X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=resources%2Flang%2FMessages.properties;h=f8c2b683863ada609d9d3613a9a35b341d2a0a01;hb=d19882378d8912834a5e196a30f78491cb1e621a;hp=fa32f12444238bc4ae04ba3e518127a133888ab0;hpb=f4b18ae31d37e694b59875f26e0863179de248f1;p=jalview.git diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties index fa32f12..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 @@ -132,6 +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 @@ -189,7 +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 @@ -201,9 +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 @@ -273,7 +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 configured path in the Preferences' Structure tab +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 @@ -403,7 +416,7 @@ 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 @@ -514,11 +527,11 @@ label.retrieve_parse_sequence_database_records_alignment_or_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 = 3D-Beacons Search +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 Uniprot References. 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.threshold_feature_display_by_score = Threshold the feature display by score. @@ -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\! @@ -876,6 +891,7 @@ label.save_text_to_file = Save Text to File 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.load_feature_colours = Load Feature Colours label.save_feature_colours = Save Feature Colour Scheme label.select_startup_file = Select startup file @@ -963,13 +979,14 @@ error.implementation_error_minlen_must_be_greater_zero = Implementation error: m error.implementation_error_msawbjob_called = Implementation error - StartJob(MsaWSJob) called on a WSJobInstance {0} error.implementation_error_cannot_attach_ws_menu_entry = IMPLEMENTATION ERROR: cannot attach WS Menu Entry without service handle reference! error.parameter_migration_not_implemented_yet = Parameter migration not implemented yet +error.implementation_error_cannot_set_jaba_option = Implementation error: cannot set Jaba Option to a value outside its allowed value range! error.implementation_error_valuetype_doesnt_support_jabaws_type = IMPLEMENTATION ERROR: jalview.ws.params.ValueConstrainI.ValueType does not support the JABAWS type : {0} error.cannot_create_jabaws_param_set = Cannot create a JabaWSParamSet from non-JabaWS parameters error.cannot_set_arguments_to_jabaws_param_set = Cannot set arguments to a JabaWSParamSet that are not JabaWS arguments 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! @@ -977,7 +994,7 @@ 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 @@ -1034,23 +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: {0}. Use URL\n{1} +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} @@ -1058,6 +1076,7 @@ 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.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 exception.couldnt_recover_sequence_properties_for_alignment = Couldn't recover sequence properties for alignment @@ -1079,7 +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 @@ -1100,6 +1119,8 @@ status.export_complete = {0} Export completed status.fetching_pdb = Fetching PDB {0} status.refreshing_news = Refreshing news 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 status.fetching_sequence_queries_from = Fetching {0} sequence queries from {1} status.finshed_querying = Finished querying status.parsing_results = Parsing results. @@ -1112,14 +1133,21 @@ 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 +label.error_loading_file_params = Error loading file {0} +label.error_loading_jalview_file = Error loading Jalview file warn.out_of_memory_when_action = Out of memory when {0}\!\!\nSee help files for increasing Java Virtual Machine memory. warn.out_of_memory_loading_file = Out of memory loading file {0}\!\!\nSee help files for increasing Java Virtual Machine memory. label.out_of_memory = Out of memory label.invalid_id_column_width = Invalid ID Column width warn.user_defined_width_requirements = The user defined width for the\nannotation and sequence ID columns\nin exported figures must be\nat least 12 pixels wide. +label.couldnt_create_sequence_fetcher = Couldn't create SequenceFetcher +warn.couldnt_create_sequence_fetcher_client = Could not create the sequence fetcher client. Check error logs for details. warn.server_didnt_pass_validation = Service did not pass validation.\nCheck the Jalview Console for more details. warn.url_must_contain = Sequence URL must contain $SEQUENCE_ID$, $DB_ACCESSION$, or a regex warn.urls_not_contacted = URLs that could not be contacted @@ -1303,6 +1331,7 @@ option.enable_disable_autosearch = When ticked, search is performed automaticall 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 @@ -1325,6 +1354,79 @@ 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 @@ -1332,6 +1434,7 @@ label.backupfiles_confirm_save_file_backupfiles_roll_wrong = Something possibly 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 @@ -1340,6 +1443,7 @@ label.backup_filename_strategy = Backup filename strategy label.append_to_filename = Append to filename (%n is replaced by the backup number) label.append_to_filename_tooltip = %n in the text will be replaced by the backup number. The text will appear after the filename. See the summary box above. label.index_digits = Number of digits to use for the backup number (%n) +label.summary_of_backups_scheme = Summary of backup scheme label.scheme_examples = Scheme examples label.increment_index = Increase appended text numbers - newest file has largest number. label.reverse_roll = "Roll" appended text numbers - newest backup file is always number 1. @@ -1368,11 +1472,13 @@ label.single_file_description = Keep the last version of the file label.keep_all_versions_description = Keep all previous versions of the file label.rolled_backups_description = Keep the last nine versions of the file from _bak.1 (newest) to _bak.9 (oldest) label.cancel_changes_description = Cancel changes made to your last saved Custom scheme +label.previously_saved_scheme = Previously saved scheme label.no_backup_files = NO BACKUP FILES label.include_backup_files = Include backup files label.cancel_changes = Cancel changes label.warning_confirm_change_reverse = Warning!\nIf you change the increment/decrement of the backup filename number, without changing the suffix or number of digits,\nthis may cause loss of backup files created with the previous backup filename scheme.\nAre you sure you wish to do this? label.change_increment_decrement = Change increment/decrement? +label.was_previous = was {0} label.newerdelete_replacement_line = Backup file\n''{0}''\t(modified {2}, size {4})\nis to be deleted and replaced by apparently older file\n''{1}''\t(modified {3}, size {5}). label.confirm_deletion_or_rename = Confirm deletion of ''{0}'' or rename to ''{1}''? label.newerdelete_line = Backup file\n''{0}''\t(modified {2}, size {4})\nis to be deleted but is newer than the oldest remaining backup file\n''{1}''\t(modified {3}, size {5}). @@ -1412,3 +1518,5 @@ label.maximum_memory_tooltip = Enter memory as an integer number optionally foll 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}.