action.merge_results = Merge Results
action.load_scheme = Load scheme
action.save_scheme = Save scheme
+label.scheme_changed = Changes to scheme ''{0}'' have not been saved.<br><br>Save changes, or continue without saving to make a new colour scheme.
+label.save_changes = Save Changes
+label.dont_save_changes = Don't Save
action.save_image = Save Image
action.paste = Paste
action.show_html_source = Show HTML Source
-action.print = Print
+action.print = Print...
action.web_service = Web Service
action.cancel_job = Cancel Job
action.start_job = Start Job
action.close_all = Close all
action.load_project = Load Project
action.save_project = Save Project
+action.save_project_as = Save Project as...
action.quit = Quit
+label.quit_jalview = Quit Jalview?
action.expand_views = Expand Views
action.gather_views = Gather Views
-action.page_setup = Page Setup
+action.page_setup = Page Setup...
action.reload = Reload
action.load = Load
action.open = Open
action.create = Create
action.update = Update
action.delete = Delete
-action.snapshot = Snapshot
action.clear = Clear
action.accept = Accept
action.select_ddbb = --- Select Database ---
action.right_justify_alignment = Right Justify Alignment
action.boxes = Boxes
action.text = Text
-action.by_pairwise_id = by Pairwise Identity
-action.by_id = by Id
-action.by_length = by Length
-action.by_group = by Group
+action.by_pairwise_id = By Pairwise Identity
+action.by_id = By Id
+action.by_length = By Length
+action.by_group = By Group
action.unmark_as_reference = Unmark as Reference
action.set_as_reference = Set as Reference
action.remove = Remove
action.remove_redundancy = Remove Redundancy...
-action.pairwise_alignment = Pairwise Alignments...
-action.by_rna_helixes = by RNA Helices
+action.pairwise_alignment = Pairwise Alignment
action.user_defined = User Defined...
action.by_conservation = By Conservation
action.wrap = Wrap
action.show_hidden_markers = Show Hidden Markers
action.find = Find
action.undefine_groups = Undefine Groups
-action.create_groups = Create Groups
action.make_groups_selection = Make Groups For Selection
action.copy = Copy
action.cut = Cut
action.scale_right = Scale Right
action.by_tree_order = By Tree Order
action.sort = Sort
-action.calculate_tree = Calculate Tree
+action.calculate_tree = Calculate Tree...
+action.calculate_tree_pca = Calculate Tree or PCA...
action.help = Help
-action.by_annotation = by Annotation...
+action.by_annotation = By Annotation...
action.invert_sequence_selection = Invert Sequence Selection
action.invert_column_selection = Invert Column Selection
action.show = Show
action.new_view = New View
action.close = Close
action.add = Add
-action.save_as_default = Save as default
-action.save_as = Save as
+action.save_as = Save as...
action.save = Save
-action.cancel_fetch = Cancel Fetch
-action.save_omit_hidden_columns = Save / Omit Hidden Columns
action.change_font = Change Font
action.change_font_tree_panel = Change Font (Tree Panel)
action.colour = Colour
action.calculate = Calculate
action.select_all = Select all
+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.using_jmol = Using Jmol
action.fetch_db_references = Fetch DB References
action.view_flanking_regions = Show flanking regions
label.view_flanking_regions = Show sequence data either side of the subsequences involved in this alignment
-label.str = Str:
-label.seq = Seq:
label.structures_manager = Structures Manager
-label.nickname = Nickname:
-label.url = URL:
+label.url = URL
+label.url\: = URL:
label.input_file_url = Enter URL or Input File
-label.select_feature = Select feature:
+label.select_feature = Select feature
label.name = Name
+label.name\: = Name:
label.name_param = Name: {0}
label.group = Group
+label.group\: = Group:
label.group_name = Group Name
label.group_description = Group Description
label.edit_group_name_description = Edit Group Name/Description
label.colour = Colour:
-label.description = Description:
+label.description = Description
+label.description\: = Description:
label.start = Start:
label.end = End:
label.current_parameter_set_name = Current parameter set name:
label.service_action = Service Action:
label.post_url = POST URL:
label.url_suffix = URL Suffix
-label.sequence_source = Sequence Source
label.per_seq = per Sequence
label.result_vertically_separable = Results are vertically separable
label.amend = Amend
label.principal_component_analysis = Principal Component Analysis
label.average_distance_identity = Average Distance Using % Identity
label.neighbour_joining_identity = Neighbour Joining Using % Identity
-label.treecalc_title = {0} Using {1}
+label.choose_calculation = Choose Calculation
+label.calc_title = {0} Using {1}
label.tree_calc_av = Average Distance
label.tree_calc_nj = Neighbour Joining
-label.select_score_model = Select score model
label.score_model_pid = % Identity
label.score_model_blosum62 = BLOSUM62
label.score_model_pam250 = PAM 250
+label.score_model_smithwatermanscore = Score between two sequences aligned with Smith-Waterman with default Peptide/Nucleotide matrix
+label.score_model_sequencefeaturesimilarity = Distance measure of average number of features not shared at sequence positions
label.score_model_conservation = Physicochemical property conservation
label.score_model_enhconservation = Physicochemical property conservation
label.status_bar = Status bar
label.out_to_textbox = Output to Textbox
-label.clustalx = Clustalx
+label.occupancy = Occupancy
+# delete Clustal - use FileFormat name instead
label.clustal = Clustal
-label.zappo = Zappo
-label.taylor = Taylor
+# label.colourScheme_<schemeName> as in JalviewColourScheme, spaces removed
+label.colourScheme_clustal = Clustalx
+label.colourScheme_blosum62 = BLOSUM62 Score
+label.colourScheme_%identity = Percentage Identity
+label.colourScheme_zappo = Zappo
+label.colourScheme_taylor = Taylor
+label.colourScheme_hydrophobic = Hydrophobicity
+label.colourScheme_helixpropensity = Helix Propensity
+label.colourScheme_strandpropensity = Strand Propensity
+label.colourScheme_turnpropensity = Turn Propensity
+label.colourScheme_buriedindex = Buried Index
+label.colourScheme_purine/pyrimidine = Purine/Pyrimidine
+label.colourScheme_nucleotide = Nucleotide
+label.colourScheme_t-coffeescores = T-Coffee Scores
+label.colourScheme_rnahelices = By RNA Helices
+label.colourScheme_sequenceid = Sequence ID Colour
label.blc = BLC
label.fasta = Fasta
label.msf = MSF
label.pfam = PFAM
label.pileup = Pileup
label.pir = PIR
-label.hydrophobicity = Hydrophobicity
-label.helix_propensity = Helix Propensity
-label.strand_propensity = Strand Propensity
-label.turn_propensity = Turn Propensity
-label.buried_index = Buried Index
-label.purine_pyrimidine = Purine/Pyrimidine
-label.percentage_identity = Percentage Identity
-label.blosum62 = BLOSUM62
-label.blosum62_score = BLOSUM62 Score
-label.tcoffee_scores = T-Coffee Scores
-label.average_distance_bloslum62 = Average Distance Using BLOSUM62
+label.average_distance_blosum62 = Average Distance Using BLOSUM62
label.neighbour_blosum62 = Neighbour Joining Using BLOSUM62
label.show_annotations = Show annotations
label.hide_annotations = Hide annotations
label.add_reference_annotations = Add reference annotations
label.find_tip = Search alignment, selection or sequence ids for a subsequence (ignoring gaps).<br>Accepts regular expressions - search Help for 'regex' for details.
label.colour_text = Colour Text
-label.show_non_conversed = Show nonconserved
+label.show_non_conserved = Show nonconserved
label.overview_window = Overview Window
label.none = None
label.above_identity_threshold = Above Identity Threshold
label.show_sequence_features = Show Sequence Features
label.nucleotide = Nucleotide
label.protein = Protein
+label.nucleotides = Nucleotides
+label.proteins = Proteins
label.to_new_alignment = To New Alignment
label.to_this_alignment = Add To This Alignment
label.apply_colour_to_all_groups = Apply Colour To All Groups
-label.modify_identity_thereshold = Modify Identity Threshold...
