X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=resources%2Flang%2FMessages.properties;h=a23bc0066b29898fbcf63c0e848868f92c41bd51;hb=6d431e1a1f18894d35c9881fe5a45ffd6bfccf67;hp=b93acdce17c4c4d64f64ac5b107acbf92b627803;hpb=14869d2b36336f1fa3e135d83abe64059ad63300;p=jalview.git diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties index b93acdc..a23bc00 100644 --- a/resources/lang/Messages.properties +++ b/resources/lang/Messages.properties @@ -80,7 +80,8 @@ action.scale_left = Scale Left action.scale_right = Scale Right action.by_tree_order = By Tree Order action.sort = Sort -action.calculate_tree = Calculate Tree +action.calculate_tree = Calculate Tree... +action.calculate_tree_pca = Calculate Tree or PCA... action.help = Help action.by_annotation = By Annotation... action.invert_sequence_selection = Invert Sequence Selection @@ -117,10 +118,8 @@ action.select = Select 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 = Save -action.cancel_fetch = Cancel Fetch action.change_font = Change Font action.change_font_tree_panel = Change Font (Tree Panel) action.colour = Colour @@ -139,7 +138,6 @@ action.fetch_db_references = Fetch DB References action.view_flanking_regions = Show flanking regions label.view_flanking_regions = Show sequence data either side of the subsequences involved in this alignment label.structures_manager = Structures Manager -label.nickname = Nickname: label.url = URL label.url\: = URL: label.input_file_url = Enter URL or Input File @@ -161,7 +159,6 @@ label.current_parameter_set_name = Current parameter set name: label.service_action = Service Action: label.post_url = POST URL: label.url_suffix = URL Suffix -label.sequence_source = Sequence Source label.per_seq = per Sequence label.result_vertically_separable = Results are vertically separable label.amend = Amend @@ -170,6 +167,7 @@ label.redo_command = Redo {0} label.principal_component_analysis = Principal Component Analysis label.average_distance_identity = Average Distance Using % Identity label.neighbour_joining_identity = Neighbour Joining Using % Identity +label.choose_calculation = Choose Calculation label.treecalc_title = {0} Using {1} label.tree_calc_av = Average Distance label.tree_calc_nj = Neighbour Joining @@ -177,10 +175,13 @@ label.select_score_model = Select score model label.score_model_pid = % Identity label.score_model_blosum62 = BLOSUM62 label.score_model_pam250 = PAM 250 +label.score_model_smithwatermanscore = Score between two sequences aligned with Smith-Waterman with default Peptide/Nucleotide matrix +label.score_model_sequencefeaturesimilarity = Distance measure of average number of features not shared at sequence positions label.score_model_conservation = Physicochemical property conservation label.score_model_enhconservation = Physicochemical property conservation label.status_bar = Status bar label.out_to_textbox = Output to Textbox +label.occupancy = Occupancy # delete Clustal - use FileFormat name instead label.clustal = Clustal # label.colourScheme_ as in JalviewColourScheme @@ -237,7 +238,6 @@ label.documentation = Documentation label.about = About... label.show_sequence_limits = Show Sequence Limits 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 @@ -262,6 +262,7 @@ 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.double_click_to_browse = Double-click to browse for file 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 @@ -269,6 +270,7 @@ label.chimera_missing = Chimera structure viewer not found.
Please enter the 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.no_colour = No Colour label.use_original_colours = Use Original Colours label.threshold_minmax = Threshold is min/max label.represent_group_with = Represent Group with {0} @@ -276,9 +278,9 @@ label.selection = Selection label.group_colour = Group Colour label.sequence = Sequence label.view_pdb_structure = View PDB Structure -label.min = Min: -label.max = Max: -label.colour_by_label = Colour by label +label.min_value = Min value +label.max_value = Max value +label.no_value = No value label.new_feature = New Feature label.match_case = Match Case label.view_alignment_editor = View in alignment editor @@ -332,6 +334,7 @@ label.colour_residues_above_occurrence = Colour residues above % occurrence label.set_this_label_text = set this label text label.sequences_from = Sequences from {0} label.successfully_loaded_file = Successfully loaded file {0} +label.successfully_loaded_matrix = Successfully loaded score matrix {0} label.successfully_saved_to_file_in_format = Successfully saved to file: {0} in {1} format. label.copied_sequences_to_clipboard = Copied {0} sequences to clipboard. label.check_file_matches_sequence_ids_alignment = Check that the file matches sequence IDs in the alignment. @@ -346,7 +349,6 @@ label.status = Status label.channels = Channels label.channel_title_item_count = {0} ({1}) 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 action.load_vamsas_session = Load Vamsas Session... @@ -362,7 +364,8 @@ label.optimise_order = Optimise Order 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 +label.load_colours_tooltip = Load feature colours and filters from file +label.save_colours_tooltip = Save feature colours and filters to file label.selected_database_to_fetch_from = Selected {0} database {1} to fetch from {2} label.database_param = Database: {0} label.example = Example @@ -375,14 +378,11 @@ label.remove_from_default_list = Remove from default list? label.remove_user_defined_colour = Remove user defined colour label.you_must_select_least_two_sequences = You must select at least 2 sequences. label.invalid_selection = Invalid Selection -label.principal_component_analysis_must_take_least_four_input_sequences = Principal component analysis must take\nat least 4 input sequences. label.sequence_selection_insufficient = Sequence selection insufficient -label.you_need_more_two_sequences_selected_build_tree = You need to have more than two sequences selected to build a tree! +label.you_need_at_least_n_sequences = You need to select at least {0} sequences label.not_enough_sequences = Not enough sequences label.selected_region_to_tree_may_only_contain_residues_or_gaps = The selected region to create a tree may\nonly contain residues or gaps.\nTry using the Pad function in the edit menu,\nor one of the multiple sequence alignment web services. label.sequences_selection_not_aligned = Sequences in selection are not aligned -label.sequences_must_be_aligned_before_creating_tree = The sequences must be aligned before creating a tree.\nTry using the Pad function in the edit menu,\n or one of the multiple sequence alignment web services. -label.sequences_not_aligned = Sequences not aligned label.problem_reading_tree_file = Problem reading tree file label.possible_problem_with_tree_file = Possible problem with tree file label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation = Please select at least three bases in at least one sequence in order to perform a cDNA translation. @@ -397,19 +397,12 @@ 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 -label.pdb_entry_is_already_displayed = {0} is already displayed.\nDo you want to re-use this viewer ? -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 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 label.couldnt_read_pasted_text = Couldn't read the pasted text {0} label.error_parsing_text = Error parsing text -label.enter_local_das_source = Enter Nickname & URL of Local DAS Source -label.you_can_only_edit_or_remove_local_das_sources = You can only edit or remove local DAS Sources! -label.public_das_source = Public DAS source - not editable label.input_alignment_from_url = Input Alignment From URL label.input_alignment = Input Alignment label.couldnt_import_as_vamsas_session = Couldn't import {0} as a new vamsas session. @@ -426,8 +419,6 @@ label.invalid_url = Invalid URL ! label.error_loading_file = Error loading file label.problems_opening_file = Encountered problems opening {0}!! label.file_open_error = File open error -label.no_das_sources_selected_warn = No das sources were selected.\nPlease select some sources and\ntry again. -label.no_das_sources_selected_title = No DAS Sources Selected label.colour_scheme_exists_overwrite = Colour scheme {0} exists.\nContinue saving colour scheme as {1}?" label.duplicate_scheme_name = Duplicate scheme name label.jalview_new_questionnaire = There is a new Questionnaire available. Would you like to complete it now ?