X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=resources%2Flang%2FMessages.properties;h=f8c2b683863ada609d9d3613a9a35b341d2a0a01;hb=d043ce47fc710d3eb2629ba926a8a7417bd67d8c;hp=8747588963d46b5b4e028c531dd5f376257f6eba;hpb=d85a2741994c169e1b81db8f9166f5214ff1f561;p=jalview.git diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties index 8747588..f8c2b68 100644 --- a/resources/lang/Messages.properties +++ b/resources/lang/Messages.properties @@ -11,6 +11,7 @@ action.paste = Paste action.show_html_source = Show HTML Source action.print = Print... action.web_service = Web Service +action.hmmer = HMMER action.cancel_job = Cancel Job action.start_job = Start Job action.revert = Revert @@ -59,6 +60,8 @@ action.boxes = Boxes action.text = Text action.by_pairwise_id = By Pairwise Identity action.by_id = By Id +action.by_evalue = By E-Value +action.by_bit_score = By Bit Score action.by_length = By Length action.by_group = By Group action.unmark_as_reference = Unmark as Reference @@ -98,6 +101,7 @@ action.edit_group = Edit Group action.border_colour = Border colour action.edit_new_group = Edit New Group action.hide_sequences = Hide Sequences +action.add_background_frequencies = Add Background Frequencies action.sequences = Sequences action.ids = IDS action.ids_sequences = IDS and sequences @@ -118,6 +122,7 @@ action.paste_annotations = Paste Annotations action.format = Format action.select = Select action.new_view = New View +action.new_structure_view_with = Open new structure view with {0} action.close = Close action.add = Add action.save_as = Save as... @@ -131,6 +136,8 @@ action.select_highlighted_columns = Select Highlighted Columns tooltip.select_highlighted_columns = Press B to mark highlighted columns, Ctrl-(or Cmd)-B to toggle, and Alt-B to mark all but highlighted columns action.deselect_all = Deselect all action.invert_selection = Invert selection +action.filter_by_evalue = Filter by E-Value +action.filter_by_score = Filter by Score action.using_jmol = Using Jmol action.undo_changes_to_feature_settings = Undo all unapplied changes to feature settings action.undo_changes_to_feature_settings_and_close_the_dialog = Undo all pending changes and close the feature settings dialog @@ -188,7 +195,7 @@ label.occupancy = Occupancy # delete Clustal - use FileFormat name instead label.clustal = Clustal # label.colourScheme_ as in JalviewColourScheme, spaces removed -label.colourScheme_clustal = Clustalx +label.colourScheme_clustal = Clustal label.colourScheme_blosum62 = BLOSUM62 Score label.colourScheme_%identity = Percentage Identity label.colourScheme_zappo = Zappo @@ -200,9 +207,16 @@ label.colourScheme_turnpropensity = Turn Propensity label.colourScheme_buriedindex = Buried Index label.colourScheme_purine/pyrimidine = Purine/Pyrimidine label.colourScheme_nucleotide = Nucleotide +label.colourScheme_hmmer-uniprot = HMMER profile v global background +label.colourScheme_hmmer-alignment = HMMER profile v alignment background +label.colourScheme_hmm_match_score = HMM Match Score label.colourScheme_t-coffeescores = T-Coffee Scores label.colourScheme_rnahelices = By RNA Helices label.colourScheme_sequenceid = Sequence ID Colour +label.colourScheme_gecos\:flower = gecos Flower +label.colourScheme_gecos\:blossom = gecos Blossom +label.colourScheme_gecos\:sunset = gecos Sunset +label.colourScheme_gecos\:ocean = gecos Ocean label.blc = BLC label.fasta = Fasta label.msf = MSF @@ -272,7 +286,7 @@ label.viewer_path = Path to {0} program label.viewer_path_tip = Jalview will first try any path entered here, else standard installation locations.
Double-click to browse for file. label.invalid_viewer_path = Path not found or not executable label.viewer_missing = Structure viewer not found.
Please enter the path to the executable (if installed),
or download and install the program. -label.open_viewer_failed = Error opening {0} - is it installed?\nCheck path in Preferences, Structure +label.open_viewer_failed = Error opening {0} - is it installed?