-label.modify_conservation_thereshold = Modify Conservation Threshold...
+label.modify_identity_threshold = Modify Identity Threshold...
+label.modify_conservation_threshold = Modify Conservation Threshold...
label.input_from_textbox = Input from textbox
label.centre_column_labels = Centre column labels
label.automatic_scrolling = Automatic Scrolling
label.documentation = Documentation
label.about = About...
label.show_sequence_limits = Show Sequence Limits
-label.feature_settings = Feature Settings...
+action.feature_settings = Feature Settings...
label.all_columns = All Columns
label.all_sequences = All Sequences
label.selected_columns = Selected Columns
label.all_but_selected_region = All but Selected Region (Shift+Ctrl+H)
label.selected_region = Selected Region
label.all_sequences_columns = All Sequences and Columns
-label.hide_insertions = Hide columns gapped for selection
label.hide_selected_annotations = Hide selected annotations
label.show_selected_annotations = Show selected annotations
label.group_consensus = Group Consensus
label.autoadd_secstr = Add secondary structure annotation to alignment
label.autoadd_temp = Add Temperature Factor annotation to alignment
label.structure_viewer = Default structure viewer
+label.double_click_to_browse = Double-click to browse for file
label.chimera_path = Path to Chimera program
label.chimera_path_tip = Jalview will first try any path entered here, else standard installation locations.<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.min_colour = Minimum Colour
label.max_colour = Maximum Colour
+label.no_colour = No Colour
label.use_original_colours = Use Original Colours
label.threshold_minmax = Threshold is min/max
label.represent_group_with = Represent Group with {0}
label.group_colour = Group Colour
label.sequence = Sequence
label.view_pdb_structure = View PDB Structure
-label.min = Min:
-label.max = Max:
-label.colour_by_label = Colour by label
+label.min_value = Min value
+label.max_value = Max value
+label.no_value = No value
label.new_feature = New Feature
label.match_case = Match Case
label.view_alignment_editor = View in alignment editor
label.font = Font:
label.size = Size:
label.style = Style:
-label.enter_redundancy_threshold = Enter the redundancy threshold
label.calculating = Calculating....
label.modify_conservation_visibility = Modify conservation visibility
-label.colour_residues_above_occurence = Colour residues above % occurence
+label.colour_residues_above_occurrence = Colour residues above % occurrence
label.set_this_label_text = set this label text
label.sequences_from = Sequences from {0}
label.successfully_loaded_file = Successfully loaded file {0}
+label.successfully_loaded_matrix = Successfully loaded score matrix {0}
label.successfully_saved_to_file_in_format = Successfully saved to file: {0} in {1} format.
label.copied_sequences_to_clipboard = Copied {0} sequences to clipboard.
label.check_file_matches_sequence_ids_alignment = Check that the file matches sequence IDs in the alignment.
label.channels = Channels
label.channel_title_item_count = {0} ({1})
label.blog_item_published_on_date = {0} {1}
-label.select_das_service_from_table = Select a DAS service from the table to read a full description here.</font></html>
label.session_update = Session Update
label.new_vamsas_session = New Vamsas Session
-label.load_vamsas_session = Load Vamsas Session
-label.save_vamsas_session = Save 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.load_colours = Load Colours
label.save_colours = Save Colours
-label.fetch_das_features = Fetch DAS Features
+label.load_colours_tooltip = Load feature colours and filters from file
+label.save_colours_tooltip = Save feature colours and filters to file
label.selected_database_to_fetch_from = Selected {0} database {1} to fetch from {2}
label.database_param = Database: {0}
label.example = Example
label.example_param = Example: {0}
label.select_file_format_before_saving = You must select a file format before saving!
label.file_format_not_specified = File format not specified
-label.alignment_contains_hidden_columns = The Alignment contains hidden columns.\nDo you want to save only the visible alignment?
label.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.you_must_select_least_two_sequences = You must select at least 2 sequences.
label.invalid_selection = Invalid Selection
-label.principal_component_analysis_must_take_least_four_input_sequences = Principal component analysis must take\nat least 4 input sequences.
label.sequence_selection_insufficient = Sequence selection insufficient
-label.you_need_more_two_sequences_selected_build_tree = You need to have more than two sequences selected to build a tree!
+label.you_need_at_least_n_sequences = You need to select at least {0} sequences
label.not_enough_sequences = Not enough sequences
label.selected_region_to_tree_may_only_contain_residues_or_gaps = The selected region to create a tree may\nonly contain residues or gaps.\nTry using the Pad function in the edit menu,\nor one of the multiple sequence alignment web services.
label.sequences_selection_not_aligned = Sequences in selection are not aligned
-label.sequences_must_be_aligned_before_creating_tree = The sequences must be aligned before creating a tree.\nTry using the Pad function in the edit menu,\n or one of the multiple sequence alignment web services.
-label.sequences_not_aligned = Sequences not aligned
label.problem_reading_tree_file = Problem reading tree file
label.possible_problem_with_tree_file = Possible problem with tree file
label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation = Please select at least three bases in at least one sequence in order to perform a cDNA translation.
label.translation_failed = Translation Failed
label.error_when_translating_sequences_submit_bug_report = Unfortunately, something went wrong when translating your sequences.\nPlease take a look in the Jalview java console\nand submit a bug report including the stacktrace.
label.implementation_error = Implementation error:
-label.automatically_associate_pdb_files_with_sequences_same_name = Do you want to automatically associate the {0} PDB files with sequences in the alignment that have the same name?
-label.automatically_associate_pdb_files_by_name = Automatically Associate PDB files by name
+label.automatically_associate_structure_files_with_sequences_same_name = Do you want to automatically associate the {0} structure file(s) with sequences in the alignment that have the same name?
+label.automatically_associate_structure_files_by_name = Automatically Associate Structure files by name
label.ignore_unmatched_dropped_files_info = <html>Do you want to <em>ignore</em> the {0} files whose names did not match any sequence IDs ?</html>
label.ignore_unmatched_dropped_files = Ignore unmatched dropped files?
label.view_name_original = Original
label.enter_view_name = Enter View Name
label.enter_label = Enter label
-label.enter_label_for_the_structure = Enter a label for the structure?
