action.by_length = by Length\r
action.by_group = by Group\r
action.remove = Remove\r
-action.remove_redundancy = Remove Redundancy...\r
+action.remove_redundancy = Remove Redundancy\r
action.pairwise_alignment = Pairwise Alignments...\r
action.by_rna_helixes = by RNA Helices\r
action.user_defined = User Defined...\r
action.invert_selection = Invert selection\r
action.using_jmol = Using Jmol\r
action.link = Link\r
-action.group_link = Group Links\r
+action.group_link = Group Link\r
action.show_chain = Show Chain\r
action.show_group = Show Group\r
action.fetch_db_references = Fetch DB References\r
-action.edit = Edit\r
action.view_flanking_regions = Show flanking regions\r
label.view_flanking_regions = Show sequence data either side of the subsequences involved in this alignment\r
label.str = Str:\r
label.to_textbox = to Textbox\r
label.jalview = Jalview\r
label.csv_spreadsheet = CSV (Spreadsheet)\r
-label.status = [Status]\r
+label.status = Status\r
label.channels = Channels\r
label.channel_title_item_count = {0} ({1})\r
label.blog_item_published_on_date = {0} {1} \r
label.enter_label_for_the_structure = Enter a label for the structure?\r
label.pdb_entry_is_already_displayed = {0} is already displayed.\nDo you want to re-use this viewer ?\r
label.map_sequences_to_visible_window = Map Sequences to Visible Window: {0}\r
-label.add_pdbentry_to_view = Do you want to add {0} to the view called\n'{1}'\n\r
+label.add_pdbentry_to_view = Do you want to add {0} to the view called\n{1}\n\r
label.align_to_existing_structure_view = Align to existing structure view\r
label.pdb_entries_couldnt_be_retrieved = The following pdb entries could not be retrieved from the PDB\:\n{0}\nPlease try downloading them manually.\r
label.couldnt_load_file = Couldn't load file\r
label.public_das_source = Public DAS source - not editable\r
label.input_alignment_from_url = Input Alignment From URL\r
label.input_alignment = Input Alignment\r
-label.couldnt_import_as_vamsas_session = Couldn't import '{0}' as a new vamsas session.\r
+label.couldnt_import_as_vamsas_session = Couldn't import {0} as a new vamsas session.\r
label.vamsas_document_import_failed = Vamsas Document Import Failed\r
label.couldnt_locate = Couldn't locate {0}\r
label.url_not_found = URL not found\r
label.view_full_application = View in Full Application\r
label.load_associated_tree = Load Associated Tree ...\r
label.load_features_annotations = Load Features/Annotations ...\r
-label.export_features = Export Features ...\r
-label.export_annotations = Export Annotations ...\r
+label.export_features = Export Features\r
+label.export_annotations = Export Annotations\r
label.jalview_copy = Copy (Jalview Only)\r
label.jalview_cut = Cut (Jalview Only)\r
label.to_upper_case = To Upper Case\r
label.open_new_jmol_view_with_all_structures_associated_current_selection_superimpose_using_alignment = Open a new Jmol view with all structures associated with the current selection and superimpose them using the alignment.\r
label.open_url_param = Open URL {0}\r
label.open_url_seqs_param = Open URL ({0}..) ({1} seqs)\r
-label.load_pdb_file_associate_with_sequence = Load a PDB file and associate it with sequence '{0}'\r
+label.load_pdb_file_associate_with_sequence = Load a PDB file and associate it with sequence {0}\r
label.reveal_hidden_columns = Reveal Hidden Columns with Right Mouse Button\r
label.dark_colour = Dark Colour\r
label.light_colour = Light Colour\r
label.show_memory_usage = Show Memory Usage\r
label.show_java_console = Show Java Console\r
label.show_jalview_news = Show Jalview News\r
+label.take_snapshot = Take snapshot\r
label.monospaced_fonts_faster_to_render = Monospaced fonts are faster to render\r
label.anti_alias_fonts = Anti-alias Fonts (Slower to render)\r
label.monospaced_font= Monospaced\r
label.separate_multiple_accession_ids = Separate multiple accession ids with semi colon ";"\r
label.replace_commas_semicolons = Replace commas with semi-colons\r
label.parsing_failed_syntax_errors_shown_below_param = Parsing failed. Syntax errors shown below {0}\r
-label.parsing_failed_unrecoverable_exception_thrown_param = \nParsing failed. An unrecoverable exception was thrown:\n {0}\r
+label.parsing_failed_unrecoverable_exception_thrown_param = \nParsing failed. An unrecoverable exception was thrown\:\n {0}\r
label.example_query_param = Example query: {0}\r
label.enter_value_increase_conservation_visibility = Enter value to increase conservation visibility\r
label.enter_percentage_identity_above_which_colour_residues = Enter % identity above which to colour residues\r
-label.wswublast_client_credits = To display sequence features an exact Uniprot id with 100% sequence identity match must be entered.\nIn order to display these features, try changing the names of your sequences to the ids suggested below.\n\nRunning WSWUBlast at EBI.\nPlease quote Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate J., Velankar S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez R.\nSOAP-based services provided by the European Bioinformatics Institute.\nNucleic Acids Res. 33(1):W25-W28 (2005));\r
+label.wswublast_client_credits = To display sequence features an exact Uniprot id with 100% sequence identity match must be entered.\nIn order to display these features, try changing the names of your sequences to the ids suggested below.\n\nRunning WSWUBlast at EBI.\nPlease quote Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate J., Velankar S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez R.\nSOAP-based services provided by the European Bioinformatics Institute.\nNucleic Acids Res. 33(1)\:W25-W28 (2005));\r
label.blasting_for_unidentified_sequence = BLASTing for unidentified sequences
label.select_columns_containing = Select columns containing\r
label.select_columns_not_containing = Select columns that do not contain\r
option.trim_retrieved_seqs = Trim retrieved sequences\r
label.trim_retrieved_sequences = When the reference sequence is longer than the sequence that you are working with, only keep the relevant subsequences.\r
+label.use_sequence_id_1 = Use $SEQUENCE_ID$ or $SEQUENCE_ID=/<regex>/=$\r
+label.use_sequence_id_2 = \nto embed sequence id in URL\r
+label.ws_parameters_for = Parameters for {0}\r
+label.switch_server = Switch server\r
+label.open_jabaws_web_page = Opens the JABAWS server's homepage in web browser\r
+label.choose_jabaws_server = Choose a server for running this service\r
+label.services_at = Services at {0}\r
+label.rest_client_submit = {0} using {1}\r
+label.fetch_retrieve_from =Retrieve from {0}</html>\r
+label.fetch_retrieve_from_all_sources = Retrieve from all {0} sources in {1}<br>First is :{2}<html> \r
+label.feature_settings_click_drag = <html>Click/drag feature types up or down to change render order.<br/>Double click to select columns containing feature in alignment/current selection<br/>Pressing Alt will select columns outside features rather than inside<br/>Pressing Shift to modify current selection (rather than clear current selection)<br/>Press CTRL or Command/Meta to toggle columns in/outside features<br/></html>\r
+label.opt_and_params_further_details = see further details by right-clicking\r
+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> \r
+label.opt_and_params_show_brief_desc = <html>Click to show brief description<br></html>\r
+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>\r
+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>\r
+label.job_created_when_checked = <html>When checked, a job is created for every sequence in the current selection.</html>\r
+label.when_checked_job_visible_region_and_results = <html>When checked, a single job is created for the visible region and results mapped back onto their location in the alignment. Otherwise, a job would be created for every contiguous region visible in the alignment or current selection (e.g. a multiple alignment).</html>\r
+label.flat_file_representation = <html>Flat file representation of this rest service using the Really Simple Bioinformatics Service formalism</html>\r
+label.result_of_parsing_rsbs = <html>Results of parsing the RSBS representation</html>\r
+label.user_preset = User Preset\r
+label.service_preset = Service Preset\r
+label.run_with_preset = Run {0} with preset\r
+label.view_service_doc_url = <html>View <a href="{0}">{1}</a></html>\r
+label.submit_sequence = <html>Submit {0} {1} {2} {3} to<br/>{4}</html>\r
+action.by_title_param = by {0}\r
+label.alignment = Alignment\r
+label.secondary_structure_prediction = Secondary Structure Prediction\r
+label.sequence_database_search = Sequence Database Search\r
+label.analysis = Analysis\r
+label.protein_disorder = Protein Disorder \r
+label.source_from_db_source = Sources from {0}\r
+label.from_msname = from {0}\r
+label.superpose_with = Superpose with ...\r
+action.do = Do\r
+label.scale_label_to_column = Scale Label to Column\r
+label.add_new_row = Add New Row\r
+label.edit_label_description = Edit Label/Description\r
+label.hide_row = Hide This Row\r
+label.delete_row = Delete This Row\r
+label.show_all_hidden_rows = Show All Hidden Rows\r
+label.export_annotation = Export Annotation\r
+label.copy_consensus_sequence = Copy Consensus Sequence\r
+label.helix = Helix\r
+label.sheet = Sheet\r
+label.rna_helix = RNA Helix\r
+label.remove_annotation = Remove Annotation\r
+label.colour_by = Colour by...\r
+label.muscle_multiple_protein_sequence_alignment = Muscle Multiple Protein Sequence Alignment\r
+label.mafft_multiple_sequence_alignment = MAFFT Multiple Sequence Alignment\r
+label.clustalw_multiple_sequence_alignment = ClustalW Multiple Sequence Alignment\r
+label.jnet_secondary_structure_prediction = JNet Secondary Structure Prediction\r
+label.multiharmony = Multi-Harmony\r
+label.unable_start_web_service_analysis = Unable to start web service analysis\r
+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.\r
+label.prompt_each_time = Prompt each time\r
+label.use_source = Use Source\r
+label.couldnt_save_project = Couldn't save project\r
+label.error_whilst_saving_current_state_to = Error whilst saving current state to {0}\r
+label.error_whilst_loading_project_from = Error whilst loading project from {0}\r
+label.couldnt_load_project = Couldn't load project\r
+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.\r
+label.invalid_name_preset_exists = Invalid name - preset already exists.\r
+label.invalid_name = Invalid name\r
+label.set_proxy_settings = Please set up your proxy settings in the 'Connections' tab of the Preferences window\r
+label.proxy_authorization_failed = Proxy Authorization Failed\r
+label.internal_jalview_error = Internal Jalview Error\r
+label.secondary_structure_prediction_service_couldnt_be_located = The Secondary Structure Prediction Service named {0} at {1} couldn't be located.\r
+label.service_called_is_not_msa_service = The Service called \n{0}\nis not a \nMultiple Sequence Alignment Service\!\r
+label.msa_service_is_unknown = The Multiple Sequence Alignment Service named {0} is unknown\r
+label.service_called_is_not_seq_search_service = The Service called \n{0}\nis not a \nSequence Search Service\!\r
+label.seq_search_service_is_unknown = The Sequence Search Service named {0} is unknown\r
+label.feature_type = Feature Type\r
+label.display = Display\r
+label.service_url = Service URL\r
+label.copied_sequences = Copied sequences\r
+label.cut_sequences = Cut Sequences\r
+label.conservation_colour_increment = Conservation Colour Increment ({0})\r
+label.percentage_identity_thereshold = Percentage Identity Thereshold ({0})\r
+label.error_unsupported_owwner_user_colour_scheme = Unsupported owner for User Colour scheme dialog\r
+label.save_alignment_to_file = Save Alignment to file\r
+label.save_features_to_file = Save Features to File\r
+label.save_annotation_to_file = Save Annotation to File\r
+label.no_features_on_alignment = No features found on alignment\r
+label.save_pdb_file = Save PDB File\r
+label.save_text_to_file = Save Text to File\r
+label.save_state = Save State\r
+label.restore_state = Restore State\r
+label.saving_jalview_project = Saving jalview project {0}\r
+label.loading_jalview_project = Loading jalview project {0}\r
+label.save_vamsas_document_archive = Save Vamsas Document Archive\r
+label.saving_vamsas_doc = Saving VAMSAS Document to {0}\r
+label.load_feature_colours = Load Feature Colours\r
+label.save_feature_colours = Save Feature Colour Scheme\r
+label.dataset_for = {0} Dataset for {1}\r
+label.select_startup_file = Select startup file\r
+label.select_default_browser = Select default web browser\r
+label.save_tree_as_newick = Save tree as newick file\r
+label.create_eps_from_tree = Create EPS file from tree\r
+label.create_png_from_tree = Create PNG image from tree\r
+label.save_colour_scheme = Save colour scheme\r
+label.edit_params_for = Edit parameters for {0}\r
+label.choose_filename_for_param_file = Choose a filename for this parameter file\r
+label.save_as_html = Save as HTML\r
+label.recently_opened = Recently Opened\r
+label.blasting_for_unidentified_sequence_jobs_running = BLASTing for unidentified sequences - {0} jobs running.\r
+label.tree_from = Tree from {0}\r
+label.webservice_job_title = {0} using {1}\r
+label.select_visible_region_of = selected {0} region of {1}\r
+label.visible = Visible\r
+label.select_unselect_visible_regions_from = select and unselected {0} regions from {1}\r
+label.visible_region_of = visible region of\r
+label.webservice_job_title_on = {0} using {1} on {2}\r
+label.updating_vamsas_session = Updating vamsas session\r
+label.loading_file = Loading File: {0}\r
+label.edit_params = Edit {0}\r
+error.not_implemented = Not implemented\r
+error.no_such_method_as_clone1_for = No such method as clone1 for {0}\r
+error.null_from_clone1 = Null from clone1!\r
+error.implementation_error_sortbyfeature = Implementation Error - sortByFeature method must be one of FEATURE_SCORE, FEATURE_LABEL or FEATURE_DENSITY.\r
+error.not_yet_implemented = Not yet implemented\r
+error.unknown_type_dna_or_pep = Unknown Type {0} - dna or pep are the only allowed values.\r
+error.implementation_error_dont_know_thereshold_annotationcolourgradient = Implementation error: don't know about threshold setting for current AnnotationColourGradient.\r
+error.implementation_error_embeddedpopup_not_null = Implementation error - embeddedPopup must be non-null\r
+error.invalid_colour_for_mycheckbox = Invalid color for MyCheckBox\r
+error.implementation_error_unrecognised_render_object_for_features_type = Implementation Error: Unrecognised render object {0} for features of type {1}\r
+error.implementation_error_unsupported_feature_colour_object = Implementation error: Unsupported feature colour object.\r
+error.invalid_separator_parameter = Invalid separator parameter - must be non-zero length\r
+error.alignment_cigararray_not_implemented = Alignment(CigarArray) not yet implemented\r
+error.weak_sequencei_equivalence_not_yet_implemented = Weak sequenceI equivalence not yet implemented.\r
+error.implementation_error_can_only_make_alignmnet_from_cigararray = Implementation Error - can only make an alignment view from a CigarArray of sequences.\r
+error.empty_view_cannot_be_updated = empty view cannot be updated.\r
+error.mismatch_between_number_of_sequences_in_block = Mismatch between number of sequences in block {0} ({1}) and the original view ({2})\r
+error.padding_not_yet_implemented = Padding not yet implemented\r
+error.mismatch_between_visible_blocks_to_update_and_number_of_contigs_in_view = Mismatch between visible blocks to update and number of contigs in view (contigs=0,blocks={0})\r
+error.unknown_seq_cigar_operation = Unknown SeqCigar operation {0}\r
+error.implementation_bug_parse_cigar_string = Implementation bug in parseCigarString\r
+error.implementation_error_invalid_operation_string = Implementation error. Invalid operation string.\r
+error.invalid_range_string = Invalid range string (must be zero or positive number)\r
+error.implementation_error_delete_range_out_of_bounds = Implementation Error: deleteRange out of bounds: start must be non-negative and less than end.\r
+error.implementation_error = Implementation error\r
+error.implementation_error_unknown_operation = Implementation Error! Unknown operation {0}\r
+error.implementation_error_unexpected_null_from_get_sequence_and_deletions = Implementation Error - unexpected null from getSequenceAndDeletions\r
+error.implementation_error_set_seq_null = Implementation Error - _setSeq(null,...)\r
+error.implementation_error_s = Implementation Error: _s= {0}\r
+error.implementation_error_seqcigar_possible = SeqCigar: Possible implementation error: sequence is longer than dataset sequence\r
+error.implmentation_bug_seq_null = Implementation Bug. Null seq\r
+error.implementation_bug_cigar_operation_list_range_list = Implementation Bug. Cigar Operation list!= range list\r
+error.not_yet_implemented_cigar_object_from_cigar_string = NOT YET Implemented: Constructing a Cigar object from a cigar string and a gapped sequence.\r
+error.implementation_bug_cigar_operation = Implementation Bug. Cigar Operation {0} {1} not one of {2}, {3}, or {4}.\r
+error.implementation_error_for_new_cigar = Implementation error for new Cigar(SequenceI)\r
+error.implementation_error_cigar_seq_no_operations = Implementation error: {0}th sequence Cigar has no operations.\r
+error.implementation_error_jmol_getting_data = Implementation error - Jmol seems to be still working on getting its data - report at http://issues.jalview.org/browse/JAL-1016\r
+error.implementation_error_no_pdbentry_from_index = Implementation error - no corresponding pdbentry (for index {0}) to add sequences mappings to\r
+error.jmol_version_not_compatible_with_jalview_version = Jmol version {0} is not compatible with this version of Jalview. Report this problem at issues.jalview.org\r
+error.not_implemented_remove = Remove: Not implemented\r
+error.not_implemented_clone = Clone: Not implemented\r
+error.implementation_error_chimera_getting_data = Implementation error - Chimera seems to be still working on getting its data - report at http://issues.jalview.org/browse/JAL-1016\r
+error.call_setprogressbar_before_registering_handler = call setProgressBar before registering the progress bar's handler.\r
+label.cancelled_params = Cancelled {0}\r
+error.implementation_error_cannot_show_view_alignment_frame = Implementation error: cannot show a view from another alignment in an AlignFrame.\r
+error.implementation_error_dont_know_about_thereshold_setting = Implementation error: don't know about threshold setting for current AnnotationColourGradient.\r
+error.eps_generation_not_implemented = EPS Generation not yet implemented\r
+error.png_generation_not_implemented = PNG Generation not yet implemented\r
+error.try_join_vamsas_session_another = Trying to join a vamsas session when another is already connected\r
+error.invalid_vamsas_session_id = Invalid vamsas session id\r
+error.implementation_error_cannot_create_groovyshell = Implementation Error. Cannot create groovyShell without Groovy on the classpath!\r
+label.groovy_support_failed = Jalview Groovy Support Failed\r
+label.couldnt_create_groovy_shell = Couldn't create the groovy Shell. Check the error log for the details of what went wrong.\r
+error.unsupported_version_calcIdparam = Unsupported Version for calcIdparam {0}\r
+error.implementation_error_cant_reorder_tree = Implementation Error: Can't reorder this tree. Not DefaultMutableTreeNode.\r
+error.invalid_value_for_option = Invalid value {0} for option {1}\r
+error.implementation_error_cannot_import_vamsas_doc = Implementation Error - cannot import existing vamsas document into an existing session, Yet!\r
+label.vamsas_doc_couldnt_be_opened_as_new_session = VAMSAS Document could not be opened as a new session - please choose another\r
+error.implementation_error_vamsas_operation_not_init = Impementation error! Vamsas Operations when client not initialised and connected\r
+error.jalview_no_connected_vamsas_session = Jalview not connected to Vamsas session\r
+error.implementation_error_cannot_recover_vamsas_object_mappings = IMPLEMENTATION ERROR: Cannot recover vamsas object mappings - no backup was made\r
+error.setstatus_called_non_existent_job_pane = setStatus called for non-existent job pane {0}\r
+error.implementation_error_cannot_find_marshaller_for_param_set =Implementation error: Can't find a marshaller for the parameter set\r
+error.implementation_error_old_jalview_object_not_bound =IMPLEMENTATION ERROR: old jalview object is not bound ! ({0})\r
+error.implementation_error_vamsas_doc_class_should_bind_to_type = Implementation Error: Vamsas Document Class {0} should bind to a {1} (found a {2})\r
+error.implementation_error_jalview_class_should_bind_to_type = Implementation Error: Jalview Class {0} should bind to a {1} (found a {2})\r
+error.invalid_vamsas_rangetype_cannot_resolve_lists = Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!\r
+error.implementation_error_maplist_is_null = Implementation error. MapList is null for initMapType.\r
+error.implementation_error_cannot_have_null_alignment = Implementation error: Cannot have null alignment property key\r
+error.implementation_error_null_fileparse = Implementation error. Null FileParse in copy constructor\r
+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.\r
+error.implementation_error_cannot_duplicate_colour_scheme = Serious implementation error: cannot duplicate colourscheme {0}\r
+error.implementation_error_structure_selection_manager_null = Implementation error. Structure selection manager's context is 'null'\r
+exception.ssm_context_is_null = SSM context is null\r
+error.idstring_seqstrings_only_one_per_sequence = idstrings and seqstrings contain one string each per sequence\r
+error.cannot_have_mixed_length_replacement_vectors = Cannot have mixed length replacement vectors. Replacement vector for {0} is {1} strings long, and have already seen a {2} length vector.\r
+error.cannot_have_zero_length_vector_replacement_strings = Cannot have zero length vector of replacement strings - either 1 value or n values.\r
+error.implementation_error_multiple_single_sequence_prediction_jobs_not_supported = Implementation Error! Multiple single sequence prediction jobs are not yet supported\r
+error.implementation_error_invalid_msa_index_for_job =Implementation Error! Invalid msaIndex for JPredJob on parent MSA input object!\r
+error.implementation_error_startjob_called = Implementation error - StartJob(JpredJob) called on {0}\r
+error.multiple_jnet_subjob_merge_not_implemented = Multiple JNet subjob merging not yet implemented\r
+label.job_never_ran = Job never ran - input returned to user.\r
+error.implementation_error_minlen_must_be_greater_zero = Implementation error: minlen must be zero or more\r
+error.implementation_error_msawbjob_called = Implementation error - StartJob(MsaWSJob) called on a WSJobInstance {0}\r
+error.implementation_error_cannot_attach_ws_menu_entry = IMPLEMENTATION ERROR: cannot attach WS Menu Entry without service handle reference!\r
+error.parameter_migration_not_implemented_yet = Parameter migration not implemented yet\r
+error.implementation_error_cannot_set_jaba_option = Implementation error: cannot set Jaba Option to a value outside its allowed value range!\r
+error.implementation_error_valuetype_doesnt_support_jabaws_type = IMPLEMENTATION ERROR: jalview.ws.params.ValueConstrainI.ValueType does not support the JABAWS type : {0}\r
+error.cannot_create_jabaws_param_set = Cannot create a JabaWSParamSet from non-JabaWS parameters\r
+error.cannot_set_arguments_to_jabaws_param_set = Cannot set arguments to a JabaWSParamSet that are not JabaWS arguments\r
+error.implementation_error_runner_config_not_available = Implementation Error: Runner Config not available for a JABAWS service of type {0} ({1})\r
+error.implementation_error_cannot_handle_jaba_param = Implementation Error: Cannot handle Jaba parameter object {0}\r
+error.implementation_error_attempt_to_delete_service_preset = Implementation error: Attempt to delete a service preset!\r
+error.implementation_error_cannot_locate_oldname_presetname = Implementation error: Can't locate either oldname ({0}) or presetName ({1}in the datastore!"\r
+error.implementation_error_jabaws_param_set_only_handled_by = Implementation error: JabaWsParamSets can only be handled by JabaParamStore\r
+error.cannot_set_source_file_for = Cannot set source file for {0}\r
+error.mismatch_service_instance_preset = Probable mismatch between service instance and preset!\r
+error.cannot_set_params_for_ws_preset = Cannot set Parameters for a Jaba Web service's preset\r
+error.implementation_error_can_only_instantiate_jaba_param_sets = Implementation error: Can only instantiate Jaba parameter sets\r
+error.no_aacon_service_found = No AACon service found\r
+error.implementation_error_couldnt_copy_value_constraint = Implementation error: could not copy ValueConstrain!\r
+error.couldnt_encode_as_utf8 = Couldn't encode {0} as UTF-8.\r
+error.tree_inputtype_not_yet_implemented = Tree InputType not yet implemented\r
+error.implementation_error_need_to_have_httpresponse = Implementation Error: need to have an HttpResponse to process\r
+error.dbrefsource_implementation_exception =DBRefSource Implementation Exception\r
+error.implementation_error_dbinstance_must_implement_interface = Implmentation Error - getDbInstances must be given a class that implements jalview.ws.seqfetcher.DbSourceProxy (was given{0})\r
+error.implementation_error_must_init_dbsources =Implementation error. Must initialise dbSources\r
+label.view_controller_toggled_marked = {0} {1} columns {2} containing features of type {3} across {4} sequence(s)\r
+label.toggled = Toggled\r
+label.marked = Marked\r
+label.not = not\r
+label.no_feature_of_type_found = No features of type {0} found.\r
+label.submission_params = Submission {0}\r
+label.empty_alignment_job = Empty Alignment Job\r
+label.add_new_sbrs_service = Add a new Simple Bioinformatics Rest Service\r
+label.edit_sbrs_entry = Edit Simple Bioinformatics Rest Service entry\r
+label.pca_recalculating = Recalculating PCA\r
+label.pca_calculating = Calculating PCA\r
+label.select_foreground_colour = Choose foreground colour\r
+label.select_colour_for_text = Select Colour for Text\r
+label.adjunst_foreground_text_colour_thereshold = Adjust Foreground Text Colour Threshold\r
+label.select_subtree_colour = Select Sub-Tree Colour\r
+label.create_new_sequence_features = Create New Sequence Feature(s)\r
+label.amend_delete_features = Amend/Delete Features for {0}\r
+exception.out_of_bounds_for_file = Out of bounds for file: i={0}, Final Buffer: i0={1} iend={2}\r
+exception.null_string_given_to_regex_search = Null String Given to Regex.search\r
+exception.null_string_like_given_to_regex_search = Null StringLike Given to Regex.search\r
+exception.null_string_given_to_regex_reverse_search = Null String Given to Regex.reverseSearch\r
+exception.null_string_like_given_to_regex_reverse_search = Null StringLike Given to Regex.reverseSearch\r
+exception.null_string_like_given_to_regex_search_from = Null String Given to Regex.searchFrom\r
+exception.null_string_like_given_to_regex_search_region = Null String Given to Regex.searchRegion\r
+exception.replace_null_regex_pointer = Replacer has null Regex pointer\r
+exception.bad_pattern_to_regex_perl_code = bad pattern to Regex.perlCode: {0}\r
