action.show_html_source = Show HTML Source
action.print = Print...
action.web_service = Web Service
+action.hmmer = HMMER
action.cancel_job = Cancel Job
action.start_job = Start Job
action.revert = Revert
label.colourScheme_nucleotide = Nucleotide
label.colourScheme_t-coffee_scores = T-Coffee Scores
label.colourScheme_rna_helices = By RNA Helices
+label.colourScheme_hmmer-uniprot = HMMER profile v global background
+label.colourScheme_hmmer-alignment = HMMER profile v alignment background
label.blc = BLC
label.fasta = Fasta
label.msf = MSF
label.about = About...
label.show_sequence_limits = Show Sequence Limits
action.feature_settings = Feature Settings...
-label.feature_settings = Feature Settings
label.all_columns = All Columns
label.all_sequences = All Sequences
label.selected_columns = Selected Columns
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_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.seq_sort_by_score = Sequence sort by Score
label.load_colours = Load Colours
label.save_colours = Save Colours
+label.load_colours_tooltip = Load feature colours and filters from file
+label.save_colours_tooltip = Save feature colours and filters to file
label.fetch_das_features = Fetch DAS Features
label.selected_database_to_fetch_from = Selected {0} database {1} to fetch from {2}
label.database_param = Database: {0}
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.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.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_url_param = Open URL {0}
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.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.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.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 = Enter one or more accession IDs separated by a semi-colon ";"
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.opt_and_params_show_brief_desc_image_link = <html>Click to show brief description<br><img src="{0}"/> Right click for further information.</html>
-label.opt_and_params_show_brief_desc = <html>Click to show brief description<br></html>
+label.opt_and_params_show_brief_desc_image_link = Click to show brief description<br><img src="{0}"/> Right click for further information.
+label.opt_and_params_show_brief_desc = Click to show brief description<br>
label.adjusts_width_generated_eps_png = <html>Adjusts the width of the generated EPS or PNG file to ensure even the longest sequence ID or annotation label is displayed</html>
label.manually_specify_width_left_column = <html>Manually specify the width of the left hand column where sequence IDs and annotation labels will be rendered in exported alignment figures. This setting will be ignored if 'Automatically set ID width' is set</html>
label.job_created_when_checked = <html>When checked, a job is created for every sequence in the current selection.</html>
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.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.couldnt_create_groovy_shell = Couldn't create the groovy Shell. Check the error log for the details of what went wrong.
error.unsupported_version_calcIdparam = Unsupported Version for calcIdparam {0}
error.implementation_error_cant_reorder_tree = Implementation Error: Can't reorder this tree. Not DefaultMutableTreeNode.
-error.invalid_value_for_option = Invalid value {0} for option {1}
error.implementation_error_cannot_import_vamsas_doc = Implementation Error - cannot import existing vamsas document into an existing session, Yet!
label.vamsas_doc_couldnt_be_opened_as_new_session = VAMSAS Document could not be opened as a new session - please choose another
error.implementation_error_vamsas_operation_not_init = Impementation error! Vamsas Operations when client not initialised and connected
status.searching_for_pdb_structures = Searching for PDB Structures
status.opening_file_for = opening file for
status.colouring_chimera = Colouring Chimera
+status.running_hmmbuild = Building Hidden Markov Model
+status.running_hmmalign = Creating alignment with Hidden Markov Model
+status.running_hmmsearch = Searching for matching sequences
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.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
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_gt = >
label.matchCondition_ge = >=
label.numeric_required = The value should be numeric
-label.no_attributes_known = No attributes known
+label.filter = Filter
label.filters = Filters
-label.match_condition = Match condition
label.join_conditions = Join conditions with
-label.feature_to_filter = Feature to filter
+label.score = Score
+label.colour_by_label = Colour by label
+label.variable_colour = Variable colour...
+label.select_colour = Select colour
+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.filters_tooltip = Click to set or amend filters
+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.hmmalign = hmmalign
+label.use_hmm = HMM profile to use
+label.hmmbuild = hmmbuild
+label.hmmsearch = hmmsearch
+label.installation = Installation
+label.hmmer_location = HMMER Binaries Installation Location
+label.cygwin_location = Cygwin Binaries Installation Location (Windows)
+label.information_annotation = Information Annotation
+label.ignore_below_background_frequency = Ignore Below Background Frequency
+label.information_description = Information content, measured in bits
+warn.no_hmm = No Hidden Markov model found.\nRun hmmbuild or load an HMM file first.
+label.no_sequences_found = No matching sequences, or an error occurred.
+label.hmmer = HMMER
+label.trim_termini = Trim Non-Matching Termini
+label.trim_termini_desc = If true, non-matching regions on either end of the resulting alignment are removed.
+label.no_of_sequences = Number of sequences returned
+label.reporting_cutoff = Reporting Cut-off
+label.freq_alignment = Use alignment background frequencies
+label.freq_uniprot = Use Uniprot background frequencies
+label.hmmalign_options = hmmalign options
+label.hmmsearch_options = hmmsearch options
+label.executable_not_found = The ''{0}'' executable file was not found
+warn.command_failed = {0} failed
+label.invalid_folder = Invalid Folder
+label.number_of_results = Number of Results to Return
+label.auto_align_seqs = Automatically Align Fetched Sequences
+label.use_accessions = Return Accessions
+label.seq_evalue = Sequence E-value Cut-off
+label.seq_score = Sequence Score Threshold
+label.dom_evalue = Domain E-value Cut-off
+label.dom_score = Domain Score Threshold
+label.number_of_results_desc = The maximum number of hmmsearch results to display
+label.auto_align_seqs_desc = If true, all fetched sequences will be aligned to the hidden Markov model with which the search was performed
+label.use_accessions_desc = If true, the accession number of each sequence is returned, rather than that sequence's name
+label.seq_e_value_desc = The E-value cutoff for returned sequences (hmmsearch -E)
+label.seq_score_desc = The score threshold for returned sequences (hmmsearch -T)
+label.dom_e_value_desc = The E-value cutoff for returned domains (hmmsearch --domE)
+label.dom_score_desc = The score threshold for returned domains (hmmsearch --domT)
+label.add_database = Add Database
+label.this_alignment = This alignment
+warn.invalid_format = This is not a valid database file format. The current supported formats are Fasta, Stockholm and Pfam.
+label.database_for_hmmsearch = The database hmmsearch will search through
+label.use_reference = Use Reference Annotation
+label.use_reference_desc = If true, hmmbuild will keep all columns defined as a reference position by the reference annotation
+label.hmm_name = Alignment HMM Name
+label.hmm_name_desc = The name given to the HMM for the alignment
+warn.no_reference_annotation = No reference annotation found
+label.hmmbuild_for = Build HMM for
+label.hmmbuild_for_desc = Build an HMM for the selected sets of sequences
+label.alignment = Alignment
+label.groups_and_alignment = All groups and alignment
+label.groups = All groups
+label.selected_group = Selected group
+label.use_info_for_height = Use Information Content as Letter Height