-label.pdb_entry_is_already_displayed = {0} is already displayed.\nDo you want to re-use this viewer ?
-label.map_sequences_to_visible_window = Map Sequences to Visible Window: {0}
-label.add_pdbentry_to_view = Do you want to add {0} to the view called\n{1}\n
-label.align_to_existing_structure_view = Align to existing structure view
+label.enter_label_for_the_structure = Enter a label for the structure
label.pdb_entries_couldnt_be_retrieved = The following pdb entries could not be retrieved from the PDB\:\n{0}\nPlease retry, or try downloading them manually.
label.couldnt_load_file = Couldn't load file
label.couldnt_find_pdb_id_in_file = Couldn't find a PDB id in the file supplied. Please enter an Id to identify this structure.
label.no_pdb_id_in_file = No PDB Id in File
label.couldnt_read_pasted_text = Couldn't read the pasted text {0}
label.error_parsing_text = Error parsing text
-label.enter_local_das_source = Enter Nickname & URL of Local DAS Source
-label.you_can_only_edit_or_remove_local_das_sources = You can only edit or remove local DAS Sources!
-label.public_das_source = Public DAS source - not editable
label.input_alignment_from_url = Input Alignment From URL
label.input_alignment = Input Alignment
label.couldnt_import_as_vamsas_session = Couldn't import {0} as a new vamsas session.
label.vamsas_document_import_failed = Vamsas Document Import Failed
-label.couldnt_locate = Couldn't locate {0}
+label.couldnt_locate = Couldn''t locate {0}
label.url_not_found = URL not found
-label.no_link_selected = No link selected
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_loading_file = Error loading file
label.problems_opening_file = Encountered problems opening {0}!!
label.file_open_error = File open error
-label.no_das_sources_selected_warn = No das sources were selected.\nPlease select some sources and\ntry again.
-label.no_das_sources_selected_title = No DAS Sources Selected
label.colour_scheme_exists_overwrite = Colour scheme {0} exists.\nContinue saving colour scheme as {1}?"
label.duplicate_scheme_name = Duplicate scheme name
label.jalview_new_questionnaire = There is a new Questionnaire available. Would you like to complete it now ?\n
label.features_can_be_added_from_searches_1 = (Features can be added from searches or
label.features_can_be_added_from_searches_2 = from Jalview / GFF features files)
label.calculating_pca= Calculating PCA
-label.reveal_columns = Reveal Columns
label.jalview_cannot_open_file = Jalview can't open file
label.jalview_applet = Jalview applet
label.loading_data = Loading data
label.calculating_tree = Calculating tree
label.state_queueing = queuing
label.state_running = running
-label.state_complete = complete
label.state_completed = finished
label.state_job_cancelled = job cancelled!!
label.state_job_error = job error!
label.structure_type = Structure type
label.settings_for_type = Settings for {0}
label.view_full_application = View in Full Application
-label.load_associated_tree = Load Associated Tree ...
-label.load_features_annotations = Load Features/Annotations ...
-label.export_features = Export Features ...
-label.export_annotations = Export Annotations ...
+label.load_associated_tree = Load Associated Tree...
+label.load_features_annotations = Load Features/Annotations...
+label.load_vcf = Load SNP variants from plain text or indexed VCF data
+label.load_vcf_file = Load VCF File
+label.searching_vcf = Loading VCF variants...
+label.added_vcf = Added {0} VCF variants to {1} sequence(s)
+label.export_features = Export Features...
+label.export_annotations = Export Annotations...
label.to_upper_case = To Upper Case
label.to_lower_case = To Lower Case
label.toggle_case = Toggle Case
-label.edit_name_description = Edit Name/Description ...
-label.create_sequence_feature = Create Sequence Feature ...
+label.edit_name_description = Edit Name/Description...
+label.create_sequence_feature = Create Sequence Feature...
label.edit_sequence = Edit Sequence
label.edit_sequences = Edit Sequences
+label.insert_gap = Insert 1 gap
+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.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.chimera_help = Chimera Help
label.all = All
label.sort_by = Sort alignment by
label.sort_by_score = Sort by Score
label.standard_databases = Standard Databases
label.fetch_embl_uniprot = Fetch from EMBL/EMBLCDS or Uniprot/PDB and any selected DAS sources
label.reset_min_max_colours_to_defaults = Reset min and max colours to defaults from user preferences.
-label.align_structures_using_linked_alignment_views = Align structures using {0} linked alignment views
+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_thereshold = No Threshold
-label.threshold_feature_above_thereshold = Above Threshold
-label.threshold_feature_below_thereshold = Below Threshold
-label.adjust_thereshold = Adjust threshold
+label.threshold_feature_no_threshold = No Threshold
+label.threshold_feature_above_threshold = Above Threshold
+label.threshold_feature_below_threshold = Below Threshold
+label.adjust_threshold = Adjust threshold
label.toggle_absolute_relative_display_threshold = Toggle between absolute and relative display threshold.
-label.display_features_same_type_different_label_using_different_colour = Display features of the same type with a different label using a different colour. (e.g. domain features)
label.select_colour_minimum_value = Select Colour for Minimum Value
label.select_colour_maximum_value = Select Colour for Maximum Value
-label.open_new_jmol_view_with_all_structures_associated_current_selection_superimpose_using_alignment = Open a new structure viewer with all structures associated with the current selection and superimpose them using the alignment.
label.open_url_param = Open URL {0}
label.open_url_seqs_param = Open URL ({0}..) ({1} seqs)
label.load_pdb_file_associate_with_sequence = Load a PDB file and associate it with sequence {0}
label.light_colour = Light Colour
label.highlightnode = Left click to select leaves.<br>Double-click to invert leaves.<br>Right click to change colour.
label.load_colour_scheme = Load colour scheme
+label.copy_format_from = Copy format from
label.toggle_enabled_views = When enabled, allows many views to be selected.
+label.select_all_views = Select all views
+label.select_many_views = Select many views
label.edit_notes_parameter_set = Click to edit the notes for this parameter set.
label.open_local_file = Open local file
label.enable_automatically_sort_alignment_when_open_new_tree = Enable this to automatically sort<br>the alignment when you open<br> a new tree.
label.window = Window
label.preferences = Preferences
label.tools = Tools
-label.fetch_sequences = Fetch Sequence(s)
+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.logo = Logo
label.non_positional_features = List Non-positional Features
label.database_references = List Database References
-label.share_selection_across_views = Share selection across views
-label.scroll_highlighted_regions = Scroll to highlighted regions
+#label.share_selection_across_views = Share selection across views
+#label.scroll_highlighted_regions = Scroll to highlighted regions
label.gap_symbol = Gap Symbol
label.prot_alignment_colour = Protein Alignment Colour
label.nuc_alignment_colour = Nucleotide Alignment Colour
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.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.connections = Connections
label.output = Output
label.editing = Editing
-label.das_settings = DAS Settings
label.web_services = Web Services
label.right_click_to_edit_currently_selected_parameter = Right click to edit currently selected parameter.
label.let_jmol_manage_structure_colours = Let Jmol manage structure colours
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.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.available_das_sources = Available DAS Sources
-label.full_details = Full Details
-label.authority = Authority
-label.type = Type
label.proxy_server = Proxy Server
label.file_output = File Output
label.select_input_type = Select input type
label.input_output = Input/Output
label.cut_paste = Cut'n'Paste
label.adjusting_parameters_for_calculation = Adjusting parameters for existing Calculation
-label.2d_rna_structure_line = 2D RNA {0}
+label.2d_rna_structure_line = 2D RNA {0} (alignment)
label.2d_rna_sequence_name = 2D RNA - {0}
-label.edit_name_and_description_current_group = Edit name and description of current group.