\nCheck configured path in Structure tab of Jalview''s Preferences label.min_colour = Minimum Colour label.max_colour = Maximum Colour label.no_colour = No Colour @@ -328,6 +342,7 @@ label.successfully_pasted_alignment_file = Successfully pasted alignment file label.paste_your_alignment_file = Paste your alignment file here label.paste_your = Paste your label.finished_searching = Finished searching +label.subsequence_matches_found = {0} subsequence matches found label.search_results= Search results {0} : {1} label.found_match_for = Found match for {0} label.font = Font: @@ -354,16 +369,11 @@ label.status = Status label.channels = Channels label.channel_title_item_count = {0} ({1}) label.blog_item_published_on_date = {0} {1} -label.session_update = Session Update -label.new_vamsas_session = New 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... label.lineart = Lineart label.dont_ask_me_again = Don't ask me again -label.select_eps_character_rendering_style = Select EPS character rendering style +label.select_character_rendering_style = {0} character rendering style +label.select_character_style_title = {0} Rendering options label.invert_selection = Invert Selection label.optimise_order = Optimise Order label.seq_sort_by_score = Sequence sort by Score @@ -377,7 +387,7 @@ 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.couldnt_save_file = Couldn't save file: {0} +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? label.remove_user_defined_colour = Remove user defined colour @@ -406,17 +416,14 @@ label.pdb_entries_couldnt_be_retrieved = The following pdb entries could not be 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.couldnt_read_pasted_text = Couldn''t read the pasted text {0} label.error_parsing_text = Error parsing text 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. label.vamsas_document_import_failed = Vamsas Document Import Failed -label.couldnt_locate = Could not locate {0} +label.couldnt_locate = Couldn''t locate {0} label.url_not_found = URL not found label.new_sequence_url_link = New sequence URL link -label.cannot_edit_annotations_in_wrapped_view = Cannot edit annotations in wrapped view -label.wrapped_view_no_edit = Wrapped view - no edit label.error_retrieving_data = Error Retrieving Data label.user_colour_scheme_must_have_name = User colour scheme must have a name label.no_name_colour_scheme = No name for colour scheme @@ -501,8 +508,7 @@ label.insert_gaps = Insert {0} gaps label.delete_gap = Delete 1 gap label.delete_gaps = Delete {0} gaps label.sequence_details = Sequence Details -label.jmol_help = Jmol Help -label.chimera_help = Chimera Help +label.viewer_help = {0} Help label.close_viewer = Close Viewer label.confirm_close_viewer = This will close Jalview''s connection to {0}.
Do you want to close the {1} window as well? label.all = All @@ -520,9 +526,14 @@ label.load_tree_file = Load a tree file label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences = Retrieve and parse sequence database records for the alignment or the currently selected sequences label.standard_databases = Standard Databases label.fetch_embl_uniprot = Fetch from EMBL/EMBLCDS or Uniprot/PDB and any selected DAS sources +label.fetch_uniprot_references = Fetch Uniprot references +label.search_3dbeacons = Search 3D-Beacons +label.find_models_from_3dbeacons = Search 3D-Beacons for 3D structures and models +label.3dbeacons = 3D-Beacons +label.fetch_references_for = Fetch database references for {0} sequences ? +label.fetch_references_for_3dbeacons = 3D Beacons needs to fetch Uniprot References for {0} sequences. Do you want to continue ? label.reset_min_max_colours_to_defaults = Reset min and max colours to defaults from user preferences. label.align_structures_using_linked_alignment_views = Superpose structures using {0} selected alignment view(s) -label.connect_to_session = Connect to session {0} label.threshold_feature_display_by_score = Threshold the feature display by score. label.threshold_feature_no_threshold = No Threshold label.threshold_feature_above_threshold = Above Threshold @@ -556,9 +567,6 @@ label.right_align_sequence_id = Right Align Sequence Id label.sequence_id_tooltip = Sequence ID Tooltip label.no_services = label.select_copy_raw_html = Select this if you want to copy raw html -label.share_data_vamsas_applications = Share data with other vamsas applications -label.connect_to = Connect to -label.join_existing_vamsas_session = Join an existing vamsas session label.from_url = from URL label.any_trees_calculated_or_loaded_alignment_automatically_sort = When selected, any trees calculated or loaded onto the alignment will automatically sort the alignment label.sort_with_new_tree = Sort With New Tree @@ -568,7 +576,6 @@ label.preferences = Preferences label.tools = Tools 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 label.show_java_console = Show Java Console @@ -591,14 +598,22 @@ label.gap_symbol = Gap Symbol label.prot_alignment_colour = Protein Alignment Colour