+exception.no_stub_implementation_for_interface = There is no stub implementation for the interface: {0}\r
+exception.cannot_set_endpoint_address_unknown_port = Cannot set Endpoint Address for Unknown Port {0}\r
+exception.querying_matching_opening_parenthesis_for_non_closing_parenthesis = Querying matching opening parenthesis for non-closing parenthesis character {0}\r
+exception.mismatched_unseen_closing_char = Mismatched (unseen) closing character {0}\r
+exception.mismatched_closing_char = Mismatched closing character {0}\r
+exception.mismatched_opening_char = Mismatched opening character {0} at {1}\r
+exception.invalid_datasource_couldnt_obtain_reader = Invalid datasource. Could not obtain Reader\r
+exception.index_value_not_in_range = {0}: Index value {1} not in range [0..{2}]\r
+exception.unterminated_cigar_string = Unterminated cigar string\r
+exception.unexpected_operation_cigar_string_pos = Unexpected operation {0} in cigar string (position {1} in {2}\r
+exception.couldnt_parse_responde_from_annotated3d_server = Couldn't parse response from Annotate3d server\r
+exception.application_test_npe = Application test: throwing an NullPointerException It should arrive at the console\r
+exception.overwriting_vamsas_id_binding = Overwriting vamsas id binding\r
+exception.overwriting_jalview_id_binding = Overwriting jalview id binding\r
+error.implementation_error_unknown_file_format_string = Implementation error: Unknown file format string\r
+exception.failed_to_resolve_gzip_stream = Failed to resolve GZIP stream\r
+exception.problem_opening_file_also_tried = Problem opening {0} (also tried {1}) : {2}\r
+exception.problem_opening_file = Problem opening {0} : {1}\r
+exception.failed_to_read_data_from_source = Failed to read data from source: {0}\r
+exception.no_init_source_stream = Unitialised Source Stream\r
+exception.invalid_source_stream = Invalid Source Stream: {0}\r
+error.implementation_error_reset_called_for_invalid_source = Implementation Error: Reset called for invalid source.\r
+exception.number_of_residues_in_query_sequence_differ_from_prediction = Number of residues in {0} supposed query sequence ({1}\n{2})\ndiffer from number of prediction sites in prediction ({3})\r
+label.mapped = mapped\r
+exception.jpredconcide_entry_has_unexpected_number_of_columns = JPredConcise: Entry ({0}) has an unexpected number of columns\r
+exception.couldnt_parse_concise_annotation_for_prediction = Couldn't parse concise annotation for prediction profile.\n{0}\r
+exception.newfile = NewickFile\: {0}\n\r
+label.no_tree_read_in = No Tree read in\r
+exception.rnaml_couldnt_access_datasource = Couldn't access datasource ({0})\r
+exception.ranml_couldnt_process_data = Couldn't process data as RNAML file ({0})\r
+exception.ranml_invalid_file = Invalid RNAML file ({0})\r
+exception.ranml_problem_parsing_data = Problem parsing data as RNAML ({0})\r
+exception.pfam_no_sequences_found = No sequences found (PFAM input)\r
+exception.stockholm_invalid_format = This file is not in valid STOCKHOLM format: First line does not contain '# STOCKHOLM'\r
+exception.couldnt_parse_sequence_line = Could not parse sequence line: {0}\r
+exception.error_parsing_line = Error parsing {0}\r
+exception.unknown_annotation_detected = Unknown annotation detected: {0} {1}\r
+exception.couldnt_store_sequence_mappings = Couldn't store sequence mappings for {0}\r
+exception.matrix_too_many_iteration = Too many iterations in {0} (max is {1})\r
+exception.browser_not_found = Exception in finding browser: {0}\r
+exception.browser_unable_to_locate = Unable to locate browser: {0}\r
+exception.invocation_target_exception_creating_aedesc = InvocationTargetException while creating AEDesc: {0}\r
+exception.illegal_access_building_apple_evt= IllegalAccessException while building AppleEvent: {0}\r
+exception.instantiation_creating_aedesc = InstantiationException while creating AEDesc: {0}\r
+exception.unable_to_launch_url = Unable to launch URL: {0}\r
+exception.unable_to_create_internet_config = Unable to create an Internet Config instance: {0}\r
+exception.invocation_target_calling_url = InvocationTargetException while calling openURL: {0}\r
+exception.illegal_access_calling_url = IllegalAccessException while calling openURL: {0}\r
+exception.interrupted_launching_browser = InterruptedException while launching browser: {0}\r
+exception.das_source_doesnt_support_sequence_command = Source {0} does not support the sequence command.\r
+exception.invalid_das_source = Invalid das source: {0}\r
+exception.ebiembl_retrieval_failed_on = EBI EMBL XML retrieval failed on {0}:{1}\r
+label.no_embl_record_found = # No EMBL record retrieved for {0}:{1}\r
+label.embl_successfully_parsed = # Successfully parsed the {0} queries into an Alignment\r
+exception.no_pdb_records_for_chain = No PDB Records for {0} chain {1}\r
+exception.unexpected_handling_rnaml_translation_for_pdb = Unexpected exception when handling RNAML translation of PDB data\r
+exception.couldnt_recover_sequence_properties_for_alignment = Couldn't recover sequence properties for alignment\r
+exception.unknown_format_for_file = Unknown format {0} for file \: \n{1}\r
+label.remove_gaps = Remove Gaps\r
+exception.couldnt_recover_sequence_props_for_jnet_query = Couldn't recover sequence properties for JNet Query sequence!\r
+exception.server_timeout_try_later = Server timed out - try again later\n\r
+exception.web_service_returned_null_try_later= Server at {0} returned null object, it probably cannot be contacted. Try again later.\r
+exception.cannot_contact_service_endpoint_at = Cannot contact service endpoint at {0}\r
+error.implementation_error_cannot_find_service_url_in_given_set = Implementation error: Cannot find service url in the given url set!\r
+error.implementation_error_cannot_find_service_url_in_given_set_param_store = Implementation error: Cannot find service url in the given url set for this service parameter store ({0}}\r
+exception.jobsubmission_invalid_params_set = Invalid parameter set. Check Jalview implementation\r
+exception.notvaliddata_group_contains_less_than_min_seqs = Group contains less than {0} sequences.\r
+exception.outofmemory_loading_pdb_file = Out of memory loading PDB File\r
+exception.eps_coudnt_write_output_file = Could not write to the output file: {0}\r
+exception.eps_method_not_supported = Method not currently supported by EpsGraphics2D version {0}\r
+exception.eps_unable_to_get_inverse_matrix = Unable to get inverse of matrix: {0}\r
+warn.job_cannot_be_cancelled_close_window = This job cannot be cancelled.\nJust close the window.\r
+warn.service_not_supported = Service not supported!\r
+warn.input_is_too_big = Input is too big!\r
+warn.invalid_job_param_set = Invalid job parameter set!\r
+info.job_couldnt_be_run_server_doesnt_support_program = Job could not be run because the server doesn't support this program.\n{0}\r
+info.job_couldnt_be_run_exceeded_hard_limit = Job could not be run because it exceeded a hard limit on the server.\n{0}\r
+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\r
+info.no_jobs_ran = No jobs ran\r
+info.failed_to_submit_prediction = Failed to submit the prediction\:\n{0} {1}\r
+info.invalid_jnet_job_result_data ={0}\n{1}\nInvalid JNet job result data\!\n{2}\r
+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\r
+info.alignment_object_method_notes = \nAlignment Object Method Notes\n\r
+info.server_exception = \n{0} Server exception\!\n{1}\r
+status.processing_commandline_args = Processing commandline arguments...\r
+status.das_features_being_retrived = DAS features being retrieved...\r
+status.searching_for_sequences_from = Searching for sequences from {0}\r
+status.finished_searching_for_sequences_from = Finished searching for sequences from {0}\r
+label.eps_file = EPS file\r
+label.png_image = PNG image\r
+status.saving_file = Saving {0}\r
+status.export_complete = Export complete.\r
+status.fetching_pdb = Fetching PDB {0}\r
+status.refreshing_news = Refreshing news\r
+status.importing_vamsas_session_from = Importing VAMSAS session from {0}\r
+status.opening_params = Opening {0}\r
+status.waiting_sequence_database_fetchers_init = Waiting for Sequence Database Fetchers to initialise\r
+status.init_sequence_database_fetchers = Initialising Sequence Database Fetchers\r
+status.fetching_sequence_queries_from = Fetching {0} sequence queries from {1}\r
+status.finshed_querying = Finished querying\r
+status.parsing_results = Parsing results.\r
+status.processing = Processing...\r
+status.refreshing_web_service_menus = Refreshing Web Service Menus\r
+status.collecting_job_results = Collecting job results.\r
+status.fetching_das_sequence_features = Fetching DAS Sequence Features\r
+status.no_das_sources_active = No DAS Sources Active\r
+status.das_feature_fetching_cancelled = DAS Feature Fetching Cancelled\r
+status.das_feature_fetching_complete = DAS Feature Fetching Complete\r
+status.fetching_db_refs = Fetching db refs\r
+label.font_doesnt_have_letters_defined = Font doesn't have letters defined\nso cannot be used\nwith alignment data\r
+label.error_loading_file_params = Error loading file {0}\r
+label.error_loading_jalview_file = Error loading Jalview file\r
+warn.out_of_memory_when_action = Out of memory when {0}\!\!\nSee help files for increasing Java Virtual Machine memory.\r
+warn.out_of_memory_loading_file = Out of memory loading file {0}\!\!\nSee help files for increasing Java Virtual Machine memory.\r
+label.out_of_memory = Out of memory\r
+label.invalid_id_column_width = Invalid ID Column width\r
+warn.user_defined_width_requirements = The user defined width for the\nannotation and sequence ID columns\nin exported figures must be\nat least 12 pixels wide.\r
+label.couldnt_create_sequence_fetcher = Couldn't create SequenceFetcher\r
+warn.couldnt_create_sequence_fetcher_client = Could not create the sequence fetcher client. Check error logs for details.\r
+warn.server_didnt_pass_validation = Service did not pass validation.\nCheck the Jalview Console for more details.\r
+warn.url_must_contain = Sequence URL must contain $SEQUENCE_ID$ or a regex $SEQUENCE_ID=/<regex>/=$\r
+info.validate_jabaws_server = Validate JabaWS Server ?\n(Look in console output for results)\r
+label.test_server = Test Server?\r
+info.you_want_jalview_to_find_uniprot_accessions = Do you want Jalview to find\nUniprot Accession ids for given sequence names?\r
+label.find_uniprot_accession_ids = Find Uniprot Accession Ids\r
+label.new_sequence_fetcher = New Sequence Fetcher\r
+label.additional_sequence_fetcher = Additional Sequence Fetcher\r
+label.select_database_retrieval_source = Select Database Retrieval Source\r
+label.overwrite_existing_file = Overwrite existing file?\r
+label.file_already_exists = File exists\r
+label.edit_jabaws_url = Edit JABAWS URL\r
+label.add_jabaws_url = Add new JABAWS URL\r
+label.news_from_jalview = News from http://www.jalview.org\r
+label.cut_paste_alignmen_file = Cut & Paste Alignment File\r
+label.enter_redundancy_thereshold = Enter the redundancy thereshold\r
+label.select_dark_light_set_thereshold = <html><i>Select a dark and light text colour, then set the threshold to<br>switch between colours, based on background colour</i></html>\r
+label.select_feature_colour = Select Feature Colour
\ No newline at end of file
+action.refresh_services = Refrescar servicios\r
+action.reset_services = Reiniciar servicios\r
+action.merge_results = Unificar resultados\r
+action.load_scheme = Cargar esquema\r
+action.save_scheme = Guardar esquema\r
+action.save_image = Guardar imagen\r
+action.paste = Pegar\r
+action.show_html_source = Mostrar código HTML\r
+action.print = Imprimir\r
+action.web_service = Servicio web\r
+action.cancel_job = Cancelar trabajo\r
+action.start_job = Arrancar trabajo\r
+action.revert = Deshacer\r
+action.move_down = Mover hacia abajo\r
+action.move_up = Mover hacia arriba\r
+action.remove_return_datatype = Borrar tipo de datos de retorno\r
+action.add_return_datatype = Añadir tipo de datos de retorno\r
+action.remove_input_parameter = Borrar el parámetro de entrada seleccionado\r
+action.add_input_parameter = Añadir parámetro de entrada seleccionado\r
+action.edit = Editar\r
+action.new = Nuevo\r
+action.open_file = Abrir fichero\r
+action.show_unconserved = Mostrar regiones no conservadas\r
+action.open_new_aligmnent = Abrir nuevo alineamiento\r
+action.raise_associated_windows = Destacar ventanas asociadas\r
+action.minimize_associated_windows = Minimizar ventanas asociadas\r
+action.close_all = Cerrar todo\r
+action.load_project = Cargar proyecto\r
+action.save_project = Guardar proyecto\r
+action.quit = Salir\r
+action.expand_views = Expandir vistas\r
+action.gather_views = Capturar vistas\r
+action.page_setup = Configuración de la página\r
+action.reload = Recargar\r
+action.load = Cargar\r
+action.open = Abrir\r
action.cancel = Cancelar\r
action.create = Crear\r
action.update = Actualizar\r
action.delete = Borrar\r
-action.snapshot = Captura\r
+action.snapshot = Imagen\r
action.clear = Limpiar\r
action.accept = Aceptar\r
+action.select_ddbb = --- Seleccionar base de datos ---\r
+action.undo = Deshacer\r
+action.redo = Rehacer\r
+action.reset = Reiniciar\r
+action.remove_left = Eliminar parte izquierda\r
+action.remove_right = Eliminar parte derecha\r
+action.remove_empty_columns = Eliminar las columnas vacías\r
+action.remove_all_gaps = Eliminar todos los huecos\r
+action.left_justify_alignment = Ajustar el alineamiento a la izquierda\r
+action.right_justify_alignment = Ajustar el alineamiento a la derecha\r
+action.boxes = Casillas\r
+action.text = Texto\r
+action.by_pairwise_id = Identificar por parejas\r
+action.by_id = Por identificador\r
+action.by_length = Por longitud\r
+action.by_group = Por grupo\r
+action.remove = Eliminar\r
+action.remove_redundancy = Eliminar redundancia...\r
+action.pairwise_alignment = Alineamiento de pares...\r
+action.by_rna_helixes = Por hélices de RNA\r
+action.user_defined = Definido por el usuario...\r
+action.by_conservation = Por conservación\r
+action.wrap = Envolver\r
+action.show_gaps = Mostrar huecos\r
+action.show_hidden_markers = Mostrar marcadores ocultos\r
+action.find = Buscar\r
+action.undefine_groups = Grupos sin definir\r
+action.create_groups = Crear grupos\r
+action.make_groups_selection = Hacer grupos para seleccionar\r
+action.copy = Copiar\r
+action.cut = Cortar\r
+action.font = Fuente...\r
+action.scale_above = Escala superior\r
+action.scale_left = Escala izquierda\r
+action.scale_right = Escala derecha\r
+action.by_tree_order = Por orden del árbol\r
+action.sort = Ordenar\r
+action.calculate_tree = Calcular árbol\r
+action.help = Ayuda\r
+action.by_annotation = Por anotación...\r
+action.invert_sequence_selection = Invertir selección de secuencias\r
+action.invert_column_selection = Invertir selección de columnas\r
+action.show = Mostrar\r
+action.hide = Ocultar\r
+action.ok = OK\r
+action.set_defaults = Defecto\r
+action.create_group = Crear grupo\r
+action.remove_group = Eliminar grupo\r
+action.edit_group = Editar grupo\r
+action.border_colour = Color del borde\r
+action.edit_new_group = Editar nuevo grupo\r
+action.hide_sequences = Ocultar secuencias\r
+action.sequences = Secuencias\r
+action.ids = IDS\r
+action.ids_sequences = IDS y secuencias\r
+action.reveal_all = Revelar todo\r
+action.reveal_sequences = Revelar secuencias\r
+action.find_all = Buscar todo\r
+action.find_next = Buscar siguiente\r
+action.file = Archivo\r
+action.view = Ver \r
+action.change_params = Cambiar parámetros\r
+action.apply = Aplicar\r
+action.apply_threshold_all_groups = Aplicar umbral a todos los grupos\r
+action.apply_all_groups = Aplicar a todos los grupos\r
+action.by_chain = Por cadena\r
+action.by_sequence = Por secuencia\r
+action.paste_annotations = Pegar anotaciones\r
+action.format = Formato\r
+action.select = Seleccionar\r
+action.new_view = Nueva vista\r
+action.close = Cerrar\r
+action.add = Añadir\r
+action.save_as_default = Guardar como por defecto\r
+action.save_as = Guardar como\r
+action.save = Guardar\r
+action.cancel_fetch = Cancelar búsqueda\r
+action.save_omit_hidden_columns = Guardar / Omitir las columnas ocultas\r
+action.change_font = Cambiar Fuente\r
+action.change_font_tree_panel = Cambiar fuente (panel del árbol)\r
+action.colour = Color\r
+action.calculate = Calcular\r
+action.select_all = Seleccionar Todo\r
+action.deselect_all = Deseleccionar Todo\r
+action.invert_selection = Invertir selección\r
+action.using_jmol = Usar Jmol\r
+action.link = Enlazar\r
+action.group_link = Enlazar grupo\r
+action.show_chain = Mostrar cadena\r
+action.show_group = Mostrar grupo\r
+action.fetch_db_references = Recuperar referencias a base de datos\r
+action.view_flanking_regions = Mostrar flancos\r
+label.view_flanking_regions = Mostrar los datos de la secuencia a ambos lados de las subsecuencias implicadas en este alineamiento\r
+label.str = Str: \r
+label.seq = Seq: \r
+label.structures_manager = Administrar estructuras\r
+label.nickname = Sobrenombre:\r
+label.url = URL: \r
+label.input_file_url = Introducir URL en el fichero de entrada\r
+label.select_feature = Seleccionar función:\r
+label.name = Nombre:\r
+label.name_param = Nombre: {0}\r
+label.group = Grupo:\r
+label.group_name = Nombre del grupo\r
+label.group_description = Descripción del grupo\r
+label.edit_group_name_description = Editar nombre/descripción del grupo\r
+label.colour = Color:\r
+label.description = Descripción:\r
+label.start = Comenzar:\r
+label.end = Terminar:\r
+label.current_parameter_set_name = Nombre actual del conjunto de parámetros:\r
+label.service_action = Acción de servicio:\r
+label.post_url = POST URL: \r
+label.url_suffix = URL Sufijo\r
+label.sequence_source = Fuente de la secuencia\r
+label.per_seq = por secuencia\r
+label.result_vertically_separable = Los resultados son separables verticalmente\r
+label.amend = Modificar\r
+label.undo_command = Deshacer {0}\r
+label.redo_command = Rehacer {0}\r
+label.principal_component_analysis = Análisis del Componente Principal\r
+label.average_distance_identity = Distancia Media Usando % de Identidad\r
+label.neighbour_joining_identity = Unir vecinos utilizando % de Identidad\r
+label.treecalc_title = {0} utilizando {1}\r
+label.tree_calc_av = Distancia media\r
+label.tree_calc_nj = Unir vecinos\r
+label.select_score_model = Selecciones modelo de puntuación\r
+label.score_model_pid = % Identidad\r
+label.score_model_blosum62 = BLOSUM62\r
+label.score_model_pam250 = PAM 250\r
+label.score_model_conservation = Conservación de las propiedades físico-químicas\r
+label.score_model_enhconservation = Conservación de las propiedades físico-químicas\r
+label.status_bar = Barra de estado\r
+label.out_to_textbox = Generar cuadro de texto\r
+label.clustalx = Clustalx\r
+label.clustal = Clustal\r
+label.zappo = Zappo\r
+label.taylor = Taylor\r
+label.blc = BLC\r
+label.fasta = Fasta\r
+label.msf = MSF\r
+label.pfam = PFAM\r
+label.pileup = Pileup\r
+label.pir = PIR\r
+label.hydrophobicity = Hidrofobicidad\r
+label.helix_propensity = Tendencia de la hélice\r
+label.strand_propensity = Tendencia de la hebra\r
+label.turn_propensity = Tendencia de giro\r
+label.buried_index = Índice de encubrimiento\r
+label.purine_pyrimidine = Purina/Pirimidina\r
+label.percentage_identity = Porcentaje de identidad\r
+label.blosum62 = BLOSUM62\r
+label.blosum62_score = Puntuación del BLOSUM62 \r
+label.tcoffee_scores = Puntuación del T-Coffee\r
+label.average_distance_bloslum62 = Distancia Media Usando BLOSUM62\r
+label.neighbour_blosum62 = Neighbour Joining usando BLOSUM62\r
+label.show_annotations = Mostrar anotaciones\r
+label.colour_text = Color del texto\r
+label.show_non_conversed = Mostrar no conservadas\r
+label.overview_window = Ventana resumen\r
+label.none = Ninguno\r
+label.above_identity_threshold = Por encima del umbral de identidad\r
+label.show_sequence_features = Mostrar las características de las secuencias\r
+label.nucleotide = Nucleótido\r
+label.to_new_alignment = A nuevo alineamiento\r
+label.to_this_alignment = Añadir a este alineamiento\r
+label.apply_colour_to_all_groups = Aplicar color a todos los grupos\r
+label.modify_identity_thereshold = Modificar el umbral de identidad...\r
+label.modify_conservation_thereshold = Modificar el umbral de conservación...\r
+label.input_from_textbox = Introducir desde el cuadro de texto\r
+label.centre_column_labels = Centrar las etiquetas de las columnas\r
+label.automatic_scrolling = Desplazamiento automático\r
+label.documentation = Documentación\r
+label.about = Acerca de...\r
+label.show_sequence_limits = Mostrar los límites de la secuencia\r
+label.feature_settings = Ajustar funciones...\r
+label.sequence_features = Funciones de la secuencia\r
+label.all_columns = Todas las columnas\r
+label.all_sequences = Todas las secuencias\r
+label.selected_columns = Columnas seleccionadas\r
+label.selected_sequences = Secuencias seleccionadas\r
+label.all_but_selected_region = Todo menos la región seleccionada (Shift+Ctrl+H)\r
+label.selected_region = Región seleccionada\r
+label.all_sequences_columns = Todas las secuencias y columnas\r
+label.group_consensus = Consenso de grupo\r
+label.group_conservation = Conservación de grupo\r
+label.show_consensus_histogram = Mostrar el histograma de consenso\r
+label.show_consensus_logo = Mostrar el logo de consenso\r
+label.norm_consensus_logo = Normalizar el logo de consenso\r
+label.apply_all_groups = Aplicar a todos los grupos\r
+label.autocalculated_annotation = Anotación autocalculada\r
+label.min_colour = Color mínimo\r
+label.max_colour = Color máximo\r
+label.use_original_colours = Usar colores originales\r
+label.threshold_minmax = El umbral es mín/máx\r
+label.represent_group_with = Representar al grupo con\r
+label.selection = Seleccionar\r
+label.group_colour = Color del grupo\r
+label.sequence = Secuencia\r
+label.view_pdb_structure = Ver estructura PDB\r
+label.min = Mín:\r
+label.max = Máx:\r
+label.colour_by_label = Color por etiquetas\r
+label.new_feature = Nueva función\r
+label.match_case = Hacer corresponder mayúsculas y minúsculas\r
+label.view_alignment_editor = Ver en el editor de alineamientos\r
+label.labels = Etiquetas\r
+label.output_values = Valores de salida...\r
+label.output_points = Puntos de salida...\r
+label.output_transformed_points = Puntos de salida transformados\r
+label.input_data = Datos de entrada...\r
+label.nucleotide_matrix = Matriz nucleotídica\r
+label.protein_matrix = Matriz proteica\r
+label.show_bootstrap_values = Mostrar valores de Bootstrap\r
+label.show_distances = Mostrar distancias\r
+label.mark_unassociated_leaves = Marcar hojas no asociadas\r
+label.fit_to_window = Ajustar a la ventana\r
+label.newick_format = Formato Newick\r
+label.select_newick_like_tree_file = Seleccione un fichero de árbol tipo Newick\r
+label.colours = Colores\r
+label.view_mapping = Ver mapeado\r
+label.wireframe = Estructura metálica\r
+label.depthcue = Clave de profundidad\r
+label.z_buffering = Tamponamiento Z\r
+label.charge_cysteine = Carga & Cisteína\r
+label.all_chains_visible = Todas las cadenas visibles\r
+label.successfully_added_features_alignment = Funciones añadidas exitosamente al alineamiento\r
+label.keyboard_editing_mode = El modo de editar teclado es {0}\r
+label.paste_features_annotations_Tcoffee_here = Pegar tus funciones / anotaciones / puntuación del fichero T-coffee aquí.\r
+label.removed_columns = {0} columnas eliminadas.\r
+label.removed_empty_columns = {0} columnas vacías eliminadas.\r
+label.paste_newick_tree_file = Pegar su fichero árbol Newick aquí. \r
+label.order_by_params = Ordenar por {0}\r
+label.html_content = <html>{0}</html>\r
+label.paste_pdb_file= Pegar tu fichero PDB aquí.\r
+label.paste_pdb_file_for_sequence = Pegar fichero PDB para la secuencia {0}\r
+label.could_not_parse_newick_file = No se pudo analizar el fichero Newick\\\!\\n {0}\r
+label.successfully_pasted_tcoffee_scores_to_alignment= Pegada exitosamente la puntuación T-Coffee al alineamiento.\r
+label.failed_add_tcoffee_scores = Fallo al añadir las puntuaciones T-Coffee: \r
+label.successfully_pasted_annotation_to_alignment = Anotación pegada exitosamente al alineamiento.\r
+label.couldnt_parse_pasted_text_as_valid_annotation_feature_GFF_tcoffee_file = No es posible parsear el texto pegado como una anotación características, GFF, o fichero T-Coffee válidos\r
+label.successfully_pasted_alignment_file = Fichero de alineamiento pegado exitosamente\r
+label.paste_your_alignment_file = Pegar su fichero de alineamiento aquí\r
+label.paste_your = Pegar su\r
+label.finished_searching = Búsqueda finalizada\r
+label.search_results= Buscar Resultados {0} : {1}\r
+label.found_match_for = Buscar coincidencia para {0}\r
+label.font = Fuente:\r
+label.size = Talla:\r
+label.style = Estilo:\r
+label.enter_redundancy_threshold = Introducir el umbral de redundancia\r
+label.calculating = Calculando....\r
+label.modify_conservation_visibility = Modificar la visibilidad de conservación\r
+label.colour_residues_above_occurence = Residuos de color por encima del % de aparición \r
+label.set_this_label_text = fijar como etiqueta \r
+label.sequences_from = Secuencias de {0}\r
+label.successfully_loaded_file = Fichero cargado exitosamente {0}\r
+label.successfully_saved_to_file_in_format = Guardado exitosamente en el fichero: {0} en formato {1}.\r
+label.copied_sequences_to_clipboard = Copiadas {0} secuencias en el portapapeles.\r
+label.check_file_matches_sequence_ids_alignment = Comprobar que el fichero coincide con el ID de la secuencia en el alineamiento.\r
+label.problem_reading_tcoffee_score_file = Problema de lectura del fichero de puntuaciones T-COFFEE\r
+label.source_to_target = {0} a '{1}'\r
+label.per_sequence_only= Sólo por secuencia\r
+label.to_file = a fichero\r
+label.to_textbox = a cuadro de texto\r
+label.jalview = Jalview\r
+label.csv_spreadsheet = CSV (Hoja de cálculo)\r
+label.status = [Estado]\r
+label.channels = Canales\r
+label.channel_title_item_count = {0} ({1})\r
+label.blog_item_published_on_date = {0} {1} \r
+label.select_das_service_from_table = Seleccionar servicio DAS de la tabla para leer una descripción completa aquí.\r
+label.session_update = Actualizar sesión\r
+label.new_vamsas_session = Nueva sesión Vamsas\r
+label.load_vamsas_session = Cargar sesión Vamsas\r
+label.save_vamsas_session = Guardar sesión Vamsas\r
+label.select_vamsas_session_opened_as_new_vamsas_session= Selecciones una sesión vamsas para abrirla como una nueva sesión.\r
+label.open_saved_vamsas_session = Abrir una sesión VAMSAS guardada\r
+label.groovy_console = Consola Groovy \r
+label.lineart = lineart\r
+label.dont_ask_me_again = No volver a preguntar\r
+label.select_eps_character_rendering_style = Seleccionar el carácter EPS como estilo de visualización \r
+label.invert_selection = Invertir selección\r
+label.optimise_order = Optimizar orden\r
+label.seq_sort_by_score = Ordenar las secuencias por puntuación\r
+label.load_colours = Cargar colores\r
+label.save_colours = Guardar colores\r
+label.fetch_das_features = Recuperar funciones DAS\r
+label.selected_database_to_fetch_from = Seleccionada {0} Base de datos {1} para buscar de {2} \r
+label.database_param = Base de datos: {0}\r
+label.example = Ejemplo\r
+label.example_param = Ejemplo: {0}\r
+label.select_file_format_before_saving = Debe seleccionar un formato de fichero antes de guardar!\r
+label.file_format_not_specified = Formato de fichero no especificado\r