-label.view_structure_for = View structure for {0}
-label.view_all_structures = View all {0} structures.
-label.view_all_representative_structures = View all {0} representative structures.
-label.open_new_jmol_view_with_all_representative_structures_associated_current_selection_superimpose_using_alignment = Opens a new structure viewer with all representative structures\nassociated with the current selection\nsuperimposed with the current alignment.
-label.associate_structure_with_sequence = Associate Structure with Sequence
-label.from_file = from file
+label.edit_name_and_description_current_group = Edit name and description of current group
+label.from_file = From File
label.enter_pdb_id = Enter PDB Id
-label.discover_pdb_ids = Discover PDB ids
-label.text_colour = Text Colour
+label.enter_pdb_id_tip = Enter PDB Id (or pdbid:chaincode)
+label.text_colour = Text Colour...
label.structure = Structure
-label.view_structure = View Structure
-label.clustalx_colours = Clustalx colours
-label.above_identity_percentage = Above % Identity
+label.show_pdbstruct_dialog = 3D Structure Data...
+label.view_rna_structure = VARNA 2D Structure
label.create_sequence_details_report_annotation_for = Annotation for {0}
label.sequence_details_for = Sequence Details for {0}
label.sequence_name = Sequence Name
label.sequence_description = Sequence Description
label.edit_sequence_name_description = Edit Sequence Name/Description
-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.export_image = Export Image
label.vamsas_store = VAMSAS store
label.translate_cDNA = Translate as cDNA
-label.linked_view_title = Linked cDNA and protein view
-label.align = Align
+label.reverse = Reverse
+label.reverse_complement = Reverse Complement
+label.linked_view_title = Linked CDS and protein view
label.extract_scores = Extract Scores
-label.get_cross_refs = Get Cross References
+label.get_cross_refs = Get Cross-References
label.sort_alignment_new_tree = Sort Alignment With New Tree
label.add_sequences = Add Sequences
label.new_window = New Window
label.split_window = Split Window
-label.refresh_available_sources = Refresh Available Sources
-label.use_registry = Use Registry
-label.add_local_source = Add Local Source
label.set_as_default = Set as Default
label.show_labels = Show labels
-label.background_colour = Background Colour
+action.background_colour = Background Colour...
label.associate_nodes_with = Associate Nodes With
-label.jalview_pca_calculation = Jalview PCA Calculation
label.link_name = Link Name
label.pdb_file = PDB file
label.colour_with_jmol = Colour with Jmol
label.colour_with_chimera = Colour with Chimera
-label.align_structures = Align structures
+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.sort_alignment_by_tree = Sort Alignment By Tree
label.mark_unlinked_leaves = Mark Unlinked Leaves
label.associate_leaves_with = Associate Leaves With
label.save_colour_scheme_with_unique_name_added_to_colour_menu = Save your colour scheme with a unique name and it will be added to the Colour menu
label.case_sensitive = Case Sensitive
-label.lower_case_colour = Lower Case Colour
-label.index_by_host = Index by host
-label.index_by_type = Index by type
+label.lower_case_colour = Colour All Lower Case
+label.lower_case_tip = Chosen colour applies to all lower case symbols
+label.index_by_host = Index by Host
+label.index_by_type = Index by Type
label.enable_jabaws_services = Enable JABAWS Services
-label.display_warnings = Display warnings
-label.move_url_up = Move URL up
-label.move_url_down = Move URL down
-label.add_sbrs_definition = Add a SBRS definition
-label.edit_sbrs_definition = Edit SBRS definition
-label.delete_sbrs_definition = Delete SBRS definition
-label.your_sequences_have_been_verified = Your sequences have been verified against known sequence databases. Some of the ids have been\n altered, most likely the start/end residue will have been updated.\n Save your alignment to maintain the updated id.\n\n
-label.sequence_names_updated = Sequence names updated
+label.display_warnings = Display Warnings
+label.move_url_up = Move URL Up
+label.move_url_down = Move URL Down
+label.add_sbrs_definition = Add a SBRS Definition
+label.edit_sbrs_definition = Edit SBRS Definition
+label.delete_sbrs_definition = Delete SBRS Definition
+label.your_sequences_have_been_verified = Your sequences have been verified against known sequence databases.\n(Use Calculate | Show flanking regions to show enclosing sequence.)\nTo preserve data changes, save your alignment.\n\n
+label.sequences_updated = Sequences updated
label.dbref_search_completed = DBRef search completed
-label.show_all_chains = Show all chains
label.fetch_all_param = Fetch all {0}
label.paste_new_window = Paste To New Window
label.settings_for_param = Settings for {0}
label.view_params = View {0}
-label.select_all_views = Select all views
+label.aacon_calculations = AACon Calculations
+label.aacon_settings = Change AACon Settings...
+tooltip.aacon_calculations = When checked, AACon calculations are updated automatically.
+tooltip.aacon_settings = Modify settings for AACon calculations.
+label.rnalifold_calculations = RNAAliFold Prediction
+label.rnalifold_settings = Change RNAAliFold settings...
+tooltip.rnalifold_calculations = When checked, RNA secondary structure predictions will be calculated for the alignment, and updated when edits are made.
+tooltip.rnalifold_settings = Modify settings for the RNAAliFold prediction. Use this to hide or show different results of the RNA calculation, and change RNA folding parameters.
label.all_views = All Views
label.align_sequences_to_existing_alignment = Align sequences to an existing alignment
label.realign_with_params = Realign with {0}
label.view_and_change_parameters_before_running_calculation = View and change parameters before running calculation
label.view_documentation = View documentation
label.select_return_type = Select return type
-label.translation_of_params = Translation of {0}
+label.translation_of_params = Translation of {0} (Table {1})
label.features_for_params = Features for - {0}
label.annotations_for_params = Annotations for - {0}
label.generating_features_for_params = Generating features for - {0}
label.original_data_for_params = Original Data for {0}
label.points_for_params = Points for {0}
label.transformed_points_for_params = Transformed points for {0}
-label.graduated_color_for_params = Graduated Feature Colour for {0}
-label.select_backgroud_colour = Select Background Colour
+label.variable_color_for = Variable Feature Colour for {0}
+label.select_background_colour = Select Background Colour
label.invalid_font = Invalid Font
-label.separate_multiple_accession_ids = Separate multiple accession ids with semi colon ";"
+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.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.parsing_failed_unrecoverable_exception_thrown_param = \nParsing failed. An unrecoverable exception was thrown\:\n {0}
label.blasting_for_unidentified_sequence = BLASTing for unidentified sequences
label.select_columns_containing = Select columns containing
label.select_columns_not_containing = Select columns that do not contain
+label.hide_columns_containing = Hide columns containing
+label.hide_columns_not_containing = Hide columns that do not contain
option.trim_retrieved_seqs = Trim retrieved sequences
label.trim_retrieved_sequences = When the reference sequence is longer than the sequence that you are working with, only keep the relevant subsequences.
