reload
 action.load = Load
 action.open = Open
@@ -53,16 +53,16 @@ action.left_justify_alignment = Left Justify Alignment
 action.right_justify_alignment = Right Justify Alignment
 action.boxes = Boxes
 action.text = Text
-action.by_pairwise_id = by Pairwise Identity
-action.by_id = by Id
-action.by_length = by Length
-action.by_group = by Group
+action.by_pairwise_id = By Pairwise Identity
+action.by_id = By Id
+action.by_length = By Length
+action.by_group = By Group
 action.unmark_as_reference = Unmark as Reference 
 action.set_as_reference = Set as Reference 
 action.remove = Remove
 action.remove_redundancy = Remove Redundancy...
-action.pairwise_alignment = Pairwise Alignments...
-action.by_rna_helixes = by RNA Helices
+action.pairwise_alignment = Pairwise Alignment
+action.by_rna_helixes = By RNA Helices
 action.user_defined = User Defined...
 action.by_conservation = By Conservation
 action.wrap = Wrap
@@ -82,7 +82,7 @@ action.by_tree_order = By Tree Order
 action.sort = Sort
 action.calculate_tree = Calculate Tree
 action.help = Help
-action.by_annotation = by Annotation...
+action.by_annotation = By Annotation...
 action.invert_sequence_selection = Invert Sequence Selection
 action.invert_column_selection = Invert Column Selection
 action.show = Show
@@ -118,7 +118,7 @@ action.new_view = New View
 action.close = Close
 action.add = Add
 action.save_as_default = Save as default
-action.save_as = Save as
+action.save_as = Save as...
 action.save = Save
 action.cancel_fetch = Cancel Fetch
 action.save_omit_hidden_columns = Save / Omit Hidden Regions
@@ -228,7 +228,8 @@ label.automatic_scrolling = Automatic Scrolling
 label.documentation = Documentation
 label.about = About...
 label.show_sequence_limits = Show Sequence Limits
-label.feature_settings = Feature Settings...
+action.feature_settings = Feature Settings...
+label.feature_settings = Feature Settings
 label.all_columns = All Columns
 label.all_sequences = All Sequences
 label.selected_columns = Selected Columns 
@@ -342,8 +343,8 @@ label.blog_item_published_on_date = {0} {1}
 label.select_das_service_from_table = Select a DAS service from the table to read a full description here.</font></html>
 label.session_update = Session Update
 label.new_vamsas_session = New Vamsas Session
-label.load_vamsas_session = Load Vamsas Session
-label.save_vamsas_session = Save Vamsas Session
+action.load_vamsas_session = Load Vamsas Session...
+action.save_vamsas_session = Save Vamsas Session
 label.select_vamsas_session_opened_as_new_vamsas_session= Select a vamsas session to be opened as a new vamsas session.
 label.open_saved_vamsas_session = Open a saved VAMSAS session
 label.groovy_console = Groovy Console...
@@ -482,15 +483,15 @@ label.fetching_pdb_data = Fetching PDB data...
 label.structure_type = Structure type
 label.settings_for_type = Settings for {0}
 label.view_full_application = View in Full Application
-label.load_associated_tree = Load Associated Tree ...
-label.load_features_annotations = Load Features/Annotations ...
-label.export_features = Export Features ...
-label.export_annotations = Export Annotations ...
+label.load_associated_tree = Load Associated Tree...
+label.load_features_annotations = Load Features/Annotations...
+label.export_features = Export Features...
+label.export_annotations = Export Annotations...
 label.to_upper_case = To Upper Case
 label.to_lower_case = To Lower Case
 label.toggle_case = Toggle Case
-label.edit_name_description = Edit Name/Description ...
-label.create_sequence_feature = Create Sequence Feature ...
+label.edit_name_description = Edit Name/Description...
+label.create_sequence_feature = Create Sequence Feature...
 label.edit_sequence = Edit Sequence
 label.edit_sequences = Edit Sequences
 label.sequence_details = Sequence Details
@@ -562,7 +563,8 @@ label.from_textbox = from Textbox
 label.window = Window
 label.preferences = Preferences
 label.tools = Tools
-label.fetch_sequences = Fetch Sequence(s)
+label.fetch_sequences = Fetch Sequences
+action.fetch_sequences = Fetch Sequences...
 label.stop_vamsas_session = Stop Vamsas Session
 label.collect_garbage = Collect Garbage
 label.show_memory_usage = Show Memory Usage
@@ -670,14 +672,15 @@ label.view_all_structures = View all {0} structures.
 label.view_all_representative_structures = View all {0} representative structures.
 label.open_new_jmol_view_with_all_representative_structures_associated_current_selection_superimpose_using_alignment = Opens a new structure viewer with all representative structures\nassociated with the current selection\nsuperimposed with the current alignment.
 label.associate_structure_with_sequence = Associate Structure with Sequence
-label.from_file = from file
+label.from_file = From File
 label.enter_pdb_id = Enter PDB Id
-label.discover_pdb_ids = Discover PDB ids
+label.discover_pdb_ids = Discover PDB IDs
 label.text_colour = Text Colour
