From c86442e455c858f4a092fbb2e9394faa3e161a89 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Sun, 6 Sep 2015 14:47:57 +0100 Subject: [PATCH] =?utf8?q?JAL-1645=20JAL-1355=20UI/i18n:=20added=20missing=20?= =?utf8?q?messages,=20moved=20=E2=80=98=E2=80=A6=E2=80=99=20into=20action=20?= =?utf8?q?messages=20for=20actions=20needing=20more=20user=20input,=20title=20?= =?utf8?q?caps=20for=20menu=20entries=20and=20dialog=20titles?= MIME-Version: 1.0 Content-Type: text/plain; charset=utf8 Content-Transfer-Encoding: 8bit --- resources/lang/Messages.properties | 83 +++++++++++--------- src/MCview/PDBViewer.java | 3 +- src/jalview/appletgui/APopupMenu.java | 4 +- src/jalview/appletgui/AlignFrame.java | 13 +-- src/jalview/appletgui/AnnotationColumnChooser.java | 2 +- src/jalview/appletgui/FeatureSettings.java | 3 +- src/jalview/gui/PopupMenu.java | 6 +- src/jalview/gui/TreePanel.java | 2 +- src/jalview/jbgui/GAlignFrame.java | 16 ++-- src/jalview/jbgui/GDesktop.java | 13 ++- src/jalview/jbgui/GPCAPanel.java | 28 +++++-- src/jalview/jbgui/GStructureViewer.java | 3 +- src/jalview/jbgui/GTreePanel.java | 3 +- src/jalview/ws/jws2/AAConClient.java | 11 ++- src/jalview/ws/jws2/RNAalifoldClient.java | 29 ++++--- 15 files changed, 123 insertions(+), 96 deletions(-) diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties index a4f6497..05d6427 100644 --- 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. 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 = View {1} label.submit_sequence = Submit {0} {1} {2} {3} to
{4} -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 = Deleting all sequences will close the alignment window.
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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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") + ""); 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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; -- 1.7.10.2