\n @@ -487,6 +478,10 @@ 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.load_vcf = Load SNP variants from plain text or indexed VCF data +label.load_vcf_file = Load VCF File +label.searching_vcf = Loading VCF variants... +label.added_vcf = Added {0} VCF variants to {1} sequence(s) label.export_features = Export Features... label.export_annotations = Export Annotations... label.to_upper_case = To Upper Case @@ -525,7 +520,6 @@ label.threshold_feature_above_threshold = Above Threshold label.threshold_feature_below_threshold = Below Threshold label.adjust_threshold = Adjust threshold label.toggle_absolute_relative_display_threshold = Toggle between absolute and relative display threshold. -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_url_param = Open URL {0} @@ -617,7 +611,6 @@ label.visual = Visual label.connections = Connections label.output = Output label.editing = Editing -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 @@ -633,10 +626,6 @@ label.delete_service_url = Delete Service URL label.details = Details label.options = Options label.parameters = Parameters -label.available_das_sources = Available DAS Sources -label.full_details = Full Details -label.authority = Authority -label.type = Type label.proxy_server = Proxy Server label.file_output = File Output label.select_input_type = Select input type @@ -670,7 +659,8 @@ label.2d_rna_structure_line = 2D RNA {0} (alignment) label.2d_rna_sequence_name = 2D RNA - {0} label.edit_name_and_description_current_group = Edit name and description of current group label.from_file = From File -label.enter_pdb_id = Enter PDB Id (or pdbid:chaincode) +label.enter_pdb_id = Enter PDB Id +label.enter_pdb_id_tip = Enter PDB Id (or pdbid:chaincode) label.text_colour = Text Colour... label.structure = Structure label.show_pdbstruct_dialog = 3D Structure Data... @@ -704,14 +694,10 @@ 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 label.set_as_default = Set as Default label.show_labels = Show labels 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 @@ -743,7 +729,6 @@ label.delete_sbrs_definition = Delete SBRS Definition label.your_sequences_have_been_verified = Your sequences have been verified against known sequence databases.\n(Use Calculate | Show flanking regions to show enclosing sequence.)\nTo preserve data changes, save your alignment.\n\n label.sequences_updated = Sequences updated label.dbref_search_completed = DBRef search completed -label.show_all_chains = Show all chains label.fetch_all_param = Fetch all {0} label.paste_new_window = Paste To New Window label.settings_for_param = Settings for {0} @@ -778,7 +763,7 @@ label.pairwise_aligned_sequences = Pairwise Aligned Sequences label.original_data_for_params = Original Data for {0} label.points_for_params = Points for {0} label.transformed_points_for_params = Transformed points for {0} -label.graduated_color_for_params = Graduated Feature Colour for {0} +label.variable_color_for = Variable Feature Colour for {0} label.select_background_colour = Select Background Colour label.invalid_font = Invalid Font label.separate_multiple_accession_ids = Enter one or more accession IDs separated by a semi-colon ";" @@ -849,12 +834,10 @@ label.multiharmony = Multi-Harmony label.unable_start_web_service_analysis = Unable to start web service analysis label.job_couldnt_be_started_check_input = The Job couldn't be started. Please check your input, and the Jalview console for any warning messages. label.prompt_each_time = Prompt each time -label.use_source = Use Source label.couldnt_save_project = Couldn't save project label.error_whilst_saving_current_state_to = Error whilst saving current state to {0} label.error_whilst_loading_project_from = Error whilst loading project from {0} label.couldnt_load_project = Couldn't load project -label.pca_sequences_not_aligned = The sequences must be aligned before calculating PCA.\nTry using the Pad function in the edit menu,\nor one of the multiple sequence alignment web services. label.invalid_name_preset_exists = Invalid name - preset already exists. label.invalid_name = Invalid name label.set_proxy_settings = Please set up your proxy settings in the 'Connections' tab of the Preferences window @@ -866,7 +849,7 @@ label.msa_service_is_unknown = The Multiple Sequence Alignment Service named {0} label.service_called_is_not_seq_search_service = The Service called \n{0}\nis not a \nSequence Search Service\! label.seq_search_service_is_unknown = The Sequence Search Service named {0} is unknown label.feature_type = Feature Type -label.display = Display +label.show = Show label.service_url = Service URL label.copied_sequences = Copied sequences label.cut_sequences = Cut Sequences @@ -876,7 +859,6 @@ label.error_unsupported_owwner_user_colour_scheme = Unsupported owner for User C label.save_alignment_to_file = Save Alignment to file label.save_features_to_file = Save Features to File label.save_annotation_to_file = Save Annotation to File -label.no_features_on_alignment = No features found on alignment label.save_pdb_file = Save PDB File label.save_text_to_file = Save Text to File label.save_state = Save State @@ -898,6 +880,7 @@ label.choose_filename_for_param_file = Choose a filename for this parameter file label.save_as_html = Save as HTML label.recently_opened = Recently Opened label.blasting_for_unidentified_sequence_jobs_running = BLASTing for unidentified sequences - {0} jobs running. +label.tree = Tree label.tree_from = Tree from {0} label.webservice_job_title = {0} using {1} label.select_visible_region_of = selected {0} region of {1} @@ -908,10 +891,10 @@ label.webservice_job_title_on = {0} using {1} on {2} label.updating_vamsas_session = Updating vamsas session label.loading_file = Loading File: {0} label.edit_params = Edit {0} +label.as_percentage = As Percentage error.not_implemented = Not implemented error.no_such_method_as_clone1_for = No such method as clone1 for {0} error.null_from_clone1 = Null from clone1! -error.implementation_error_sortbyfeature = Implementation Error - sortByFeature method must be one of FEATURE_SCORE, FEATURE_LABEL or FEATURE_DENSITY. error.not_yet_implemented = Not yet implemented error.unknown_type_dna_or_pep = Unknown Type {0} - dna or pep are the only allowed values. error.implementation_error_dont_know_threshold_annotationcolourgradient = Implementation error: don't know about threshold setting for current AnnotationColourGradient. @@ -1075,8 +1058,6 @@ exception.unable_to_create_internet_config = Unable to create an Internet Config exception.invocation_target_calling_url = InvocationTargetException while calling openURL: {0} exception.illegal_access_calling_url = IllegalAccessException while calling openURL: {0} exception.interrupted_launching_browser = InterruptedException while launching browser: {0} -exception.das_source_doesnt_support_sequence_command = Source {0} does not support the sequence command. -exception.invalid_das_source = Invalid das source: {0} exception.ebiembl_retrieval_failed_on = EBI EMBL XML retrieval failed on {0}:{1} exception.no_pdb_records_for_chain = No PDB Records for {0} chain {1} exception.unexpected_handling_rnaml_translation_for_pdb = Unexpected exception when handling RNAML translation of PDB data @@ -1131,10 +1112,6 @@ status.parsing_results = Parsing results. status.processing = Processing... status.refreshing_web_service_menus = Refreshing Web Service Menus status.collecting_job_results = Collecting job results. -status.fetching_das_sequence_features = Fetching DAS Sequence Features -status.no_das_sources_active = No DAS Sources Active -status.das_feature_fetching_cancelled = DAS Feature Fetching Cancelled -status.das_feature_fetching_complete = DAS Feature Fetching Complete status.fetching_db_refs = Fetching db refs status.loading_cached_pdb_entries = Loading Cached PDB Entries status.searching_for_pdb_structures = Searching for PDB Structures @@ -1157,8 +1134,6 @@ warn.urls_not_contacted = URLs that could not be contacted warn.urls_no_jaba = URLs without any JABA Services info.validate_jabaws_server = Validate JabaWS Server ?\n(Look in console output for results) label.test_server = Test Server? -info.you_want_jalview_to_find_uniprot_accessions = Do you want Jalview to find\nUniprot Accession ids for given sequence names? -label.find_uniprot_accession_ids = Find Uniprot Accession Ids label.new_sequence_fetcher = New Sequence Fetcher label.additional_sequence_fetcher = Additional Sequence Fetcher label.select_database_retrieval_source = Select Database Retrieval Source @@ -1211,7 +1186,6 @@ label.pdb_sequence_fetcher = PDB Sequence Fetcher label.result = result label.results = results label.structure_chooser = Structure Chooser -label.select = Select : label.invert = Invert label.select_pdb_file = Select PDB File info.select_filter_option = Select Filter Option/Manual Entry @@ -1222,6 +1196,7 @@ label.configure_displayed_columns = Customise Displayed Options