+action.set_text_colour = Text Colour...
 label.structure = Structure
 label.view_structure = View Structure
 label.view_protein_structure = View Protein Structure
-label.show_pdbstruct_dialog = 3D Structure Data ...
+label.show_pdbstruct_dialog = 3D Structure Data...
 label.view_rna_structure = VARNA 2D Structure
 label.clustalx_colours = Clustalx colours
 label.above_identity_percentage = Above % Identity
@@ -715,13 +718,14 @@ label.add_local_source = Add Local Source
 label.set_as_default = Set as Default
 label.show_labels = Show labels
 label.background_colour = Background Colour
+action.background_colour = Background Colour...
 label.associate_nodes_with = Associate Nodes With
 label.jalview_pca_calculation = Jalview PCA Calculation
 label.link_name = Link Name
 label.pdb_file = PDB file
 label.colour_with_jmol = Colour with Jmol
 label.colour_with_chimera = Colour with Chimera
-label.align_structures = Align structures
+label.align_structures = Align Structures
 label.jmol = Jmol
 label.chimera = Chimera
 label.sort_alignment_by_tree = Sort Alignment By Tree
@@ -730,15 +734,15 @@ label.associate_leaves_with = Associate Leaves With
 label.save_colour_scheme_with_unique_name_added_to_colour_menu = Save your colour scheme with a unique name and it will be added to the Colour menu
 label.case_sensitive = Case Sensitive
 label.lower_case_colour = Lower Case Colour
-label.index_by_host = Index by host
-label.index_by_type = Index by type
+label.index_by_host = Index by Host
+label.index_by_type = Index by Type
 label.enable_jabaws_services = Enable JABAWS Services
-label.display_warnings = Display warnings
-label.move_url_up = Move URL up
-label.move_url_down = Move URL down
-label.add_sbrs_definition = Add a SBRS definition
-label.edit_sbrs_definition = Edit SBRS definition
-label.delete_sbrs_definition = Delete SBRS definition
+label.display_warnings = Display Warnings
+label.move_url_up = Move URL Up
+label.move_url_down = Move URL Down
+label.add_sbrs_definition = Add a SBRS Definition
+label.edit_sbrs_definition = Edit SBRS Definition
+label.delete_sbrs_definition = Delete SBRS Definition
 label.your_sequences_have_been_verified = Your sequences have been verified against known sequence databases. Some of the ids have been\n altered, most likely the start/end residue will have been updated.\n Save your alignment to maintain the updated id.\n\n
 label.sequence_names_updated = Sequence names updated
 label.dbref_search_completed = DBRef search completed
@@ -747,6 +751,14 @@ label.fetch_all_param = Fetch all {0}
 label.paste_new_window = Paste To New Window
 label.settings_for_param = Settings for {0}
 label.view_params = View {0}
+label.aacon_calculations = AACon Calculations
+label.aacon_settings = Change AACon Settings...
+tooltip.aacon_calculations = When checked, AACon calculations are updated automatically.
+tooltip.aacon_settings = Modify settings for AACon calculations.
+label.rnalifold_calculations = RNAAliFold Prediction
+label.rnalifold_settings = Change RNAAliFold settings...
+tooltip.rnalifold_calculations = When checked, RNA secondary structure predictions will be calculated for the alignment, and updated when edits are made.
+tooltip.rnalifold_settings = Modify settings for the RNAAliFold prediction. Use this to hide or show different results of the RNA calculation, and change RNA folding parameters.
 label.all_views = All Views
 label.align_sequences_to_existing_alignment = Align sequences to an existing alignment
 label.realign_with_params = Realign with {0}
@@ -813,7 +825,7 @@ label.service_preset = Service Preset
 label.run_with_preset = Run {0} with preset
 label.view_service_doc_url = <html>View <a href="{0}">{1}</a></html>
 label.submit_sequence = <html>Submit {0} {1} {2} {3} to<br/>{4}</html>
-action.by_title_param = by {0}
+action.by_title_param = By {0}
 label.alignment = Alignment
 label.secondary_structure_prediction = Secondary Structure Prediction
 label.sequence_database_search = Sequence Database Search
@@ -821,7 +833,7 @@ label.analysis = Analysis
 label.protein_disorder = Protein Disorder 
 label.source_from_db_source = Sources from {0}
 label.from_msname = from {0}
-label.superpose_with = Superpose with ...
+label.superpose_with = Superpose with
 action.do = Do
 label.scale_label_to_column = Scale Label to Column
 label.add_new_row = Add New Row
@@ -1187,7 +1199,8 @@ label.select_feature_colour = Select Feature Colour
 label.delete_all = Delete all sequences
 warn.delete_all = <html>Deleting all sequences will close the alignment window.<br>Confirm deletion or Cancel.
 label.add_annotations_for = Add annotations for
-label.choose_annotations = Choose annotations
+action.choose_annotations = Choose Annotations...
+label.choose_annotations = Choose Annotations
 label.find = Find
 label.invalid_search = Search string invalid
 error.invalid_regex = Invalid regular expression

