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
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
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
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...
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
# delete Clustal - use FileFormat name instead
label.clustal = Clustal
# label.colourScheme_<schemeName> 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
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
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.<br>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.<br/>Please enter the path to Chimera (if installed),<br/>or download and install UCSF Chimera.
-label.chimera_failed = Error opening Chimera - is it installed?\nCheck path in Preferences, Structure
+label.viewer_path = Path to {0} program
+label.viewer_path_tip = Jalview will first try any path entered here, else standard installation locations.<br>Double-click to browse for file.
+label.invalid_viewer_path = Path not found or not executable
+label.viewer_missing = Structure viewer not found.<br/>Please enter the path to the executable (if installed),<br/>or download and install the program.
+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
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:
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
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
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
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_chimera = This will close Jalview''s connection to {0}.<br>Do you want to close the Chimera window as well?
+label.confirm_close_viewer = This will close Jalview''s connection to {0}.<br>Do you want to close the {1} window as well?
label.all = All
label.sort_by = Sort alignment by
label.sort_by_score = Sort by Score
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
label.sequence_id_tooltip = Sequence ID Tooltip
label.no_services = <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
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
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
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.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<br>when a web service URL cannot be accessed by Jalview<br>when it starts up
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
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."
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.let_viewer_manage_structure_colours = Let viewer manage structure colours
+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
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}
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\!
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
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
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
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!
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
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}
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}
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.
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
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
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.colouring_chimera = Colouring Chimera
+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}
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
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
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
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
label.click_to_edit = Click to edit, right-click for menu
label.by_annotation_tooltip = Annotation Colour is configured from the main Colour menu
label.show_linked_features = Show {0} features
-label.show_linked_feature_settings = Open {0} settings
label.on_top = on top
label.include_linked_features = Include {0} features
-label.include_linked_tooltip = Include visible {0} features<br>converted to local sequence coordinates
\ No newline at end of file
+label.include_linked_tooltip = Include visible {0} features<br>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).<br>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}.
git://source.jalview.org / jalview.git / blobdiff