+label.alignment_contains_hidden_columns = El alineamiento contiene columnas ocultas.\\nQuieres guardar s\u00F3lo el alineamiento visible?\r
+label.couldnt_save_file = No se pudo guardar el fichero: {0}\r
+label.error_saving_file = Error guardando el fichero\r
+label.remove_from_default_list = eliminar de la lista de defectuosos?\r
+label.remove_user_defined_colour = Eliminar el color definido por el usuario\r
+label.you_must_select_least_two_sequences = Debes seleccionar al menos 2 secuencias.\r
+label.invalid_selection = Selección inválida\r
+label.principal_component_analysis_must_take_least_four_input_sequences = El an\u00E1lisis de la componente principal debe tomar\\nal menos 4 secuencias de entrada.\r
+label.sequence_selection_insufficient = Selección de secuencias insuficiente\r
+label.you_need_more_two_sequences_selected_build_tree = necesitas seleccionar más de dos secuencias para construir un árbol!\r
+label.not_enough_sequences = No suficientes secuencias\r
+label.selected_region_to_tree_may_only_contain_residues_or_gaps = La regi\u00F3n seleccionada para construir un \u00E1rbol puede\\ncontener s\u00F3lo residuos o espacios.\\nPrueba usando la funci\u00F3n Pad en el men\u00FA de edici\u00F3n,\\n o uno de los m\u00FAltiples servicios web de alineamiento de secuencias.\r
+label.sequences_selection_not_aligned = Las secuencias seleccionadas no están alineadas\r
+label.sequences_must_be_aligned_before_creating_tree = Las secuencias deben estar alineadas antes de crear el \u00E1rbol.\\nPrueba usando la funci\u00F3n Pad en el men\u00FA de editar,\\n o uno de los m\u00FAltiples servicios web de alineamiento de secuencias.\r
+label.sequences_not_aligned = Secuencias no alineadas\r
+label.problem_reading_tree_file = Problema al leer el fichero del árbol\r
+label.possible_problem_with_tree_file = Posible problema con el fichero del árbol\r
+label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation = Por favor seleccionar al menos tres bases de al menos una secuencia para poder realizar la traducción de cDNA.\r
+label.translation_failed = Translation Failed\r
+label.error_when_translating_sequences_submit_bug_report = Desafortunadamente, algo fue mal a la hora de traducir tus secuencias.\\nPor favor, revisa la consola Jalview java \\ny presenta un informe de error que incluya el seguimiento.\r
+label.implementation_error = Error de implementación:\r
+label.automatically_associate_pdb_files_with_sequences_same_name = Quieres asociar automáticamente los {0} ficheros PDB con las secuencias del alineamiento que tengan el mismo nombre?\r
+label.automatically_associate_pdb_files_by_name = Asociar los ficheros PDB por nombre automáticamente\r
+label.ignore_unmatched_dropped_files_info = Quieres <em>ignorar</em> los {0} ficheros cuyos nombres no coincidan con ningún IDs de las secuencias ?\r
+label.ignore_unmatched_dropped_files = Ignorar los ficheros sin coincidencias?\r
+label.enter_view_name = Introducir nombre visible (¿?)\r
+label.enter_label = Introducir etiqueta\r
+label.enter_label_for_the_structure = Introducir una etiqueta para la estructura?\r
+label.pdb_entry_is_already_displayed = {0} Ya est\u00E1 mostrado.\\nQuieres volver a usar este visor?\r
+label.map_sequences_to_visible_window = Mapa de secuencias en ventana visible: {0}\r
+label.add_pdbentry_to_view = Quieres a\u00F1adir {0} a la vista llamada\\n'{1}'\\n\r
+label.align_to_existing_structure_view = Alinear a una estructura ya existente\r
+label.pdb_entries_couldnt_be_retrieved = Las siguientes entradas pdb no pueden ser extra\u00EDdas del PDB\\\:\\n{0}\\nPor favor, prueba descarg\u00E1ndolas manualmente.\r
+label.couldnt_load_file = No se pudo cargar el fichero\r
+label.couldnt_find_pdb_id_in_file = No se pudo encontrar un Id PDB en el fichero suministrado. Por favor, introduzca un Id para identificar esta estructura.\r
+label.no_pdb_id_in_file = No hay un Id PDB en el fichero\r
+label.couldnt_read_pasted_text = No se pudo leer el texto pegado {0}\r
+label.error_parsing_text = Error analizando el texto\r
+label.enter_local_das_source = Intruduzca el Nickname & URL de la fuente DAS local\r
+label.you_can_only_edit_or_remove_local_das_sources = Sólo puedes editar o eliminar fuentes DAS locales!\r
+label.public_das_source = Fuente pública DAS - no editable\r
+label.input_alignment_from_url = Alineamiento de entrada desde URL\r
+label.input_alignment = Alineamiento de entrada\r
+label.couldnt_import_as_vamsas_session = No se pudo importar '{0}' como una nueva sesión Vamsas.\r
+label.vamsas_document_import_failed = Fallo en la importación del documento Vamsas\r
+label.couldnt_locate = No se pudo localizar {0}\r
+label.url_not_found = URL no encontrada\r
+label.no_link_selected = Enlace no seleccionado\r
+label.new_sequence_url_link = Enlace a una nueva secuencia URL\r
+label.cannot_edit_annotations_in_wrapped_view = No se pueden editar anotaciones en vista envolvente\r
+label.wrapped_view_no_edit = Vista envolvente - no editar\r
+label.error_retrieving_data = Error en la recuperación de datos\r
+label.user_colour_scheme_must_have_name = El esquema de colores del usuario debe tener un nombre\r
+label.no_name_colour_scheme = No hay nombre para el esquema de colores \r
+label.invalid_url = URL Invalido!\r
+label.error_loading_file = Error al cargar el fichero\r
+label.problems_opening_file = Encontrados problemas al abrir el fichero {0}!!\r
+label.file_open_error = Error al abrir el fichero\r
+label.no_das_sources_selected_warn = No han sido seleccionadas fuentes DAS.\\nPor favor, seleccione algunas fuentes y\\npruebe de nuevo.\r
+label.no_das_sources_selected_title = No han sido seleccionadas fuentes DAS\r
+label.colour_scheme_exists_overwrite = El esquema de colores {0} ya existe.\\nContinuar guardando el esquema de colores como {1}?"\r
+label.duplicate_scheme_name = Duplicar nombre de esquema\r
+label.jalview_new_questionnaire = Hay un nuevo cuestionario disponible. Querr\u00EDa completarlo ahora ?\\n\r
+label.jalview_user_survey = Encuesta de usuario Jalview \r
+label.alignment_properties = Propiedades del alineamiento: {0}\r
+label.alignment_props = Propiedades del alineamiento\r
+label.input_cut_paste = Cortar y pegar la entrada\r
+label.input_cut_paste_params = Cortar y pegar la entrada - {0}\r
+label.alignment_output_command = Alineamiento de salida - {0}\r
+label.annotations = Anotaciones\r
+label.features = Funciones\r
+label.overview_params = Visión general {0}\r
+label.paste_newick_file = Pegar nuevo fichero Newick\r
+label.load_tree_from_file = desde fichero - \r
+label.colour_by_annotation = Color por anotación\r
+label.selection_output_command = Seleccionar salida - {0}\r
+label.annotation_for_displayid = <p><h2>Anotación para {0} </h2></p><p>\r
+label.pdb_sequence_mapping = PDB - Mapeado de secuencia\r
+label.pca_details = detalles de la PCA\r
+label.redundancy_threshold_selection = Selección del umbral de redundancia\r
+label.user_defined_colours = Colores definidos del usuario\r
+label.jalviewLite_release = JalviewLite - versión {0}\r
+label.jaview_build_date = Fecha de creación: {0}\r
+label.jalview_authors_1 = Authors: Jim Procter, Andrew Waterhouse, Jan Engelhardt, Lauren Lui,\r
+label.jalview_authors_2 = Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton.\r
+label.jalview_dev_managers = Desarrollo gestionado por The Barton Group, University of Dundee, Scotland, UK.\r
+label.jalview_distribution_lists = Para ayuda, ver el FAQ at www.jalview.org y/o adjuntar la lista de envío jalview-discuss@jalview.org\r
+label.jalview_please_cite = Si usa Jalview incluya la siguiente cita, por favor:\r
+label.jalview_cite_1_authors = Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)\r
+label.jalview_cite_1_title = Jalview Version 2 - un editor de alineamiento múltiple de secuencias y banco de trabajo de análisis\r
+label.jalview_cite_1_ref = Bioinformaticos doi: 10.1093/bioinformatics/btp033\r
+label.right_click = clic en el botón derecho\r
+label.to_add_annotation = para añadir anotación\r
+label.alignment_has_no_annotations = El alineamiento no tiene anotaciones\r
+label.retrieving_pdb_data = Recuperación de datos PDB...\r
+label.label = Etiqueta\r
+label.no_features_added_to_this_alignment = No hay funciones asociadas a este alineamiento!!\r
+label.features_can_be_added_from_searches_1 = (Las funciones pueden ser añadidas de búsquedas o\r
+label.features_can_be_added_from_searches_2 = de ficheros de funciones Jalview / GFF)\r
+label.calculating_pca= Calculando PCA\r
+label.reveal_columns = Mostrar Columnas\r
+label.jalview_cannot_open_file = Jalview no puede abrir el fichero\r
+label.jalview_applet = Aplicación Jalview \r
+label.loading_data = Cargando datos\r
+label.memory_stats = Memoria libre total: {0} MB; Memoria máxima: {1} MB; {2} %\r
+label.calculating_tree = Calculando árbol\r
+label.state_queueing = En cola \r
+label.state_running = Procesando\r
+label.state_complete = Completar\r
+label.state_completed = Finalizado\r
+label.state_job_cancelled = ¡Trabajo cancelado!\r
+label.state_job_error = Error del trabajo!\r
+label.server_error_try_later = ¡Error del servidor! (Intentar más tarde)\r
+label.error_loading_pdb_data = ¡Error cargando los datos PDB!\r
+label.fetching_pdb_data = Buscando los datos PDB...\r
+label.structure_type = Estructura_tipo\r
+label.settings_for_type = Ajustes para {0}\r
+label.view_full_application = Ver en la aplicación completa \r
+label.load_associated_tree = Cargar árbol asociado ...\r
+label.load_features_annotations = Cargar características/anotaciones ...\r
+label.export_features = Exportar características...\r
+label.export_annotations = Exportar anotaciones ...\r
+label.jalview_copy = Copiar (sólo Jalview)\r
+label.jalview_cut = Cortar (sólo Jalview)\r
+label.to_upper_case = Pasar a mayúsculas\r
+label.to_lower_case = Pasar a minúsculas\r
+label.toggle_case = Alternar mayúsculas y minúsculas\r
+label.edit_name_description = Editar nombre/descripción\r
+label.create_sequence_feature = Crear función de secuencia\r
+label.edit_sequence = Editar secuencia\r
+label.edit_sequences = Editar secuencias\r
+label.sequence_details = Detalles de la secuencia\r
+label.jmol_help = Ayuda de Jmol \r
+label.all = Todo\r
+label.sort_by = Ordenar por\r
+label.sort_by_score = Ordenar por puntuación\r
+label.sort_by_density = Ordenar por densidad\r
+label.sequence_sort_by_density = Ordenar las secuencias por densidad\r
+label.reveal = Revelar\r
+label.hide_columns = Ocultar columnas\r
+label.load_jalview_annotations = Cargar un fichero de anotación de Jalivew o un fichero de características\r
+label.load_tree_file = Cargar un fichero de árbol\r
+label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences = Recuperar y parsear un registro de secuencia de base de datos para el alineamiento o secuencias actualmente seleccionados\r
+label.standard_databases = Bases de datos estándar\r
+label.fetch_embl_uniprot = Recuperar de EMBL/EMBLCDS o Uniprot/PDB y de cualquier fuente DAS seleccionada\r
+label.reset_min_max_colours_to_defaults = Reiniciar los colores min y max colours a los valores por defecto establecidos en las preferencias de usuario\r
+label.align_structures_using_linked_alignment_views = Alinear las estructuras utlizando las {0} vistas de alineamiento enlazadas\r
+label.connect_to_session = Conectar a la sesión {0}\r
+label.threshold_feature_display_by_score = Filtrar la característica mostrada por puntuación.\r
+label.threshold_feature_no_thereshold = Sin umbral\r
+label.threshold_feature_above_thereshold = Por encima del umbral\r
+label.threshold_feature_below_thereshold = Por debajo del umbral\r
+label.adjust_thereshold = Ajustar umbral\r
+label.toggle_absolute_relative_display_threshold = Cambiar entre mostrar el umbral absoluto y el relativo.\r
+label.display_features_same_type_different_label_using_different_colour = Mostrar las características del mismo tipo con una etiqueta diferente y empleando un color distinto (p.e. características del dominio)\r
+label.select_colour_minimum_value = Seleccionar el color para el valor mínimo\r
+label.select_colour_maximum_value = Seleccionar el color para el valor máximo\r
+label.open_new_jmol_view_with_all_structures_associated_current_selection_superimpose_using_alignment = Abrir una nueva vista Jmol con todas las estructuras asociadas con la selección acxtual y superponer las utilizando el alineamiento.\r
+label.open_url_param = Abrir URL {0}\r
+label.open_url_seqs_param = Abrir URL ({0}..) ({1} secuencias)\r
+label.load_pdb_file_associate_with_sequence = Cargar un fichero PDB y asociarlo con la secuencia '{0}'\r
+label.reveal_hidden_columns = Revelar las columnas ocultas con el botón derecho del ratón\r
+label.dark_colour = Oscurecer color\r
+label.light_colour = Aclarar color\r
+label.highlightnode = Pulse el botón izquierdo para seleccionar las hojas.<br>Haga doble clic para invertir las hojas.<br>Pulse el botón derecho para cambiar el color.\r
+label.load_colour_scheme = Cargar esquema cromático\r
+label.toggle_enabled_views = Cuando está habilitado, permite que se seleccionen varias vistas.\r
+label.edit_notes_parameter_set = Haga clic para editar las notas de este conjunto de parámetros.\r
+label.open_local_file = Abrir fichero local\r
+label.enable_automatically_sort_alignment_when_open_new_tree = Habilite esta opción para ordenar automáticamente<br>el alineamiento cuando abra<br> un nuevo árbol.\r
+label.listen_for_selections = Atención a las selecciones\r
+label.selections_mirror_selections_made_same_sequences_other_views = Cuando está habilitado, las selecciones de esta vista serán un reflejo<br>de las selecciones realizadas en las mismas secuencias de otras vistas.\r
+label.toggle_sequence_visibility = Shift+H cambia la visibilidad de la secuencia\r
+label.toggle_columns_visibility = Ctrl+H cambia la visibilidad de la columna\r
+label.toggles_visibility_hidden_selected_regions = H cambiar la visibilidad de las regiones ocultas o seleccionadas\r
+label.rename_tab_eXpand_reGroup= Haga clic en el botón derecho para renombrar la pestaña<br>Presione X para expandir las tablas y G para reagrupar.\r
+label.right_align_sequence_id = Alinear a la derecha el ID de la secuencia\r
+label.sequence_id_tooltip = Ayuda del ID de la secuencia\r
+label.no_services = <Sin Servicios>\r
+label.select_copy_raw_html = Seleccione esta opción si desea copiar el html en bruto\r
+label.share_data_vamsas_applications = Compartir datos con otras aplicaciones vamsas\r
+label.connect_to = Conectar a\r
+label.join_existing_vamsas_session = Unirse a una sesión vamsas existente\r
+label.from_url = desde una URL\r
+label.any_trees_calculated_or_loaded_alignment_automatically_sort = Cuando está habilitado, cualquier árbol calculado o cargado en el alineamiento lo ordenará\r
+label.sort_with_new_tree = Ordenar con el nuevo árbol\r
+label.from_textbox = desde un área de texto\r
+label.window = Ventana\r
+label.preferences = Preferencias\r
+label.tools = Herramientas\r
+label.fetch_sequences = Recuperar secuencia(s)\r
+label.stop_vamsas_session = Parar sesión vamsas\r
+label.collect_garbage = Recolector de basura\r
+label.show_memory_usage = Mostrar uso de memoria\r
+label.show_java_console = Mostrar consola de Java\r
+label.show_jalview_news = Mostrar las noticias de Jalview\r
+label.take_snapshot = Tomar captura\r
+label.monospaced_fonts_faster_to_render = Las fuentes monoespaciadas son más rápidas de pintar\r
+label.anti_alias_fonts = Fuentes anti-alias (más lentas de pintar)\r
+label.monospaced_font= Monoespaciadas\r
+label.quality = Calidad\r
+label.maximize_window = Maximizar ventana\r
+label.conservation = Conservación\r
+label.consensus = Consenso\r
+label.histogram = Histograma\r
+label.logo = Logo\r
+label.non_positional_features = Características no posicionales\r
+label.database_references = Referencias a base de datos\r
+label.share_selection_across_views = Compartir la selección en todas las vistas\r
+label.scroll_highlighted_regions = Desplazarse hasta las regiones resaltadas\r
+label.gap_symbol = Símbolo del hueco\r
+label.alignment_colour = Color del alineamiento\r
+label.address = Dirección\r
+label.port = Puerto\r
+label.default_browser_unix = Navegador por defecto (Unix)\r
+label.send_usage_statistics = Enviar estadísticas de uso\r
+label.check_for_questionnaires = Comprobar los cuestionarios\r
+label.check_for_latest_version = Comprobar la última versión\r
+label.url_linkfrom_sequence_id = URL del enlace del ID de la secuencia\r
+label.use_proxy_server = Utilizar un servidor proxy\r
+label.eps_rendering_style = Estilo de visualización EPS\r
+label.append_start_end = Añadir /inicio-fin (/15-380)\r
+label.full_sequence_id = ID de la secuencia completo\r
+label.smooth_font = Fuente alargada\r
+label.autocalculate_consensus = Autocalcular consenso\r
+label.pad_gaps = Rellenar huecos\r
+label.pad_gaps_when_editing = Rellenar huecos al editar\r
+label.automatically_set_id_width = Establecer automáticamente al anchura del ID\r
+label.figure_id_column_width = Anchura de la columna del ID de la Figura\r
+label.use_modeller_output = Utilizar la salidad del Modeller\r
+label.wrap_alignment = Envolver alineamiento\r
+label.right_align_ids = Alinear IDs a la derecha\r
+label.sequence_name_italics = Nombre de la secuencia en cursiva\r
+label.open_overview = Abrir resumen\r
+label.default_colour_scheme_for_alignment = Esquema cromático por defecto para el alineamiento\r
+label.annotation_shading_default = Sombreado por defecto de la anotación\r
+label.default_minimum_colour_annotation_shading = Por mínimo por defecto para el sombreado de la anotación\r
+label.default_maximum_colour_annotation_shading = Por máximo por defecto para el sombreado de la anotación\r
+label.visual = Visual\r
+label.connections = Conexiones\r
+label.output = Salida\r
+label.editing = Edición\r
+label.das_settings = Configuración DAS\r
+label.web_services = Servicios web\r
+label.right_click_to_edit_currently_selected_parameter = Haga clic en el botón derecho para editar el parámetro seleccionado actualmente.\r
+label.let_jmol_manage_structure_colours = Permitir que Jmol gestione la estructuras cromáticas\r
+label.marks_leaves_tree_not_associated_with_sequence = Marcar las hojas del árbol que no están asociadas a una secuencia\r
+label.index_web_services_menu_by_host_site = Indizar los servicios web en el menú por el host que los aloja\r
+label.option_want_informed_web_service_URL_cannot_be_accessed_jalview_when_starts_up = Marque esta opción si desea ser informado<br>cuando no se pueda acceder a la URL de un servicio web<br>al arrancar Jalview.\r
+label.new_service_url = Nueva URL del servicio\r
+label.edit_service_url = Editar la URL del servicio\r
+label.delete_service_url = Borrar la URL del servicio\r
+label.details = Detalles\r
+label.options = Opciones\r
+label.parameters = Paramétros\r
+label.available_das_sources = Fuentes DAS disponibles\r
+label.full_details = Detalles completos\r
+label.authority = Autoridad\r
+label.type = Tipo\r
+label.proxy_server = Servidor proxy\r
+label.file_output = Fichero de salida\r
+label.select_input_type = Seleccionar el tipo de entrada\r
+label.set_options_for_type = Establecer opciones para el tipo\r
+label.data_input_parameters = Datos de los parámetros de entrada\r
+label.data_returned_by_service = Datos devueltos por el servicio\r
+label.rsbs_encoded_service = Servicio RSBS codificado\r
+label.parsing_errors = Errores de parseo\r
+label.simple_bioinformatics_rest_services = Simple Bioinformatics Rest Services\r
+label.web_service_discovery_urls = URL de descubrimiento de servicios web\r
+label.input_parameter_name = Nombre del parámetro de entrada\r
+label.short_descriptive_name_for_service = Nombre corto descriptivo del servicio\r
+label.function_service_performs = Tipo de función que realiza el servicio (p.e. alineamiento, análisis, búsqueda, etc).\r
+label.brief_description_service = Descripción breve del servicio\r
+label.url_post_data_service = URL a la que enviar los datos del servicio. Incluya cualquier parámetro especial que se necesite aquí\r
+label.optional_suffix = Sufijo opcional añadido a la URL al recuperar los resultados del servicio\r
+label.preferred_gap_character = ¿Qué caracter para el hueco prefiere el servicio?\r
+label.gap_character = Carácter para hueco\r
+label.move_return_type_up_order= Mover el tipo de returno hacia arriba en el orden\r
+label.move_return_type_down_order= Mover el tipo de returno hacia abajo en el orden\r
+label.update_user_parameter_set = Actualizar el conjunto de parámetros de usuario existente\r
+label.delete_user_parameter_set = Borrar el conjunto de parámetros de usuario existente\r
+label.create_user_parameter_set = Crear un nuevo conjunto de parámetro con la configuración actual.\r
+label.revert_changes_user_parameter_set = Deshacer todos los cambios en el conjunto de parámetros actual\r
+label.start_job_current_settings = Arrancar trabajo con la configuración actual\r
+label.cancel_job_close_dialog = Cerrar este diálogo y cancelar el trabajo\r
+label.input_output = Entrada/Salida\r
+label.cut_paste = Cortar y pegar\r
+label.adjusting_parameters_for_calculation = Ajustar los parámetros para el cálculo existente\r
+label.2d_rna_structure_line = 2D RNA {0}\r
+label.2d_rna_sequence_name = 2D RNA - {0}\r
+label.edit_name_and_description_current_group = Editar el nombre y la descripción del grupo actual.\r
+label.view_structure_for = Visualizar la estructura para {0}\r
+label.view_all_structures = Visualizar todas las {0} estructuras.\r
+label.view_all_representative_structures = Visualizar todas las {0} estructuras representativas.\r
+label.open_new_jmol_view_with_all_representative_structures_associated_current_selection_superimpose_using_alignment = Abrir una nueva vista de Jmol con todas las estructuras representativas\nasociadas con la selecci\u00F3n actual\nsuperpuesta con el alineamiento actual.\r
+label.associate_structure_with_sequence = Asociar estructura con la secuencia\r
+label.from_file = desde fichero\r
+label.enter_pdb_id = Introducir PDB Id\r
+label.discover_pdb_ids = Buscar PDB ids\r
+label.text_colour = Color del texto\r
+label.structure = Estructura\r
+label.view_structure = Visualizar estructura\r
+label.clustalx_colours = Colores de Clustalx\r
+label.above_identity_percentage = Sobre % identidad\r
+label.create_sequence_details_report_annotation_for = Anotación para {0}\r
+label.sequece_details_for = Detalles de la secuencia para {0}\r
+label.sequence_name = Nombre de la secuencia\r
+label.sequence_description = Descripción de la secuencia\r
+label.edit_sequence_name_description = Editar el nombre/descripción de la secuencia\r
+label.spaces_converted_to_backslashes = Los espacios se han convertido en _\r
+label.no_spaces_allowed_sequence_name = No se permiten espacios en el nombre de la secuencia\r
+label.select_outline_colour = Seleccionar el color del límite\r
+label.web_browser_not_found_unix = Unixers\: No es posible encontrar el navegador web por defecto.\nA\u00F1ada la ruta completa de su navegador en la pesta\u00F1a de Preferencias.\r
+label.web_browser_not_found = No se encuentra el navegador web\r
+label.select_pdb_file_for = Seleccione un fichero PDB para {0}\r
+label.html = HTML\r
+label.wrap = Envolver\r
+label.show_database_refs = Mostrar las referencias en base de datos\r
+label.show_non_positional_features = Mostrar las características no posicionales\r
+label.save_png_image = Guardar como imagen PNG\r
+label.load_tree_for_sequence_set = Cargar un árbol para este conjunto de secuencias\r
+label.export_image = Exportar imagen\r
+label.vamsas_store = Almacén VAMSAS\r
+label.translate_cDNA = Traducir cDNA\r
+label.extract_scores = Extraer puntuaciones\r
+label.get_cross_refs = Obtener referencias cruzadas\r
+label.sort_alignment_new_tree = Alinear el alineamiento con el nuevo árbol\r
+label.add_sequences = Añadir secuencias\r
+label.new_window = Nueva ventana\r
+label.refresh_available_sources = Refrescar las fuentes disponibles\r
+label.use_registry = Utilizar el registro\r
+label.add_local_source = Añadir fuente local\r
+label.set_as_default = Establecer por defecto\r
+label.show_labels = Mostrar etiquetas\r
+label.background_colour = Color de fondo\r
+label.associate_nodes_with = Asociar nodos con\r
+label.jalview_pca_calculation = Cálculo del PCA por Jalview\r
+label.link_name = Nombre del enalce\r
+label.pdb_file = Fichero PDB\r
+label.colour_with_jmol = Colorear con Jmol\r
+label.align_structures = Alinear estructuras\r
+label.jmol = Jmol\r
+label.sort_alignment_by_tree = Ordenar alineamiento por árbol\r
+label.mark_unlinked_leaves = Marcar las hojas como no enlazadas\r
+label.associate_leaves_with = Asociar hojas con\r
+label.save_colour_scheme_with_unique_name_added_to_colour_menu = Guarde el esquema cromáticos con un nombre único y se añadirá al menú de colores\r
+label.case_sensitive = Sensible a mayúsculas\r
+label.lower_case_colour = Color para las minúsculas\r
+label.index_by_host = Indizar por host\r
+label.index_by_type = Indizar por tipo\r
+label.enable_jabaws_services = Habilitar servicios JABAWS\r
+label.display_warnings = Mostrar advertencias\r
+label.move_url_up = Mover la URL hacia arriba\r
+label.move_url_down = Mover la URL hacia abajo\r
+label.add_sbrs_definition = Añadir una definición SBRS \r
+label.edit_sbrs_definition = Editar una definición SBRS \r
+label.delete_sbrs_definition = Borrar una definición SBRS \r
+label.your_sequences_have_been_verified = Sus secuencias has sido verificadas en una base de datos de secuencias conocidas. Algunos de sus ID se han alterado y\n, probablemente, el residuo de inicio/fin se haya actualizado.\nGuarde su alineamiento para mantener el ID actualizado.\n\n \r
+label.sequence_names_updated = Nombres de secuencia actualizados\r
+label.dbref_search_completed = Búsqueda de DBRef terminada\r
+label.show_all_chains = Mostrar todas las cadenas\r
+label.fetch_all_param = Recuperar todas {0}\r
+label.paste_new_window = Pegar en una nueva ventana\r
+label.settings_for_param = Configuración para {0}\r
+label.view_params = Visualizar {0}\r
+label.select_all_views = Seleccionar todas las vistas\r
+label.align_sequences_to_existing_alignment = Alinear las secuencias con el alineamiento existente\r
+label.realign_with_params = Realinear con {0}\r
+label.calcname_with_default_settings = {0} por defecto\r
+label.action_with_default_settings = {0} con la configuración por defecto\r
+label.edit_settings_and_run = Editar la configuración y ejecutar...\r
+label.view_and_change_parameters_before_alignment = Ver y cambiar los parámetros antes del alineamiento\r
+label.run_with_preset_params = Ejecutar {0} con preconfiguración\r
+label.view_and_change_parameters_before_running_calculation = Ver y cambiar los parámetros antes de lanzar el cálculo\r
+label.view_documentation = Ver documentación\r
+label.select_return_type = Seleccionar el tipo de retorno\r
+label.translation_of_params = Traducción de {0}\r
+label.features_for_params = Características de - {0}\r
+label.annotations_for_params = Anotaciones de - {0}\r
+label.generating_features_for_params = Generando características de - {0}\r
+label.generating_annotations_for_params = Generando anotaciones de - {0}\r
+label.varna_params = VARNA - {0}\r
+label.sequence_feature_settings = Configuración de las características de la secuencia\r
+label.pairwise_aligned_sequences = Secuencias alineadas a pares\r
+label.original_data_for_params = Datos originales de {0}\r
+label.points_for_params = Puntos de {0}\r