diff --git a/src/MCview/PDBViewer.java b/src/MCview/PDBViewer.java
index f9c7602..12367b2 100755 (executable)
--- a/src/MCview/PDBViewer.java
+++ b/src/MCview/PDBViewer.java
@@ -329,8 +329,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
       }
     });
     viewMenu.setText(MessageManager.getString("action.view"));
-    background.setText(MessageManager.getString("label.background_colour")
-            + "...");
+    background.setText(MessageManager.getString("action.background_colour"));
     background.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 9e16329..30f2e7f 100644 (file)
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -175,10 +175,10 @@ public class APopupMenu extends java.awt.PopupMenu implements
           MessageManager.getString("label.edit_sequence"));
 
   MenuItem sequenceDetails = new MenuItem(
-          MessageManager.getString("label.sequence_details") + "...");
+          MessageManager.getString("label.sequence_details"));
 
   MenuItem selSeqDetails = new MenuItem(
-          MessageManager.getString("label.sequence_details") + "...");
+          MessageManager.getString("label.sequence_details"));
 
   MenuItem makeReferenceSeq = new MenuItem();
   

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 698fafc..0861f2d 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -2991,10 +2991,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
           MessageManager.getString("label.load_features_annotations"));
 
   MenuItem outputFeatures = new MenuItem(
-          MessageManager.getString("label.export_features").concat("..."));
+          MessageManager.getString("label.export_features"));
 
   MenuItem outputAnnotations = new MenuItem(
-          MessageManager.getString("label.export_annotations").concat("..."));
+          MessageManager.getString("label.export_annotations"));
 
   MenuItem closeMenuItem = new MenuItem(
           MessageManager.getString("action.close"));
@@ -3243,8 +3243,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     removeAllGapsMenuItem.setLabel(MessageManager
             .getString("action.remove_all_gaps"));
     removeAllGapsMenuItem.addActionListener(this);
-    removeRedundancyMenuItem.setLabel(MessageManager.getString(
-            "action.remove_redundancy").concat("..."));
+    removeRedundancyMenuItem.setLabel(MessageManager
+            .getString("action.remove_redundancy"));
     removeRedundancyMenuItem.addActionListener(this);
 
