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.create = Create
action.update = Update
action.delete = Delete
-action.snapshot = Snapshot
action.clear = Clear
action.accept = Accept
action.select_ddbb = --- Select Database ---
action.remove = Remove
action.remove_redundancy = Remove Redundancy...
action.pairwise_alignment = Pairwise Alignment
-action.by_rna_helixes = By RNA Helices
action.user_defined = User Defined...
action.by_conservation = By Conservation
action.wrap = Wrap
action.show_gaps = Show Gaps
+action.show_occupancy = Show Occupancy
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.save_as = Save as...
action.save = Save
action.cancel_fetch = Cancel Fetch
-action.save_omit_hidden_columns = Save / Omit Hidden Regions
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.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
+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_helix_propensity = Helix Propensity
+label.colourScheme_strand_propensity = Strand Propensity
+label.colourScheme_turn_propensity = Turn Propensity
+label.colourScheme_buried_index = Buried Index
+label.colourScheme_purine/pyrimidine = Purine/Pyrimidine
+label.colourScheme_nucleotide = Nucleotide
+label.colourScheme_t-coffee_scores = T-Coffee Scores
+label.colourScheme_rna_helices = By RNA Helices
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.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.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.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.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 regions (hidden sequences/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.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.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.vamsas_document_import_failed = Vamsas Document Import Failed
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.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.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.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.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.adjusting_parameters_for_calculation = Adjusting parameters for existing Calculation
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.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
-action.set_text_colour = Text Colour...
+label.enter_pdb_id = Enter PDB Id (or pdbid:chaincode)
+label.text_colour = Text Colour...
label.structure = Structure
-label.view_structure = View Structure
-label.view_protein_structure = View Protein Structure
label.show_pdbstruct_dialog = 3D Structure Data...
label.view_rna_structure = VARNA 2D Structure
-label.clustalx_colours = Clustalx colours
-label.above_identity_percentage = Above % Identity
label.create_sequence_details_report_annotation_for = Annotation for {0}
label.sequence_details_for = Sequence Details for {0}
label.sequence_name = Sequence Name
label.reverse = Reverse
label.reverse_complement = Reverse Complement
label.linked_view_title = Linked CDS and protein view
-label.align = Align
label.extract_scores = Extract Scores
label.get_cross_refs = Get Cross-References
label.sort_alignment_new_tree = Sort Alignment With New Tree
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.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.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.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.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.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.select_background_colour = Select Background Colour
label.invalid_font = Invalid Font
label.separate_multiple_accession_ids = Enter one or more accession IDs separated by a semi-colon ";"
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.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.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
label.source_from_db_source = Sources from {0}
label.from_msname = from {0}
label.superpose_with = Superpose with
-action.do = Do
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.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.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.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.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
-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 containing features of type {2} across {3} 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.containing = containing
+label.not_containing = not containing
label.no_feature_of_type_found = No features of type {0} found.
label.submission_params = Submission {0}
label.empty_alignment_job = Empty Alignment Job
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.adjunst_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.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}
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.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 = opening file
+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.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.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.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
action.no = No
action.yes = Yes
label.for = for
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.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_fetcher = PDB Sequence Fetcher
label.result = result
label.results = results
action.export_hidden_sequences = Export Hidden Sequences
action.export_features = Export Features
label.export_settings = Export Settings
-label.save_as_biojs_html = Save as BioJs HTML
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.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.
+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
-info.error_creating_file = Error creating {0} 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.prev_page_tooltip=Previous Page
exception.bad_request=Bad request. There is a problem with your input.
exception.service_not_available=Service not available. The server is being updated, try again later.
+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_miriam_id = {0} is a MIRIAM id and cannot be used as a custom url name
+exception.url_cannot_have_duplicate_id = {0} cannot be used as a label for more than one line
+label.filter = Filter text:
+action.customfilter = Custom only
+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.invalid_name = Invalid Name !
+label.output_seq_details = Output Sequence Details to list all database references
+<<<<<<< HEAD
+label.phyre2_model_prediction = 3D Protein Model prediction with Phyre2
+label.run_phyre2_prediction = Run Phyre2 Prediction
+status.obtaining_mapping_with_phyre2_template_alignment = Obtaining mapping with Phyre2 Template alignment
+=======
+label.urllinks = Links
+>>>>>>> develop
git://source.jalview.org / jalview.git / blobdiff