+label.transformed_points_for_params = Puntos transformados de {0}\r
+label.graduated_color_for_params = Color graduado para la característica de {0}\r
+label.select_backgroud_colour = Seleccionar color de fondo\r
+label.invalid_font = Fuente no válida\r
+label.separate_multiple_accession_ids = Separar los accession id con un punto y coma ";"\r
+label.replace_commas_semicolons = Cambiar comas por puntos y comas\r
+label.parsing_failed_syntax_errors_shown_below_param = Parseo erróneo. A continuación, se muestras los errores de sintaxis {0}\r
+label.parsing_failed_unrecoverable_exception_thrown_param = \nParseo err\u00F3neo. Se ha lanzado una excepci\u00F3n fatal\:\n {0}\r
+label.example_query_param = Consulta de ejemplo: {0}\r
+label.enter_value_increase_conservation_visibility = Introduzca un valor para incrementar la visibilidad de la conservación\r
+label.enter_percentage_identity_above_which_colour_residues = Introduza un % de identidad por encima del cual se colorearán los residuos\r
+label.wswublast_client_credits = Para mostrar las caracter\u00EDsticas de una secuencia, debe indicarse un id de Uniprot cuya secuencia se corresponda al 100 % con la introducida.\nPara mostrar estas caracter\u00EDsticas, prueba a cambar los nombre de sus secuencia con los ID que se sugieren a continuaci\u00F3n.\n\nRunning WSWUBlast at EBI.\nPlease quote Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate J., Velankar S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez R.\nSOAP-based services provided by the European Bioinformatics Institute.\nNucleic Acids Res. 33(1)\:W25-W28 (2005));\r
+label.blasting_for_unidentified_sequence = Ejecutar BLAST para la secuencias sin identificar\r
+label.select_columns_containing = Seleccione las columnas que contengan\r
+label.select_columns_not_containing = Seleccione las columnas que no contengan\r
+option.trim_retrieved_seqs = Ajustar las secuencias recuperadas\r
+label.trim_retrieved_sequences = Cuando la secuencia de referencia es más larga que la secuencia con la que está trabajando, sólo se mantienen las subsecuencias relevantes.\r
+label.use_sequence_id_1 = Utilice $SEQUENCE_ID$ o $SEQUENCE_ID=/<regex>/=$\r
+label.use_sequence_id_2 = \nto para embeber el id de la secuencia en una URL\r
+label.ws_parameters_for = Parámetros para {0}\r
+label.switch_server = Cambiar servidor\r
+label.open_jabaws_web_page = Abre el página principal del servidor JABAWS en un navegador web\r
+label.choose_jabaws_server = Escoja un servidor para ejecutar este servicio\r
+label.services_at = Servicios en {0}\r
+label.rest_client_submit = {0} utilizando {1}\r
+label.fetch_retrieve_from =Recuperar de {0}\r
+label.fetch_retrieve_from_all_sources = Recuperar de todas las fuentes {0} en {1}<br>La primera es :{2} \r
+label.feature_settings_click_drag = Haga clic o arrastre los tipos de las características hacia arriba o hacia abajo para cambiar el orden de visualización.<br/>Haga doble clic para seleccionar las columnas que contienen las características del alineamiento/selección actual.<br/>Presionando Alt seleccionará las columnas exteriores a las características en lugar de las interiores<br/>Presione Shift para modificar la selección actual (en lugar de borrarla)<br/>Presione CTRL o Command/Meta para cambiar las columans externas o internas a las características<br/>\r
+label.opt_and_params_further_details = ver los detalles adicionales haciendo clic en el botón derecho\r
+label.opt_and_params_show_brief_desc_image_link = Haga clic para ver una descripción breve<br><img src="{0}"/>Haga clic en el botón derecho para obtener información adicional. \r
+label.opt_and_params_show_brief_desc = Haga clic para ver una descripción breve<br>\r
+label.adjusts_width_generated_eps_png = Ajusta la anchura del fichero EPS o PNG generado para asegurar incluso que el ID de la secuencia más larga o las etiquetas de anotación se muestran\r
+label.manually_specify_width_left_column = Especificar manualmente la anchura de la columna izquierda en las etiquetas de los ID de la secuencia y las anotaciones se mostrar en las figuras del alineamiento exportado.Esta configuraicón se ignorará si está marcada la opción 'Establecer automáticamente al anchura del ID'\r
+label.job_created_when_checked = Cuando está habilitado, se crea un trabajo para cada secuencia de la selección actual\r
+label.when_checked_job_visible_region_and_results = Cuando está habilitado, se crea un único trabajo para la región visible y los resultados de mapean en su ubicación dentro del alineamiento. En caso contrario, se creará un trabajo para cada región visible y contigua en el alineamiento o selección actual (p.e. un alineamiento múlitple).\r
+label.flat_file_representation = La representación del fichero plano de este servicio utilizando el formalismo Really Simple Bioinformatics Service\r
+label.result_of_parsing_rsbs = Resultados de parsear la representación RSBS\r
+label.user_preset = Preselección de usuario\r
+label.service_preset = Preselección del servicio\r
+label.run_with_preset = Ejecutar {0} con preselección\r
+label.view_service_doc_url = Visualizar <a href="{0}">{1}</a>\r
+label.submit_sequence = Enviar {0} {1} {2} {3} a<br/>{4}\r
+action.by_title_param = por {0}\r
+label.alignment = Alineamiento\r
+label.secondary_structure_prediction = Predicción de la estructura secundaria\r
+label.sequence_database_search = Búsqueda en base de datos de secuencias\r
+label.analysis = Análisis\r
+label.protein_disorder = Desorden en la proteína \r
+label.source_from_db_source = Fuentes de {0}\r
+label.from_msname = de '{0}'\r
+label.superpose_with = Superponer con...\r
+action.do = Hacer\r
+label.scale_label_to_column = Ajustar la etiqueta a la columna\r
+label.add_new_row = Añadir nuevo fila\r
+label.edit_label_description = Editar etiqueta/descripción\r
+label.hide_row = Ocultar esta fila\r
+label.delete_row = Borrar esta fila\r
+label.show_all_hidden_rows = Mostrar todas las filas ocultas\r
+label.export_annotation = Exportar anotación\r
+label.copy_consensus_sequence = Copiar secuencia de consenso\r
+label.helix = Hélice\r
+label.sheet = Hoja\r
+label.rna_helix = Hélice de ARN\r
+label.remove_annotation = Borrar anotación\r
+label.colour_by = Colorear por...\r
+label.muscle_multiple_protein_sequence_alignment = Alineamiento múltiple de secuencias de proteínas con Muscle\r
+label.mafft_multiple_sequence_alignment = Alineamiento múltiple de secuencias con MAFFT\r
+label.clustalw_multiple_sequence_alignment = Alineamiento múltiple de secuencias con ClustalW\r
+label.jnet_secondary_structure_prediction = Predicción de la estructura secundaria con JNet\r
+label.multiharmony = Multi-Harmony\r
+label.unable_start_web_service_analysis = No es posible iniciar el servicio web de análisis\r
+label.job_couldnt_be_started_check_input = El trabajo no puede arrancarse. Por favor, compruebe los parámetros de entrada y los mensajes de advertencia de la consola de Jalview.\r
+label.prompt_each_time = Preguntar siempre\r
+label.use_source = Fuente\r
+label.couldnt_save_project = No es posible guardar el proyecto\r
+label.error_whilst_saving_current_state_to = Error mientras se guardaba el estado a {0}\r
+label.error_whilst_loading_project_from = Error cargado el proyecto desde {0}\r
+label.couldnt_load_project = No es posible cargar el proyecto\r
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Save PDB File");
+ chooser.setDialogTitle(MessageManager.getString("label.save_pdb_file"));
chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
import jalview.analysis.AlignSeq;
import jalview.datamodel.*;
import jalview.io.FileParse;
+import jalview.util.MessageManager;
public class PDBfile extends jalview.io.AlignFile
{
} catch (OutOfMemoryError er)
{
System.out.println("OUT OF MEMORY LOADING PDB FILE");
- throw new IOException("Out of memory loading PDB File");
+ throw new IOException(
+ MessageManager
+ .getString("exception.outofmemory_loading_pdb_file"));
} catch (NumberFormatException ex)
{
if (line != null)
;
}
+ /**
+ * matches ochains against al and populates seqs with the best match between
+ * each ochain and the set in al
+ *
+ * @param ochains
+ * @param al
+ * @param dnaOrProtein
+ */
private void replaceMatchingSeqsWith(ArrayList<SequenceI> ochains,
AlignmentI al, String dnaOrProtein)
{
//
package com.stevesoft.pat;
+import jalview.util.MessageManager;
+
import java.util.*;
/**
*/
Pattern clone1(Hashtable h)
{
- throw new Error("No such method as clone1 for " + getClass().getName());
+ throw new Error(MessageManager.formatMessage("error.no_such_method_as_clone1_for", new String[]{getClass().getName()}));
}
Pattern clone(Hashtable h)
p = clone1(h);
if (p == null)
{
- throw new Error("Null from clone1!");
+ throw new Error(MessageManager.getString("error.null_from_clone1"));
}
h.put(this, p);
h.put(p, p);
//
package com.stevesoft.pat;
+import jalview.util.MessageManager;
+
import java.io.*;
import java.util.*;
{
if (s == null)
{
- throw new NullPointerException("Null String Given to Regex.search");
+ throw new NullPointerException(MessageManager.getString("exception.null_string_given_to_regex_search"));
}
return _search(s, 0, s.length());
}
{
if (sl == null)
{
- throw new NullPointerException(
- "Null StringLike Given to Regex.search");
+ throw new NullPointerException(MessageManager.getString("exception.null_string_like_given_to_regex_search"));
}
return _search(sl, 0, sl.length());
}
{
if (s == null)
{
- throw new NullPointerException(
- "Null String Given to Regex.reverseSearch");
+ throw new NullPointerException(MessageManager.getString("exception.null_string_given_to_regex_reverse_search"));
}
return _reverseSearch(s, 0, s.length());
}
{
if (sl == null)
{
- throw new NullPointerException(
- "Null StringLike Given to Regex.reverseSearch");
+ throw new NullPointerException(MessageManager.getString("exception.null_string_like_given_to_regex_reverse_search"));
}
return _reverseSearch(sl, 0, sl.length());
}
{
if (s == null)
{
- throw new NullPointerException(
- "Null String Given to Regex.searchFrom");
+ throw new NullPointerException(MessageManager.getString("exception.null_string_like_given_to_regex_search_from"));
}
return _search(s, start, s.length());
}
{
if (s == null)
{
- throw new NullPointerException(
- "Null String Given to Regex.searchFrom");
+ throw new NullPointerException(MessageManager.getString("exception.null_string_like_given_to_regex_search_from"));
}
return _search(s, start, s.length());
}
{
if (s == null)
{
- throw new NullPointerException(
- "Null String Given to Regex.searchRegion");
+ throw new NullPointerException(MessageManager.getString("exception.null_string_like_given_to_regex_search_region"));
}
return _search(s, start, end);
}
//
package com.stevesoft.pat;
+import jalview.util.MessageManager;
+
import com.stevesoft.pat.wrap.*;
/** Internally used class. */
lastMatchedTo = 0;
if (rh.me == null)
{
- throw new NullPointerException("Replacer has null Regex pointer");
+ throw new NullPointerException(MessageManager.getString("exception.replace_null_regex_pointer"));
}
if (rh.me._search(s, start, end))
{
//
package com.stevesoft.pat;
+import jalview.util.MessageManager;
+
import com.stevesoft.pat.wrap.*;
/**
Regex r = Regex.perlCode(rs);
if (r == null)
{
- throw new NullPointerException("bad pattern to Regex.perlCode: " + rs);
+ throw new NullPointerException(MessageManager.formatMessage("exception.bad_pattern_to_regex_perl_code", new String[]{rs}));
}
add(r);
}
//
package com.stevesoft.pat.wrap;
+import jalview.util.MessageManager;
+
import java.io.*;
import com.stevesoft.pat.*;
{
}
- throw new ArrayIndexOutOfBoundsException("Out of bounds for file:"
- + " i=" + i + ", Final Buffer: i0=" + i0 + " iend=" + iend);
+ throw new ArrayIndexOutOfBoundsException(MessageManager.formatMessage("exception.out_of_bounds_for_file", new String[]{
+ Integer.valueOf(i).toString(),
+ Integer.valueOf(i0).toString(),
+ Integer.valueOf(iend).toString()
+ }));
}
public String toString()
{
- throw new Error("Not implemented");
+ throw new Error(MessageManager.getString("error.not_implemented"));
}
public int length()
*/
package ext.vamsas;
+import jalview.util.MessageManager;
+
public class IRegistryServiceLocator extends org.apache.axis.client.Service
implements ext.vamsas.IRegistryService
{
{
throw new javax.xml.rpc.ServiceException(t);
}
- throw new javax.xml.rpc.ServiceException(
- "There is no stub implementation for the interface: "
- + (serviceEndpointInterface == null ? "null"
- : serviceEndpointInterface.getName()));
+ throw new javax.xml.rpc.ServiceException(MessageManager.formatMessage("exception.no_stub_implementation_for_interface", new String[]{(serviceEndpointInterface == null ? "null": serviceEndpointInterface.getName())}));
}
/**
}
else
{ // Unknown Port Name
- throw new javax.xml.rpc.ServiceException(
- " Cannot set Endpoint Address for Unknown Port" + portName);
+ throw new javax.xml.rpc.ServiceException(MessageManager.formatMessage("exception.cannot_set_endpoint_address_unknown_port", new String[]{portName}));
}
}
*/
package ext.vamsas;
+import jalview.util.MessageManager;
+
public class JpredServiceLocator extends org.apache.axis.client.Service
implements ext.vamsas.JpredService
{
{
throw new javax.xml.rpc.ServiceException(t);
}
- throw new javax.xml.rpc.ServiceException(
- "There is no stub implementation for the interface: "
- + (serviceEndpointInterface == null ? "null"
- : serviceEndpointInterface.getName()));
+ throw new javax.xml.rpc.ServiceException(MessageManager.formatMessage("exception.no_stub_implementation_for_interface", new String[]{(serviceEndpointInterface == null ? "null": serviceEndpointInterface.getName())}));
}
/**
}
else
{ // Unknown Port Name
- throw new javax.xml.rpc.ServiceException(
- " Cannot set Endpoint Address for Unknown Port" + portName);
+ throw new javax.xml.rpc.ServiceException(MessageManager.formatMessage("exception.cannot_set_endpoint_address_unknown_port", new String[]{portName}));
}
}
*/
package ext.vamsas;
+import jalview.util.MessageManager;
+
public class MuscleWSServiceLocator extends org.apache.axis.client.Service
implements ext.vamsas.MuscleWSService
{
throw new javax.xml.rpc.ServiceException(t);
}
- throw new javax.xml.rpc.ServiceException(
- "There is no stub implementation for the interface: "
- + ((serviceEndpointInterface == null) ? "null"
- : serviceEndpointInterface.getName()));
+ throw new javax.xml.rpc.ServiceException(MessageManager.formatMessage("exception.no_stub_implementation_for_interface", new String[]{(serviceEndpointInterface == null ? "null": serviceEndpointInterface.getName())}));
}
/**
}
else
{ // Unknown Port Name
- throw new javax.xml.rpc.ServiceException(
- " Cannot set Endpoint Address for Unknown Port" + portName);
+ throw new javax.xml.rpc.ServiceException(MessageManager.formatMessage("exception.cannot_set_endpoint_address_unknown_port", new String[]{portName}));
}
}
*/
package ext.vamsas;
+import jalview.util.MessageManager;
+
public class SeqSearchServiceLocator extends org.apache.axis.client.Service
implements ext.vamsas.SeqSearchServiceService
{
{
throw new javax.xml.rpc.ServiceException(t);
}
- throw new javax.xml.rpc.ServiceException(
- "There is no stub implementation for the interface: "
- + (serviceEndpointInterface == null ? "null"
- : serviceEndpointInterface.getName()));
+ throw new javax.xml.rpc.ServiceException(MessageManager.formatMessage("exception.no_stub_implementation_for_interface", new String[]{(serviceEndpointInterface == null ? "null": serviceEndpointInterface.getName())}));
}
/**
}
else
{ // Unknown Port Name
- throw new javax.xml.rpc.ServiceException(
- " Cannot set Endpoint Address for Unknown Port" + portName);
+ throw new javax.xml.rpc.ServiceException(MessageManager.formatMessage("exception.cannot_set_endpoint_address_unknown_port", new String[]{portName}));
}
}
else
{
output.append("Wrong type = dna or pep only");
- throw new Error("Unknown Type " + type2
- + " - dna or pep are the only allowed values.");
+ throw new Error(MessageManager.formatMessage("error.unknown_type_dna_or_pep", new String[]{type2}));
}
}
if (method != FEATURE_SCORE && method != FEATURE_LABEL
&& method != FEATURE_DENSITY)
{
- throw new Error(
- "Implementation Error - sortByFeature method must be one of FEATURE_SCORE, FEATURE_LABEL or FEATURE_DENSITY.");
+ throw new Error(MessageManager.getString("error.implementation_error_sortbyfeature"));
}
boolean ignoreScore = method != FEATURE_SCORE;
StringBuffer scoreLabel = new StringBuffer();
{
if (method == FEATURE_LABEL)
{
- throw new Error("Not yet implemented.");
+ throw new Error(MessageManager.getString("error.not_yet_implemented"));
}
}
if (lastSortByFeatureScore == null
import jalview.analysis.SecStrConsensus.SimpleBP;
import jalview.datamodel.SequenceFeature;
+import jalview.util.MessageManager;
public class Rna
{
{
if (!isClosingParenthesis(closingParenthesis))
{
- throw new WUSSParseException(
- "Querying matching opening parenthesis for non-closing parenthesis character "
- + closingParenthesis, -1);
+ throw new WUSSParseException(MessageManager.formatMessage("exception.querying_matching_opening_parenthesis_for_non_closing_parenthesis", new String[]{new StringBuffer(closingParenthesis).toString()}), -1);
}
return closingToOpening.get(closingParenthesis);
if (!stacks.containsKey(opening))
{
- throw new WUSSParseException(
- "Mismatched (unseen) closing character " + base, i);
+ throw new WUSSParseException(MessageManager.formatMessage("exception.mismatched_unseen_closing_char", new String[]{new StringBuffer(base).toString()}), i);
}
Stack<Integer> stack = stacks.get(opening);
if (stack.isEmpty())
{
// error whilst parsing i'th position. pass back
- throw new WUSSParseException("Mismatched closing character "
- + base, i);
+ throw new WUSSParseException(MessageManager.formatMessage("exception.mismatched_closing_char", new String[]{new StringBuffer(base).toString()}), i);
}
int temp = stack.pop();
Stack<Integer> stack = stacks.get(opening);
if (!stack.empty())
{
- throw new WUSSParseException("Mismatched opening character "
- + opening + " at " + stack.pop(), i);
+ throw new WUSSParseException(MessageManager.formatMessage("exception.mismatched_opening_char", new String[]{new StringBuffer(opening).toString(),Integer.valueOf(stack.pop()).toString()}), i);
}
}
return pairs;
if (dialog.accept)
{
- EditCommand editCommand = new EditCommand("Edit Sequences",
+ EditCommand editCommand = new EditCommand(MessageManager.getString("label.edit_sequences"),
EditCommand.REPLACE, dialog.getName().replace(' ',
ap.av.getGapCharacter()),
sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
colourMenu.add(abovePIDColour);
colourMenu.add(conservationMenuItem);
- noColourmenuItem.setLabel("None");
+ noColourmenuItem.setLabel(MessageManager.getString("label.none"));
noColourmenuItem.addActionListener(this);
- clustalColour.setLabel("Clustalx colours");
+ clustalColour.setLabel(MessageManager.getString("label.clustalx_colours"));
clustalColour.addActionListener(this);
- zappoColour.setLabel("Zappo");
+ zappoColour.setLabel(MessageManager.getString("label.zappo"));
zappoColour.addActionListener(this);
- taylorColour.setLabel("Taylor");
+ taylorColour.setLabel(MessageManager.getString("label.taylor"));
taylorColour.addActionListener(this);
- hydrophobicityColour.setLabel("Hydrophobicity");
+ hydrophobicityColour.setLabel(MessageManager.getString("label.hydrophobicity"));
hydrophobicityColour.addActionListener(this);
- helixColour.setLabel("Helix propensity");
+ helixColour.setLabel(MessageManager.getString("label.helix_propensity"));
helixColour.addActionListener(this);
- strandColour.setLabel("Strand propensity");
+ strandColour.setLabel(MessageManager.getString("label.strand_propensity"));
strandColour.addActionListener(this);
- turnColour.setLabel("Turn propensity");
+ turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
turnColour.addActionListener(this);
- buriedColour.setLabel("Buried Index");
+ buriedColour.setLabel(MessageManager.getString("label.buried_index"));
buriedColour.addActionListener(this);
- abovePIDColour.setLabel("Above % Identity");
+ abovePIDColour.setLabel(MessageManager.getString("label.above_identity_percentage"));
- userDefinedColour.setLabel("User Defined");
+ userDefinedColour.setLabel(MessageManager.getString("action.user_defined"));
userDefinedColour.addActionListener(this);
- PIDColour.setLabel("Percentage Identity");
+ PIDColour.setLabel(MessageManager.getString("action.percentage_identity"));
PIDColour.addActionListener(this);
BLOSUM62Colour.setLabel("BLOSUM62");
BLOSUM62Colour.addActionListener(this);
- conservationMenuItem.setLabel("Conservation");
+ conservationMenuItem.setLabel(MessageManager.getString("label.conservation"));
editMenu.add(copy);
copy.addActionListener(this);
if (newAlignment)
{
- String newtitle = new String("Copied sequences");
- if (getTitle().startsWith("Copied sequences"))
+ String newtitle = MessageManager.getString("label.copied_sequences");
+ if (getTitle().startsWith(MessageManager.getString("label.copied_sequences")))
{
newtitle = getTitle();
}
else
{
- newtitle = newtitle.concat("- from " + getTitle());
+ newtitle = newtitle.concat(MessageManager.formatMessage("label.from_msname", new String[]{getTitle()}));
}
AlignFrame af = new AlignFrame(new Alignment(newSeqs),
viewport.applet, newtitle, false);
}
// !newAlignment
- addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
+ addHistoryItem(new EditCommand(MessageManager.getString("label.add_sequences"), EditCommand.PASTE,
seqs, 0, viewport.getAlignment().getWidth(),
viewport.getAlignment()));
/*
* //ADD HISTORY ITEM
*/
- addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
+ addHistoryItem(new EditCommand(MessageManager.getString("label.cut_sequences"), EditCommand.CUT, cut,
sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
viewport.getAlignment()));
MessageManager.getString("label.load_features_annotations"));
MenuItem outputFeatures = new MenuItem(
- MessageManager.getString("label.export_features"));
+ MessageManager.getString("label.export_features").concat("..."));
MenuItem outputAnnotations = new MenuItem(
- MessageManager.getString("label.export_annotations"));
+ MessageManager.getString("label.export_annotations").concat("..."));
MenuItem closeMenuItem = new MenuItem(
MessageManager.getString("action.close"));
sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
sortGroupMenuItem.addActionListener(this);
removeRedundancyMenuItem.setLabel(MessageManager
- .getString("action.remove_redundancy"));
+ .getString("action.remove_redundancy").concat("..."));
removeRedundancyMenuItem.addActionListener(this);
pairwiseAlignmentMenuItem.setLabel(MessageManager
.getString("action.pairwise_alignment"));
threshold.select(1);
break;
default:
- throw new Error(
- "Implementation error: don't know about threshold setting for current AnnotationColourGradient.");
+ throw new Error(MessageManager.getString("error.implementation_error_dont_know_thereshold_annotationcolourgradient"));
}
thresholdIsMin.setState(acg.thresholdIsMinMax);
thresholdValue.setText("" + acg.getAnnotationThreshold());
String[][] boundchains, boolean align, AlignmentPanel ap,
String protocol)
{
- throw new Error("Not yet implemented.");
+ throw new Error(MessageManager.getString("error.not_yet_implemented"));
}
public AppletJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
}
if (freader == null)
{
- throw new Exception(
- "Invalid datasource. Could not obtain Reader.");
+ throw new Exception(MessageManager.getString("exception.invalid_datasource_couldnt_obtain_reader"));
}
jmb.viewer.openReader(pdbentry.getFile(), pdbentry.getId(),
freader);
*/
package jalview.appletgui;
+import jalview.util.MessageManager;
+
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.FlowLayout;
{
if (embeddedPopup == null)
{
- throw new Error(
- "Implementation error - embeddedPopup must be non-null");
+ throw new Error(MessageManager.getString("error.implementation_error_embeddedpopup_not_null"));
}
if (overrideFonts)
{
}
else
{
- throw new Error("Invalid color for MyCheckBox");
+ throw new Error(MessageManager.getString("error.invalid_colour_for_mycheckbox"));
}
if (col != null)
{
}
}
- String title = newFeatures ? "Create New Sequence Feature(s)"
- : "Amend/Delete Features for " + sequences[0].getName();
+ String title = newFeatures ? MessageManager.getString("label.create_new_sequence_features")
+ : MessageManager.formatMessage("label.amend_delete_features", new String[]{sequences[0].getName()});
final JVDialog dialog = new JVDialog(ap.alignFrame, title, true, 385,
240);
return ((GraduatedColor) fc).getMaxColor();
}
}
- throw new Error("Implementation Error: Unrecognised render object "
- + fc.getClass() + " for features of type " + featureType);
+ throw new Error(MessageManager.formatMessage("error.implementation_error_unrecognised_render_object_for_features_type", new String[]{fc.getClass().getCanonicalName(),featureType}));
}
/**
}
else
{
- throw new Error(
- "Implementation error: Unsupported feature colour object.");
+ throw new Error(MessageManager.getString("error.implementation_error_unsupported_feature_colour_object"));
}
refreshTable();
}
}
else
{
- throw new Error("Invalid color for MyCheckBox");
+ throw new Error(MessageManager.getString("error.invalid_colour_for_mycheckbox"));
}
if (col != null)
{
}
}
- EditCommand cut = new EditCommand("Remove Redundancy",
+ EditCommand cut = new EditCommand(MessageManager.getString("action.remove_redundancy"),
EditCommand.CUT, deleted, 0, width, ap.av.getAlignment());
AlignmentI alignment = ap.av.getAlignment();
for (int i = 0; i < del.size(); i++)
import jalview.structure.SelectionSource;
import jalview.structure.SequenceListener;
import jalview.structure.StructureSelectionManager;
+import jalview.util.MessageManager;
public class SeqPanel extends Panel implements MouseMotionListener,
MouseListener, SequenceListener
StringBuffer message = new StringBuffer();
if (groupEditing)
{
- message.append("Edit group:");
+ message.append(MessageManager.getString("action.edit_group")).append(":");
if (editCommand == null)
{
- editCommand = new EditCommand("Edit Group");
+ editCommand = new EditCommand(MessageManager.getString("action.edit_group"));
}
}
else
{
- message.append("Edit sequence: " + seq.getName());
+ message.append(MessageManager.getString("label.edit_sequence")).append(" " + seq.getName());
String label = seq.getName();
if (label.length() > 10)
{
}
if (editCommand == null)
{
- editCommand = new EditCommand("Edit " + label);
+ editCommand = new EditCommand(MessageManager.formatMessage("label.edit_params", new String[]{label}));
}
}
sp.cs = cs;
}
- conservationSlider.setTitle("Conservation Colour Increment (" + source
- + ")");
+ conservationSlider.setTitle(MessageManager.formatMessage("label.conservation_colour_increment", new String[]{source}));
if (ap.av.getAlignment().getGroups() != null)
{
sp.setAllGroupsCheckEnabled(true);
pid = (SliderPanel) PIDSlider.getComponent(0);
pid.cs = cs;
}
- PIDSlider.setTitle("Percentage Identity Threshold (" + source + ")");
+ PIDSlider.setTitle(MessageManager.formatMessage("label.percentage_identity_thereshold", new String[]{source}));
if (ap.av.getAlignment().getGroups() != null)
{
setTargetColour(colour);
okcancelPanel.setBounds(new Rectangle(0, 113, 400, 35));
- frame.setTitle("User Defined Colours - " + label);
+ frame.setTitle(MessageManager.getString("label.user_defined_colours") + " - " + label);
frame.setSize(420, 200);
}
// // not 1.1 compatible!
