X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=resources%2Flang%2FMessages.properties;h=1f5d4cbfaec2b20c57b1220ab0b6b63e3eb1250e;hb=6066400ed6b0fe288ebbea82389f59838a534706;hp=0f935ca7e947be757906707310e38fd04301a519;hpb=c920b3c897f5d20d839a3fc84c2bfa097970b5d1;p=jalview.git
diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index 0f935ca..1f5d4cb 100644
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -21,7 +21,7 @@ action.edit = Edit
action.new = New
action.open_file = Open file
action.show_unconserved = Show Unconserved
-action.open_new_aligmnent = Open new alignment
+action.open_new_alignment = Open new alignment
action.raise_associated_windows = Raise Associated Windows
action.minimize_associated_windows = Minimize Associated Windows
action.close_all = Close all
@@ -57,8 +57,10 @@ 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.remove_redundancy = Remove Redundancy...
action.pairwise_alignment = Pairwise Alignments...
action.by_rna_helixes = by RNA Helices
action.user_defined = User Defined...
@@ -102,11 +104,12 @@ action.find_all = Find all
action.find_next = Find next
action.file = File
action.view = View
+action.annotations = Annotations
action.change_params = Change Parameters
action.apply = Apply
action.apply_threshold_all_groups = Apply threshold to all groups
action.apply_all_groups = Apply to all Groups
-action.by_chain = By chain
+action.by_chain = By Chain
action.by_sequence = By Sequence
action.paste_annotations = Paste Annotations
action.format = Format
@@ -118,7 +121,7 @@ action.save_as_default = Save as default
action.save_as = Save as
action.save = Save
action.cancel_fetch = Cancel Fetch
-action.save_omit_hidden_columns = Save / Omit Hidden Columns
+action.save_omit_hidden_columns = Save / Omit Hidden Regions
action.change_font = Change Font
action.change_font_tree_panel = Change Font (Tree Panel)
action.colour = Colour
@@ -198,6 +201,14 @@ label.tcoffee_scores = T-Coffee Scores
label.average_distance_bloslum62 = Average Distance Using BLOSUM62
label.neighbour_blosum62 = Neighbour Joining Using BLOSUM62
label.show_annotations = Show annotations
+label.hide_annotations = Hide annotations
+label.show_all_seq_annotations = Show sequence related
+label.hide_all_seq_annotations = Hide sequence related
+label.show_all_al_annotations = Show alignment related
+label.hide_all_al_annotations = Hide alignment related
+label.hide_all = Hide all
+label.add_reference_annotations = Add reference annotations
+label.find_tip = Search alignment, selection or sequence ids for a subsequence (ignoring gaps).
Accepts regular expressions - search Help for 'regex' for details.
label.colour_text = Colour Text
label.show_non_conversed = Show nonconserved
label.overview_window = Overview Window
@@ -205,6 +216,7 @@ label.none = None
label.above_identity_threshold = Above Identity Threshold
label.show_sequence_features = Show Sequence Features
label.nucleotide = Nucleotide
+label.protein = Protein
label.to_new_alignment = To New Alignment
label.to_this_alignment = Add To This Alignment
label.apply_colour_to_all_groups = Apply Colour To All Groups
@@ -217,14 +229,17 @@ label.documentation = Documentation
label.about = About...
label.show_sequence_limits = Show Sequence Limits
label.feature_settings = Feature Settings...
-label.sequence_features = Sequence Features
label.all_columns = All Columns
label.all_sequences = All Sequences
label.selected_columns = Selected Columns
label.selected_sequences = Selected Sequences
+label.except_selected_sequences = All except selected sequences
label.all_but_selected_region = All but Selected Region (Shift+Ctrl+H)
label.selected_region = Selected Region
label.all_sequences_columns = All Sequences and Columns
+label.hide_insertions = Hide columns gapped for selection
+label.hide_selected_annotations = Hide selected annotations
+label.show_selected_annotations = Show selected annotations
label.group_consensus = Group Consensus
label.group_conservation = Group Conservation
label.show_consensus_histogram = Show Consensus Histogram
@@ -232,6 +247,18 @@ label.show_consensus_logo = Show Consensus Logo
label.norm_consensus_logo = Normalise Consensus Logo
label.apply_all_groups = Apply to all groups
label.autocalculated_annotation = Autocalculated Annotation
+label.show_first = Show first
+label.show_last = Show last
+label.struct_from_pdb = Process secondary structure from PDB
+label.use_rnaview = Use RNAView for secondary structure
+label.autoadd_secstr = Add secondary structure annotation to alignment
+label.autoadd_temp = Add Temperature Factor annotation to alignment
+label.structure_viewer = Default structure viewer
+label.chimera_path = Path to Chimera program
+label.chimera_path_tip = Jalview will first try any path entered here, else standard installation locations.