label.start_jalview = Start Jalview label.biojs_html_export = BioJS label.scale_as_cdna = Scale protein residues to codons +label.font_as_cdna = Use same font for cDNA and peptide label.scale_protein_to_cdna = Scale Protein to cDNA label.scale_protein_to_cdna_tip = Make protein residues same width as codons in split frame views info.select_annotation_row = Select Annotation Row @@ -1279,7 +1254,6 @@ label.SEQUENCE_ID_no_longer_used = $SEQUENCE_ID$ is no longer used for DB access label.SEQUENCE_ID_for_DB_ACCESSION1 = Please review your URL links in the 'Connections' tab of the Preferences window: label.SEQUENCE_ID_for_DB_ACCESSION2 = URL links using '$SEQUENCE_ID$' for DB accessions now use '$DB_ACCESSION$'. label.do_not_display_again = Do not display this message again -exception.url_cannot_have_miriam_id = {0} is a MIRIAM id and cannot be used as a custom url name exception.url_cannot_have_duplicate_id = {0} cannot be used as a label for more than one line label.filter = Filter text: action.customfilter = Custom only @@ -1294,7 +1268,68 @@ label.database = Database label.urltooltip = Only one url, which must use a sequence id, can be selected for the 'On Click' option label.edit_sequence_url_link = Edit sequence URL link warn.name_cannot_be_duplicate = User-defined URL names must be unique and cannot be MIRIAM ids -label.invalid_name = Invalid Name ! label.output_seq_details = Output Sequence Details to list all database references label.urllinks = Links -label.togglehidden = Toggle hidden columns on/off \ No newline at end of file +action.clear_cached_items = Clear Cached Items +label.togglehidden = Show hidden regions +label.quality_descr = Alignment Quality based on Blosum62 scores +label.conservation_descr = Conservation of total alignment less than {0}% gaps +label.consensus_descr = PID +label.complement_consensus_descr = PID for cDNA +label.strucconsensus_descr = PID for base pairs +label.occupancy_descr = Number of aligned positions +label.show_experimental = Enable experimental features +label.show_experimental_tip = Enable any new and currently 'experimental' features (see Latest Release Notes for details) +label.warning_hidden = Warning: {0} {1} is currently hidden +label.overview_settings = Overview settings +label.ov_legacy_gap = Use legacy gap colouring (gaps are white) +label.gap_colour = Gap colour: +label.ov_show_hide_default = Show hidden regions when opening overview +label.hidden_colour = Hidden colour: +label.select_gap_colour = Select gap colour +label.select_hidden_colour = Select hidden colour +label.overview = Overview +label.reset_to_defaults = Reset to defaults +label.oview_calc = Recalculating overview... +label.feature_details = Feature details +label.matchCondition_contains = Contains +label.matchCondition_notcontains = Does not contain +label.matchCondition_matches = Matches +label.matchCondition_notmatches = Does not match +label.matchCondition_present = Is present +label.matchCondition_notpresent = Is not present +label.matchCondition_eq = = +label.matchCondition_ne = not = +label.matchCondition_lt = < +label.matchCondition_le = <= +label.matchCondition_gt = > +label.matchCondition_ge = >= +label.numeric_required = The value should be numeric +label.filter = Filter +label.filters = Filters +label.join_conditions = Join conditions with +label.score = Score +label.colour_by_label = Colour by label +label.variable_colour = Variable colour... +label.select_colour = Select colour +option.enable_disable_autosearch = When ticked, search is performed automatically +option.autosearch = Autosearch +label.retrieve_ids = Retrieve IDs +label.display_settings_for = Display settings for {0} features +label.simple = Simple +label.simple_colour = Simple Colour +label.colour_by_text = Colour by text +label.graduated_colour = Graduated Colour +label.by_text_of = By text of +label.by_range_of = By range of +label.filters_tooltip = Click to set or amend filters +label.or = Or +label.and = And +label.sequence_feature_colours = Sequence Feature Colours +label.best_quality = Best Quality +label.best_resolution = Best Resolution +label.most_protein_chain = Most Protein Chain +label.most_bound_molecules = Most Bound Molecules +label.most_polymer_residues = Most Polymer Residues +label.cached_structures = Cached Structures +label.free_text_search = Free Text Search