// dialog = new Dialog(((JVDialog)alignframe), title, true);
// } else {
- throw new Error("Unsupported owner for User Colour scheme dialog.");
+ throw new Error(MessageManager.getString("label.error_unsupported_owwner_user_colour_scheme"));
}
dialog.add(this);
import javax.swing.*;
import jalview.gui.*;
+import jalview.util.MessageManager;
import jalview.util.Platform;
/**
{
if (!headless)
{
- desktop.setProgressBar("Processing commandline arguments...",
+ desktop.setProgressBar(MessageManager.getString("status.processing_commandline_args"),
progress = System.currentTimeMillis());
}
System.out.println("Opening file: " + file);
running++;
}
- af.setProgressBar("DAS features being retrieved...", id);
+ af.setProgressBar(MessageManager.getString("status.das_features_being_retrived"), id);
af.featureSettings_actionPerformed(null);
af.featureSettings.fetchDasFeatures(dasSources, true);
af.setProgressBar(null, id);
}
else
{
- throw new Error(
- "Invalid separator parameter - must be non-zero length");
+ throw new Error(MessageManager.getString("error.invalid_separator_parameter"));
}
}
int r = 255;
//- Imported classes and packages -/
//---------------------------------/
+import jalview.util.MessageManager;
+
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
// check bounds for index
if (index < 0 || index >= this._annotationElementList.size())
{
- throw new IndexOutOfBoundsException(
- "getAnnotationElement: Index value '" + index
- + "' not in range [0.."
- + (this._annotationElementList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "getAnnotationElement",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._annotationElementList.size() - 1)).toString()
+ }));
}
return (jalview.binding.AnnotationElement) _annotationElementList
// check bounds for index
if (index < 0 || index >= this._annotationElementList.size())
{
- throw new IndexOutOfBoundsException(
- "setAnnotationElement: Index value '" + index
- + "' not in range [0.."
- + (this._annotationElementList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "setAnnotationElement",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._annotationElementList.size() - 1)).toString()
+ }));
}
this._annotationElementList.set(index, vAnnotationElement);
//- Imported classes and packages -/
//---------------------------------/
+import jalview.util.MessageManager;
+
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
// check bounds for index
if (index < 0 || index >= this._settingList.size())
{
- throw new IndexOutOfBoundsException("getSetting: Index value '"
- + index + "' not in range [0.."
- + (this._settingList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "getSetting",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._settingList.size() - 1)).toString()
+ }));
}
return (jalview.binding.Setting) _settingList.get(index);
// check bounds for index
if (index < 0 || index >= this._settingList.size())
{
- throw new IndexOutOfBoundsException("setSetting: Index value '"
- + index + "' not in range [0.."
- + (this._settingList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "setSetting",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._settingList.size() - 1)).toString()
+ }));
}
this._settingList.set(index, vSetting);
//- Imported classes and packages -/
//---------------------------------/
+import jalview.util.MessageManager;
+
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
// check bounds for index
if (index < 0 || index >= this._seqList.size())
{
- throw new IndexOutOfBoundsException("getSeq: Index value '" + index
- + "' not in range [0.." + (this._seqList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "getSeq",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._seqList.size() - 1)).toString()
+ }));
}
return ((java.lang.Integer) _seqList.get(index)).intValue();
// check bounds for index
if (index < 0 || index >= this._seqList.size())
{
- throw new IndexOutOfBoundsException("setSeq: Index value '" + index
- + "' not in range [0.." + (this._seqList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "setSeq",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._seqList.size() - 1)).toString()
+ }));
}
this._seqList.set(index, new java.lang.Integer(vSeq));
//- Imported classes and packages -/
//---------------------------------/
+import jalview.util.MessageManager;
+
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
// check bounds for index
if (index < 0 || index >= this._featuresList.size())
{
- throw new IndexOutOfBoundsException("getFeatures: Index value '"
- + index + "' not in range [0.."
- + (this._featuresList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "getFeatures",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._featuresList.size() - 1)).toString()
+ }));
}
return (jalview.binding.Features) _featuresList.get(index);
// check bounds for index
if (index < 0 || index >= this._pdbidsList.size())
{
- throw new IndexOutOfBoundsException("getPdbids: Index value '"
- + index + "' not in range [0.."
- + (this._pdbidsList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "getPdbids",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._pdbidsList.size() - 1)).toString()
+ }));
}
return (jalview.binding.Pdbids) _pdbidsList.get(index);
// check bounds for index
if (index < 0 || index >= this._featuresList.size())
{
- throw new IndexOutOfBoundsException("setFeatures: Index value '"
- + index + "' not in range [0.."
- + (this._featuresList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "setFeatures",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._featuresList.size() - 1)).toString()
+ }));
}
this._featuresList.set(index, vFeatures);
// check bounds for index
if (index < 0 || index >= this._pdbidsList.size())
{
- throw new IndexOutOfBoundsException("setPdbids: Index value '"
- + index + "' not in range [0.."
- + (this._pdbidsList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "setPdbids",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._pdbidsList.size() - 1)).toString()
+ }));
}
this._pdbidsList.set(index, vPdbids);
//- Imported classes and packages -/
//---------------------------------/
+import jalview.util.MessageManager;
+
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
// check bounds for index
if (index < 0 || index >= this._JGroupList.size())
{
- throw new IndexOutOfBoundsException("getJGroup: Index value '"
- + index + "' not in range [0.."
- + (this._JGroupList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "getJGroup",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._JGroupList.size() - 1)).toString()
+ }));
}
return (jalview.binding.JGroup) _JGroupList.get(index);
// check bounds for index
if (index < 0 || index >= this._JSeqList.size())
{
- throw new IndexOutOfBoundsException("getJSeq: Index value '" + index
- + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "getJSeq",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._JSeqList.size() - 1)).toString()
+ }));
}
return (jalview.binding.JSeq) _JSeqList.get(index);
// check bounds for index
if (index < 0 || index >= this._treeList.size())
{
- throw new IndexOutOfBoundsException("getTree: Index value '" + index
- + "' not in range [0.." + (this._treeList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "getJgetTreeSeq",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._treeList.size() - 1)).toString()
+ }));
}
return (jalview.binding.Tree) _treeList.get(index);
// check bounds for index
if (index < 0 || index >= this._userColoursList.size())
{
- throw new IndexOutOfBoundsException("getUserColours: Index value '"
- + index + "' not in range [0.."
- + (this._userColoursList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "getUserColours",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._userColoursList.size() - 1)).toString()
+ }));
}
return (jalview.binding.UserColours) _userColoursList.get(index);
// check bounds for index
if (index < 0 || index >= this._viewportList.size())
{
- throw new IndexOutOfBoundsException("getViewport: Index value '"
- + index + "' not in range [0.."
- + (this._viewportList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "getViewport",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._viewportList.size() - 1)).toString()
+ }));
}
return (jalview.binding.Viewport) _viewportList.get(index);
// check bounds for index
if (index < 0 || index >= this._JGroupList.size())
{
- throw new IndexOutOfBoundsException("setJGroup: Index value '"
- + index + "' not in range [0.."
- + (this._JGroupList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "setJGroup",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._JGroupList.size() - 1)).toString()
+ }));
}
this._JGroupList.set(index, vJGroup);
// check bounds for index
if (index < 0 || index >= this._JSeqList.size())
{
- throw new IndexOutOfBoundsException("setJSeq: Index value '" + index
- + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "setJSeq",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._JSeqList.size() - 1)).toString()
+ }));
}
this._JSeqList.set(index, vJSeq);
// check bounds for index
if (index < 0 || index >= this._treeList.size())
{
- throw new IndexOutOfBoundsException("setTree: Index value '" + index
- + "' not in range [0.." + (this._treeList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "setTree",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._treeList.size() - 1)).toString()
+ }));
}
this._treeList.set(index, vTree);
// check bounds for index
if (index < 0 || index >= this._userColoursList.size())
{
- throw new IndexOutOfBoundsException("setUserColours: Index value '"
- + index + "' not in range [0.."
- + (this._userColoursList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "setUserColours",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._userColoursList.size() - 1)).toString()
+ }));
}
this._userColoursList.set(index, vUserColours);
// check bounds for index
if (index < 0 || index >= this._viewportList.size())
{
- throw new IndexOutOfBoundsException("setViewport: Index value '"
- + index + "' not in range [0.."
- + (this._viewportList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "setViewport",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._viewportList.size() - 1)).toString()
+ }));
}
this._viewportList.set(index, vViewport);
//- Imported classes and packages -/
//---------------------------------/
+import jalview.util.MessageManager;
+
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
// check bounds for index
if (index < 0 || index >= this._colourList.size())
{
- throw new IndexOutOfBoundsException("getColour: Index value '"
- + index + "' not in range [0.."
- + (this._colourList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "getColour",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._colourList.size() - 1)).toString()
+ }));
}
return (Colour) _colourList.get(index);
// check bounds for index
if (index < 0 || index >= this._colourList.size())
{
- throw new IndexOutOfBoundsException("setColour: Index value '"
- + index + "' not in range [0.."
- + (this._colourList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "setColour",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._colourList.size() - 1)).toString()
+ }));
}
this._colourList.set(index, vColour);
//- Imported classes and packages -/
//---------------------------------/
+import jalview.util.MessageManager;
+
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
// check bounds for index
if (index < 0 || index >= this._items.size())
{
- throw new IndexOutOfBoundsException("getPdbentryItem: Index value '"
- + index + "' not in range [0.." + (this._items.size() - 1)
- + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "getPdbentryItem",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._items.size() - 1)).toString()
+ }));
}
return (jalview.binding.PdbentryItem) _items.get(index);
// check bounds for index
if (index < 0 || index >= this._items.size())
{
- throw new IndexOutOfBoundsException("setPdbentryItem: Index value '"
- + index + "' not in range [0.." + (this._items.size() - 1)
- + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "setPdbentryItem",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._items.size() - 1)).toString()
+ }));
}
this._items.set(index, vPdbentryItem);
*/
package jalview.binding;
+import jalview.util.MessageManager;
+
/**
* Class PdbentryItem.
*
// check bounds for index
if (index < 0 || index >= this._propertyList.size())
{
- throw new IndexOutOfBoundsException("getProperty: Index value '"
- + index + "' not in range [0.."
- + (this._propertyList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "getProperty",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._propertyList.size() - 1)).toString()
+ }));
}
return (jalview.binding.Property) _propertyList.get(index);
// check bounds for index
if (index < 0 || index >= this._propertyList.size())
{
- throw new IndexOutOfBoundsException("setProperty: Index value '"
- + index + "' not in range [0.."
- + (this._propertyList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "setProperty",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._propertyList.size() - 1)).toString()
+ }));
}
this._propertyList.set(index, vProperty);
//- Imported classes and packages -/
//---------------------------------/
+import jalview.util.MessageManager;
+
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
// check bounds for index
if (index < 0 || index >= this._annotationList.size())
{
- throw new IndexOutOfBoundsException("getAnnotation: Index value '"
- + index + "' not in range [0.."
- + (this._annotationList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "getAnnotation",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._annotationList.size() - 1)).toString()
+ }));
}
return (jalview.binding.Annotation) _annotationList.get(index);
// check bounds for index
if (index < 0 || index >= this._sequenceList.size())
{
- throw new IndexOutOfBoundsException("getSequence: Index value '"
- + index + "' not in range [0.."
- + (this._sequenceList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "getSequence",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._sequenceList.size() - 1)).toString()
+ }));
}
return (jalview.binding.Sequence) _sequenceList.get(index);
// check bounds for index
if (index < 0 || index >= this._annotationList.size())
{
- throw new IndexOutOfBoundsException("setAnnotation: Index value '"
- + index + "' not in range [0.."
- + (this._annotationList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "setAnnotation",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._annotationList.size() - 1)).toString()
+ }));
}
this._annotationList.set(index, vAnnotation);
// check bounds for index
if (index < 0 || index >= this._sequenceList.size())
{
- throw new IndexOutOfBoundsException("setSequence: Index value '"
- + index + "' not in range [0.."
- + (this._sequenceList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "setSequence",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._sequenceList.size() - 1)).toString()
+ }));
}
this._sequenceList.set(index, vSequence);
//- Imported classes and packages -/
//---------------------------------/
+import jalview.util.MessageManager;
+
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
// check bounds for index
if (index < 0 || index >= this._alignmentList.size())
{
- throw new IndexOutOfBoundsException("getAlignment: Index value '"
- + index + "' not in range [0.."
- + (this._alignmentList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "getAlignment",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._alignmentList.size() - 1)).toString()
+ }));
}
return (Alignment) _alignmentList.get(index);
// check bounds for index
if (index < 0 || index >= this._sequenceSetList.size())
{
- throw new IndexOutOfBoundsException("getSequenceSet: Index value '"
- + index + "' not in range [0.."
- + (this._sequenceSetList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "getSequenceSet",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._sequenceSetList.size() - 1)).toString()
+ }));
}
return (SequenceSet) _sequenceSetList.get(index);
// check bounds for index
if (index < 0 || index >= this._treeList.size())
{
- throw new IndexOutOfBoundsException("getTree: Index value '" + index
- + "' not in range [0.." + (this._treeList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "getTree",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._treeList.size() - 1)).toString()
+ }));
}
return (java.lang.String) _treeList.get(index);
// check bounds for index
if (index < 0 || index >= this._alignmentList.size())
{
- throw new IndexOutOfBoundsException("setAlignment: Index value '"
- + index + "' not in range [0.."
- + (this._alignmentList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "setAlignment",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._alignmentList.size() - 1)).toString()
+ }));
}
this._alignmentList.set(index, vAlignment);
// check bounds for index
if (index < 0 || index >= this._sequenceSetList.size())
{
- throw new IndexOutOfBoundsException("setSequenceSet: Index value '"
- + index + "' not in range [0.."
- + (this._sequenceSetList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "setSequenceSet",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._sequenceSetList.size() - 1)).toString()
+ }));
}
this._sequenceSetList.set(index, vSequenceSet);
// check bounds for index
if (index < 0 || index >= this._treeList.size())
{
- throw new IndexOutOfBoundsException("setTree: Index value '" + index
- + "' not in range [0.." + (this._treeList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "setTree",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._treeList.size() - 1)).toString()
+ }));
}
this._treeList.set(index, vTree);
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
public class AlignViewController implements AlignViewControllerI
{
}
viewport.setColumnSelection(cs);
alignPanel.paintAlignment(true);
- avcg.setStatus((toggle ? "Toggled " : "Marked ")
- + (invert ? (alw - alStart) - bs.cardinality() : bs
- .cardinality()) + " columns "
- + (invert ? "not " : "") + "containing features of type "
- + featureType + " across " + nseq + " sequence(s)");
+ avcg.setStatus(MessageManager.formatMessage("label.view_controller_toggled_marked",
+ new String[]{
+ (toggle ? MessageManager.getString("label.toggled") : MessageManager.getString("label.marked")),
+ (invert ? (Integer.valueOf((alw - alStart) - bs.cardinality()).toString()):(Integer.valueOf(bs.cardinality()).toString())),
+ featureType, Integer.valueOf(nseq).toString()
+ }));
return true;
}
else
{
- avcg.setStatus("No features of type " + featureType + " found.");
+ avcg.setStatus(MessageManager.formatMessage("label.no_feature_of_type_found", new String[]{featureType}));
if (!extendCurrent && cs != null)
{
cs.clear();
*/
package jalview.datamodel;
+import jalview.util.MessageManager;
+
import java.util.*;
/**
*/
public static AlignmentI createAlignment(CigarArray compactAlignment)
{
- throw new Error("Alignment(CigarArray) not yet implemented");
+ throw new Error(MessageManager.getString("error.alignment_cigararray_not_implemented"));
// this(compactAlignment.refCigars);
}
*/
package jalview.datamodel;
+import jalview.util.MessageManager;
+
import java.util.*;
public class AlignmentOrder
{
if (!identity)
{
- throw new Error("Weak sequenceI equivalence not yet implemented.");
+ throw new Error(MessageManager.getString("error.weak_sequencei_equivalence_not_yet_implemented"));
}
else
{
}
if (!identity)
{
- throw new Error("Weak sequenceI equivalence not yet implemented.");
+ throw new Error(MessageManager.getString("error.weak_sequencei_equivalence_not_yet_implemented"));
}
else
{
*/
package jalview.datamodel;
+import jalview.util.MessageManager;
import jalview.util.ShiftList;
import java.io.PrintStream;
{
if (!seqcigararray.isSeqCigarArray())
{
- throw new Error(
- "Implementation Error - can only make an alignment view from a CigarArray of sequences.");
+ throw new Error(MessageManager.getString("error.implementation_error_can_only_make_alignmnet_from_cigararray"));
}
// contigs = seqcigararray.applyDeletions();
contigs = seqcigararray.getDeletedRegions();
{
if (sequences == null || width <= 0)
{
- throw new Error("empty view cannot be updated.");
+ throw new Error(MessageManager.getString("error.empty_view_cannot_be_updated"));
}
if (nvismsa == null)
{
j++;
if (mseq.length != sequences.length)
{
- throw new Error(
- "Mismatch between number of sequences in block "
- + j + " (" + mseq.length
- + ") and the original view ("
- + sequences.length + ")");
+ throw new Error(MessageManager.formatMessage("error.mismatch_between_number_of_sequences_in_block", new String[]{Integer.valueOf(j).toString(),Integer.valueOf(mseq.length).toString(),Integer.valueOf(sequences.length).toString() }));
}
swidth = mseq[0].getLength(); // JBPNote: could ensure padded
// here.
else
{
// place gaps.
- throw new Error("Padding not yet implemented.");
+ throw new Error(MessageManager.getString("error.padding_not_yet_implemented"));
}
}
}
{
if (nvismsa.length != 1)
{
- throw new Error(
- "Mismatch between visible blocks to update and number of contigs in view (contigs=0,blocks="
- + nvismsa.length);
+ throw new Error(MessageManager.formatMessage("error.mismatch_between_visible_blocks_to_update_and_number_of_contigs_in_view", new String[]{Integer.valueOf(nvismsa.length).toString()}));
}
if (nvismsa[0] != null)
{
*/
package jalview.datamodel;
+import jalview.util.MessageManager;
+
import java.util.*;
public abstract class CigarBase
endpos = alcursor;
break;
default:
- throw new Error("Unknown SeqCigar operation '" + operation[i] + "'");
+ throw new Error(MessageManager.formatMessage("error.unknown_seq_cigar_operation", new String[]{new StringBuffer(operation[i]).toString()}));
}
}
if (++delcount > 0)
} while (c >= '0' && c <= '9' && j < l);
if (j >= l && c >= '0' && c <= '9')
{
- throw new Exception("Unterminated cigar string.");
+ throw new Exception(MessageManager.getString("exception.unterminated_cigar_string"));
}
try
{
i = j;
} catch (Exception e)
{
- throw new Error("Implementation bug in parseCigarString");
+ throw new Error(MessageManager.getString("error.implementation_bug_parse_cigar_string"));
}
if (c >= 'a' && c <= 'z')
{
}
else
{
- throw new Exception("Unexpected operation '" + c
- + "' in cigar string (position " + i + " in '"
- + cigarString + "'");
+ throw new Exception(MessageManager.formatMessage("exception.unexpected_operation_cigar_string_pos", new String[]{
+ new StringBuffer(c).toString(),
+ Integer.valueOf(i).toString(),
+ cigarString
+ }));
}
}
return new Object[]
}
if (op != M && op != D && op != I)
{
- throw new Error("Implementation error. Invalid operation string.");
+ throw new Error(MessageManager.getString("error.implementation_error_invalid_operation_string"));
}
if (range == 0)
{
}
if (range < 0)
{
- throw new Error(
- "Invalid range string (must be zero or positive number)");
+ throw new Error(MessageManager.getString("error.invalid_range_string"));
}
int lngth = 0;
if (operation == null)
}
if (start < 0 || start > end)
{
- throw new Error(
- "Implementation Error: deleteRange out of bounds: start must be non-negative and less than end.");
+ throw new Error(MessageManager.getString("error.implementation_error_delete_range_out_of_bounds"));
}
// find beginning
int cursor = 0; // mark the position for the current operation being edited.
}
break;
case D:
- throw new Error("Implementation error."); // do nothing;
+ throw new Error(MessageManager.getString("error.implementation_error")); // do nothing;
default:
- throw new Error("Implementation Error! Unknown operation '"
- + oldops[o] + "'");
+ throw new Error(MessageManager.formatMessage("error.implementation_error_unknown_operation", new String[]{new StringBuffer(oldops[o]).toString()}));
}
rlength -= remain;
remain = oldrange[++o]; // number of op characters left to edit
refseq.getSequenceAsString(start, end), GapChar);
if (edit_result == null)
{
- throw new Error(
- "Implementation Error - unexpected null from getSequenceAndDeletions");
+ throw new Error(MessageManager.getString("error.implementation_error_unexpected_null_from_get_sequence_and_deletions"));
}
int bounds[] = (int[]) edit_result[1];
seq = new Sequence(refseq.getName(), (String) edit_result[0],
boolean hasgaps = false;
if (seq == null)
{
- throw new Error("Implementation Error - _setSeq(null,...)");
+ throw new Error(MessageManager.getString("error.implementation_error_set_seq_null"));
}
if (_s < 0)
{
- throw new Error("Implementation Error: _s=" + _s);
+ throw new Error(MessageManager.formatMessage("error.implementation_error_s", new String[]{Integer.valueOf(_s).toString()}));
}
String seq_string = seq.getSequenceAsString();
if (_e == 0 || _e < _s || _e > seq_string.length())
// Check offsets
if (end > ds.getLength())
{
- throw new Error(
- "SeqCigar: Possible implementation error: sequence is longer than dataset sequence");
+ throw new Error(MessageManager.getString("error.implementation_error_seqcigar_possible"));
// end = ds.getLength();
}
super();
if (seq == null)
{
- throw new Error("Implementation Bug. Null seq !");
+ throw new Error(MessageManager.getString("error.implmentation_bug_seq_null"));
}
if (operation.length != range.length)
{
- throw new Error(
- "Implementation Bug. Cigar Operation list!= range list");
+ throw new Error(MessageManager.getString("error.implementation_bug_cigar_operation_list_range_list"));
}
if (operation != null)
if (_setSeq(seq, false, 0, 0))
{
- throw new Error(
- "NOT YET Implemented: Constructing a Cigar object from a cigar string and a gapped sequence.");
+ throw new Error(MessageManager.getString("error.not_yet_implemented_cigar_object_from_cigar_string"));
}
for (int i = this.length, j = 0; j < operation.length; i++, j++)
{
char op = operation[j];
if (op != M && op != I && op != D)
{
- throw new Error("Implementation Bug. Cigar Operation '" + j
- + "' '" + op + "' not one of '" + M + "', '" + I
- + "', or '" + D + "'.");
+ throw new Error(MessageManager.formatMessage("error.implementation_bug_cigar_operation", new String[]{Integer.valueOf(j).toString(),Integer.valueOf(op).toString(),Integer.valueOf(M).toString(),Integer.valueOf(I).toString(),Integer.valueOf(D).toString()}));
}
this.operation[i] = op;
this.range[i] = range[j];
this.length = 0;
if (_setSeq(seq, false, 0, 0))
{
- throw new Error(
- "NOT YET Implemented: Constructing a Cigar object from a cigar string and a gapped sequence.");
+ throw new Error(MessageManager.getString("error.not_yet_implemented_cigar_object_from_cigar_string"));
}
}
}
super();
if (seq == null)
{
- throw new Error("Implementation error for new Cigar(SequenceI)");
+ throw new Error(MessageManager.getString("error.implementation_error_for_new_cigar"));
}
_setSeq(seq, false, 0, 0);
// there is still work to do
super();
if (seq == null)
{
- throw new Error("Implementation error for new Cigar(SequenceI)");
+ throw new Error(MessageManager.getString("error.implementation_error_for_new_cigar"));
}
_setSeq(seq, false, start, end + 1);
// there is still work to do
// endcol}, hidden regions {{start, end, col}})
if (gs_regions[i] == null)
{
- throw new Error("Implementation error: " + i
- + "'th sequence Cigar has no operations.");
+ throw new Error(MessageManager.formatMessage("error.implementation_error_cigar_seq_no_operations", new String[]{Integer.valueOf(i).toString()}));
}
g_seqs[i] = new StringBuffer((String) ((Object[]) gs_regions[i])[0]); // the
// visible
/**
* This annotation is displayed below the alignment but the positions are tied
* to the residues of this sequence
+ *
+ * TODO: change to List<>
*/
- Vector annotation;
+ Vector<AlignmentAnnotation> annotation;
/**
* The index of the sequence in a MSA
datasetSequence.updatePDBIds();
if (annotation != null)
{
- Vector<AlignmentAnnotation> _annot = annotation;
- annotation = null;
- for (AlignmentAnnotation aa : _annot)
+ for (AlignmentAnnotation aa : annotation)
{
- aa.sequenceRef = datasetSequence;
- aa.adjustForAlignment(); // uses annotation's own record of
+ AlignmentAnnotation _aa = new AlignmentAnnotation(aa);
+ _aa.sequenceRef = datasetSequence;
+ _aa.adjustForAlignment(); // uses annotation's own record of
// sequence-column mapping
- datasetSequence.addAlignmentAnnotation(aa);
+ datasetSequence.addAlignmentAnnotation(_aa);
}
}
}
-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.datamodel;
-
-import java.util.Vector;
-
-import fr.orsay.lri.varna.models.rna.RNA;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public interface SequenceI
-{
- /**
- * Set the display name for the sequence
- *
- * @param name
- */
- public void setName(String name);
-
- /**
- * Get the display name
- */
- public String getName();
-
- /**
- * Set start position of first non-gapped symbol in sequence
- *
- * @param start
- * new start position
- */
- public void setStart(int start);
-
- /**
- * get start position of first non-gapped residue in sequence
- *
- * @return
- */
- public int getStart();
-
- /**
- * get the displayed id of the sequence
- *
- * @return true means the id will be returned in the form
- * DisplayName/Start-End
- */
- public String getDisplayId(boolean jvsuffix);
-
- /**
- * set end position for last residue in sequence
- *
- * @param end
- */
- public void setEnd(int end);
-
- /**
- * get end position for last residue in sequence getEnd()>getStart() unless
- * sequence only consists of gap characters
- *
- * @return
- */
- public int getEnd();
-
- /**
- * @return length of sequence including gaps
- *
- */
- public int getLength();
-
- /**
- * Replace the sequence with the given string
- *
- * @param sequence
- * new sequence string
- */
- public void setSequence(String sequence);
-
- /**
- * @return sequence as string
- */
- public String getSequenceAsString();
-
- /**
- * get a range on the sequence as a string
- *
- * @param start
- * position relative to start of sequence including gaps (from 0)
- * @param end
- * position relative to start of sequence including gaps (from 0)
- *
- * @return String containing all gap and symbols in specified range
- */
- public String getSequenceAsString(int start, int end);
-
- /**
- * Get the sequence as a character array
- *
- * @return seqeunce and any gaps
- */
- public char[] getSequence();
-
- /**
- * get stretch of sequence characters in an array
- *
- * @param start
- * absolute index into getSequence()
- * @param end
- * exclusive index of last position in segment to be returned.
- *
- * @return char[max(0,end-start)];
- */
- public char[] getSequence(int start, int end);
-
- /**
- * create a new sequence object from start to end of this sequence
- *
- * @param start
- * int
- * @param end
- * int
- * @return SequenceI
- */
- public SequenceI getSubSequence(int start, int end);
-
- /**
- * DOCUMENT ME!
- *
- * @param i
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public char getCharAt(int i);
-
- /**
- * DOCUMENT ME!
