X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=resources%2Flang%2FMessages.properties;h=bf9cc186b74390b6f06182ad2a82d63270c2fd20;hb=c794c5033adeee182b03a5ea92c0a7495a29661f;hp=1762a06d516a5dd2f14aa97cfb6f50d0499fc6ca;hpb=e1dbbc5edc07f65706eeb1dda9f4c9bcdee9d3a5;p=jalview.git diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties index 1762a06..bf9cc18 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 @@ -59,6 +60,8 @@ action.boxes = Boxes action.text = Text action.by_pairwise_id = By Pairwise Identity action.by_id = By Id +action.by_evalue = By E-Value +action.by_bit_score = By Bit Score action.by_length = By Length action.by_group = By Group action.unmark_as_reference = Unmark as Reference @@ -98,6 +101,7 @@ action.edit_group = Edit Group action.border_colour = Border colour action.edit_new_group = Edit New Group action.hide_sequences = Hide Sequences +action.add_background_frequencies = Add Background Frequencies action.sequences = Sequences action.ids = IDS action.ids_sequences = IDS and sequences @@ -131,6 +135,8 @@ 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.filter_by_evalue = Filter by E-Value +action.filter_by_score = Filter by Score action.using_jmol = Using Jmol action.undo_changes_to_feature_settings = Undo all unapplied changes to feature settings action.undo_changes_to_feature_settings_and_close_the_dialog = Undo all pending changes and close the feature settings dialog @@ -200,6 +206,9 @@ label.colourScheme_turnpropensity = Turn Propensity label.colourScheme_buriedindex = Buried Index label.colourScheme_purine/pyrimidine = Purine/Pyrimidine label.colourScheme_nucleotide = Nucleotide +label.colourScheme_hmmer-uniprot = HMMER profile v global background +label.colourScheme_hmmer-alignment = HMMER profile v alignment background +label.colourScheme_hmm_match_score = HMM Match Score label.colourScheme_t-coffeescores = T-Coffee Scores label.colourScheme_rnahelices = By RNA Helices label.colourScheme_sequenceid = Sequence ID Colour @@ -810,8 +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. @@ -946,7 +955,6 @@ 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 @@ -1054,6 +1062,7 @@ exception.ranml_couldnt_process_data = Couldn't process data as RNAML file ({0}) exception.ranml_invalid_file = Invalid RNAML file ({0}) exception.ranml_problem_parsing_data = Problem parsing data as RNAML ({0}) exception.pfam_no_sequences_found = No sequences found (PFAM input) +exception.hmmer_no_valid_sequences_found = No valid sequences found 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.unknown_annotation_detected = Unknown annotation detected: {0} {1} @@ -1125,6 +1134,9 @@ 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_search = 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} @@ -1341,6 +1353,79 @@ 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.hmmalign = hmmalign +label.use_hmm = HMM profile to use +label.use_sequence = Sequence to use +label.hmmbuild = hmmbuild +label.hmmsearch = hmmsearch +label.jackhmmer = jackhmmer +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.inclusion_threshold = Inlcusion Threshold +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.jackhmmer_options = jackhmmer 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.number_of_iterations = Number of jackhmmer Iterations +label.auto_align_seqs = Automatically Align Fetched Sequences +label.new_returned = new sequences returned +label.use_accessions = Return Accessions +label.check_for_new_sequences = Return Number of New Sequences +label.evalue = E-Value +label.reporting_seq_evalue = Reporting Sequence E-value Cut-off +label.reporting_seq_score = Reporting Sequence Score Threshold +label.reporting_dom_evalue = Reporting Domain E-value Cut-off +label.reporting_dom_score = Reporting Domain Score Threshold +label.inclusion_seq_evalue = Inclusion Sequence E-value Cut-off +label.inclusion_seq_score = Inclusion Sequence Score Threshold +label.inclusion_dom_evalue = Inclusion Domain E-value Cut-off +label.inclusion_dom_score = Inclusion Domain Score Threshold +label.number_of_results_desc = The maximum number of hmmsearch results to display +label.number_of_iterations_desc = The number of iterations jackhmmer will complete when searching for new sequences +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.check_for_new_sequences_desc = Display number of new sequences returned from hmmsearch compared to the previous alignment +label.use_accessions_desc = If true, the accession number of each sequence is returned, rather than that sequence's name +label.reporting_seq_e_value_desc = The E-value cutoff for returned sequences +label.reporting_seq_score_desc = The score threshold for returned sequences +label.reporting_dom_e_value_desc = The E-value cutoff for returned domains +label.reporting_dom_score_desc = The score threshold for returned domains +label.inclusion_seq_e_value_desc = Sequences with an E-value less than this cut-off are classed as significant +label.inclusion_seq_score_desc = Sequences with a bit score greater than this threshold are classed as significant +label.inclusion_dom_e_value_desc = Domains with an E-value less than this cut-off are classed as significant +label.inclusion_dom_score_desc = Domains with a bit score greater than this threshold are classed as significant +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 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 @@ -1413,3 +1498,4 @@ label.include_linked_features = Include {0} features label.include_linked_tooltip = Include visible {0} features
converted to local sequence coordinates label.features_not_shown = {0} feature(s) not shown label.no_features_to_sort_by = No features to sort by +