-label.use_sequence_id_1 = Use $SEQUENCE_ID$ or $SEQUENCE_ID=/<regex>/=$
-label.use_sequence_id_2 = \nto embed sequence id in URL
+label.use_sequence_id_1 = Use $DB_ACCESSION$ or $DB_ACCESSION=/<regex>/=$
+label.use_sequence_id_2 = to embed accession id in URL
+label.use_sequence_id_3 = Use $SEQUENCE_ID$ similarly to embed sequence id
+label.use_sequence_id_4 =
label.ws_parameters_for = Parameters for {0}
label.switch_server = Switch server
label.choose_jabaws_server = Choose a server for running this service
label.rest_client_submit = {0} using {1}
label.fetch_retrieve_from =Retrieve from {0}</html>
label.fetch_retrieve_from_all_sources = Retrieve from all {0} sources in {1}<br>First is :{2}<html>
-#label.feature_settings_click_drag = <html>Click/drag feature types up or down to change render order.<br/>Double click to select columns containing feature in alignment/current selection<br/>Pressing Alt will select columns outside features rather than inside<br/>Pressing Shift to modify current selection (rather than clear current selection)<br/>Press CTRL or Command/Meta to toggle columns in/outside features<br/></html>
label.feature_settings_click_drag = Drag up or down to change render order.<br/>Double click to select columns containing feature.
label.transparency_tip = Adjust transparency to 'see through' feature colours.
label.opt_and_params_further_details = see further details by right-clicking
label.service_preset = Service Preset
label.run_with_preset = Run {0} with preset
label.view_service_doc_url = <html>View <a href="{0}">{1}</a></html>
-label.submit_sequence = <html>Submit {0} {1} {2} {3} to<br/>{4}</html>
-action.by_title_param = by {0}
-label.alignment = Alignment
-label.secondary_structure_prediction = Secondary Structure Prediction
-label.sequence_database_search = Sequence Database Search
-label.analysis = Analysis
-label.protein_disorder = Protein Disorder
+action.by_title_param = By {0}
label.source_from_db_source = Sources from {0}
label.from_msname = from {0}
-label.superpose_with = Superpose with ...
-action.do = Do
+label.superpose_with = Superpose with
label.scale_label_to_column = Scale Label to Column
label.add_new_row = Add New Row
label.edit_label_description = Edit Label/Description
label.muscle_multiple_protein_sequence_alignment = Muscle Multiple Protein Sequence Alignment
label.mafft_multiple_sequence_alignment = MAFFT Multiple Sequence Alignment
label.clustalw_multiple_sequence_alignment = ClustalW Multiple Sequence Alignment
-label.jnet_secondary_structure_prediction = JNet Secondary Structure Prediction
+label.jnet_secondary_structure_prediction = JPred Secondary Structure Prediction
label.multiharmony = Multi-Harmony
label.unable_start_web_service_analysis = Unable to start web service analysis
label.job_couldnt_be_started_check_input = The Job couldn't be started. Please check your input, and the Jalview console for any warning messages.
label.prompt_each_time = Prompt each time
-label.use_source = Use Source
label.couldnt_save_project = Couldn't save project
label.error_whilst_saving_current_state_to = Error whilst saving current state to {0}
label.error_whilst_loading_project_from = Error whilst loading project from {0}
label.couldnt_load_project = Couldn't load project
-label.pca_sequences_not_aligned = The sequences must be aligned before calculating PCA.\nTry using the Pad function in the edit menu,\nor one of the multiple sequence alignment web services.
label.invalid_name_preset_exists = Invalid name - preset already exists.
label.invalid_name = Invalid name
label.set_proxy_settings = Please set up your proxy settings in the 'Connections' tab of the Preferences window
label.service_called_is_not_seq_search_service = The Service called \n{0}\nis not a \nSequence Search Service\!
label.seq_search_service_is_unknown = The Sequence Search Service named {0} is unknown
label.feature_type = Feature Type
-label.display = Display
+label.show = Show
label.service_url = Service URL
label.copied_sequences = Copied sequences
label.cut_sequences = Cut Sequences
label.conservation_colour_increment = Conservation Colour Increment ({0})
-label.percentage_identity_thereshold = Percentage Identity Threshold ({0})
+label.percentage_identity_threshold = Percentage Identity Threshold ({0})
label.error_unsupported_owwner_user_colour_scheme = Unsupported owner for User Colour scheme dialog
label.save_alignment_to_file = Save Alignment to file
label.save_features_to_file = Save Features to File
label.save_annotation_to_file = Save Annotation to File
-label.no_features_on_alignment = No features found on alignment
label.save_pdb_file = Save PDB File
label.save_text_to_file = Save Text to File
label.save_state = Save State
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.dataset_for = {0} Dataset for {1}
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.save_as_html = Save as HTML
label.recently_opened = Recently Opened
label.blasting_for_unidentified_sequence_jobs_running = BLASTing for unidentified sequences - {0} jobs running.
+label.tree = Tree
label.tree_from = Tree from {0}
label.webservice_job_title = {0} using {1}
label.select_visible_region_of = selected {0} region of {1}
label.updating_vamsas_session = Updating vamsas session
label.loading_file = Loading File: {0}
label.edit_params = Edit {0}
+label.as_percentage = As Percentage
error.not_implemented = Not implemented
error.no_such_method_as_clone1_for = No such method as clone1 for {0}
error.null_from_clone1 = Null from clone1!
-error.implementation_error_sortbyfeature = Implementation Error - sortByFeature method must be one of FEATURE_SCORE, FEATURE_LABEL or FEATURE_DENSITY.
error.not_yet_implemented = Not yet implemented
error.unknown_type_dna_or_pep = Unknown Type {0} - dna or pep are the only allowed values.
-error.implementation_error_dont_know_thereshold_annotationcolourgradient = Implementation error: don't know about threshold setting for current AnnotationColourGradient.
-error.implementation_error_embeddedpopup_not_null = Implementation error - embeddedPopup must be non-null
-error.invalid_colour_for_mycheckbox = Invalid color for MyCheckBox
-error.implementation_error_unrecognised_render_object_for_features_type = Implementation Error: Unrecognised render object {0} for features of type {1}
-error.implementation_error_unsupported_feature_colour_object = Implementation error: Unsupported feature colour object.
+error.implementation_error_dont_know_threshold_annotationcolourgradient = Implementation error: don't know about threshold setting for current AnnotationColourGradient.
error.invalid_separator_parameter = Invalid separator parameter - must be non-zero length
error.alignment_cigararray_not_implemented = Alignment(CigarArray) not yet implemented
-error.weak_sequencei_equivalence_not_yet_implemented = Weak sequenceI equivalence not yet implemented.