label.nuc_alignment_colour = Nucleotide Alignment Colour label.address = Address +label.host = Host label.port = Port -label.default_browser_unix = Default Browser (Unix) +label.default_browser_unix_windows = Default Browser (Unix, Windows) label.send_usage_statistics = Send usage statistics label.check_for_questionnaires = Check for questionnaires label.check_for_latest_version = Check for latest version label.url_linkfrom_sequence_id = URL link from Sequence ID -label.use_proxy_server = Use a proxy server -label.eps_rendering_style = EPS rendering style +label.no_proxy = No proxy servers +label.system_proxy = System proxy servers (http={0}; https={1}) +label.use_proxy_server = Use these proxy servers +label.auth_required = Authentication required +label.username = Username +label.password = Password +label.proxy_password_required = Proxy password required +label.not_stored = not stored in Preferences file +label.rendering_style = {0} rendering style label.append_start_end = Append /start-end (/15-380) label.full_sequence_id = Full Sequence Id label.smooth_font = Smooth Font @@ -623,8 +638,8 @@ label.editing = Editing 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.fetch_chimera_attributes = Fetch Chimera attributes -label.fetch_chimera_attributes_tip = Copy Chimera attribute to Jalview feature +label.fetch_viewer_attributes = Fetch {0} attributes +label.fetch_viewer_attributes_tip = Copy {0} attribute to Jalview feature 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 @@ -634,7 +649,7 @@ label.delete_service_url = Delete Service URL label.details = Details label.options = Options label.parameters = Parameters -label.proxy_server = Proxy Server +label.proxy_servers = Proxy Servers label.file_output = File Output label.select_input_type = Select input type label.set_options_for_type = Set options for type @@ -678,7 +693,7 @@ 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 -label.spaces_converted_to_backslashes = Spaces have been converted to _ +label.spaces_converted_to_underscores = Spaces have been converted to _ label.no_spaces_allowed_sequence_name = No spaces allowed in Sequence Name label.select_outline_colour = Select Outline Colour label.web_browser_not_found_unix = Unixers\: Couldn't find default web browser.\nAdd the full path to your browser in Preferences." @@ -714,11 +729,9 @@ label.colour_with_viewer = Colour in structure viewer label.superpose_structures = Superpose Structures error.superposition_failed = Superposition failed: {0} label.insufficient_residues = Not enough aligned residues ({0}) to perform superposition -label.jmol = Jmol -label.chimera = Chimera -label.create_chimera_attributes = Write Jalview features -label.create_chimera_attributes_tip = Set Chimera residue attributes for visible features -label.attributes_set = {0} attribute values set on Chimera +label.create_viewer_attributes = Write Jalview features +label.create_viewer_attributes_tip = Set structure residue attributes for Jalview features +label.attributes_set = {0} attribute values set on {1} label.sort_alignment_by_tree = Sort Alignment By Tree label.mark_unlinked_leaves = Mark Unlinked Leaves label.associate_leaves_with = Associate Leaves With @@ -778,8 +791,10 @@ label.transformed_points_for_params = Transformed points for {0} label.variable_color_for = Variable Feature Colour for {0} label.select_background_colour = Select Background Colour label.invalid_font = Invalid Font +label.search_db_all = Search all of {0} +label.search_db_index = Search {0} index {1} label.separate_multiple_accession_ids = Enter one or more accession IDs separated by a semi-colon ";" -label.separate_multiple_query_values = Enter one or more {0}s separated by a semi-colon ";" +label.separate_multiple_query_values = Enter one or more {0} separated by a semi-colon ";" label.search_all = Enter one or more search values separated by a semi-colon ";" (Note: This searches the entire 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} @@ -855,7 +870,7 @@ label.invalid_name = Invalid name label.set_proxy_settings = Please set up your proxy settings in the 'Connections' tab of the Preferences window label.proxy_authorization_failed = Proxy Authorization Failed label.internal_jalview_error = Internal Jalview Error -label.secondary_structure_prediction_service_couldnt_be_located = The Secondary Structure Prediction Service named {0} at {1} couldn't be located. +label.secondary_structure_prediction_service_couldnt_be_located = The Secondary