Double-click to browse for file.
+label.invalid_chimera_path = Chimera path not found or not executable
+label.chimera_missing = Chimera structure viewer not found.
Please enter the path to Chimera (if installed),
or download and install UCSF Chimera.
+label.chimera_failed = Error opening Chimera - is it installed?\nCheck path in Preferences, Structure
label.min_colour = Minimum Colour
label.max_colour = Maximum Colour
label.use_original_colours = Use Original Colours
@@ -325,7 +352,7 @@ label.dont_ask_me_again = Don't ask me again
label.select_eps_character_rendering_style = Select EPS character rendering style
label.invert_selection = Invert Selection
label.optimise_order = Optimise Order
-label.seq_sort_by_score = Seq sort by Score
+label.seq_sort_by_score = Sequence sort by Score
label.load_colours = Load Colours
label.save_colours = Save Colours
label.fetch_das_features = Fetch DAS Features
@@ -335,7 +362,7 @@ label.example = Example
label.example_param = Example: {0}
label.select_file_format_before_saving = You must select a file format before saving!
label.file_format_not_specified = File format not specified
-label.alignment_contains_hidden_columns = The Alignment contains hidden columns.\nDo you want to save only the visible alignment?
+label.alignment_contains_hidden_columns = The Alignment contains hidden regions (hidden sequences/columns).\nDo you want to save only the visible alignment?
label.couldnt_save_file = Couldn't save file: {0}
label.error_saving_file = Error Saving File
label.remove_from_default_list = Remove from default list?
@@ -360,6 +387,7 @@ label.automatically_associate_pdb_files_with_sequences_same_name = Do you want t
label.automatically_associate_pdb_files_by_name = Automatically Associate PDB files by name
label.ignore_unmatched_dropped_files_info = Do you want to ignore the {0} files whose names did not match any sequence IDs ?
label.ignore_unmatched_dropped_files = Ignore unmatched dropped files?
+label.view_name_original = Original
label.enter_view_name = Enter View Name
label.enter_label = Enter label
label.enter_label_for_the_structure = Enter a label for the structure?
@@ -367,7 +395,7 @@ label.pdb_entry_is_already_displayed = {0} is already displayed.\nDo you want to
label.map_sequences_to_visible_window = Map Sequences to Visible Window: {0}
label.add_pdbentry_to_view = Do you want to add {0} to the view called\n{1}\n
label.align_to_existing_structure_view = Align to existing structure view
-label.pdb_entries_couldnt_be_retrieved = The following pdb entries could not be retrieved from the PDB\:\n{0}\nPlease try downloading them manually.
+label.pdb_entries_couldnt_be_retrieved = The following pdb entries could not be retrieved from the PDB\:\n{0}\nPlease retry, or try downloading them manually.
label.couldnt_load_file = Couldn't load file
label.couldnt_find_pdb_id_in_file = Couldn't find a PDB id in the file supplied. Please enter an Id to identify this structure.
label.no_pdb_id_in_file = No PDB Id in File
@@ -405,6 +433,7 @@ label.input_cut_paste = Cut & Paste Input
label.input_cut_paste_params = Cut & Paste Input - {0}
label.alignment_output_command = Alignment output - {0}
label.annotations = Annotations
+label.structure_options = Structure Options
label.features = Features
label.overview_params = Overview {0}
label.paste_newick_file = Paste Newick file
@@ -418,8 +447,8 @@ label.redundancy_threshold_selection = Redundancy threshold selection
label.user_defined_colours = User defined colours
label.jalviewLite_release = JalviewLite - Release {0}
label.jaview_build_date = Build date: {0}
-label.jalview_authors_1 = Authors: : Jim Procter, Andrew Waterhouse, Lauren Lui, Jan Engelhardt, Natasha Sherstnev,
-label.jalview_authors_2 = Daniel Barton, Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton.