-error.implementation_error_can_only_make_alignmnet_from_cigararray = Implementation Error - can only make an alignment view from a CigarArray of sequences.
error.empty_view_cannot_be_updated = empty view cannot be updated.
error.mismatch_between_number_of_sequences_in_block = Mismatch between number of sequences in block {0} ({1}) and the original view ({2})
error.padding_not_yet_implemented = Padding not yet implemented
error.implementation_bug_cigar_operation = Implementation Bug. Cigar Operation {0} {1} not one of {2}, {3}, or {4}.
error.implementation_error_for_new_cigar = Implementation error for new Cigar(SequenceI)
error.implementation_error_cigar_seq_no_operations = Implementation error: {0}th sequence Cigar has no operations.
-error.implementation_error_jmol_getting_data = Implementation error - Jmol seems to be still working on getting its data - report at http://issues.jalview.org/browse/JAL-1016
error.implementation_error_no_pdbentry_from_index = Implementation error - no corresponding pdbentry (for index {0}) to add sequences mappings to
error.jmol_version_not_compatible_with_jalview_version = Jmol version {0} is not compatible with this version of Jalview. Report this problem at issues.jalview.org
error.not_implemented_remove = Remove: Not implemented
error.not_implemented_clone = Clone: Not implemented
-error.implementation_error_chimera_getting_data = Implementation error - Chimera seems to be still working on getting its data - report at http://issues.jalview.org/browse/JAL-1016
error.call_setprogressbar_before_registering_handler = call setProgressBar before registering the progress bar's handler.
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_thereshold_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.implementation_error_dont_know_about_threshold_setting = Implementation error: don't know about threshold setting for current AnnotationColourGradient.
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
-error.implementation_error_cannot_create_groovyshell = Implementation Error. Cannot create groovyShell without Groovy on the classpath!
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_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.implementation_error_jalview_class_should_bind_to_type = Implementation Error: Jalview 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_cannot_duplicate_colour_scheme = Serious implementation error: cannot duplicate colourscheme {0}
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_multiple_single_sequence_prediction_jobs_not_supported = Implementation Error! Multiple single sequence prediction jobs are not yet supported
error.implementation_error_invalid_msa_index_for_job =Implementation Error! Invalid msaIndex for JPredJob on parent MSA input object!
error.implementation_error_startjob_called = Implementation error - StartJob(JpredJob) called on {0}
-error.multiple_jnet_subjob_merge_not_implemented = Multiple JNet subjob merging not yet implemented
+error.multiple_jnet_subjob_merge_not_implemented = Multiple JPred subjob merging not yet implemented
label.job_never_ran = Job never ran - input returned to user.
error.implementation_error_minlen_must_be_greater_zero = Implementation error: minlen must be zero or more
error.implementation_error_msawbjob_called = Implementation error - StartJob(MsaWSJob) called on a WSJobInstance {0}
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} containing features of type {3} across {4} sequence(s)
+label.view_controller_toggled_marked = {0} {1} columns {2} features of type {3} across {4} sequence(s)
label.toggled = Toggled
label.marked = Marked
-label.not = not
-label.no_feature_of_type_found = No features of type {0} found.
+label.containing = containing
+label.not_containing = not containing
+label.no_feature_of_type_found = No features of type {0} found
+label.no_feature_found_selection = No features of type {0} found in selection
label.submission_params = Submission {0}
label.empty_alignment_job = Empty Alignment Job
label.add_new_sbrs_service = Add a new Simple Bioinformatics Rest Service
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_thereshold = 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.bad_pattern_to_regex_perl_code = bad pattern to Regex.perlCode: {0}
exception.no_stub_implementation_for_interface = There is no stub implementation for the interface: {0}
exception.cannot_set_endpoint_address_unknown_port = Cannot set Endpoint Address for Unknown Port {0}
-exception.querying_matching_opening_parenthesis_for_non_closing_parenthesis = Querying matching opening parenthesis for non-closing parenthesis character {0}
exception.mismatched_unseen_closing_char = Mismatched (unseen) closing character {0}
exception.mismatched_closing_char = Mismatched closing character {0}
exception.mismatched_opening_char = Mismatched opening character {0} at {1}
exception.invalid_datasource_couldnt_obtain_reader = Invalid datasource. Could not obtain Reader
-exception.index_value_not_in_range = {0}: Index value {1} not in range [0..{2}]
exception.unterminated_cigar_string = Unterminated cigar string
exception.unexpected_operation_cigar_string_pos = Unexpected operation {0} in cigar string (position {1} in {2}
exception.couldnt_parse_responde_from_annotated3d_server = Couldn't parse response from Annotate3d server
exception.application_test_npe = Application test: throwing an NullPointerException It should arrive at the console
exception.overwriting_vamsas_id_binding = Overwriting vamsas id binding
exception.overwriting_jalview_id_binding = Overwriting jalview id binding
-error.implementation_error_unknown_file_format_string = Implementation error: Unknown file format string
exception.failed_to_resolve_gzip_stream = Failed to resolve GZIP stream
exception.problem_opening_file_also_tried = Problem opening {0} (also tried {1}) : {2}
exception.problem_opening_file = Problem opening {0} : {1}
exception.pfam_no_sequences_found = No sequences found (PFAM input)
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.error_parsing_line = Error parsing {0}
exception.unknown_annotation_detected = Unknown annotation detected: {0} {1}
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_unable_to_locate = Unable to locate browser: {0}
exception.invocation_target_exception_creating_aedesc = InvocationTargetException while creating AEDesc: {0}
exception.illegal_access_building_apple_evt= IllegalAccessException while building AppleEvent: {0}
-exception.instantiation_creating_aedesc = InstantiationException while creating AEDesc: {0}
exception.unable_to_launch_url = Unable to launch URL: {0}
exception.unable_to_create_internet_config = Unable to create an Internet Config instance: {0}
exception.invocation_target_calling_url = InvocationTargetException while calling openURL: {0}
exception.illegal_access_calling_url = IllegalAccessException while calling openURL: {0}
exception.interrupted_launching_browser = InterruptedException while launching browser: {0}
-exception.das_source_doesnt_support_sequence_command = Source {0} does not support the sequence command.
-exception.invalid_das_source = Invalid das source: {0}
exception.ebiembl_retrieval_failed_on = EBI EMBL XML retrieval failed on {0}:{1}
-label.no_embl_record_found = # No EMBL record retrieved for {0}:{1}
-label.embl_successfully_parsed = # Successfully parsed the {0} queries into an Alignment
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
exception.unknown_format_for_file = Unknown format {0} for file \: \n{1}
label.remove_gaps = Remove Gaps
-exception.couldnt_recover_sequence_props_for_jnet_query = Couldn't recover sequence properties for JNet Query sequence!
+exception.couldnt_recover_sequence_props_for_jnet_query = Couldn't recover sequence properties for JPred Query sequence!
exception.server_timeout_try_later = Server timed out - try again later\n
exception.web_service_returned_null_try_later= Server at {0} returned null object, it probably cannot be contacted. Try again later.
exception.cannot_contact_service_endpoint_at = Cannot contact service endpoint at {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.