Structure Prediction Service named {0} at {1} couldn''t be located. label.service_called_is_not_msa_service = The Service called \n{0}\nis not a \nMultiple Sequence Alignment Service\! label.msa_service_is_unknown = The Multiple Sequence Alignment Service named {0} is unknown label.service_called_is_not_seq_search_service = The Service called \n{0}\nis not a \nSequence Search Service\! @@ -877,15 +892,11 @@ label.save_state = Save State label.restore_state = Restore State label.saving_jalview_project = Saving jalview project {0} label.loading_jalview_project = Loading jalview project {0} -label.save_vamsas_document_archive = Save Vamsas Document Archive -label.saving_vamsas_doc = Saving VAMSAS Document to {0} label.load_feature_colours = Load Feature Colours label.save_feature_colours = Save Feature Colour Scheme label.select_startup_file = Select startup file label.select_default_browser = Select default web browser label.save_tree_as_newick = Save tree as newick file -label.create_eps_from_tree = Create EPS file from tree -label.create_png_from_tree = Create PNG image from tree label.save_colour_scheme = Save colour scheme label.edit_params_for = Edit parameters for {0} label.choose_filename_for_param_file = Choose a filename for this parameter file @@ -900,7 +911,6 @@ label.visible = Visible label.select_unselect_visible_regions_from = select and unselected {0} regions from {1} label.visible_region_of = visible region of 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 @@ -941,29 +951,20 @@ error.call_setprogressbar_before_registering_handler = call setProgressBar befor label.cancelled_params = Cancelled {0} error.implementation_error_cannot_show_view_alignment_frame = Implementation error: cannot show a view from another alignment in an AlignFrame. error.implementation_error_dont_know_about_threshold_setting = Implementation error: don't know about threshold setting for current AnnotationColourGradient. -error.eps_generation_not_implemented = EPS Generation not yet implemented -error.png_generation_not_implemented = PNG Generation not yet implemented -error.try_join_vamsas_session_another = Trying to join a vamsas session when another is already connected -error.invalid_vamsas_session_id = Invalid vamsas session id label.groovy_support_failed = Jalview Groovy Support Failed label.couldnt_create_groovy_shell = Couldn't create the groovy Shell. Check the error log for the details of what went wrong. error.unsupported_version_calcIdparam = Unsupported Version for calcIdparam {0} error.implementation_error_cant_reorder_tree = Implementation Error: Can't reorder this tree. Not DefaultMutableTreeNode. -error.invalid_value_for_option = Invalid value {0} for option {1} +error.invalid_value_for_option = Invalid value ''{0}'' for option ''{1}'' error.implementation_error_cannot_import_vamsas_doc = Implementation Error - cannot import existing vamsas document into an existing session, Yet! label.vamsas_doc_couldnt_be_opened_as_new_session = VAMSAS Document could not be opened as a new session - please choose another -error.implementation_error_vamsas_operation_not_init = Impementation error! Vamsas Operations when client not initialised and connected -error.jalview_no_connected_vamsas_session = Jalview not connected to Vamsas session -error.implementation_error_cannot_recover_vamsas_object_mappings = IMPLEMENTATION ERROR: Cannot recover vamsas object mappings - no backup was made error.setstatus_called_non_existent_job_pane = setStatus called for non-existent job pane {0} error.implementation_error_cannot_find_marshaller_for_param_set =Implementation error: Can't find a marshaller for the parameter set error.implementation_error_old_jalview_object_not_bound =IMPLEMENTATION ERROR: old jalview object is not bound ! ({0}) error.implementation_error_vamsas_doc_class_should_bind_to_type = Implementation Error: Vamsas Document Class {0} should bind to a {1} (found a {2}) error.invalid_vamsas_rangetype_cannot_resolve_lists = Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice! -error.implementation_error_maplist_is_null = Implementation error. MapList is null for initMapType. error.implementation_error_cannot_have_null_alignment = Implementation error: Cannot have null alignment property key error.implementation_error_null_fileparse = Implementation error. Null FileParse in copy constructor -error.implementation_error_cannot_map_alignment_sequences = IMPLEMENTATION ERROR: Cannot map an alignment of sequences from different