     /*
@@ -3268,7 +3268,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     grpsFromSelection.addActionListener(this);
     createGroup.setLabel(MessageManager.getString("action.create_group"));
     unGroup.setLabel(MessageManager.getString("action.remove_group"));
-    annotationColumnSelection.setLabel("Select by Annotation");
+    annotationColumnSelection.setLabel(MessageManager
+            .getString("action.select_by_annotation"));
     annotationColumnSelection.addActionListener(this);
 
     /*
@@ -3298,7 +3299,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     hideAllSelection.addActionListener(this);
     showAllHidden.addActionListener(this);
     featureSettings.setLabel(MessageManager
-            .getString("label.feature_settings"));
+            .getString("action.feature_settings"));
     featureSettings.addActionListener(this);
     sequenceFeatures.setLabel(MessageManager
             .getString("label.show_sequence_features"));

diff --git a/src/jalview/appletgui/AnnotationColumnChooser.java b/src/jalview/appletgui/AnnotationColumnChooser.java
index 0375de2..6ad8648 100644 (file)
--- a/src/jalview/appletgui/AnnotationColumnChooser.java
+++ b/src/jalview/appletgui/AnnotationColumnChooser.java
@@ -783,7 +783,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
 
       });
 
-      displayName.setLabel(MessageManager.getString("label.display_name"));
+      displayName.setLabel(MessageManager.getString("label.label"));
       displayName.setEnabled(false);
       displayName.addItemListener(this);
 

diff --git a/src/jalview/appletgui/FeatureSettings.java b/src/jalview/appletgui/FeatureSettings.java
index 2b79256..f1e9835 100755 (executable)
--- a/src/jalview/appletgui/FeatureSettings.java
+++ b/src/jalview/appletgui/FeatureSettings.java
@@ -179,7 +179,8 @@ public class FeatureSettings extends Panel implements ItemListener,
     height = Math.min(400, height);
     int width = 300;
     jalview.bin.JalviewLite.addFrame(frame,
-            MessageManager.getString("label.feature_settings"), width,
+            MessageManager.getString("label.sequence_feature_settings"),
+            width,
             height);
   }
 

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 45b5394..4e11581 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -1128,7 +1128,7 @@ public class PopupMenu extends JPopupMenu
       }
     });
     chooseAnnotations.setText(MessageManager
-            .getString("label.choose_annotations") + "...");
+            .getString("action.choose_annotations"));
     chooseAnnotations.addActionListener(new java.awt.event.ActionListener()
     {
       @Override
@@ -1138,7 +1138,7 @@ public class PopupMenu extends JPopupMenu
       }
     });
     sequenceDetails.setText(MessageManager
-            .getString("label.sequence_details") + "...");
+            .getString("label.sequence_details"));
     sequenceDetails.addActionListener(new java.awt.event.ActionListener()
     {
       @Override
@@ -1148,7 +1148,7 @@ public class PopupMenu extends JPopupMenu
       }
     });
     sequenceSelDetails.setText(MessageManager
-            .getString("label.sequence_details") + "...");
+            .getString("label.sequence_details"));
     sequenceSelDetails
             .addActionListener(new java.awt.event.ActionListener()
             {

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 7177e43..a806183 100755 (executable)
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -244,7 +244,7 @@ public class TreePanel extends GTreePanel
     }
 
     final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
-            "label.all_views");
+            MessageManager.getString("label.all_views"));
     buttonGroup.add(itemf);
     itemf.setSelected(treeCanvas.applyToAllViews);
     itemf.addActionListener(new ActionListener()

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index c6a042b..3504ea4 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -454,7 +454,7 @@ public class GAlignFrame extends JInternalFrame
   private void jbInit() throws Exception
   {
     JMenuItem saveAs = new JMenuItem(
-            MessageManager.getString("action.save_as") + "...");
+            MessageManager.getString("action.save_as"));
     ActionListener al = new ActionListener()
     {
       @Override
@@ -704,7 +704,7 @@ public class GAlignFrame extends JInternalFrame
     });
 
     JMenuItem removeRedundancyMenuItem = new JMenuItem(MessageManager
-            .getString("action.remove_redundancy").concat("..."));
+.getString("action.remove_redundancy"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D, Toolkit
             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
@@ -1124,7 +1124,7 @@ public class GAlignFrame extends JInternalFrame
     });
 