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
info.failed_to_submit_prediction = Failed to submit the prediction\:\n{0} {1}
-info.invalid_jnet_job_result_data ={0}\n{1}\nInvalid JNet job result data\!\n{2}
+info.invalid_jnet_job_result_data ={0}\n{1}\nInvalid JPred job result data\!\n{2}
info.failed_to_submit_sequences_for_alignment = Failed to submit sequences for alignment.\nIt is most likely that there is a problem with the server.\nJust close the window\n
info.alignment_object_method_notes = \nAlignment Object Method Notes\n
info.server_exception = \n{0} Server exception\!\n{1}
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 = Export complete.
+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.processing = Processing...
status.refreshing_web_service_menus = Refreshing Web Service Menus
status.collecting_job_results = Collecting job results.
-status.fetching_das_sequence_features = Fetching DAS Sequence Features
-status.no_das_sources_active = No DAS Sources Active
-status.das_feature_fetching_cancelled = DAS Feature Fetching Cancelled
-status.das_feature_fetching_complete = DAS Feature Fetching Complete
status.fetching_db_refs = Fetching db refs
+status.loading_cached_pdb_entries = Loading Cached PDB Entries
+status.searching_for_pdb_structures = Searching for PDB Structures
+status.opening_file_for = opening file for
+status.colouring_chimera = Colouring Chimera
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.
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 $SEQUENCE_ID$ or a regex $SEQUENCE_ID=/<regex>/=$
+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
+warn.urls_no_jaba = URLs without any JABA Services
info.validate_jabaws_server = Validate JabaWS Server ?\n(Look in console output for results)
label.test_server = Test Server?
-info.you_want_jalview_to_find_uniprot_accessions = Do you want Jalview to find\nUniprot Accession ids for given sequence names?
-label.find_uniprot_accession_ids = Find Uniprot Accession Ids
label.new_sequence_fetcher = New Sequence Fetcher
label.additional_sequence_fetcher = Additional Sequence Fetcher
label.select_database_retrieval_source = Select Database Retrieval Source
label.add_jabaws_url = Add new JABAWS URL
label.news_from_jalview = News from http://www.jalview.org
label.cut_paste_alignmen_file = Cut & Paste Alignment File
-label.enter_redundancy_thereshold = Enter the redundancy threshold
-label.select_dark_light_set_thereshold = <html><i>Select a dark and light text colour, then set the threshold to<br>switch between colours, based on background colour</i></html>
+label.enter_redundancy_threshold = Enter the redundancy threshold
+label.select_dark_light_set_threshold = <html><i>Select a dark and light text colour, then set the threshold to<br>switch between colours, based on background colour</i></html>
label.select_feature_colour = Select Feature Colour
label.delete_all = Delete all sequences
warn.delete_all = <html>Deleting all sequences will close the alignment window.<br>Confirm deletion or Cancel.
label.add_annotations_for = Add annotations for
-label.choose_annotations = Choose annotations
+action.choose_annotations = Choose Annotations...
+label.choose_annotations = Choose Annotations
label.find = Find
label.invalid_search = Search string invalid
error.invalid_regex = Invalid regular expression
label.show_histogram = Show Histogram
label.show_logo = Show Logo
label.normalise_logo = Normalise Logo
-label.no_colour_selection_in_scheme = Please, make a colour selection before to apply colour scheme
+label.no_colour_selection_in_scheme = Please make a colour selection before applying colour scheme
label.no_colour_selection_warn = Error saving colour scheme
label.open_split_window? = Would you like to open as a split window, with cDNA and protein linked?
label.open_split_window = Open split window
-label.no_mappings = No mappings found
-label.mapping_failed = No sequence mapping could be made between the alignments.<br>A mapping requires sequence names to match, and equivalent sequence lengths.
action.no = No
action.yes = Yes
label.for = for
-label.select_by_annotation = Select By Annotation
-action.select_by_annotation = Select by Annotation...
+label.select_by_annotation = Select/Hide Columns by Annotation
+action.select_by_annotation = Select/Hide Columns by Annotation...
label.threshold_filter = Threshold Filter
-action.hide = Hide
-action.select = Select
label.alpha_helix = Alpha Helix
label.beta_strand = Beta Strand
label.turn = Turn
label.select_all = Select All
label.structures_filter = Structures Filter
label.search_filter = Search Filter
-label.display_name = Display Label
-label.description = Description
label.include_description= Include Description
action.back = Back
label.hide_insertions = Hide Insertions
label.mark_as_representative = Mark as representative
label.open_jabaws_web_page = Open JABAWS web page
-label.opens_the_jabaws_server_homepage = Opens the JABAWS server's homepage in web browser
-label.pdb_sequence_getcher = PDB Sequence Fetcher
+label.pdb_sequence_fetcher = PDB Sequence Fetcher
label.result = result
label.results = results
label.structure_chooser = Structure Chooser
-label.select = Select :
label.invert = Invert
label.select_pdb_file = Select PDB File
info.select_filter_option = Select Filter Option/Manual Entry
info.associate_wit_sequence = Associate with Sequence
label.search_result = Search Result
label.found_structures_summary = Found Structures Summary
-label.configure_displayed_columns = Configure Displayed Columns
+label.configure_displayed_columns = Customise Displayed Options
label.start_jalview = Start Jalview
label.biojs_html_export = BioJS
-action.back = Back
-label.hide_insertions = Hide Insertions
-label.mark_as_representative = Mark as representative
-label.open_jabaws_web_page = Open JABAWS web page
-label.opens_the_jabaws_server_homepage = Opens the JABAWS server's homepage in web browser
-label.pdb_sequence_getcher = PDB Sequence Fetcher
-label.result = result
-label.results = results
-label.structure_chooser = Structure Chooser
-label.select = Select :
-label.invert = Invert
-label.select_pdb_file = Select PDB File
-info.select_filter_option = Select Filter Option/Manual Entry
-info.associate_wit_sequence = Associate with Sequence
-label.search_result = Search Result
-label.found_structures_summary = Found Structures Summary
-label.configure_displayed_columns = Configure Displayed Columns
-label.scale_as_cdna = Scale residues to width of codons
+label.scale_as_cdna = Scale protein residues to codons
+label.font_as_cdna = Use same font for cDNA and peptide
label.scale_protein_to_cdna = Scale Protein to cDNA
label.scale_protein_to_cdna_tip = Make protein residues same width as codons in split frame views
+info.select_annotation_row = Select Annotation Row
+info.enter_search_text_here = Enter Search Text Here
+info.enter_search_text_to_enable = Enter Search Text to Enable
+info.search_in_annotation_label = Search in {0} Label
+info.search_in_annotation_description = Search in {0} Description
+info.change_threshold_mode_to_enable = Change Threshold Mode to Enable
+label.couldnt_read_data = Couldn't read data
+label.embbed_biojson = Embed BioJSON to HTML export
+action.export_groups = Export Groups
+action.export_annotations = Export Annotations
+action.export_hidden_columns = Export Hidden Columns
+action.export_hidden_sequences = Export Hidden Sequences
+action.export_features = Export Features
+label.export_settings = Export Settings
+label.pdb_web-service_error = PDB Web-service Error
+label.structure_chooser_manual_association = Structure Chooser - Manual association
+label.structure_chooser_filter_time = Structure Chooser - Filter time ({0})
+label.structure_chooser_no_of_structures = Structure Chooser - {0} Found ({1})
+info.no_pdb_entry_found_for = No PDB entry found for {0}
+exception.unable_to_detect_internet_connection = Jalview is unable to detect an internet connection
+exception.fts_server_unreachable = Jalview is unable to reach the {0} server. \nPlease ensure that you are connected to the internet and try again.