datasets into a single alignment in the vamsas document. error.implementation_error_structure_selection_manager_null = Implementation error. Structure selection manager's context is 'null' exception.ssm_context_is_null = SSM context is null error.idstring_seqstrings_only_one_per_sequence = idstrings and seqstrings contain one string each per sequence @@ -985,7 +986,7 @@ error.cannot_set_arguments_to_jabaws_param_set = Cannot set arguments to a JabaW error.implementation_error_runner_config_not_available = Implementation Error: Runner Config not available for a JABAWS service of type {0} ({1}) error.implementation_error_cannot_handle_jaba_param = Implementation Error: Cannot handle Jaba parameter object {0} error.implementation_error_attempt_to_delete_service_preset = Implementation error: Attempt to delete a service preset! -error.implementation_error_cannot_locate_oldname_presetname = Implementation error: Can't locate either oldname ({0}) or presetName ({1}in the datastore!" +error.implementation_error_cannot_locate_oldname_presetname = Implementation error: Can''t locate either oldname ({0}) or presetName ({1}) in the datastore!" error.implementation_error_jabaws_param_set_only_handled_by = Implementation error: JabaWsParamSets can only be handled by JabaParamStore error.cannot_set_source_file_for = Cannot set source file for {0} error.mismatch_service_instance_preset = Probable mismatch between service instance and preset! @@ -993,13 +994,14 @@ error.cannot_set_params_for_ws_preset = Cannot set Parameters for a Jaba Web ser error.implementation_error_can_only_instantiate_jaba_param_sets = Implementation error: Can only instantiate Jaba parameter sets error.no_aacon_service_found = No AACon service found error.implementation_error_couldnt_copy_value_constraint = Implementation error: could not copy ValueConstrain! -error.couldnt_encode_as_utf8 = Couldn't encode {0} as UTF-8. +error.couldnt_encode_as_utf8 = Couldn''t encode {0} as UTF-8. error.tree_inputtype_not_yet_implemented = Tree InputType not yet implemented error.implementation_error_need_to_have_httpresponse = Implementation Error: need to have an HttpResponse to process error.dbrefsource_implementation_exception =DBRefSource Implementation Exception error.implementation_error_dbinstance_must_implement_interface = Implmentation Error - getDbInstances must be given a class that implements jalview.ws.seqfetcher.DbSourceProxy (was given{0}) error.implementation_error_must_init_dbsources =Implementation error. Must initialise dbSources label.view_controller_toggled_marked = {0} {1} columns {2} features of type {3} across {4} sequence(s) +label.no_highlighted_regions_marked = No highlighted regions marked label.toggled = Toggled label.marked = Marked label.containing = containing @@ -1014,7 +1016,7 @@ label.pca_recalculating = Recalculating PCA label.pca_calculating = Calculating PCA label.select_foreground_colour = Choose foreground colour label.select_colour_for_text = Select Colour for Text -label.adjunst_foreground_text_colour_threshold = Adjust Foreground Text Colour Threshold +label.adjust_foreground_text_colour_threshold = Adjust Foreground Text Colour Threshold label.select_subtree_colour = Select Sub-Tree Colour label.create_new_sequence_features = Create New Sequence Feature(s) label.amend_delete_features = Amend/Delete Features for {0} @@ -1049,21 +1051,24 @@ error.implementation_error_reset_called_for_invalid_source = Implementation Erro exception.number_of_residues_in_query_sequence_differ_from_prediction = Number of residues in {0} supposed query sequence ({1}\n{2})\ndiffer from number of prediction sites in prediction ({3}) label.mapped = mapped exception.jpredconcide_entry_has_unexpected_number_of_columns = JPredConcise: Entry ({0}) has an unexpected number of columns -exception.couldnt_parse_concise_annotation_for_prediction = Couldn't parse concise annotation for prediction profile.\n{0} +exception.couldnt_parse_concise_annotation_for_prediction = Couldn''t parse concise annotation for prediction profile.