+label.jalview_authors_1 = Authors: Jim Procter, Andrew Waterhouse, Mungo Carstairs, Tochukwu Ofoegbu, Lauren Lui, Jan Engelhardt,
+label.jalview_authors_2 = Natasha Sherstnev, Daniel Barton, Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton.
label.jalview_dev_managers = Development managed by The Barton Group, University of Dundee, Scotland, UK.
label.jalview_distribution_lists = For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list
label.jalview_please_cite = If you use Jalview, please cite:
@@ -455,10 +484,8 @@ 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.jalview_copy = Copy (Jalview Only)
-label.jalview_cut = Cut (Jalview Only)
+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
@@ -468,11 +495,18 @@ label.edit_sequence = Edit Sequence
label.edit_sequences = Edit Sequences
label.sequence_details = Sequence Details
label.jmol_help = Jmol Help
+label.chimera_help = Chimera Help
+label.close_viewer = Close Viewer
+label.confirm_close_chimera = This will close Jalview''s connection to {0}.
Do you want to close the Chimera window as well?
+label.chimera_help = Chimera Help
label.all = All
-label.sort_by = Sort by
+label.sort_by = Sort alignment by
label.sort_by_score = Sort by Score
label.sort_by_density = Sort by Density
label.sequence_sort_by_density = Sequence sort by Density
+label.sort_ann_by = Sort annotations by
+label.sort_annotations_by_sequence = Sort by sequence
+label.sort_annotations_by_label = Sort by label
label.reveal = Reveal
label.hide_columns = Hide Columns
label.load_jalview_annotations = Load Jalview Annotations or Features File
@@ -492,7 +526,7 @@ label.toggle_absolute_relative_display_threshold = Toggle between absolute and r
label.display_features_same_type_different_label_using_different_colour = Display features of the same type with a different label using a different colour. (e.g. domain features)
label.select_colour_minimum_value = Select Colour for Minimum Value
label.select_colour_maximum_value = Select Colour for Maximum Value
-label.open_new_jmol_view_with_all_structures_associated_current_selection_superimpose_using_alignment = Open a new Jmol view with all structures associated with the current selection and superimpose them using the alignment.
+label.open_new_jmol_view_with_all_structures_associated_current_selection_superimpose_using_alignment = Open a new structure viewer with all structures associated with the current selection and superimpose them using the alignment.
label.open_url_param = Open URL {0}
label.open_url_seqs_param = Open URL ({0}..) ({1} seqs)
label.load_pdb_file_associate_with_sequence = Load a PDB file and associate it with sequence {0}
@@ -501,7 +535,10 @@ label.dark_colour = Dark Colour
label.light_colour = Light Colour
label.highlightnode = Left click to select leaves.
Double-click to invert leaves.
Right click to change colour.
label.load_colour_scheme = Load colour scheme
+label.copy_format_from = Copy format from
label.toggle_enabled_views = When enabled, allows many views to be selected.
+label.select_all_views = Select all views
+label.select_many_views = Select many views
label.edit_notes_parameter_set = Click to edit the notes for this parameter set.
label.open_local_file = Open local file
label.enable_automatically_sort_alignment_when_open_new_tree = Enable this to automatically sort
the alignment when you open
a new tree.
@@ -541,12 +578,13 @@ label.conservation = Conservation
label.consensus = Consensus
label.histogram = Histogram
label.logo = Logo
-label.non_positional_features = Non-positional Features
-label.database_references = Database References
+label.non_positional_features = List Non-positional Features
+label.database_references = List Database References
label.share_selection_across_views = Share selection across views
label.scroll_highlighted_regions = Scroll to highlighted regions
label.gap_symbol = Gap Symbol
-label.alignment_colour = Alignment Colour
+label.prot_alignment_colour = Protein Alignment Colour
+label.nuc_alignment_colour = Nucleotide Alignment Colour
label.address = Address
label.port = Port
label.default_browser_unix = Default Browser (Unix)
@@ -567,7 +605,7 @@ label.figure_id_column_width = Figure ID column width
label.use_modeller_output = Use Modeller Output
label.wrap_alignment = Wrap Alignment
label.right_align_ids = Right Align Ids
-label.sequence_name_italics = Sequence Name Italics
+label.sequence_name_italics = Italic Sequence Ids
label.open_overview = Open Overview
label.default_colour_scheme_for_alignment = Default Colour Scheme for alignment
label.annotation_shading_default = Annotation Shading Default
@@ -581,6 +619,7 @@ label.das_settings = DAS Settings
label.web_services = Web Services
label.right_click_to_edit_currently_selected_parameter = Right click to edit currently selected parameter.
