X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=resources%2Flang%2FMessages.properties;h=c25cda8be57ee517ebaebe96aedc4f45dd667b2b;hb=02c1474aa3b80a034a475edd9dc77fe8928ad1f1;hp=00888d5aa8fa80363c6f4135959e8241356cc0c1;hpb=3013ab968530be65871281fc548c5ffa92a7b7b0;p=jalview.git diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties index 00888d5..c25cda8 100644 --- a/resources/lang/Messages.properties +++ b/resources/lang/Messages.properties @@ -11,6 +11,7 @@ action.paste = Paste 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 @@ -203,6 +204,8 @@ 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.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 @@ -266,6 +269,7 @@ label.use_rnaview = Use RNAView for secondary structure 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.
Double-click to browse for file. label.invalid_chimera_path = Chimera path not found or not executable @@ -368,6 +372,8 @@ 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.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} @@ -400,10 +406,6 @@ 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.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. @@ -676,7 +678,8 @@ 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.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... @@ -816,8 +819,8 @@ label.fetch_retrieve_from_all_sources = Retrieve from all {0} sources in {1}
label.feature_settings_click_drag = Drag up or down to change render order.
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 = Click to show brief description
Right click for further information. -label.opt_and_params_show_brief_desc = Click to show brief description
+label.opt_and_params_show_brief_desc_image_link = Click to show brief description
Right click for further information. +label.opt_and_params_show_brief_desc = Click to show brief description
label.adjusts_width_generated_eps_png = Adjusts the width of the generated EPS or PNG file to ensure even the longest sequence ID or annotation label is displayed label.manually_specify_width_left_column = 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 label.job_created_when_checked = When checked, a job is created for every sequence in the current selection. @@ -879,7 +882,6 @@ label.error_unsupported_owwner_user_colour_scheme = Unsupported owner for User C 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 @@ -958,7 +960,6 @@ label.groovy_support_failed = Jalview Groovy Support Failed label.couldnt_create_groovy_shell = Couldn't create the groovy Shell. Check the error log for the details of what went wrong. error.unsupported_version_calcIdparam = Unsupported Version for calcIdparam {0} error.implementation_error_cant_reorder_tree = Implementation Error: Can't reorder this tree. Not DefaultMutableTreeNode. -error.invalid_value_for_option = Invalid value {0} for option {1} error.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 @@ -1144,6 +1145,9 @@ 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 +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} @@ -1215,7 +1219,6 @@ 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 @@ -1341,9 +1344,9 @@ label.filters = Filters label.join_conditions = Join conditions with label.score = Score label.colour_by_label = Colour by label -label.variable_colour = Variable colour +label.variable_colour = Variable colour... label.select_colour = Select colour -option.enable_disable_autosearch = When ticked, search is performed automatically. +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 @@ -1355,4 +1358,67 @@ 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 \ No newline at end of file +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 +action.search = Search \ No newline at end of file