\n{0} exception.newfile = NewickFile\: {0}\n label.no_tree_read_in = No Tree read in -exception.rnaml_couldnt_access_datasource = Couldn't access datasource ({0}) -exception.ranml_couldnt_process_data = Couldn't process data as RNAML file ({0}) +exception.rnaml_couldnt_access_datasource = Couldn''t access datasource ({0}) +exception.ranml_couldnt_process_data = Couldn''t process data as RNAML file ({0}) exception.ranml_invalid_file = Invalid RNAML file ({0}) exception.ranml_problem_parsing_data = Problem parsing data as RNAML ({0}) exception.pfam_no_sequences_found = No sequences found (PFAM input) +exception.hmmer_no_valid_sequences_found = No valid sequences found exception.stockholm_invalid_format = This file is not in valid STOCKHOLM format: First line does not contain '# STOCKHOLM' exception.couldnt_parse_sequence_line = Could not parse sequence line: {0} exception.unknown_annotation_detected = Unknown annotation detected: {0} {1} -exception.couldnt_store_sequence_mappings = Couldn't store sequence mappings for {0} +exception.couldnt_store_sequence_mappings = Couldn''t store sequence mappings for {0} exception.matrix_too_many_iteration = Too many iterations in {0} (max is {1}) exception.browser_not_found = Exception in finding browser: {0} +exception.browser_unable_to_launch = Unable to launch browser: {0} exception.browser_unable_to_locate = Unable to locate browser: {0} +exception.browser_os_not_supported = Launching browser on this operating system not supported. Use URL\n{0} exception.invocation_target_exception_creating_aedesc = InvocationTargetException while creating AEDesc: {0} exception.illegal_access_building_apple_evt= IllegalAccessException while building AppleEvent: {0} exception.unable_to_launch_url = Unable to launch URL: {0} @@ -1086,7 +1091,6 @@ error.implementation_error_cannot_find_service_url_in_given_set_param_store = Im exception.jobsubmission_invalid_params_set = Invalid parameter set. Check Jalview implementation exception.notvaliddata_group_contains_less_than_min_seqs = Group contains less than {0} sequences. exception.outofmemory_loading_pdb_file = Out of memory loading PDB File -exception.eps_coudnt_write_output_file = Could not write to the output file: {0} exception.eps_method_not_supported = Method not currently supported by EpsGraphics2D version {0} exception.eps_unable_to_get_inverse_matrix = Unable to get inverse of matrix: {0} warn.job_cannot_be_cancelled_close_window = This job cannot be cancelled.\nJust close the window. @@ -1094,7 +1098,7 @@ warn.service_not_supported = Service not supported! warn.input_is_too_big = Input is too big! warn.invalid_job_param_set = Invalid job parameter set! warn.oneseq_msainput_selection = The current selection only contains a single sequence. Do you want to submit all sequences for alignment instead ? -info.job_couldnt_be_run_server_doesnt_support_program = Job could not be run because the server doesn't support this program.\n{0} +info.job_couldnt_be_run_server_doesnt_support_program = Job could not be run because the server doesn''t support this program.\n{0} info.job_couldnt_be_run_exceeded_hard_limit = Job could not be run because it exceeded a hard limit on the server.\n{0} info.job_couldnt_be_run_incorrect_param_setting = Job could not be run because some of the parameter settings are not supported by the server.\n{0}\nPlease check to make sure you have used the correct parameter set for this service\!\n info.no_jobs_ran = No jobs ran @@ -1111,11 +1115,9 @@ status.searching_for_sequences_from = Searching for sequences from {0} status.finished_searching_for_sequences_from = Finished searching for sequences from {0} label.eps_file = EPS file label.png_image = PNG image -status.saving_file = Saving {0} -status.export_complete = {0} Export completed. +status.export_complete = {0} Export completed status.fetching_pdb = Fetching PDB {0} status.refreshing_news = Refreshing news -status.importing_vamsas_session_from = Importing VAMSAS session from {0} status.opening_params = Opening {0} status.waiting_sequence_database_fetchers_init = Waiting for Sequence Database Fetchers to initialise status.init_sequence_database_fetchers = Initialising Sequence Database Fetchers @@ -1128,7 +1130,12 @@ status.collecting_job_results = Collecting job results. 