- *
- * @param desc
- * DOCUMENT ME!
- */
- public void setDescription(String desc);
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public String getDescription();
-
- /**
- * Return the alignment column for a sequence position * Return the alignment
- * position for a sequence position
- *
- * @param pos
- * lying from start to end
- *
- * @return aligned column for residue (0 if residue is upstream from
- * alignment, -1 if residue is downstream from alignment) note.
- * Sequence object returns sequence.getEnd() for positions upstream
- * currently. TODO: change sequence for
- * assert(findIndex(seq.getEnd()+1)==-1) and fix incremental bugs
- *
- */
- public int findIndex(int pos);
-
- /**
- * Returns the sequence position for an alignment position
- *
- * @param i
- * column index in alignment (from 1)
- *
- * @return residue number for residue (left of and) nearest ith column
- */
- public int findPosition(int i);
-
- /**
- * Returns an int array where indices correspond to each residue in the
- * sequence and the element value gives its position in the alignment
- *
- * @return int[SequenceI.getEnd()-SequenceI.getStart()+1] or null if no
- * residues in SequenceI object
- */
- public int[] gapMap();
-
- /**
- * Returns an int array where indices correspond to each position in sequence
- * char array and the element value gives the result of findPosition for that
- * index in the sequence.
- *
- * @return int[SequenceI.getLength()]
- */
- public int[] findPositionMap();
-
- /**
- * Delete a range of aligned sequence columns, creating a new dataset sequence
- * if necessary and adjusting start and end positions accordingly.
- *
- * @param i
- * first column in range to delete
- * @param j
- * last column in range to delete
- */
- public void deleteChars(int i, int j);
-
- /**
- * DOCUMENT ME!
- *
- * @param i
- * DOCUMENT ME!
- * @param c
- * DOCUMENT ME!
- */
- public void insertCharAt(int i, char c);
-
- /**
- * DOCUMENT ME!
- *
- * @param i
- * DOCUMENT ME!
- * @param c
- * DOCUMENT ME!
- */
- public void insertCharAt(int i, int length, char c);
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public SequenceFeature[] getSequenceFeatures();
-
- /**
- * DOCUMENT ME!
- *
- * @param v
- * DOCUMENT ME!
- */
- public void setSequenceFeatures(SequenceFeature[] features);
-
- /**
- * DOCUMENT ME!
- *
- * @param id
- * DOCUMENT ME!
- */
- public void setPDBId(Vector ids);
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public Vector getPDBId();
-
- /**
- * add entry to the vector of PDBIds, if it isn't in the list already
- *
- * @param entry
- */
- public void addPDBId(PDBEntry entry);
-
- /**
- * update the list of PDBEntrys to include any DBRefEntrys citing structural
- * databases
- *
- * @return true if PDBEntry list was modified
- */
- public boolean updatePDBIds();
-
- public String getVamsasId();
-
- public void setVamsasId(String id);
-
- public void setDBRef(DBRefEntry[] dbs);
-
- public DBRefEntry[] getDBRef();
-
- /**
- * add the given entry to the list of DBRefs for this sequence, or replace a
- * similar one if entry contains a map object and the existing one doesnt.
- *
- * @param entry
- */
- public void addDBRef(DBRefEntry entry);
-
- public void addSequenceFeature(SequenceFeature sf);
-
- public void deleteFeature(SequenceFeature sf);
-
- public void setDatasetSequence(SequenceI seq);
-
- public SequenceI getDatasetSequence();
-
- public AlignmentAnnotation[] getAnnotation();
-
- public void addAlignmentAnnotation(AlignmentAnnotation annotation);
-
- public void removeAlignmentAnnotation(AlignmentAnnotation annotation);
-
- /**
- * Derive a sequence (using this one's dataset or as the dataset)
- *
- * @return duplicate sequence with valid dataset sequence
- */
- public SequenceI deriveSequence();
-
- /**
- * set the array of associated AlignmentAnnotation for this sequenceI
- *
- * @param revealed
- */
- public void setAlignmentAnnotation(AlignmentAnnotation[] annotation);
-
- /**
- * Get one or more alignment annotations with a particular label.
- *
- * @param label
- * string which each returned annotation must have as a label.
- * @return null or array of annotations.
- */
- public AlignmentAnnotation[] getAnnotation(String label);
-
- /**
- * create a new dataset sequence (if necessary) for this sequence and sets
- * this sequence to refer to it. This call will move any features or
- * references on the sequence onto the dataset.
- *
- * @return dataset sequence for this sequence
- */
- public SequenceI createDatasetSequence();
-
- /**
- * Transfer any database references or annotation from entry under a sequence
- * mapping.
- *
- * @param entry
- * @param mp
- * null or mapping from entry's numbering to local start/end
- */
- public void transferAnnotation(SequenceI entry, Mapping mp);
-
- /**
- * @param index
- * The sequence index in the MSA
- */
- public void setIndex(int index);
-
- /**
- * @return The index of the sequence in the alignment
- */
- public int getIndex();
-
- /**
- * @return The RNA of the sequence in the alignment
- */
-
- public RNA getRNA();
-
- /**
- * @param rna
- * The RNA.
- */
- public void setRNA(RNA rna);
-
-}
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)\r
+ * Copyright (C) 2014 The Jalview Authors\r
+ * \r
+ * This file is part of Jalview.\r
+ * \r
+ * Jalview is free software: you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License \r
+ * as published by the Free Software Foundation, either version 3\r
+ * of the License, or (at your option) any later version.\r
+ * \r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License\r
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
+ * The Jalview Authors are detailed in the 'AUTHORS' file.\r
+ */\r
+package jalview.datamodel;\r
+\r
+import java.util.Vector;\r
+\r
+import fr.orsay.lri.varna.models.rna.RNA;\r
+\r
+/**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public interface SequenceI\r
+{\r
+ /**\r
+ * Set the display name for the sequence\r
+ * \r
+ * @param name\r
+ */\r
+ public void setName(String name);\r
+\r
+ /**\r
+ * Get the display name\r
+ */\r
+ public String getName();\r
+\r
+ /**\r
+ * Set start position of first non-gapped symbol in sequence\r
+ * \r
+ * @param start\r
+ * new start position\r
+ */\r
+ public void setStart(int start);\r
+\r
+ /**\r
+ * get start position of first non-gapped residue in sequence\r
+ * \r
+ * @return\r
+ */\r
+ public int getStart();\r
+\r
+ /**\r
+ * get the displayed id of the sequence\r
+ * \r
+ * @return true means the id will be returned in the form\r
+ * DisplayName/Start-End\r
+ */\r
+ public String getDisplayId(boolean jvsuffix);\r
+\r
+ /**\r
+ * set end position for last residue in sequence\r
+ * \r
+ * @param end\r
+ */\r
+ public void setEnd(int end);\r
+\r
+ /**\r
+ * get end position for last residue in sequence getEnd()>getStart() unless\r
+ * sequence only consists of gap characters\r
+ * \r
+ * @return\r
+ */\r
+ public int getEnd();\r
+\r
+ /**\r
+ * @return length of sequence including gaps\r
+ * \r
+ */\r
+ public int getLength();\r
+\r
+ /**\r
+ * Replace the sequence with the given string\r
+ * \r
+ * @param sequence\r
+ * new sequence string\r
+ */\r
+ public void setSequence(String sequence);\r
+\r
+ /**\r
+ * @return sequence as string\r
+ */\r
+ public String getSequenceAsString();\r
+\r
+ /**\r
+ * get a range on the sequence as a string\r
+ * \r
+ * @param start\r
+ * position relative to start of sequence including gaps (from 0)\r
+ * @param end\r
+ * position relative to start of sequence including gaps (from 0)\r
+ * \r
+ * @return String containing all gap and symbols in specified range\r
+ */\r
+ public String getSequenceAsString(int start, int end);\r
+\r
+ /**\r
+ * Get the sequence as a character array\r
+ * \r
+ * @return seqeunce and any gaps\r
+ */\r
+ public char[] getSequence();\r
+\r
+ /**\r
+ * get stretch of sequence characters in an array\r
+ * \r
+ * @param start\r
+ * absolute index into getSequence()\r
+ * @param end\r
+ * exclusive index of last position in segment to be returned.\r
+ * \r
+ * @return char[max(0,end-start)];\r
+ */\r
+ public char[] getSequence(int start, int end);\r
+\r
+ /**\r
+ * create a new sequence object from start to end of this sequence\r
+ * \r
+ * @param start\r
+ * int\r
+ * @param end\r
+ * int\r
+ * @return SequenceI\r
+ */\r
+ public SequenceI getSubSequence(int start, int end);\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param i\r
+ * DOCUMENT ME!\r
+ * \r
+ * @return DOCUMENT ME!\r
+ */\r
+ public char getCharAt(int i);\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param desc\r
+ * DOCUMENT ME!\r
+ */\r
+ public void setDescription(String desc);\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @return DOCUMENT ME!\r
+ */\r
+ public String getDescription();\r
+\r
+ /**\r
+ * Return the alignment column for a sequence position * Return the alignment\r
+ * position for a sequence position\r
+ * \r
+ * @param pos\r
+ * lying from start to end\r
+ * \r
+ * @return aligned column for residue (0 if residue is upstream from\r
+ * alignment, -1 if residue is downstream from alignment) note.\r
+ * Sequence object returns sequence.getEnd() for positions upstream\r
+ * currently. TODO: change sequence for\r
+ * assert(findIndex(seq.getEnd()+1)==-1) and fix incremental bugs\r
+ * \r
+ */\r
+ public int findIndex(int pos);\r
+\r
+ /**\r
+ * Returns the sequence position for an alignment position\r
+ * \r
+ * @param i\r
+ * column index in alignment (from 1)\r
+ * \r
+ * @return residue number for residue (left of and) nearest ith column\r
+ */\r
+ public int findPosition(int i);\r
+\r
+ /**\r
+ * Returns an int array where indices correspond to each residue in the\r
+ * sequence and the element value gives its position in the alignment\r
+ * \r
+ * @return int[SequenceI.getEnd()-SequenceI.getStart()+1] or null if no\r
+ * residues in SequenceI object\r
+ */\r
+ public int[] gapMap();\r
+\r
+ /**\r
+ * Returns an int array where indices correspond to each position in sequence\r
+ * char array and the element value gives the result of findPosition for that\r
+ * index in the sequence.\r
+ * \r
+ * @return int[SequenceI.getLength()]\r
+ */\r
+ public int[] findPositionMap();\r
+\r
+ /**\r
+ * Delete a range of aligned sequence columns, creating a new dataset sequence\r
+ * if necessary and adjusting start and end positions accordingly.\r
+ * \r
+ * @param i\r
+ * first column in range to delete\r
+ * @param j\r
+ * last column in range to delete\r
+ */\r
+ public void deleteChars(int i, int j);\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param i\r
+ * DOCUMENT ME!\r
+ * @param c\r
+ * DOCUMENT ME!\r
+ */\r
+ public void insertCharAt(int i, char c);\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param i\r
+ * DOCUMENT ME!\r
+ * @param c\r
+ * DOCUMENT ME!\r
+ */\r
+ public void insertCharAt(int i, int length, char c);\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @return DOCUMENT ME!\r
+ */\r
+ public SequenceFeature[] getSequenceFeatures();\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param v\r
+ * DOCUMENT ME!\r
+ */\r
+ public void setSequenceFeatures(SequenceFeature[] features);\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param id\r
+ * DOCUMENT ME!\r
+ */\r
+ public void setPDBId(Vector ids);\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @return DOCUMENT ME!\r
+ */\r
+ public Vector getPDBId();\r
+\r
+ /**\r
+ * add entry to the vector of PDBIds, if it isn't in the list already\r
+ * \r
+ * @param entry\r
+ */\r
+ public void addPDBId(PDBEntry entry);\r
+\r
+ /**\r
+ * update the list of PDBEntrys to include any DBRefEntrys citing structural\r
+ * databases\r
+ * \r
+ * @return true if PDBEntry list was modified\r
+ */\r
+ public boolean updatePDBIds();\r
+\r
+ public String getVamsasId();\r
+\r
+ public void setVamsasId(String id);\r
+\r
+ public void setDBRef(DBRefEntry[] dbs);\r
+\r
+ public DBRefEntry[] getDBRef();\r
+\r
+ /**\r
+ * add the given entry to the list of DBRefs for this sequence, or replace a\r
+ * similar one if entry contains a map object and the existing one doesnt.\r
+ * \r
+ * @param entry\r
+ */\r
+ public void addDBRef(DBRefEntry entry);\r
+\r
+ public void addSequenceFeature(SequenceFeature sf);\r
+\r
+ public void deleteFeature(SequenceFeature sf);\r
+\r
+ public void setDatasetSequence(SequenceI seq);\r
+\r
+ public SequenceI getDatasetSequence();\r
+\r
+ public AlignmentAnnotation[] getAnnotation();\r
+\r
+ public void addAlignmentAnnotation(AlignmentAnnotation annotation);\r
+\r
+ public void removeAlignmentAnnotation(AlignmentAnnotation annotation);\r
+\r
+ /**\r
+ * Derive a sequence (using this one's dataset or as the dataset)\r
+ * \r
+ * @return duplicate sequence with valid dataset sequence\r
+ */\r
+ public SequenceI deriveSequence();\r
+\r
+ /**\r
+ * set the array of associated AlignmentAnnotation for this sequenceI\r
+ * \r
+ * @param revealed\r
+ */\r
+ public void setAlignmentAnnotation(AlignmentAnnotation[] annotation);\r
+\r
+ /**\r
+ * Get one or more alignment annotations with a particular label.\r
+ * \r
+ * @param label\r
+ * string which each returned annotation must have as a label.\r
+ * @return null or array of annotations.\r
+ */\r
+ public AlignmentAnnotation[] getAnnotation(String label);\r
+\r
+ /**\r
+ * create a new dataset sequence (if necessary) for this sequence and sets\r
+ * this sequence to refer to it. This call will move any features or\r
+ * references on the sequence onto the dataset. It will also make a duplicate\r
+ * of existing annotation rows for the dataset sequence, rather than relocate\r
+ * them in order to preserve external references (since 2.8.2).\r
+ * \r
+ * @return dataset sequence for this sequence\r
+ */\r
+ public SequenceI createDatasetSequence();\r
+\r
+ /**\r
+ * Transfer any database references or annotation from entry under a sequence\r
+ * mapping. <br/>\r
+ * <strong>Note: DOES NOT transfer sequence associated alignment\r
+ * annotation </strong><br/>\r
+ * \r
+ * @param entry\r
+ * @param mp\r
+ * null or mapping from entry's numbering to local start/end\r
+ */\r
+ public void transferAnnotation(SequenceI entry, Mapping mp);\r
+\r
+ /**\r
+ * @param index\r
+ * The sequence index in the MSA\r
+ */\r
+ public void setIndex(int index);\r
+\r
+ /**\r
+ * @return The index of the sequence in the alignment\r
+ */\r
+ public int getIndex();\r
+\r
+ /**\r
+ * @return The RNA of the sequence in the alignment\r
+ */\r
+\r
+ public RNA getRNA();\r
+\r
+ /**\r
+ * @param rna\r
+ * The RNA.\r
+ */\r
+ public void setRNA(RNA rna);\r
+\r
+}\r
import jalview.structure.StructureMapping;
import jalview.structure.StructureSelectionManager;
import jalview.structures.models.SequenceStructureBindingModel;
+import jalview.util.MessageManager;
import java.awt.Color;
import java.awt.Container;
// Jmol callback has completed.
if (mapping == null || mapping.length < 1)
{
- throw new Error(
- "Implementation error - Jmol seems to be still working on getting its data - report at http://issues.jalview.org/browse/JAL-1016");
+ throw new Error(MessageManager.getString("error.implementation_error_jmol_getting_data"));
}
int lastPos = -1;
for (int s = 0; s < sequence[pdbfnum].length; s++)
{
if (pe < 0 || pe >= pdbentry.length)
{
- throw new Error(
- "Implementation error - no corresponding pdbentry (for index "
- + pe + ") to add sequences mappings to");
+ throw new Error(MessageManager.formatMessage("error.implementation_error_no_pdbentry_from_index", new String[]{Integer.valueOf(pe).toString()}));
}
final String nullChain = "TheNullChain";
Vector s = new Vector();
import jalview.datamodel.SequenceI;
import jalview.io.AlignFile;
import jalview.io.FileParse;
+import jalview.util.MessageManager;
/**
* Import and process PDB files with Jmol
jmolApp.startViewer(viewer, null);
} catch (ClassCastException x)
{
- throw new Error(
- "Jmol version "
- + JmolViewer.getJmolVersion()
- + " is not compatible with this version of Jalview. Report this problem at issues.jalview.org",
+ throw new Error(MessageManager.formatMessage("error.jmol_version_not_compatible_with_jalview_version", new String[]{JmolViewer.getJmolVersion()}),
x);
}
}
*/
package jalview.ext.paradise;
+import jalview.util.MessageManager;
import jalview.ws.HttpClientUtils;
import java.io.IOException;
@Override
public void remove()
{
- throw new Error("Remove: Not implemented");
+ throw new Error(MessageManager.getString("error.not_implemented_remove"));
}
@Override
protected Object clone() throws CloneNotSupportedException
{
- throw new CloneNotSupportedException("Clone: Not implemented");
+ throw new CloneNotSupportedException(MessageManager.getString("error.not_implemented_clone"));
}
@Override
};
} catch (Exception foo)
{
- throw new Exception(
- "Couldn't parse response from Annotate3d server.", foo);
+ throw new Exception(MessageManager.getString("exception.couldnt_parse_responde_from_annotated3d_server"), foo);
}
}
import jalview.structure.StructureMapping;
import jalview.structure.StructureSelectionManager;
import jalview.structures.models.SequenceStructureBindingModel;
+import jalview.util.MessageManager;
import java.awt.Color;
import java.awt.event.ComponentEvent;
// Jmol callback has completed.
if (mapping == null || mapping.length < 1)
{
- throw new Error(
- "Implementation error - Chimera seems to be still working on getting its data - report at http://issues.jalview.org/browse/JAL-1016");
+ throw new Error(MessageManager.getString("error.implementation_error_chimera_getting_data"));
}
int lastPos = -1;
for (int s = 0; s < sequence[pdbfnum].length; s++)
{
if (pe < 0 || pe >= pdbentry.length)
{
- throw new Error(
- "Implementation error - no corresponding pdbentry (for index "
- + pe + ") to add sequences mappings to");
+ throw new Error(MessageManager.formatMessage("error.implementation_error_no_pdbentry_from_index", new String[]{Integer.valueOf(pe).toString()}));
}
final String nullChain = "TheNullChain";
Vector s = new Vector();
{
if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
{
- throw new Error(
- "call setProgressBar before registering the progress bar's handler.");
+ throw new Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
}
progressBarHandlers.put(new Long(id), handler);
final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
public void actionPerformed(ActionEvent e)
{
handler.cancelActivity(id);
- us.setProgressBar(
- "Cancelled "
- + ((JLabel) progressPanel.getComponent(0))
- .getText(), id);
+ us.setProgressBar(MessageManager.formatMessage("label.cancelled_params", new String[]{((JLabel) progressPanel.getComponent(0)).getText()}), id);
}
});
progressPanel.add(cancel, BorderLayout.EAST);
currentFileFormat, false);
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Save Alignment to file");
+ chooser.setDialogTitle(MessageManager.getString("label.save_alignment_to_file"));
chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
// /////
// ADD HISTORY ITEM
//
- addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
+ addHistoryItem(new EditCommand(MessageManager.getString("label.add_sequences"), EditCommand.PASTE,
sequences, 0, alignment.getWidth(), alignment));
}
// Add any annotations attached to sequences
/*
* //ADD HISTORY ITEM
*/
- addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
+ addHistoryItem(new EditCommand(MessageManager.getString("label.cut_sequences"), EditCommand.CUT, cut,
sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
viewport.getAlignment()));
boolean addFirstIndex = false;
if (viewTitle == null || viewTitle.trim().length() == 0)
{
- viewTitle = "View";
+ viewTitle = MessageManager.getString("action.view");
addFirstIndex = true;
}
else
public void addSortByOrderMenuItem(String title,
final AlignmentOrder order)
{
- final JMenuItem item = new JMenuItem("by " + title);
+ final JMenuItem item = new JMenuItem(MessageManager.formatMessage("action.by_title_param", new String[]{title}));
sort.add(item);
item.addActionListener(new java.awt.event.ActionListener()
{
// object broker mechanism.
final Vector<JMenu> wsmenu = new Vector<JMenu>();
final IProgressIndicator af = me;
- final JMenu msawsmenu = new JMenu("Alignment");
- final JMenu secstrmenu = new JMenu(
- "Secondary Structure Prediction");
- final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
- final JMenu analymenu = new JMenu("Analysis");
- final JMenu dismenu = new JMenu("Protein Disorder");
+ final JMenu msawsmenu = new JMenu(MessageManager.getString("label.alignment"));
+ final JMenu secstrmenu = new JMenu(MessageManager.getString("label.secondary_structure_prediction"));
+ final JMenu seqsrchmenu = new JMenu(MessageManager.getString("label.sequence_database_search"));
+ final JMenu analymenu = new JMenu(MessageManager.getString("label.analysis"));
+ final JMenu dismenu = new JMenu(MessageManager.getString("label.protein_disorder"));
// JAL-940 - only show secondary structure prediction services from
// the legacy server
if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
public void run()
{
final long sttime = System.currentTimeMillis();
- ths.setProgressBar("Searching for sequences from " + fsrc, sttime);
+ ths.setProgressBar(MessageManager.formatMessage("status.searching_for_sequences_from", new String[]{fsrc}), sttime);
try
{
Alignment ds = ths.getViewport().getAlignment().getDataset(); // update
jalview.bin.Cache.log.error("Error when finding crossreferences",
e);
}
- ths.setProgressBar("Finished searching for sequences from " + fsrc,
+ ths.setProgressBar(MessageManager.formatMessage("status.finished_searching_for_sequences_from", new String[]{fsrc}),
sttime);
}
}
});
- fetchr.setToolTipText("<html>"
- + JvSwingUtils.wrapTooltip("Retrieve from "
- + src.getDbName()) + "<html>");
+ fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from", new String[]{src.getDbName()})));
dfetch.add(fetchr);
comp++;
}
}
});
- fetchr.setToolTipText("<html>"
- + JvSwingUtils.wrapTooltip("Retrieve from all "
- + otherdb.size() + " sources in "
- + src.getDbSource() + "<br>First is :"
- + src.getDbName()) + "<html>");
+ fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from_all_sources", new String[]{Integer.valueOf(otherdb.size()).toString(), src.getDbSource(), src.getDbName()})));
dfetch.add(fetchr);
comp++;
// and then build the rest of the individual menus
- ifetch = new JMenu("Sources from " + src.getDbSource());
+ ifetch = new JMenu(MessageManager.formatMessage("label.source_from_db_source", new String[]{src.getDbSource()}));
icomp = 0;
String imname = null;
int i = 0;
0, 10) + "..." : dbname;
if (imname == null)
{
- imname = "from '" + sname + "'";
+ imname = MessageManager.formatMessage("label.from_msname", new String[]{sname});
}
fetchr = new JMenuItem(msname);
final DbSourceProxy[] dassrc =
});
fetchr.setToolTipText("<html>"
- + JvSwingUtils.wrapTooltip("Retrieve from "
- + dbname) + "</html>");
+ + MessageManager.formatMessage("label.fetch_retrieve_from", new String[]{dbname}));
ifetch.add(fetchr);
++i;
if (++icomp >= mcomp || i == (otherdb.size()))
if (!viewport.getSequenceSetId().equals(
alignmentPanel.av.getSequenceSetId()))
{
- throw new Error(
- "Implementation error: cannot show a view from another alignment in an AlignFrame.");
+ throw new Error(MessageManager.getString("error.implementation_error_cannot_show_view_alignment_frame"));
}
if (tabbedPane != null
& alignPanels.indexOf(alignmentPanel) != tabbedPane
import jalview.jbgui.*;
import jalview.schemes.*;
import jalview.structure.StructureSelectionManager;
+import jalview.util.MessageManager;
/**
* DOCUMENT ME!
