X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=resources%2Flang%2FMessages.properties;h=c25cda8be57ee517ebaebe96aedc4f45dd667b2b;hb=02c1474aa3b80a034a475edd9dc77fe8928ad1f1;hp=d44c48a58487512df7f24fefe6ad29c6a8d398cf;hpb=bd6ce8f5f9fc8e5bc8a6188d15987ce0ffd2c1ee;p=jalview.git diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties index d44c48a..c25cda8 100644 --- a/resources/lang/Messages.properties +++ b/resources/lang/Messages.properties @@ -204,6 +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 @@ -267,6 +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 @@ -403,10 +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. @@ -820,8 +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. @@ -883,7 +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 @@ -962,7 +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 @@ -1222,7 +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 @@ -1372,64 +1368,57 @@ 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.hmmbuild_group = Build HMM from Selected Group -label.group_hmmbuild = Build HMM from Group label.hmmsearch = hmmsearch +label.installation = Installation label.hmmer_location = HMMER Binaries Installation Location -warn.null_hmm = Please ensure the alignment contains a hidden Markov model. +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_selected_hmm = Please select a hidden Markov model sequence. -label.select_hmm = Select HMM -warn.no_sequence_data = No sequence data found. -warn.empty_grp_or_alignment = An empty group or alignment was found. +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 = Sequences Returned -label.freq_alignment = Use Alignment Background Frequencies -label.freq_uniprot = Use Uniprot Background Frequencies -label.hmmalign_label = hmmalign Options -label.hmmsearch_label = hmmsearch Options -label.hmmbuild_not_found = The hmmbuild binary was not found -label.hmmalign_not_found = The hmmalign binary was not found -label.hmmsearch_not_found = The hmmsearch binary was not found -warn.hmm_command_failed = hmm command not found +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.folder_not_exists = HMMER binaries not found. \n Please enter the path to the HMMER binaries (if installed). -label.hmmer_installed = HMMER installed -label.hmmer_no_sequences_found = No sequences found label.number_of_results = Number of Results to Return label.auto_align_seqs = Automatically Align Fetched Sequences label.use_accessions = Return Accessions -label.seq_e_value = Sequence E-value Cutoff +label.seq_evalue = Sequence E-value Cut-off label.seq_score = Sequence Score Threshold -label.dom_e_value = Domain E-value Cutoff +label.dom_evalue = Domain E-value Cut-off label.dom_score = Domain Score Threshold -label.number_of_results_desc = The maximum number of results that hmmsearch will return +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 sequences name -label.seq_e_value_desc = The E-value cutoff for returned sequences -label.seq_score_desc = The score threshold for returned sequences -label.dom_e_value_desc = The E-value cutoff for returned domains -label.dom_score_desc = The score threshold for returned domains -label.not_enough_sequences = There are not enough sequences to run {0} +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.file_not_exists = File does not exist 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 = HMM Name -label.hmm_name_desc = The name given to the HMM. -warn.no_reference_annotation = No reference annotation found. +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 sequence groups. +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