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 +status.searching_3d_beacons = Searching 3D Beacons +status.no_structures_discovered_from_3d_beacons = No models discovered from 3D Beacons status.opening_file_for = opening file for +status.running_hmmbuild = Building Hidden Markov Model +status.running_hmmalign = Creating alignment with Hidden Markov Model +status.running_search = Searching for matching sequences status.colouring_structures = Colouring structures label.font_doesnt_have_letters_defined = Font doesn't have letters defined\nso cannot be used\nwith alignment data label.font_too_small = Font size is too small @@ -1165,6 +1172,7 @@ label.add_annotations_for = Add annotations for action.choose_annotations = Choose Annotations... label.choose_annotations = Choose Annotations label.find = Find +label.in = in label.invalid_search = Search string invalid error.invalid_regex = Invalid regular expression label.ignore_gaps_consensus = Ignore Gaps In Consensus @@ -1236,7 +1244,6 @@ exception.fts_server_unreachable = Jalview is unable to reach the {0} server. \n label.nw_mapping = Needleman & Wunsch Alignment label.sifts_mapping = SIFTs Mapping label.mapping_method = Sequence \u27f7 Structure mapping method -status.waiting_for_user_to_select_output_file = Waiting for user to select {0} file status.cancelled_image_export_operation = Cancelled {0} export operation info.error_creating_file = Error creating {0} file exception.outofmemory_loading_mmcif_file = Out of memory loading mmCIF File @@ -1319,7 +1326,7 @@ label.delete_condition = Delete this condition label.score = Score label.colour_by_label = Colour by label label.variable_colour = Variable colour... -label.select_colour = Select colour +label.select_colour_for = Select colour for {0} option.enable_disable_autosearch = When ticked, search is performed automatically option.autosearch = Autosearch label.retrieve_ids = Retrieve IDs @@ -1340,12 +1347,94 @@ 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 +label.annotation_name = Annotation Name +label.annotation_description = Annotation Description +label.edit_annotation_name_description = Edit Annotation Name/Description +label.alignment = alignment +label.pca = PCA +label.create_image_of = Create {0} image of {1} +label.click_to_edit = Click to edit, right-click for menu +label.hmmalign = hmmalign +label.use_hmm = HMM profile to use +label.use_sequence = Sequence to use +label.hmmbuild = hmmbuild +label.hmmsearch = hmmsearch +label.jackhmmer = jackhmmer +label.installation = Installation +label.hmmer_location = HMMER Binaries Installation Location +label.cygwin_location = Cygwin Binaries Installation Location (Windows) +label.information_annotation = Information Annotation +label.ignore_below_background_frequency = Ignore Below Background Frequency +label.information_description = Information content, measured in bits +warn.no_hmm = No Hidden Markov model found.\nRun hmmbuild or load an HMM file first. +label.no_sequences_found = No matching sequences, or an error occurred. +label.hmmer = HMMER +label.trim_termini = Trim Non-Matching Termini +label.trim_termini_desc = If true, non-matching regions on either end of the resulting alignment are removed. +label.no_of_sequences = Number of sequences returned +label.reporting_cutoff = Reporting Cut-off +label.inclusion_threshold = Inlcusion Threshold +label.freq_alignment = Use alignment background frequencies +label.freq_uniprot = Use Uniprot background frequencies +label.hmmalign_options = hmmalign options +label.hmmsearch_options = hmmsearch options +label.jackhmmer_options = jackhmmer options +label.executable_not_found = The ''{0}'' executable file was not found +warn.command_failed = {0} failed +label.invalid_folder = Invalid Folder +label.number_of_results = Number of Results to Return +label.number_of_iterations = Number of jackhmmer Iterations +label.auto_align_seqs = Automatically Align Fetched Sequences +label.new_returned = new sequences returned +label.use_accessions = Return Accessions +label.check_for_new_sequences = Return Number of New Sequences +label.evalue = E-Value +label.reporting_seq_evalue = Reporting Sequence E-value Cut-off +label.reporting_seq_score = Reporting Sequence Score Threshold +label.reporting_dom_evalue = Reporting Domain E-value Cut-off +label.reporting_dom_score = Reporting Domain Score Threshold +label.inclusion_seq_evalue = Inclusion Sequence E-value Cut-off +label.inclusion_seq_score = Inclusion Sequence Score Threshold +label.inclusion_dom_evalue = Inclusion Domain E-value Cut-off +label.inclusion_dom_score = Inclusion Domain Score Threshold +label.number_of_results_desc = The maximum number of hmmsearch results to display +label.number_of_iterations_desc = The number of iterations jackhmmer will complete when searching for new sequences +label.auto_align_seqs_desc = If true, all fetched sequences will be aligned to the hidden Markov model with which the search was performed +label.check_for_new_sequences_desc = Display number of new sequences returned from hmmsearch compared to the previous alignment +label.use_accessions_desc = If true, the accession number