.getProperty("java.awt.headless").equals("true"));
if (alignFrame != null && !headless)
{
- alignFrame.setProgressBar("Saving "
- + (type == jalview.util.ImageMaker.PNG ? "PNG image"
- : "EPS file"), progress);
+ alignFrame.setProgressBar(MessageManager.formatMessage("status.saving_file", new String[]{(type == jalview.util.ImageMaker.PNG ? MessageManager.getString("label.png_image") : MessageManager.getString("label.eps_file"))}), progress);
}
try
{
{
if (alignFrame != null && !headless)
{
- alignFrame.setProgressBar("Export complete.", progress);
+ alignFrame.setProgressBar(MessageManager.getString("status.export_complete"), progress);
}
}
}
threshold.setSelectedIndex(2);
break;
default:
- throw new Error(
- "Implementation error: don't know about threshold setting for current AnnotationColourGradient.");
+ throw new Error(MessageManager.getString("error.implementation_error_dont_know_about_thereshold_setting"));
}
thresholdIsMin.setSelected(acg.thresholdIsMinMax);
thresholdValue.setText("" + acg.getAnnotationThreshold());
public void minColour_actionPerformed()
{
Color col = JColorChooser.showDialog(this,
- "Select Colour for Minimum Value", minColour.getBackground());
+ MessageManager.getString("label.select_colour_minimum_value"), minColour.getBackground());
if (col != null)
{
minColour.setBackground(col);
public void maxColour_actionPerformed()
{
Color col = JColorChooser.showDialog(this,
- "Select Colour for Maximum Value", maxColour.getBackground());
+ MessageManager.getString("label.select_colour_maximum_value"), maxColour.getBackground());
if (col != null)
{
maxColour.setBackground(col);
this.ap = ap;
features = true;
CSVFormat.setVisible(false);
- frame.setTitle("Export Features");
+ frame.setTitle(MessageManager.getString("label.export_features"));
}
public void exportAnnotations(AlignmentPanel ap,
this.annotations = annotations;
this.sequenceGroups = list;
this.alignmentProperties = alProperties;
- frame.setTitle("Export Annotations");
+ frame.setTitle(MessageManager.getString("label.export_annotations"));
}
public void toFile_actionPerformed(ActionEvent e)
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(features ? "Save Features to File"
- : "Save Annotation to File");
+ chooser.setDialogTitle(features ? MessageManager.getString("label.save_features_to_file")
+ : MessageManager.getString("label.save_annotation_to_file"));
chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
if (value == JalviewFileChooser.APPROVE_OPTION)
{
- String text = "No features found on alignment";
+ String text = MessageManager.getString("label.no_features_on_alignment");
if (features)
{
if (GFFFormat.isSelected())
public void toTextbox_actionPerformed(ActionEvent e)
{
- String text = "No features found on alignment";
+ String text = MessageManager.getString("label.no_features_on_alignment");
if (features)
{
if (GFFFormat.isSelected())
public class AnnotationLabels extends JPanel implements MouseListener,
MouseMotionListener, ActionListener
{
- static String TOGGLE_LABELSCALE = "Scale Label to Column";
+ String TOGGLE_LABELSCALE = MessageManager.getString("label.scale_label_to_column");
- static String ADDNEW = "Add New Row";
+ String ADDNEW = MessageManager.getString("label.add_new_row");
- static String EDITNAME = "Edit Label/Description";
+ String EDITNAME = MessageManager.getString("label.edit_label_description");
- static String HIDE = "Hide This Row";
+ String HIDE = MessageManager.getString("label.hide_row");
- static String DELETE = "Delete This Row";
+ String DELETE = MessageManager.getString("label.delete_row");
- static String SHOWALL = "Show All Hidden Rows";
+ String SHOWALL = MessageManager.getString("label.show_all_hidden_rows");
- static String OUTPUT_TEXT = "Export Annotation";
+ String OUTPUT_TEXT = MessageManager.getString("label.export_annotation");
- static String COPYCONS_SEQ = "Copy Consensus Sequence";
+ String COPYCONS_SEQ = MessageManager.getString("label.copy_consensus_sequence");
boolean resizePanel = false;
MouseListener, MouseWheelListener, MouseMotionListener,
ActionListener, AdjustmentListener, Scrollable
{
- final String HELIX = "Helix";
+ String HELIX = MessageManager.getString("label.helix");
- final String SHEET = "Sheet";
+ String SHEET = MessageManager.getString("label.sheet");
/**
* For RNA secondary structure "stems" aka helices
*/
- final String STEM = "RNA Helix";
+ String STEM = MessageManager.getString("label.rna_helix");
- final String LABEL = "Label";
+ String LABEL = MessageManager.getString("label.label");
- final String REMOVE = "Remove Annotation";
+ String REMOVE = MessageManager.getString("label.remove_annotation");
- final String COLOUR = "Colour";
+ String COLOUR = MessageManager.getString("action.colour");
public final Color HELIX_COLOUR = Color.red.darker();
else if (evt.getActionCommand().equals(COLOUR))
{
Color col = JColorChooser.showDialog(this,
- "Choose foreground colour", Color.black);
+ MessageManager.getString("label.select_foreground_colour"), Color.black);
for (int i = 0; i < av.getColumnSelection().size(); i++)
{
&& aa[row].annotations[res].description != null
&& aa[row].annotations[res].description.length() > 0)
{
- this.setToolTipText("<html>"
- + JvSwingUtils
- .wrapTooltip(aa[row].annotations[res].description)
- + "</html>");
+ this.setToolTipText(JvSwingUtils
+ .wrapTooltip(true, aa[row].annotations[res].description));
}
else
{
_alignwith = new Vector<AlignmentPanel>();
}
- seqColourBy = new ViewSelectionMenu("Colour by ..", this, _colourwith,
+ seqColourBy = new ViewSelectionMenu(MessageManager.getString("label.colour_by"), this, _colourwith,
new ItemListener()
{
});
viewMenu.add(seqColourBy);
final ItemListener handler;
- JMenu alpanels = new ViewSelectionMenu("Superpose with ..", this,
+ JMenu alpanels = new ViewSelectionMenu(MessageManager.getString("label.superpose_with"), this,
_alignwith, handler = new ItemListener()
{
long hdl = pdbid.hashCode() - System.currentTimeMillis();
if (progressBar != null)
{
- progressBar.setProgressBar("Fetching PDB " + pdbid, hdl);
+ progressBar.setProgressBar(MessageManager.formatMessage("status.fetching_pdb", new String[]{pdbid}), hdl);
}
try
{
}
if (progressBar != null)
{
- progressBar.setProgressBar("Finished.", hdl);
+ progressBar.setProgressBar(MessageManager.getString("label.state_completed"), hdl);
}
if (pdbseq != null)
{
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Save PDB File");
+ chooser.setDialogTitle(MessageManager.getString("label.save_pdb_file"));
chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
public void backGround_actionPerformed(ActionEvent actionEvent)
{
java.awt.Color col = JColorChooser.showDialog(this,
- "Select Background Colour", null);
+ MessageManager.getString("label.select_backgroud_colour"), null);
if (col != null)
{
jmb.setBackgroundColour(col);
{
createDialog();
bounds = new Rectangle(5, 5, 550, 350);
- jd.initDialogFrame(me, false, false, "News from www.jalview.org",
+ jd.initDialogFrame(me, false, false, MessageManager.getString("label.news_from_jalview"),
bounds.width, bounds.height);
jd.frame.setModalExclusionType(ModalExclusionType.NO_EXCLUDE);
Cache.log.info("Displaying news.");
topBottomSplitPane.setBottomComponent(bottomPanel);
JScrollPane spTextDescription = new JScrollPane(textDescription);
textDescription.setText("");
- statusBar.setText(MessageManager.getString("label.status"));
+ statusBar.setText(new StringBuffer("[").append(MessageManager.getString("label.status")).append("]").toString());
buttonRefresh.addActionListener(new ActionListener()
{
_alignwith = new Vector<AlignmentPanel>();
}
- seqColourBy = new ViewSelectionMenu("Colour by ..", this, _colourwith,
+ seqColourBy = new ViewSelectionMenu(MessageManager.getString("label.colour_by"), this, _colourwith,
new ItemListener()
{
});
viewMenu.add(seqColourBy);
final ItemListener handler;
- JMenu alpanels = new ViewSelectionMenu("Superpose with ..", this,
+ JMenu alpanels = new ViewSelectionMenu(MessageManager.getString("label.superpose_with"), this,
_alignwith, handler = new ItemListener()
{
long hdl = pdbid.hashCode() - System.currentTimeMillis();
if (progressBar != null)
{
- progressBar.setProgressBar("Fetching PDB " + pdbid, hdl);
+ progressBar.setProgressBar(MessageManager.formatMessage("status.fetching_pdb", new String[]{pdbid}), hdl);
}
try
{
}
if (progressBar != null)
{
- progressBar.setProgressBar("Finished.", hdl);
+ progressBar.setProgressBar(MessageManager.getString("label.state_completed"), hdl);
}
if (pdbseq != null)
{
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Save PDB File");
+ chooser.setDialogTitle(MessageManager.getString("label.save_pdb_file"));
chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
*/
public void eps_actionPerformed(ActionEvent e)
{
- throw new Error("EPS Generation not yet implemented.");
+ throw new Error(MessageManager.getString("error.eps_generation_not_implemented"));
}
/**
*/
public void png_actionPerformed(ActionEvent e)
{
- throw new Error("PNG Generation not yet implemented.");
+ throw new Error(MessageManager.getString("error.png_generation_not_implemented"));
}
public void jmolColour_actionPerformed(ActionEvent actionEvent)
public void backGround_actionPerformed(ActionEvent actionEvent)
{
java.awt.Color col = JColorChooser.showDialog(this,
- "Select Background Colour", null);
+ MessageManager.getString("label.select_backgroud_colour"), null);
if (col != null)
{
jmb.setBackgroundColour(col);
} catch (InterruptedException ie)
{
}
- throw new NullPointerException(
- "Application test: throwing an NullPointerException It should arrive at the console");
+ throw new NullPointerException(MessageManager.getString("exception.application_test_npe"));
}
}
chooser.setAcceptAllFileFilterUsed(false);
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Save Text to File");
+ chooser.setDialogTitle(MessageManager.getString("label.save_text_to_file"));
chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
chooser.setAcceptAllFileFilterUsed(false);
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Save Text to File");
+ chooser.setDialogTitle(MessageManager.getString("label.save_text_to_file"));
chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
}
private String[] columnNames = new String[]
- { "Nickname", "Use Source" };
+ { MessageManager.getString("label.nickname"), MessageManager.getString("label.use_source") };
private Object[][] data;
public void run()
{
long instance = System.currentTimeMillis();
- Desktop.instance.setProgressBar("Refreshing news", instance);
+ Desktop.instance.setProgressBar(MessageManager.getString("status.refreshing_news"), instance);
jvnews.refreshNews();
Desktop.instance.setProgressBar(null, instance);
jvnews.showNews();
if (format.equals("URL NOT FOUND"))
{
JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "Couldn't locate " + url, "URL not found",
+ MessageManager.formatMessage("label.couldnt_locate", new String[]{url}), MessageManager.getString("label.url_not_found"),
JOptionPane.WARNING_MESSAGE);
return;
{
CutAndPasteTransfer cap = new CutAndPasteTransfer();
cap.setForInput(viewport);
- Desktop.addInternalFrame(cap, "Cut & Paste Alignment File", 600, 500);
+ Desktop.addInternalFrame(cap, MessageManager.getString("label.cut_paste_alignmen_file"), 600, 500);
}
/*
{ "Jalview Project" }, "Jalview Project");
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Save State");
+ chooser.setDialogTitle(MessageManager.getString("label.save_state"));
int value = chooser.showSaveDialog(this);
public void run()
{
- setProgressBar("Saving jalview project " + choice.getName(),
+ setProgressBar(MessageManager.formatMessage("label.saving_jalview_project", new String[]{choice.getName()}),
choice.hashCode());
jalview.bin.Cache.setProperty("LAST_DIRECTORY",
choice.getParent());
ex);
JOptionPane.showMessageDialog(
me,
- "Error whilst saving current state to "
- + choice.getName(), "Couldn't save project",
+ MessageManager.formatMessage("label.error_whilst_saving_current_state_to", new String[]{ choice.getName()}),
+ MessageManager.getString("label.couldnt_save_project"),
JOptionPane.WARNING_MESSAGE);
}
setProgressBar(null, choice.hashCode());
{ "Jalview Project", "Jalview Project (old)" },
"Jalview Project");
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Restore state");
+ chooser.setDialogTitle(MessageManager.getString("label.restore_state"));
int value = chooser.showOpenDialog(this);
{
public void run()
{
- setProgressBar("loading jalview project " + choice,
+ setProgressBar(MessageManager.formatMessage("label.loading_jalview_project", new String[]{choice}),
choice.hashCode());
try
{
Cache.log.error("Problems whilst loading project from "
+ choice, ex);
JOptionPane.showMessageDialog(Desktop.desktop,
- "Error whilst loading project from " + choice,
- "Couldn't load project", JOptionPane.WARNING_MESSAGE);
+ MessageManager.formatMessage("label.error_whilst_loading_project_from", new String[]{choice}),
+ MessageManager.getString("label.couldnt_load_project"), JOptionPane.WARNING_MESSAGE);
}
setProgressBar(null, choice.hashCode());
}
{
if (fileLoadingCount == 0)
{
- fileLoadingPanels.add(addProgressPanel("Loading File: " + fileName
- + " "));
+ fileLoadingPanels.add(addProgressPanel(MessageManager.formatMessage("label.loading_file", new String[]{fileName})));
}
fileLoadingCount++;
}
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Open a saved VAMSAS session");
+ chooser.setDialogTitle(MessageManager.getString("label.open_saved_vamsas_session"));
chooser.setToolTipText(MessageManager
.getString("label.select_vamsas_session_opened_as_new_vamsas_session"));
return false;
}
- setProgressBar("Importing VAMSAS session from " + file.getName(),
+ setProgressBar(MessageManager.formatMessage("status.importing_vamsas_session_from", new String[]{file.getName()}),
file.hashCode());
try
{
v_client = new jalview.gui.VamsasApplication(this, file, null);
} catch (Exception ex)
{
- setProgressBar("Importing VAMSAS session from " + file.getName(),
- file.hashCode());
+ setProgressBar(MessageManager.formatMessage("status.importing_vamsas_session_from", new String[]{file.getName()}),
+ file.hashCode());
jalview.bin.Cache.log.error(
"New vamsas session from existing session file failed:", ex);
return false;
}
setupVamsasConnectedGui();
v_client.initial_update(); // TODO: thread ?
- setProgressBar("Importing VAMSAS session from " + file.getName(),
+ setProgressBar(MessageManager.formatMessage("status.importing_vamsas_session_from", new String[]{file.getName()}),
file.hashCode());
return v_client.inSession();
}
{
if (v_client != null)
{
- throw new Error(
- "Trying to join a vamsas session when another is already connected.");
+ throw new Error(MessageManager.getString("error.try_join_vamsas_session_another"));
}
if (mysesid == null)
{
- throw new Error("Invalid vamsas session id.");
+ throw new Error(MessageManager.getString("error.invalid_vamsas_session_id"));
}
v_client = new VamsasApplication(this, mysesid);
setupVamsasConnectedGui();
{ "Vamsas Document" }, "Vamsas Document");
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Save Vamsas Document Archive");
+ chooser.setDialogTitle(MessageManager.getString("label.save_vamsas_document_archive"));
int value = chooser.showSaveDialog(this);
if (value == JalviewFileChooser.APPROVE_OPTION)
{
java.io.File choice = chooser.getSelectedFile();
- JPanel progpanel = addProgressPanel("Saving VAMSAS Document to "
- + choice.getName());
+ JPanel progpanel = addProgressPanel(MessageManager.formatMessage("label.saving_vamsas_doc", new String[]{choice.getName()}));
jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
String warnmsg = null;
String warnttl = null;
}
if (b)
{
- vamUpdate = this.addProgressPanel("Updating vamsas session");
+ vamUpdate = this.addProgressPanel(MessageManager.getString("label.updating_vamsas_session"));
}
vamsasStart.setVisible(!b);
vamsasStop.setVisible(!b);
// use reflection to avoid creating compilation dependency.
if (!jalview.bin.Cache.groovyJarsPresent())
{
- throw new Error(
- "Implementation Error. Cannot create groovyShell without Groovy on the classpath!");
+ throw new Error(MessageManager.getString("error.implementation_error_cannot_create_groovyshell"));
}
try
{
.showInternalMessageDialog(
Desktop.desktop,
- "Couldn't create the groovy Shell. Check the error log for the details of what went wrong.",
- "Jalview Groovy Support Failed",
+ MessageManager.getString("label.couldnt_create_groovy_shell"),
+ MessageManager.getString("label.groovy_support_failed"),
JOptionPane.ERROR_MESSAGE);
}
}
{
if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
{
- throw new Error(
- "call setProgressBar before registering the progress bar's handler.");
+ throw new Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
}
progressBarHandlers.put(new Long(id), handler);
final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
public void actionPerformed(ActionEvent e)
{
handler.cancelActivity(id);
- us.setProgressBar(
- "Cancelled "
- + ((JLabel) progressPanel.getComponent(0))
- .getText(), id);
+ us.setProgressBar(MessageManager.formatMessage("label.cancelled_params", new String[]{((JLabel) progressPanel.getComponent(0)).getText()}), id);
}
});
progressPanel.add(cancel, BorderLayout.EAST);
{
if (progress != null)
{
- progress.setProgressBar("Opening " + url, this.hashCode());
+ progress.setProgressBar(MessageManager.formatMessage("status.opening_params", new String[]{url}), this.hashCode());
}
jalview.util.BrowserLauncher.openURL(url);
} catch (Exception ex)
JOptionPane
.showInternalMessageDialog(
Desktop.desktop,
- "Unixers: Couldn't find default web browser."
- + "\nAdd the full path to your browser in Preferences.",
- "Web browser not found",
+ MessageManager.getString("label.web_browser_not_found_unix"),
+ MessageManager.getString("label.web_browser_not_found"),
JOptionPane.WARNING_MESSAGE);
ex.printStackTrace();
return ((GraduatedColor) fc).getMaxColor();
}
}
- throw new Error("Implementation Error: Unrecognised render object "
- + fc.getClass() + " for features of type " + featureType);
+ throw new Error(MessageManager.formatMessage("error.implementation_error_unrecognised_render_object_for_features_type", new String[]{fc.getClass().toString(),featureType}));
}
/**
return ((GraduatedColor) fc).findColor(feature);
}
}
- throw new Error("Implementation Error: Unrecognised render object "
- + fc.getClass() + " for features of type " + feature.getType());
+ throw new Error(MessageManager.formatMessage("error.implementation_error_unrecognised_render_object_for_features_type", new String[]{fc.getClass().toString(),feature.getType()}));
}
private boolean showFeature(SequenceFeature sequenceFeature)
if (fcol instanceof Color)
{
Color col = JColorChooser.showDialog(Desktop.desktop,
- "Select Feature Colour", ((Color) fcol));
+ MessageManager.getString("label.select_feature_colour"), ((Color) fcol));
if (col != null)
{
fcol = col;
{ "OK", "Cancel" };
}
- String title = newFeatures ? "Create New Sequence Feature(s)"
- : "Amend/Delete Features for " + sequences[0].getName();
+ String title = newFeatures ? MessageManager.getString("label.create_new_sequence_features")
+ : MessageManager.formatMessage("label.amend_delete_features", new String[]{sequences[0].getName()});
int reply = JOptionPane.showInternalOptionDialog(Desktop.desktop,
bigPanel, title, JOptionPane.YES_NO_CANCEL_OPTION,
- JOptionPane.QUESTION_MESSAGE, null, options, "OK");
+ JOptionPane.QUESTION_MESSAGE, null, options, MessageManager.getString("action.ok"));
jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
}
}
});
- table.setToolTipText("<html>"
- + JvSwingUtils
- .wrapTooltip("Click/drag feature types up or down to change render order.<br/>Double click to select columns containing feature in alignment/current selection<br/>Pressing Alt will select columns outside features rather than inside<br/>Pressing Shift to modify current selection (rather than clear current selection)<br/>Press CTRL or Command/Meta to toggle columns in/outside features<br/>")
- + "</html>");
+ table.setToolTipText(JvSwingUtils
+ .wrapTooltip(true, MessageManager.getString("label.feature_settings_click_drag")));
scrollPane.setViewportView(table);
dassourceBrowser = new DasSourceBrowser(this);
{ "fc" }, new String[]
{ "Sequence Feature Colours" }, "Sequence Feature Colours");
chooser.setFileView(new jalview.io.JalviewFileView());
- chooser.setDialogTitle("Load Feature Colours");
+ chooser.setDialogTitle(MessageManager.getString("label.load_feature_colours"));
chooser.setToolTipText(MessageManager.getString("action.load"));
int value = chooser.showOpenDialog(this);
{ "fc" }, new String[]
{ "Sequence Feature Colours" }, "Sequence Feature Colours");
chooser.setFileView(new jalview.io.JalviewFileView());
- chooser.setDialogTitle("Save Feature Colour Scheme");
+ chooser.setDialogTitle(MessageManager.getString("label.save_feature_colours"));
chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
}
});
this.add(tabbedPane, java.awt.BorderLayout.CENTER);
- tabbedPane.addTab("Feature Settings", settingsPane);
- tabbedPane.addTab("DAS Settings", dasSettingsPane);
+ tabbedPane.addTab(MessageManager.getString("label.feature_settings"), settingsPane);
+ tabbedPane.addTab(MessageManager.getString("label.das_settings"), dasSettingsPane);
bigPanel.add(transPanel, java.awt.BorderLayout.SOUTH);
transbuttons.add(optimizeOrder);
transbuttons.add(invert);
}
private String[] columnNames =
- { "Feature Type", "Colour", "Display" };
+ { MessageManager.getString("label.feature_type"), MessageManager.getString("action.colour"), MessageManager.getString("label.display") };
private Object[][] data;
JOptionPane
.showInternalMessageDialog(
this,
- "Font doesn't have letters defined\nso cannot be used\nwith alignment data.",
- "Invalid Font", JOptionPane.WARNING_MESSAGE);
+ MessageManager.getString("label.font_doesnt_have_letters_defined"),
+ MessageManager.getString("label.invalid_font"), JOptionPane.WARNING_MESSAGE);
return;
}
if (tp != null)
import jalview.datamodel.*;
import jalview.io.SequenceAnnotationReport;
+import jalview.util.MessageManager;
import jalview.util.UrlLink;
/**
JOptionPane
.showInternalMessageDialog(
Desktop.desktop,
- "Unixers: Couldn't find default web browser."
- + "\nAdd the full path to your browser in Preferences.",
- "Web browser not found", JOptionPane.WARNING_MESSAGE);
+ MessageManager.getString("label.web_browser_not_found_unix"),
+ MessageManager.getString("label.web_browser_not_found"), JOptionPane.WARNING_MESSAGE);
ex.printStackTrace();
}
public JDatabaseTree(jalview.ws.SequenceFetcher sfetch)
{
- initDialogFrame(this, true, false, "Select Database Retrieval Source",
+ initDialogFrame(this, true, false, MessageManager.getString("label.select_database_retrieval_source"),
650, 490);
/*
* Dynamically generated database list will need a translation function from
}
else
{
- throw new Error(
- "Implementation Error: Can't reorder this tree. Not DefaultMutableTreeNode.");
+ throw new Error(MessageManager.getString("error.implementation_error_cant_reorder_tree"));
}
}
jalview.util.QuickSort.sort(names, nodes);
import jalview.datamodel.SequenceI;
import jalview.schemabinding.version2.*;
import jalview.schemes.*;
+import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.util.jarInputStreamProvider;
import jalview.viewmodel.AlignmentViewport;
for (String dssids : dsses.keySet())
{
AlignFrame _af = dsses.get(dssids);
- String jfileName = fileName + " Dataset for " + _af.getTitle();
+ String jfileName = MessageManager.formatMessage("label.dataset_for", new String[]{fileName,_af.getTitle()});
if (!jfileName.endsWith(".xml"))
{
jfileName = jfileName + ".xml";
return false;
}
}
- throw new Error("Unsupported Version for calcIdparam "
- + calcIdParam.toString());
+ throw new Error(MessageManager.formatMessage("error.unsupported_version_calcIdparam", new String[]{calcIdParam.toString()}));
}
/**
{
JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "Error loading " + file, "Error loading Jalview file",
+ MessageManager.formatMessage("label.error_loading_file_params", new String[]{file}), MessageManager.getString("label.error_loading_jalview_file"),
JOptionPane.WARNING_MESSAGE);
}
});
* <table width=350>
* <tr>
* <td></td> field
+ * @param enclose TODO
+ * @param ttext
*
- * @param ttext
* @return
*/
- public static String wrapTooltip(String ttext)
+ public static String wrapTooltip(boolean enclose, String ttext)
{
+
if (ttext.length() < 60)
{
- return ttext;
+ return enclose ? "<html>"+ttext+"</html>" : ttext;
}
else
{
- return "<table width=350 border=0><tr><td>" + ttext
- + "</td></tr></table>";
+ return (enclose ? "<html>" : "") + "<table width=350 border=0><tr><td>" + ttext
+ + "</td></tr></table>" + ((enclose ? "</html>" : ""));
}
}
*/
package jalview.gui;
+import jalview.util.MessageManager;
+
import java.awt.Component;
public class OOMWarning implements Runnable
javax.swing.JOptionPane
.showInternalMessageDialog(
desktop,
- "Out of memory when "
- + action
- + "!!"
- + "\nSee help files for increasing Java Virtual Machine memory.",
- "Out of memory",
+ MessageManager.formatMessage("warn.out_of_memory_when_action", new String[]{action}),
+ MessageManager.getString("label.out_of_memory"),
javax.swing.JOptionPane.WARNING_MESSAGE);
// hope that there's enough memory left that no more appear.
oomInprogress = false;
{
hasLink = true;
- enabled.setToolTipText("<html>"
- + JvSwingUtils
- .wrapTooltip(((desc == null || desc.trim().length() == 0) ? "see further details by right-clicking"
+ enabled.setToolTipText(
+ JvSwingUtils
+ .wrapTooltip(true, ((desc == null || desc.trim().length() == 0) ? MessageManager.getString("label.opt_and_params_further_details ")
: desc)
+ "<br><img src=\"" + linkImageURL + "\"/>")
- + "</html>");
+ );
enabled.addMouseListener(this);
}
else
{
if (desc != null && desc.trim().length() > 0)
{
- enabled.setToolTipText("<html>"
- + JvSwingUtils.wrapTooltip(opt.getDescription())
- + "</html>");
+ enabled.setToolTipText(
+ JvSwingUtils.wrapTooltip(true, opt.getDescription())
+ );
}
}
add(enabled, BorderLayout.NORTH);
&& parm.getDescription().trim().length() > 0)
{
// Only create description boxes if there actually is a description.
- ttipText = ("<html>"
- + JvSwingUtils
- .wrapTooltip(parm.getDescription()
+ ttipText = (JvSwingUtils
+ .wrapTooltip(true, parm.getDescription()
+ (finfo != null ? "<br><img src=\""
+ linkImageURL
- + "\"/> Right click for further information."
- : "")) + "</html>");
+ + "\"/>"+MessageManager.getString("label.opt_and_params_further_detail")
+ : "")));
}
JvSwingUtils.mgAddtoLayout(this, ttipText,
// Only create description boxes if there actually is a description.
if (finfo != null)
{
- showDesc.setToolTipText("<html>"
- + JvSwingUtils
- .wrapTooltip("Click to show brief description<br><img src=\""
- + linkImageURL
- + "\"/> Right click for further information.")
- + "</html>");
+ showDesc.setToolTipText(JvSwingUtils.wrapTooltip(false, MessageManager.formatMessage("label.opt_and_params_show_brief_desc_image_link", new String[]{linkImageURL.toExternalForm()})));
showDesc.addMouseListener(this);
}
else
{
- showDesc.setToolTipText("<html>"
- + JvSwingUtils
- .wrapTooltip("Click to show brief description.")
- + "</html>");
+ showDesc.setToolTipText(JvSwingUtils.wrapTooltip(false, MessageManager.getString("label.opt_and_params_show_brief_desc")));
}
showDesc.addActionListener(new ActionListener()
{
}
else
{
- throw new Error("Invalid value " + string + " for option " + option);
+ throw new Error(MessageManager.formatMessage("error.invalid_value_for_option", new String[]{string,option.getName()}));
}
}
JOptionPane
.showMessageDialog(
Desktop.desktop,
- "The sequences must be aligned before calculating PCA.\n"
- + "Try using the Pad function in the edit menu,\n"
- + "or one of the multiple sequence alignment web services.",
- "Sequences not aligned", JOptionPane.WARNING_MESSAGE);
+ MessageManager.getString("label.pca_sequences_not_aligned"),
+ MessageManager.getString("label.sequences_not_aligned"), JOptionPane.WARNING_MESSAGE);
return;
}
public void bgcolour_actionPerformed(ActionEvent e)
{
- Color col = JColorChooser.showDialog(this, "Select Background Colour",
+ Color col = JColorChooser.showDialog(this, MessageManager.getString("label.select_backgroud_colour"),
rc.bgColour);
if (col != null)
{
long progId = System.currentTimeMillis();
IProgressIndicator progress = this;
- String message = "Recalculating PCA";
+ String message = MessageManager.getString("label.pca_recalculating");
if (getParent() == null)
{
progress = ap.alignFrame;
- message = "Calculating PCA";
+ message = MessageManager.getString("label.pca_calculating");
}
progress.setProgressBar(message, progId);
try
{
if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
{
- throw new Error(
- "call setProgressBar before registering the progress bar's handler.");
+ throw new Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
}
progressBarHandlers.put(new Long(id), handler);
final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
public void actionPerformed(ActionEvent e)
{
handler.cancelActivity(id);
- us.setProgressBar(
- "Cancelled "
- + ((JLabel) progressPanel.getComponent(0))
- .getText(), id);
+ us.setProgressBar(MessageManager.formatMessage("label.cancelled_params", new String[]{((JLabel) progressPanel.getComponent(0)).getText()}), id);
}
});
progressPanel.add(cancel, BorderLayout.EAST);
sortby.addItem("Pairwise Identity");
sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
- epsRendering.addItem("Prompt each time");
- epsRendering.addItem("Lineart");
- epsRendering.addItem("Text");
- epsRendering.setSelectedItem(Cache.getDefault("EPS_RENDERING",
- "Prompt each time"));
+ epsRendering.addItem(MessageManager.getString("label.prompt_each_time"));
+ epsRendering.addItem(MessageManager.getString("label.lineart"));
+ epsRendering.addItem(MessageManager.getString("action.text"));
+ epsRendering.setSelectedIndex(0);
autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
userIdWidth.setEnabled(autoIdWidth.isSelected());
userIdWidthlabel.setEnabled(autoIdWidth.isSelected());
{ "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" },
jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Select startup file");
+ chooser.setDialogTitle(MessageManager.getString("label.select_startup_file"));
int value = chooser.showOpenDialog(this);
public void defaultBrowser_mouseClicked(MouseEvent e)
{
JFileChooser chooser = new JFileChooser(".");
- chooser.setDialogTitle("Select default web browser");
+ chooser.setDialogTitle(MessageManager.getString("label.select_default_browser"));
int value = chooser.showOpenDialog(this);
public void minColour_actionPerformed()
{
Color col = JColorChooser.showDialog(this,
- "Select Colour for Minimum Value", minColour.getBackground());
+ MessageManager.getString("label.select_colour_minimum_value"), minColour.getBackground());
if (col != null)
{
minColour.setBackground(col);
public void maxColour_actionPerformed()
{
Color col = JColorChooser.showDialog(this,
- "Select Colour for Maximum Value", maxColour.getBackground());
+ MessageManager.getString("label.select_colour_maximum_value"), maxColour.getBackground());
if (col != null)
{
maxColour.setBackground(col);
JOptionPane
.showInternalMessageDialog(
Desktop.desktop,
- "The user defined width for the\nannotation and sequence ID columns\nin exported figures must be\nat least 12 pixels wide.",
- "Invalid ID Column width",
+ MessageManager.getString("warn.user_defined_width_requirements"),
+ MessageManager.getString("label.invalid_id_column_width"),
JOptionPane.WARNING_MESSAGE);
userIdWidth.setText("");
}
progress.setVisible(false);
progress = null;
- label.setText("Enter the redundancy threshold");
+ label.setText(MessageManager.getString("label.enter_redundancy_thereshold"));
slider.setVisible(true);
applyButton.setEnabled(true);
valueField.setVisible(true);
}
}
- EditCommand cut = new EditCommand("Remove Redundancy",
+ EditCommand cut = new EditCommand(MessageManager.getString("action.remove_redundancy"),
EditCommand.CUT, deleted, 0, width, ap.av.getAlignment());
for (int i = 0; i < del.size(); i++)
message.append("Edit group:");
if (editCommand == null)
{
- editCommand = new EditCommand("Edit Group");
+ editCommand = new EditCommand(MessageManager.getString("action.edit_group"));
}
}
else
}
if (editCommand == null)
{
- editCommand = new EditCommand("Edit " + label);
+ editCommand = new EditCommand(MessageManager.formatMessage("label.edit_params", new String[]{label}));
}
}
if (guiWindow != null)
{
guiWindow.setProgressBar(
- "Waiting for Sequence Database Fetchers to initialise",
+ MessageManager.getString("status.waiting_sequence_database_fetchers_init"),
Thread.currentThread().hashCode());
}
// initting happening on another thread - so wait around to see if it
if (guiWindow != null)
{
guiWindow.setProgressBar(
- "Waiting for Sequence Database Fetchers to initialise",
+ MessageManager.getString("status.waiting_sequence_database_fetchers_init"),
Thread.currentThread().hashCode());
}
}
*/
if (guiWindow != null)
{
- guiWindow.setProgressBar("Initialising Sequence Database Fetchers",
+ guiWindow.setProgressBar(MessageManager.getString("status.init_sequence_database_fetchers"),
Thread.currentThread().hashCode());
}
dasRegistry = jalview.bin.Cache.getDasSourceRegistry();
jalview.ws.SequenceFetcher sf = new jalview.ws.SequenceFetcher();
if (guiWindow != null)
{
- guiWindow.setProgressBar("Initialising Sequence Database Fetchers",
+ guiWindow.setProgressBar(MessageManager.getString("status.init_sequence_database_fetchers"),
Thread.currentThread().hashCode());
}
lastDasSourceRegistry = (dasRegistry.getDasRegistryURL() + dasRegistry
JOptionPane
.showInternalMessageDialog(
Desktop.desktop,
- "Could not create the sequence fetcher client. Check error logs for details.",
- "Couldn't create SequenceFetcher",
+ MessageManager.getString("warn.couldnt_create_sequence_fetcher_client"),
+ MessageManager.getString("label.couldnt_create_sequence_fetcher"),
JOptionPane.ERROR_MESSAGE);
}
});
private String getFrameTitle()
{
- return ((alignFrame == null) ? "New " : "Additional ")
- + "Sequence Fetcher";
+ return ((alignFrame == null) ? MessageManager.getString("label.new_sequence_fetcher") : MessageManager.getString("label.additional_sequence_fetcher"));
}
private void jbInit() throws Exception
try
{
// update status
- guiWindow.setProgressBar("Fetching " + nqueries
- + " sequence queries from " + proxy.getDbName(), Thread
+ guiWindow.setProgressBar(MessageManager.formatMessage("status.fetching_sequence_queries_from", new String[]{Integer.valueOf(nqueries).toString(),proxy.getDbName()}), Thread
.currentThread().hashCode());
isAliSource = proxy.isA(DBRefSource.ALIGNMENTDB);
if (proxy.getAccessionSeparator() == null)
presultTitle.add(titl);
}
}
- guiWindow.setProgressBar("Finished querying", Thread.currentThread()
+ guiWindow.setProgressBar(MessageManager.getString("status.finshed_querying"), Thread.currentThread()
.hashCode());
}
- guiWindow.setProgressBar((presult.size() > 0) ? "Parsing results."