label.let_jmol_manage_structure_colours = Let Jmol manage structure colours
+label.let_chimera_manage_structure_colours = Let Chimera manage structure colours
label.marks_leaves_tree_not_associated_with_sequence = Marks leaves of tree not associated with a sequence
label.index_web_services_menu_by_host_site = Index web services in menu by the host site
label.option_want_informed_web_service_URL_cannot_be_accessed_jalview_when_starts_up = Check this option if you want to be informed
when a web service URL cannot be accessed by Jalview
when it starts up
@@ -629,7 +668,7 @@ label.edit_name_and_description_current_group = Edit name and description of cur
label.view_structure_for = View structure for {0}
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 Jmol view with all representative structures\nassociated with the current selection\nsuperimposed with the current alignment.
+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.enter_pdb_id = Enter PDB Id
@@ -637,10 +676,12 @@ label.discover_pdb_ids = Discover PDB ids
label.text_colour = Text Colour
label.structure = Structure
label.view_structure = View Structure
+label.view_protein_structure = View Protein Structure
+label.view_rna_structure = View Nucleotide Structure
label.clustalx_colours = Clustalx colours
label.above_identity_percentage = Above % Identity
label.create_sequence_details_report_annotation_for = Annotation for {0}
-label.sequece_details_for = Sequece Details for {0}
+label.sequence_details_for = Sequence Details for {0}
label.sequence_name = Sequence Name
label.sequence_description = Sequence Description
label.edit_sequence_name_description = Edit Sequence Name/Description
@@ -658,12 +699,15 @@ label.save_png_image = Save As PNG Image
label.load_tree_for_sequence_set = Load a tree for this sequence set
label.export_image = Export Image
label.vamsas_store = VAMSAS store
-label.translate_cDNA = Translate cDNA
+label.translate_cDNA = Translate as cDNA
+label.linked_view_title = Linked cDNA and protein view
+label.align = Align
label.extract_scores = Extract Scores
-label.get_cross_refs = Get Cross References
+label.get_cross_refs = Get Cross-References
label.sort_alignment_new_tree = Sort Alignment With New Tree
label.add_sequences = Add Sequences
label.new_window = New Window
+label.split_window = Split Window
label.refresh_available_sources = Refresh Available Sources
label.use_registry = Use Registry
label.add_local_source = Add Local Source
@@ -675,8 +719,10 @@ 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.jmol = Jmol
+label.chimera = Chimera
label.sort_alignment_by_tree = Sort Alignment By Tree
label.mark_unlinked_leaves = Mark Unlinked Leaves
label.associate_leaves_with = Associate Leaves With
@@ -700,7 +746,7 @@ 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.select_all_views = Select all views
+label.all_views = All Views
label.align_sequences_to_existing_alignment = Align sequences to an existing alignment
label.realign_with_params = Realign with {0}
label.calcname_with_default_settings = {0} with Defaults
@@ -725,7 +771,9 @@ label.transformed_points_for_params = Transformed points for {0}
label.graduated_color_for_params = Graduated Feature Colour for {0}
label.select_backgroud_colour = Select Background Colour
label.invalid_font = Invalid Font
-label.separate_multiple_accession_ids = Separate multiple accession ids with semi colon ";"
+label.separate_multiple_accession_ids = Enter one or more PDB Ids
+label.separate_multiple_query_values = Enter one or more {0}s separated by a semi-colon ";"
+label.search_all = Enter one or more search values separated by a semi-colon ";" (Note: This Searches the entire PDB database)
label.replace_commas_semicolons = Replace commas with semi-colons
label.parsing_failed_syntax_errors_shown_below_param = Parsing failed. Syntax errors shown below {0}
label.parsing_failed_unrecoverable_exception_thrown_param = \nParsing failed. An unrecoverable exception was thrown\:\n {0}
@@ -742,13 +790,14 @@ label.use_sequence_id_1 = Use $SEQUENCE_ID$ or $SEQUENCE_ID=//=$
label.use_sequence_id_2 = \nto embed sequence id in URL
label.ws_parameters_for = Parameters for {0}
label.switch_server = Switch server
-label.open_jabaws_web_page = Opens the JABAWS server's homepage in web browser
label.choose_jabaws_server = Choose a server for running this service
label.services_at = Services at {0}
label.rest_client_submit = {0} using {1}
label.fetch_retrieve_from =Retrieve from {0}