of each sequence is returned, rather than that sequence's name +label.reporting_seq_e_value_desc = The E-value cutoff for returned sequences +label.reporting_seq_score_desc = The score threshold for returned sequences +label.reporting_dom_e_value_desc = The E-value cutoff for returned domains +label.reporting_dom_score_desc = The score threshold for returned domains +label.inclusion_seq_e_value_desc = Sequences with an E-value less than this cut-off are classed as significant +label.inclusion_seq_score_desc = Sequences with a bit score greater than this threshold are classed as significant +label.inclusion_dom_e_value_desc = Domains with an E-value less than this cut-off are classed as significant +label.inclusion_dom_score_desc = Domains with a bit score greater than this threshold are classed as significant +label.add_database = Add Database +label.this_alignment = This alignment +warn.invalid_format = This is not a valid database file format. The current supported formats are Fasta, Stockholm and Pfam. +label.database_for_hmmsearch = The database hmmsearch will search through +label.use_reference = Use Reference Annotation +label.use_reference_desc = If true, hmmbuild will keep all columns defined as a reference position by the reference annotation +label.hmm_name = Alignment HMM Name +label.hmm_name_desc = The name given to the HMM for the alignment +warn.no_reference_annotation = No reference annotation found +label.hmmbuild_for = Build HMM for +label.hmmbuild_for_desc = Build an HMM for the selected sets of sequences +label.alignment = Alignment +label.groups_and_alignment = All groups and alignment +label.groups = All groups +label.selected_group = Selected group +label.use_info_for_height = Use Information Content as Letter Height +action.search = Search label.backupfiles_confirm_delete = Confirm delete label.backupfiles_confirm_delete_old_files = Delete the following older backup files? (see the Backups tab in Preferences for more options) label.backupfiles_confirm_save_file = Confirm save file label.backupfiles_confirm_save_file_backupfiles_roll_wrong = Something possibly went wrong with the backups of this file. label.backupfiles_confirm_save_new_saved_file_ok = The new saved file seems okay. label.backupfiles_confirm_save_new_saved_file_not_ok = The new saved file might not be okay. +label.continue_operation = Continue operation? +label.continue = Continue label.backups = Backups label.backup = Backup label.backup_files = Backup Files @@ -1412,3 +1501,22 @@ label.include_linked_features = Include {0} features label.include_linked_tooltip = Include visible {0} features
converted to local sequence coordinates label.features_not_shown = {0} feature(s) not shown label.no_features_to_sort_by = No features to sort by +label.ignore_hidden = Ignore hidden columns +label.ignore_hidden_tooltip = Ignore any characters in hidden columns when matching +label.log_level = Log level +label.log_level_tooltip = Temporarily set the log level for this console. The log level will revert to {0} when this Java console is closed. +label.copy_to_clipboard = Copy to clipboard +label.copy_to_clipboard_tooltip = Copy all of the log text in this console to the system clipboard +label.startup = Startup +label.memory = Memory +label.customise_memory_settings = Customise maximum memory settings +label.memory_setting_text = New memory settings will only come into effect the next time you start Jalview +label.maximum_memory_used = Maximum memory limited to both +label.percent_of_physical_memory = Maximum percent of physical memory +label.maximum_memory = Maximum absolute memory +label.maximum_memory_tooltip = Enter memory as an integer number optionally followed by 'b', 'k', 'm', 'g' or 't' +label.adjustments_for_this_computer = Adjustments for this computer +label.memory_example_text = Maximum memory that would be used with these settings on this computer +label.memory_example_tooltip = The memory allocated to Jalview is the smaller of the percentage of physical memory (default 90%) and the maximum absolute memory (default 32GB). If your computer's memory cannot be ascertained then the maximum absolute memory defaults to 8GB (if not customised).
Jalview will always try and reserve 512MB for the OS and at least 512MB for itself. +warning.wrong_jvm_version_title = Wrong Java Version +warning.wrong_jvm_version_message = The Java version being used (Java {0}) may lead to problems.\nThis installation of Jalview should be used with Java {1}.