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.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_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.invert_sequence_selection = Invert Sequence Selection
label.view_flanking_regions = Show sequence data either side of the subsequences involved in this alignment
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.name = Name
label.principal_component_analysis = Principal Component Analysis
label.average_distance_identity = Average Distance Using % Identity
label.neighbour_joining_identity = Neighbour Joining Using % Identity
+label.choose_calculation = Choose Calculation
label.treecalc_title = {0} Using {1}
label.tree_calc_av = Average Distance
label.tree_calc_nj = Neighbour Joining
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
+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_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.style = Style:
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.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.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.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_threshold = No Threshold
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.2d_rna_sequence_name = 2D RNA - {0}
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 (or pdbid:chaincode)
-label.text_colour = Text Colour
-action.set_text_colour = Text Colour...
+label.enter_pdb_id = Enter PDB Id
+label.enter_pdb_id_tip = Enter PDB Id (or pdbid:chaincode)
+label.text_colour = Text Colour...
label.structure = Structure
label.show_pdbstruct_dialog = 3D Structure Data...
label.view_rna_structure = VARNA 2D Structure
-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.show_labels = Show labels
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.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.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.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.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.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_threshold_annotationcolourgradient = Implementation error: don't know about threshold setting for current AnnotationColourGradient.
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}
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.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.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}
label.start_jalview = Start Jalview
label.biojs_html_export = BioJS
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
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.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
+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.output_seq_details = Output Sequence Details to list all database references
+label.urllinks = Links
+label.default_cache_size = Default Cache Size
+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...
+option.enable_disable_autosearch = When ticked, search is performed automatically
+option.autosearch = Autosearch
+label.retrieve_ids = Retrieve IDs
+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
git://source.jalview.org / jalview.git / blobdiff