     JMenuItem printMenuItem = new JMenuItem(
-            MessageManager.getString("action.print") + "...");
+            MessageManager.getString("action.print"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P, Toolkit
             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
@@ -1687,7 +1687,7 @@ public class GAlignFrame extends JInternalFrame
     });
 
     JMenuItem extractScores = new JMenuItem(
-            MessageManager.getString("label.extract_scores") + "...");
+            MessageManager.getString("label.extract_scores"));
     extractScores.addActionListener(new ActionListener()
     {
       @Override
@@ -1703,7 +1703,7 @@ public class GAlignFrame extends JInternalFrame
     showProducts.setText(MessageManager.getString("label.get_cross_refs"));
 
     JMenuItem openFeatureSettings = new JMenuItem(
-            MessageManager.getString("label.feature_settings"));
+            MessageManager.getString("action.feature_settings"));
     openFeatureSettings.addActionListener(new ActionListener()
     {
       @Override
@@ -2051,7 +2051,7 @@ public class GAlignFrame extends JInternalFrame
             + MessageManager.getString("label.rename_tab_eXpand_reGroup")
             + "</i></html>");
     JMenuItem textColour = new JMenuItem(
-            MessageManager.getString("label.colour_text") + "...");
+            MessageManager.getString("action.set_text_colour"));
     textColour.addActionListener(new ActionListener()
     {
       @Override
@@ -2100,7 +2100,7 @@ public class GAlignFrame extends JInternalFrame
     addMenuActionAndAccelerator(keyStroke, expandViews, al);
 
     JMenuItem pageSetup = new JMenuItem(
-            MessageManager.getString("action.page_setup") + "...");
+            MessageManager.getString("action.page_setup"));
     pageSetup.addActionListener(new ActionListener()
     {
       @Override
@@ -2110,7 +2110,7 @@ public class GAlignFrame extends JInternalFrame
       }
     });
     JMenuItem alignmentProperties = new JMenuItem(
-            MessageManager.getString("label.alignment_props") + "...");
+            MessageManager.getString("label.alignment_props"));
     alignmentProperties.addActionListener(new ActionListener()
     {
       @Override

diff --git a/src/jalview/jbgui/GDesktop.java b/src/jalview/jbgui/GDesktop.java
index 7a55444..1c37e86 100755 (executable)
--- a/src/jalview/jbgui/GDesktop.java
+++ b/src/jalview/jbgui/GDesktop.java
@@ -209,8 +209,7 @@ public class GDesktop extends JFrame
             });
     this.getContentPane().setLayout(flowLayout1);
     windowMenu.setText(MessageManager.getString("label.window"));
-    preferences.setText(MessageManager.getString("label.preferences")
-            + "...");
+    preferences.setText(MessageManager.getString("label.preferences"));
     preferences.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -237,7 +236,7 @@ public class GDesktop extends JFrame
     });
     inputMenu.setText(MessageManager.getString("label.input_alignment"));
     vamsasStart.setText(MessageManager
-            .getString("label.new_vamsas_session") + "...");
+            .getString("label.new_vamsas_session"));
     vamsasStart.setVisible(false);
     vamsasStart.addActionListener(new ActionListener()
     {
@@ -247,7 +246,7 @@ public class GDesktop extends JFrame
       }
     });
     vamsasImport.setText(MessageManager
-            .getString("label.load_vamsas_session") + "...");
+            .getString("action.load_vamsas_session"));
     vamsasImport.setVisible(false);
     vamsasImport.addActionListener(new ActionListener()
     {
@@ -257,7 +256,7 @@ public class GDesktop extends JFrame
       }
     });
     vamsasSave.setText(MessageManager
-            .getString("label.save_vamsas_session") + "...");
+            .getString("action.save_vamsas_session"));
     vamsasSave.setVisible(false);
     vamsasSave.addActionListener(new ActionListener()
     {
@@ -266,8 +265,8 @@ public class GDesktop extends JFrame
         vamsasSave_actionPerformed(e);
       }
     });
-    inputSequence.setText(MessageManager.getString("label.fetch_sequences")
-            + "...");
+    inputSequence.setText(MessageManager
+            .getString("action.fetch_sequences"));
     inputSequence.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)

diff --git a/src/jalview/jbgui/GPCAPanel.java b/src/jalview/jbgui/GPCAPanel.java
index 9fa7d06..0bc6cac 100755 (executable)
--- a/src/jalview/jbgui/GPCAPanel.java
+++ b/src/jalview/jbgui/GPCAPanel.java
@@ -22,11 +22,24 @@ package jalview.jbgui;
 
 import jalview.util.MessageManager;
 