+label.nw_mapping = Needleman & Wunsch Alignment
+label.sifts_mapping = SIFTs Mapping
+label.mapping_method = Sequence \u27f7 Structure mapping method
+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.run_groovy = Run Groovy console script
+label.run_groovy_tip = Run the script in the Groovy console over this alignment
+label.couldnt_run_groovy_script = Failed to run Groovy script
+label.uniprot_sequence_fetcher = UniProt Sequence Fetcher
+action.next_page= >>
+action.prev_page= <<
+label.next_page_tooltip=Next Page
+label.prev_page_tooltip=Previous Page
+status.launching_3d_structure_viewer = Launching 3D Structure viewer...
+status.fetching_3d_structures_for_selected_entries = Fetching 3D Structures for selected entries...
+status.fetching_dbrefs_for_sequences_without_valid_refs = Fetching db refs for {0} sequence(s) without valid db ref required for SIFTS mapping
+status.fetching_3d_structures_for = Fetching 3D Structure for {0}
+status.obtaining_mapping_with_sifts = Obtaining mapping with SIFTS
+status.obtaining_mapping_with_nw_alignment = Obtaining mapping with NW alignment
+status.exporting_alignment_as_x_file = Exporting alignment as {0} file
+label.column = Column
+label.cant_map_cds = Unable to map CDS to protein\nCDS missing or incomplete
+label.operation_failed = Operation failed
+label.SEQUENCE_ID_no_longer_used = $SEQUENCE_ID$ is no longer used for DB accessions
+label.SEQUENCE_ID_for_DB_ACCESSION1 = Please review your URL links in the 'Connections' tab of the Preferences window:
+label.SEQUENCE_ID_for_DB_ACCESSION2 = URL links using '$SEQUENCE_ID$' for DB accessions now use '$DB_ACCESSION$'.
+label.do_not_display_again = Do not display this message again
+exception.url_cannot_have_duplicate_id = {0} cannot be used as a label for more than one line
+action.customfilter = Custom only
+action.showall = Show All
+label.insert = Insert:
+action.seq_id = $SEQUENCE_ID$
+action.db_acc = $DB_ACCESSION$
+label.primary = Double Click
+label.inmenu = In Menu
+label.id = ID
+label.database = Database
+label.urltooltip = Only one url, which must use a sequence id, can be selected for the 'On Click' option
+label.edit_sequence_url_link = Edit sequence URL link
+warn.name_cannot_be_duplicate = User-defined URL names must be unique and cannot be MIRIAM ids
+label.output_seq_details = Output Sequence Details to list all database references
+label.urllinks = Links
+action.clear_cached_items = Clear Cached Items
+label.togglehidden = Show hidden regions
+label.quality_descr = Alignment Quality based on Blosum62 scores
+label.conservation_descr = Conservation of total alignment less than {0}% gaps
+label.consensus_descr = PID
+label.complement_consensus_descr = PID for cDNA
+label.strucconsensus_descr = PID for base pairs
+label.occupancy_descr = Number of aligned positions
+label.show_experimental = Enable experimental features
+label.show_experimental_tip = Enable any new and currently 'experimental' features (see Latest Release Notes for details)
+label.warning_hidden = Warning: {0} {1} is currently hidden
+label.overview_settings = Overview settings
+label.ov_legacy_gap = Use legacy gap colouring (gaps are white)
+label.gap_colour = Gap colour:
+label.ov_show_hide_default = Show hidden regions when opening overview
+label.hidden_colour = Hidden colour:
+label.select_gap_colour = Select gap colour
+label.select_hidden_colour = Select hidden colour
+label.overview = Overview
+label.reset_to_defaults = Reset to defaults
+label.oview_calc = Recalculating overview...
+label.feature_details = Feature details
+label.matchCondition_contains = Contains
+label.matchCondition_notcontains = Does not contain
+label.matchCondition_matches = Matches
+label.matchCondition_notmatches = Does not match
+label.matchCondition_present = Is present
+label.matchCondition_notpresent = Is not present
+label.matchCondition_eq = =
+label.matchCondition_ne = not =
+label.matchCondition_lt = <
+label.matchCondition_le = <=
+label.matchCondition_gt = >
+label.matchCondition_ge = >=
+label.numeric_required = The value should be numeric
+label.filter = Filter
+label.filters = Filters
+label.join_conditions = Join conditions with
+label.delete_condition = Delete this condition
+label.score = Score
+label.colour_by_label = Colour by label
+label.variable_colour = Variable 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.display_settings_for = Display settings for {0} features
+label.simple = Simple
+label.simple_colour = Simple Colour
+label.colour_by_text = Colour by text
+label.graduated_colour = Graduated Colour
+label.by_text_of = By text of
+label.by_range_of = By range of
+label.or = Or
+label.and = And
+label.sequence_feature_colours = Sequence Feature Colours
+label.best_quality = Best Quality
+label.best_resolution = Best Resolution
+label.most_protein_chain = Most Protein Chain
+label.most_bound_molecules = Most Bound Molecules
+label.most_polymer_residues = Most Polymer Residues
+label.cached_structures = Cached Structures
+label.free_text_search = Free Text Search
+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.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.backups = Backups
+label.backup = Backup
+label.backup_files = Backup Files
+label.enable_backupfiles = Enable backup files
+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.
+label.keep_files = Deleting old backup files
+label.keep_all_backup_files = Do not delete old backup files
+label.keep_only_this_number_of_backup_files = Keep only this number of most recent backup files
+label.autodelete_old_backup_files = Auto-delete old backup files:
+label.always_ask = Always ask
+label.auto_delete = Automatically delete
+label.filename = filename
+label.braced_oldest = (oldest)
+label.braced_newest = (most recent)
+label.configuration = Configuration
+label.configure_feature_tooltip = Click to configure variable colour or filters
+label.schemes = Schemes
+label.customise = Customise
+label.custom = Custom
+label.default = Default
+label.single_file = Single backup
+label.keep_all_versions = Keep all versions
+label.rolled_backups = Rolled backup files
+label.customise_description = Select Customise, make changes, and click on OK to save your own custom scheme
+label.custom_description = Your own saved scheme
+label.default_description = Keep the last three versions of the file
+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}).
+label.confirm_deletion = Confirm deletion of ''{0}''?
+label.delete = Delete
+label.rename = Rename
+label.keep = Keep
+label.file_info = (modified {0}, size {1})
+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.by_annotation_tooltip = Annotation Colour is configured from the main Colour menu
+label.show_linked_features = Show {0} features
+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