-import java.awt.*;
-import java.awt.event.*;
-
-import javax.swing.*;
-import javax.swing.event.*;
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.FlowLayout;
+import java.awt.GridLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import javax.swing.JButton;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JComboBox;
+import javax.swing.JInternalFrame;
+import javax.swing.JLabel;
+import javax.swing.JMenu;
+import javax.swing.JMenuBar;
+import javax.swing.JMenuItem;
+import javax.swing.JPanel;
+import javax.swing.event.MenuEvent;
+import javax.swing.event.MenuListener;
 
 public class GPCAPanel extends JInternalFrame
 {
@@ -195,7 +208,7 @@ public class GPCAPanel extends JInternalFrame
       }
     });
     outputProjPoints.setText(MessageManager
-            .getString("label.output_transformed_points") + "...");
+            .getString("label.output_transformed_points"));
     outputProjPoints.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -252,8 +265,7 @@ public class GPCAPanel extends JInternalFrame
       }
     });
     print.setText(MessageManager.getString("action.print"));
-    bgcolour.setText(MessageManager.getString("label.background_colour")
-            + "...");
+    bgcolour.setText(MessageManager.getString("action.background_colour"));
     bgcolour.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)

diff --git a/src/jalview/jbgui/GStructureViewer.java b/src/jalview/jbgui/GStructureViewer.java
index 7885f74..982036d 100644 (file)
--- a/src/jalview/jbgui/GStructureViewer.java
+++ b/src/jalview/jbgui/GStructureViewer.java
@@ -166,8 +166,7 @@ public abstract class GStructureViewer extends JInternalFrame implements
     colourMenu.setText(MessageManager.getString("label.colours"));
 
     JMenuItem backGround = new JMenuItem();
-    backGround.setText(MessageManager.getString("label.background_colour")
-            + "...");
+    backGround.setText(MessageManager.getString("action.background_colour"));
     backGround.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent actionEvent)

diff --git a/src/jalview/jbgui/GTreePanel.java b/src/jalview/jbgui/GTreePanel.java
index d067753..fa5e905 100755 (executable)
--- a/src/jalview/jbgui/GTreePanel.java
+++ b/src/jalview/jbgui/GTreePanel.java
@@ -199,8 +199,7 @@ public class GTreePanel extends JInternalFrame
         placeholdersMenu_actionPerformed(e);
       }
     });
-    textbox.setText(MessageManager.getString("label.out_to_textbox")
-            + "...");
+    textbox.setText(MessageManager.getString("label.out_to_textbox"));
     textbox.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)

diff --git a/src/jalview/ws/jws2/AAConClient.java b/src/jalview/ws/jws2/AAConClient.java
index 09fb6ae..b9abb84 100644 (file)
--- a/src/jalview/ws/jws2/AAConClient.java
+++ b/src/jalview/ws/jws2/AAConClient.java
@@ -22,8 +22,7 @@ package jalview.ws.jws2;
 
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.gui.AlignFrame;
-import jalview.gui.AlignmentPanel;
-import jalview.ws.jws2.dm.AAConSettings;
+import jalview.util.MessageManager;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
 import jalview.ws.params.WsParamSetI;
 import jalview.ws.uimodel.AlignAnalysisUIText;
@@ -121,9 +120,9 @@ public class AAConClient extends JabawsCalcWorker
     return new AlignAnalysisUIText(
             compbio.ws.client.Services.AAConWS.toString(),
             jalview.ws.jws2.AAConClient.class, CALC_ID, false, true, true,
-            "AACon Calculations",
-            "When checked, AACon calculations are updated automatically.",
-            "Change AACon Settings...",
-            "Modify settings for AACon calculations.");
+            MessageManager.getString("label.aacon_calculations"),
+            MessageManager.getString("tooltip.aacon_calculations"),
+            MessageManager.getString("label.aacon_settings"),
+            MessageManager.getString("tooltip.aacon_settings"));
   }
 }

diff --git a/src/jalview/ws/jws2/RNAalifoldClient.java b/src/jalview/ws/jws2/RNAalifoldClient.java
index 55ade66..ca1fd50 100644 (file)
--- a/src/jalview/ws/jws2/RNAalifoldClient.java
+++ b/src/jalview/ws/jws2/RNAalifoldClient.java
@@ -24,7 +24,7 @@ import jalview.api.AlignCalcWorkerI;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
 import jalview.gui.AlignFrame;
-import jalview.ws.jws2.dm.AAConSettings;
+import jalview.util.MessageManager;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
 import jalview.ws.params.WsParamSetI;
 import jalview.ws.uimodel.AlignAnalysisUIText;
@@ -36,8 +36,8 @@ import java.util.List;
 import java.util.TreeSet;
 import java.util.regex.Pattern;
 
-import compbio.data.sequence.RNAStructReader.AlifoldResult;
 import compbio.data.sequence.FastaSequence;
+import compbio.data.sequence.RNAStructReader.AlifoldResult;
 import compbio.data.sequence.RNAStructScoreManager;
 import compbio.data.sequence.Range;
 import compbio.data.sequence.Score;
@@ -86,16 +86,11 @@ public class RNAalifoldClient extends JabawsCalcWorker implements
   {
     return new AlignAnalysisUIText(
             compbio.ws.client.Services.RNAalifoldWS.toString(),
-            jalview.ws.jws2.RNAalifoldClient.class,
-            CALC_ID,
-            true,
-            false,
-            true,
-            "RNAAliFold Prediction",
-            "When checked, RNA secondary structure predictions will be calculated for the alignment, and updated when edits are made.",
-            "Change RNAAliFold settings...",
-            "Modify settings for the RNAAliFold prediction. Use this to hide or show different results of the RNA calculation, and change RNA folding parameters");
-
+            jalview.ws.jws2.RNAalifoldClient.class, CALC_ID, true, false,
+            true, MessageManager.getString("label.rnalifold_calculations"),
+            MessageManager.getString("tooltip.rnalifold_calculations"),
+            MessageManager.getString("label.rnalifold_settings"),
+            MessageManager.getString("tooltip.rnalifold_settings"));
   }
 
   @Override
@@ -185,11 +180,15 @@ public class RNAalifoldClient extends JabawsCalcWorker implements
      * same data object as was overwritten with the contact probabilites data.
      */
     if (data == null)
+    {
       data = compbio.data.sequence.RNAStructReader
               .newEmptyScore(AlifoldResult.consensusAlignment);
+    }
 
     if (descriptionData == null)
+    {
       descriptionData = data;
+    }
 
     String[] typenameAndDescription = constructTypenameAndDescription(descriptionData
             .first());
@@ -269,7 +268,9 @@ public class RNAalifoldClient extends JabawsCalcWorker implements
           {
             float t = contacts.get(contact);
             if (t > prob)
+            {
               prob = t;
+            }
             description += Integer.toString(contact.from) + "->"
                     + Integer.toString(contact.to) + ": "
                     + Float.toString(t) + "%  |  ";
@@ -349,7 +350,9 @@ public class RNAalifoldClient extends JabawsCalcWorker implements
                 score.getScores().get(0), score.getScores().get(1));
       }
       else
+      {
         description = "Stochastic Backtrack Structure";
+      }
     }
     else if (datatype.equals(AlifoldResult.MEAStucture.toString()))
     {
@@ -386,7 +389,9 @@ public class RNAalifoldClient extends JabawsCalcWorker implements
       // ordering of the Scores TreeSet in ScoreManager which is, descending
       // probability
       if (contact.from == i || contact.to == i)
+      {
         contacts.put(contact, basePairs.get(contact));
+      }
     }
 
     return contacts;