- : "Processing ..", Thread.currentThread().hashCode());
+ guiWindow.setProgressBar((presult.size() > 0) ? MessageManager.getString("status.parsing_results")
+ : MessageManager.getString("status.processing"), Thread.currentThread().hashCode());
// process results
while (presult.size() > 0)
{
sp.cs = cs;
}
- conservationSlider.setTitle("Conservation Colour Increment (" + source
- + ")");
+ conservationSlider.setTitle(MessageManager.formatMessage("label.conservation_colour_increment", new String[]{source}));
if (ap.av.getAlignment().getGroups() != null)
{
pid.cs = cs;
}
- PIDSlider.setTitle("Percentage Identity Threshold (" + source + ")");
+ PIDSlider.setTitle(MessageManager.formatMessage("label.percentage_identity_thereshold", new String[]{source}));
if (ap.av.getAlignment().getGroups() != null)
{
JPanel panel = new JPanel();
bigpanel.add(panel, BorderLayout.CENTER);
bigpanel.add(
- new JLabel(
- "<html><i>Select a dark and light text colour, then set the threshold to"
- + "<br>switch between colours, based on background colour</i></html>"),
+ new JLabel(MessageManager.getString("label.select_dark_light_set_thereshold")),
BorderLayout.NORTH);
panel.add(col1);
panel.add(slider);
public void mousePressed(MouseEvent e)
{
Color col = JColorChooser.showDialog(bigpanel,
- "Select Colour for Text", col1.getBackground());
+ MessageManager.getString("label.select_colour_for_text"), col1.getBackground());
if (col != null)
{
colour1Changed(col);
public void mousePressed(MouseEvent e)
{
Color col = JColorChooser.showDialog(bigpanel,
- "Select Colour for Text", col2.getBackground());
+ MessageManager.getString("label.select_colour_for_text"), col2.getBackground());
if (col != null)
{
colour2Changed(col);
});
int reply = JOptionPane.showInternalOptionDialog(ap, bigpanel,
- "Adjust Foreground Text Colour Threshold",
+ MessageManager.getString("label.adjunst_foreground_text_colour_thereshold"),
JOptionPane.OK_CANCEL_OPTION, JOptionPane.QUESTION_MESSAGE,
null, null, null);
if (SwingUtilities.isRightMouseButton(evt))
{
Color col = JColorChooser.showDialog(this,
- "Select Sub-Tree Colour", highlightNode.color);
+ MessageManager.getString("label.select_subtree_colour"), highlightNode.color);
if (col != null)
{
setColor(highlightNode, col);
JalviewFileChooser chooser = new JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Save tree as newick file");
+ chooser.setDialogTitle(MessageManager.getString("label.save_tree_as_newick"));
chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(null);
{ "eps" }, new String[]
{ "Encapsulated Postscript" }, "Encapsulated Postscript");
chooser.setFileView(new jalview.io.JalviewFileView());
- chooser.setDialogTitle("Create EPS file from tree");
+ chooser.setDialogTitle(MessageManager.getString("label.create_eps_from_tree"));
chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
{ "Portable network graphics" }, "Portable network graphics");
chooser.setFileView(new jalview.io.JalviewFileView());
- chooser.setDialogTitle("Create PNG image from tree");
+ chooser.setDialogTitle(MessageManager.getString("label.create_png_from_tree"));
chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
{ "Jalview User Colours" }, "Jalview User Colours");
chooser.setFileView(new jalview.io.JalviewFileView());
- chooser.setDialogTitle("Save colour scheme");
+ chooser.setDialogTitle(MessageManager.getString("label.save_colour_scheme"));
chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
import jalview.structure.StructureSelectionManager;
import jalview.structure.VamsasListener;
import jalview.structure.VamsasSource;
+import jalview.util.MessageManager;
import java.beans.PropertyChangeEvent;
import java.beans.PropertyChangeListener;
{
if (sess != null)
{
- throw new Error(
- "Implementation Error - cannot import existing vamsas document into an existing session, Yet!");
+ throw new Error(MessageManager.getString("error.implementation_error_cannot_import_vamsas_doc"));
}
try
{
.showInternalMessageDialog(
Desktop.desktop,
- "VAMSAS Document could not be opened as a new session - please choose another",
- "VAMSAS Document Import Failed",
+ MessageManager.getString("label.vamsas_doc_couldnt_be_opened_as_new_session"),
+ MessageManager.getString("label.vamsas_document_import_failed"),
JOptionPane.ERROR_MESSAGE);
}
{
if (!inSession())
{
- throw new Error(
- "Impementation error! Vamsas Operations when client not initialised and connected.");
+ throw new Error(MessageManager.getString("error.implementation_error_vamsas_operation_not_init"));
}
addDocumentUpdateHandler();
addStoreDocumentHandler();
public void end_session(boolean promptUser)
{
if (!inSession())
- throw new Error("Jalview not connected to Vamsas session.");
+ throw new Error(MessageManager.getString("error.jalview_no_connected_vamsas_session"));
Cache.log.info("Jalview disconnecting from the Vamsas Session.");
try
{
return;
}
- throw new Error(
- "IMPLEMENTATION ERROR: Cannot recover vamsas object mappings - no backup was made.");
+ throw new Error(MessageManager.getString("error.implementation_error_cannot_recover_vamsas_object_mappings"));
}
jv2vobj.clear();
Iterator el = _backup_jv2vobj.entrySet().iterator();
{
if (jobpane < 0 || jobpane >= jobPanes.size())
{
- throw new Error("setStatus called for non-existent job pane."
- + jobpane);
+ throw new Error(MessageManager.formatMessage("error.setstatus_called_non_existent_job_pane", new String[]{Integer.valueOf(jobpane).toString()}));
}
switch (status)
{
// anyhow - it has to stop threads and clean up
// JBPNote : TODO: Instead of a warning, we should have an optional 'Are
// you sure?' prompt
- warnUser("This job cannot be cancelled.\nJust close the window.",
- "Cancel job");
+ warnUser(MessageManager.getString("warn.job_cannot_be_cancelled_close_window"),
+ MessageManager.getString("action.cancel_job"));
}
else
{
{
if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
{
- throw new Error(
- "call setProgressBar before registering the progress bar's handler.");
+ throw new Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
}
progressBarHandlers.put(new Long(id), handler);
final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
public void actionPerformed(ActionEvent e)
{
handler.cancelActivity(id);
- us.setProgressBar(
- "Cancelled "
- + ((JLabel) progressPanel.getComponent(0))
- .getText(), id);
+ us.setProgressBar(MessageManager.formatMessage("label.cancelled_params", new String[]{((JLabel) progressPanel.getComponent(0)).getText()}), id);
}
});
progressPanel.add(cancel, BorderLayout.EAST);
frame = new JDialog(Desktop.instance, true);
- frame.setTitle("Edit parameters for " + service.getActionText());
+ frame.setTitle(MessageManager.formatMessage("label.edit_params_for", new String[]{service.getActionText()}));
Rectangle deskr = Desktop.instance.getBounds();
Dimension pref = this.getPreferredSize();
frame.setBounds(new Rectangle(
}
WsJobParameters pgui = new WsJobParameters(lastserv,
new JabaPreset(lastserv, pr));
- JFrame jf = new JFrame("Parameters for "
- + lastserv.getActionText());
+ JFrame jf = new JFrame(MessageManager.formatMessage("label.ws_parameters_for", new String[]{lastserv.getActionText()}));
JPanel cont = new JPanel(new BorderLayout());
pgui.validate();
cont.setPreferredSize(pgui.getPreferredSize());
public void run()
{
JOptionPane.showMessageDialog(ourframe,
- "Invalid name - preset already exists.",
- "Invalid name", JOptionPane.WARNING_MESSAGE);
+ MessageManager.getString("label.invalid_name_preset_exists"),
+ MessageManager.getString("label.invalid_name"), JOptionPane.WARNING_MESSAGE);
}
});
}
if (parser == null)
{
- throw new Error(
- "Implementation error: Can't find a marshaller for the parameter set");
+ throw new Error(MessageManager.getString("error.implementation_error_cannot_find_marshaller_for_param_set"));
}
if (filename == null)
{
{ "Web Service Parameter File" },
"Web Service Parameter File");
chooser.setFileView(new jalview.io.JalviewFileView());
- chooser.setDialogTitle("Choose a filename for this parameter file");
+ chooser.setDialogTitle(MessageManager.getString("label.choose_filename_for_param_file"));
chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(Desktop.instance);
if (value == JalviewFileChooser.APPROVE_OPTION)
}
wsList.setModel(new WsUrlTableModel(tdat));
- wsList.getColumn("Status").setMinWidth(10);
+ wsList.getColumn(MessageManager.getString("label.status")).setMinWidth(10);
}
private class JabaWSStatusRenderer extends JPanel implements
{
private Object[][] data;
+ private String[] columnNames = new String[]
+ { MessageManager.getString("label.service_url"), MessageManager.getString("label.status") };
public WsUrlTableModel(Object[][] tdat)
{
@Override
public String getColumnName(int column)
{
- if (column == 1)
- {
- return "Status";
- }
- return "Service URL";
+ return columnNames[column];
}
@Override
int sel = wsList.getSelectedRow();
if (sel > -1)
{
- String url = editUrl(wsUrls.elementAt(sel), "Edit JABAWS URL");
+ String url = editUrl(wsUrls.elementAt(sel), MessageManager.getString("label.edit_jabaws_url"));
if (url != null)
{
int present = wsUrls.indexOf(url);
protected void newSbrsUrl_actionPerformed(ActionEvent e)
{
RestServiceEditorPane rse = new RestServiceEditorPane();
- rse.showDialog("Add a new Simple Bioinformatics Rest Service");
+ rse.showDialog(MessageManager.getString("label.add_new_sbrs_service"));
String rservice = rse.getEditedRestService();
if (rservice != null && !rsbsUrls.contains(rservice))
{
{
RestServiceEditorPane rse = new RestServiceEditorPane(
new RestServiceDescription(rsbsUrls.elementAt(sel)));
- rse.showDialog("Edit Simple Bioinformatics Rest Service entry");
+ rse.showDialog(MessageManager.getString("label.edit_sbrs_entry"));
String rservice = rse.getEditedRestService();
if (rservice != null)
{
int validate = JOptionPane
.showInternalConfirmDialog(
Desktop.desktop,
- "Validate JabaWS Server ?\n(Look in console output for results)",
- "Test Server?", JOptionPane.YES_NO_OPTION);
+ MessageManager.getString("info.validate_jabaws_server"),
+ MessageManager.getString("label.test_server"), JOptionPane.YES_NO_OPTION);
if (validate == JOptionPane.OK_OPTION)
{
if (jalview.ws.jws2.Jws2Discoverer.testServiceUrl(foo))
JOptionPane
.showInternalMessageDialog(
Desktop.desktop,
- "Service did not pass validation.\nCheck the Jalview Console for more details.");
+ MessageManager.getString("warn.server_didnt_pass_validation"));
}
}
else
@Override
protected void newWsUrl_actionPerformed(ActionEvent e)
{
- String url = editUrl(null, "Add new JABAWS URL");
+ String url = editUrl(null, MessageManager.getString("label.add_jabaws_url"));
if (url != null)
{
if (!wsUrls.contains(url))
public void run()
{
long ct = System.currentTimeMillis();
- Desktop.instance.setProgressBar("Refreshing Web Service Menus",
+ Desktop.instance.setProgressBar(MessageManager.getString("status.refreshing_web_service_menus"),
ct);
if (lastrefresh != update)
{
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
import java.io.IOException;
import java.util.Enumeration;
{
if (key == null)
{
- throw new Error(
- "Implementation error: Cannot have null alignment property key.");
+ throw new Error(MessageManager.getString("error.implementation_error_cannot_have_null_alignment"));
}
if (value == null)
{
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
+import jalview.util.MessageManager;
import java.io.File;
import java.io.InputStream;
else
{
- throw new Exception(
- "Implementation error: Unknown file format string");
+ throw new Exception(MessageManager.getString("error.implementation_error_unknown_file_format_string"));
}
afile.setNewlineString(newline);
afile.addJVSuffix(jvsuffix);
javax.swing.JOptionPane
.showInternalMessageDialog(
Desktop.desktop,
- "Out of memory loading file "
- + file
- + "!!"
- + "\nSee help files for increasing Java Virtual Machine memory.",
- "Out of memory",
+ MessageManager.formatMessage("warn.out_of_memory_loading_file", new String[]{file}),
+ MessageManager.getString("label.out_of_memory"),
javax.swing.JOptionPane.WARNING_MESSAGE);
}
});
*/
package jalview.io;
+import jalview.util.MessageManager;
+
import java.io.*;
import java.net.*;
import java.util.zip.GZIPInputStream;
{
if (from == null)
{
- throw new Error(
- "Implementation error. Null FileParse in copy constructor");
+ throw new Error(MessageManager.getString("error.implementation_error_null_fileparse"));
}
if (from == this)
return;
{
if (e != null)
{
- throw new IOException("Failed to resolve GZIP stream", e);
+ throw new IOException(MessageManager.getString("exception.failed_to_resolve_gzip_stream"), e);
}
throw q;
}
{
if (checkFileSource(suffixLess))
{
- throw new IOException("Problem opening " + inFile
- + " (also tried " + suffixLess + ") : " + errormessage);
+ throw new IOException(MessageManager.formatMessage("exception.problem_opening_file_also_tried", new String[]{inFile.getName(),suffixLess,errormessage}));
}
}
else
{
- throw new IOException("Problem opening " + inFile + " : "
- + errormessage);
+ throw new IOException(MessageManager.formatMessage("exception.problem_opening_file", new String[]{inFile.getName(),errormessage}));
}
}
}
if (dataIn == null || error)
{
// pass up the reason why we have no source to read from
- throw new IOException("Failed to read data from source:\n"
- + errormessage);
+ throw new IOException(MessageManager.formatMessage("exception.failed_to_read_data_from_source", new String[]{errormessage}));
}
error = false;
dataIn.mark(READAHEAD_LIMIT);
}
else
{
- throw new IOException("Unitialised Source Stream");
+ throw new IOException(MessageManager.getString("exception.no_init_source_stream"));
}
}
{
if (!error)
return dataIn.readLine();
- throw new IOException("Invalid Source Stream:" + errormessage);
+ throw new IOException(MessageManager.formatMessage("exception.invalid_source_stream", new String[]{errormessage}));
}
public boolean isValid()
}
else
{
- throw new IOException(
- "Implementation Error: Reset called for invalid source.");
+ throw new IOException(MessageManager.getString("error.implementation_error_reset_called_for_invalid_source"));
}
}
{ "HTML files" }, "HTML files");
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Save as HTML");
+ chooser.setDialogTitle(MessageManager.getString("label.save_as_html"));
chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(null);
import java.util.*;
import jalview.datamodel.*;
+import jalview.util.MessageManager;
/**
* Parser for the JPred/JNet concise format. This is a series of CSV lines, each
if (maxLength != seq_entries.elementAt(i).toString().length())
{
- throw new IOException("JPredConcise: Entry ("
- + ids.elementAt(i).toString()
- + ") has an unexpected number of columns");
+ throw new IOException(MessageManager.formatMessage("exception.jpredconcide_entry_has_unexpected_number_of_columns", new String[]{ids.elementAt(i).toString()}));
}
if ((newSeq.getName().startsWith("QUERY") || newSeq.getName()
} catch (Exception e)
{
tal = null;
- IOException ex = new IOException(
- "Couldn't parse concise annotation for prediction profile.\n"
- + e);
+ IOException ex = new IOException(MessageManager.formatMessage("exception.couldnt_parse_concise_annotation_for_prediction", new String[]{e.getMessage()}));
e.printStackTrace(); // java 1.1 does not have :
// ex.setStackTrace(e.getStackTrace());
throw ex;
&& getSelectedFile().exists())
{
int confirm = JOptionPane.showConfirmDialog(parent,
- "Overwrite existing file?", "File exists",
+ MessageManager.getString("label.overwrite_existing_file"), MessageManager.getString("label.file_already_exists"),
JOptionPane.YES_NO_OPTION);
if (confirm != JOptionPane.YES_OPTION)
}
});
- this.setBorder(new javax.swing.border.TitledBorder("Recently Opened"));
+ this.setBorder(new javax.swing.border.TitledBorder(MessageManager.getString("label.recently_opened")));
final JScrollPane scroller = new JScrollPane(list);
scroller.setPreferredSize(new Dimension(130, 200));
package jalview.io;
import jalview.datamodel.*;
+import jalview.util.MessageManager;
public class JnetAnnotationMaker
{
if ((delMap != null && delMap.length > width)
|| (delMap == null && gapmap.length != width))
{
- throw (new Exception("Number of residues in "
- + (delMap == null ? "" : " mapped ")
- + "supposed query sequence ('"
- + al.getSequenceAt(firstSeq).getName() + "'\n"
- + al.getSequenceAt(firstSeq).getSequenceAsString()
- + ")\ndiffer from number of prediction sites in prediction ("
- + width + ")"));
+ throw (new Exception(MessageManager.formatMessage("exception.number_of_residues_in_query_sequence_differ_from_prediction", new String[]{
+ (delMap == null ? "" : MessageManager.getString("label.mapped")),
+ al.getSequenceAt(firstSeq).getName(),
+ al.getSequenceAt(firstSeq).getSequenceAsString(),
+ Integer.valueOf(width).toString()
+ })));
}
AlignmentAnnotation annot;
import java.util.StringTokenizer;
import jalview.datamodel.*;
+import jalview.util.MessageManager;
/**
* Parse a new hanpshire style tree Caveats: NHX files are NOT supported and the
if (Error != null)
{
- throw (new IOException("NewickFile: " + Error + "\n"));
+ throw (new IOException(MessageManager.formatMessage("exception.newfile", new String[]{Error.toString()})));
}
if (root == null)
{
- throw (new IOException("NewickFile: No Tree read in\n"));
+ throw (new IOException(MessageManager.formatMessage("exception.newfile", new String[]{MessageManager.getString("label.no_tree_read_in")})));
}
// THe next line is failing for topali trees - not sure why yet. if
// (root.right()!=null && root.isDummy())
if (noSeqs < 1)
{
- throw new IOException("No sequences found (PFAM input)");
+ throw new IOException(MessageManager.getString("exception.pfam_no_sequences_found"));
}
for (i = 0; i < headers.size(); i++)
import jalview.datamodel.Annotation;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
_parse();
} catch (ExceptionPermissionDenied pdx)
{
- errormessage = "Couldn't access datasource (" + pdx.getMessage()
- + ")";
+ errormessage = MessageManager.formatMessage("exception.rnaml_couldnt_access_datasource", new String[]{pdx.getMessage()});
throw new IOException(pdx);
} catch (ExceptionLoadingFailed lf)
{
- errormessage = "Couldn't process data as RNAML file ("
- + lf.getMessage() + ")";
+ errormessage = MessageManager.formatMessage("exception.ranml_couldnt_process_data", new String[]{lf.getMessage()});
throw new IOException(lf);
} catch (ExceptionFileFormatOrSyntax iff)
{
- errormessage = "Invalid RNAML file (" + iff.getMessage() + ")";
+ errormessage = MessageManager.formatMessage("exception.ranml_invalid_file", new String[]{iff.getMessage()});
throw new IOException(iff);
} catch (Exception x)
{
error = true;
- errormessage = "Problem parsing data as RNAML (" + x.getMessage()
- + ")";
- throw new IOException("Couldn't parse the datasource as RNAML", x);
+ errormessage = MessageManager.formatMessage("exception.ranml_problem_parsing_data", new String[]{x.getMessage()});
+ throw new IOException(errormessage , x);
}
}
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.util.Format;
+import jalview.util.MessageManager;
import java.io.BufferedReader;
import java.io.FileReader;
r = new Regex("# STOCKHOLM ([\\d\\.]+)");
if (!r.search(nextLine()))
{
- throw new IOException(
- "This file is not in valid STOCKHOLM format: First line does not contain '# STOCKHOLM'");
+ throw new IOException(MessageManager.getString("exception.stockholm_invalid_format"));
}
else
{
if (!x.search(line))
{
// logger.error("Could not parse sequence line: " + line);
- throw new IOException("Could not parse sequence line: " + line);
+ throw new IOException(MessageManager.formatMessage("exception.couldnt_parse_sequence_line", new String[]{line}));
}
String ns = (String) seqs.get(x.stringMatched(1));
if (ns == null)
}
else
{
- throw new IOException("Error parsing " + line);
+ throw new IOException(MessageManager.formatMessage("exception.error_parsing_line", new String[]{line}));
}
}
else if (annType.equals("GC"))
}
else
{
- throw new IOException("Unknown annotation detected: " + annType
- + " " + annContent);
+ throw new IOException(MessageManager.formatMessage("exception.unknown_annotation_detected", new String[]{annType,annContent}));
}
}
}
import jalview.io.vamsas.DatastoreItem;
import jalview.io.vamsas.DatastoreRegistry;
import jalview.io.vamsas.Rangetype;
+import jalview.util.MessageManager;
+
import java.io.IOException;
import java.util.Enumeration;
import java.util.HashMap;
{
Cache.log.debug(
"Warning? Overwriting existing vamsas id binding for "
- + vobj.getVorbaId(), new Exception(
- "Overwriting vamsas id binding."));
+ + vobj.getVorbaId(), new Exception(MessageManager.getString("exception.overwriting_vamsas_id_binding")));
}
else if (jv2vobj.containsKey(jvobj)
&& !((VorbaId) jv2vobj.get(jvobj)).equals(vobj.getVorbaId()))
if (vbound.getV_parent() != null
&& dataset != vbound.getV_parent())
{
- throw new Error(
- "IMPLEMENTATION ERROR: Cannot map an alignment of sequences from different datasets into a single alignment in the vamsas document.");
+ throw new Error(MessageManager.getString("error.implementation_error_cannot_map_alignment_sequences"));
// This occurs because the dataset for the alignment we are
// trying to
}
{
// NOTE: this happens if user deletes object in one session then updates
// from another client
- throw new Error(
- "IMPLEMENTATION ERROR: old jalview object is not bound ! ("
- + oldjvobject + ")");
+ throw new Error(MessageManager.formatMessage("error.implementation_error_old_jalview_object_not_bound", new String[]{oldjvobject.toString()}));
}
if (newjvobject != null)
{
int[] se = null;
if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
{
- throw new Error(
- "Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");
+ throw new Error(MessageManager.getString("error.invalid_vamsas_rangetype_cannot_resolve_lists"));
}
if (dseta.getSegCount() > 0)
{
int[] se = null;
if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
{
- throw new Error(
- "Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");
+ throw new Error(MessageManager.getString("error.invalid_vamsas_rangetype_cannot_resolve_lists"));
}
if (dseta.getSegCount() > 0)
{
}
} catch (Exception e)
{
- throw new Exception("Couldn't store sequence mappings for " + title,
- e);
+ throw new Exception(MessageManager.formatMessage("exception.couldnt_store_sequence_mappings", new String[]{title}),e);
}
}
imageIndex++;
imageIndex %= 9;
output.setFrameIcon(imageIcon[imageIndex]);
- output.setTitle("BLASTing for unidentified sequences - "
- + jobsRunning + " jobs running.");
+ output.setTitle(MessageManager.formatMessage("label.blasting_for_unidentified_sequence_jobs_running", new String[]{Integer.valueOf(jobsRunning).toString()}));
} catch (Exception ex)
{
}
import jalview.bin.Cache;
import jalview.io.VamsasAppDatastore;
+import jalview.util.MessageManager;
import java.util.Enumeration;
import java.util.Hashtable;
{
Cache.log.debug(
"Warning? Overwriting existing vamsas id binding for "
- + vobj.getVorbaId(), new Exception(
- "Overwriting vamsas id binding."));
+ + vobj.getVorbaId(), new Exception(MessageManager.getString("exception.overwriting_vamsas_id_binding")));
}
else if (jv2vobj.containsKey(jvobj)
&& !((VorbaId) jv2vobj.get(jvobj)).equals(vobj.getVorbaId()))
{
Cache.log.debug(
"Warning? Overwriting existing jalview object binding for "
- + jvobj, new Exception(
- "Overwriting jalview object binding."));
+ + jvobj, new Exception(MessageManager.getString("exception.overwriting_jalview_id_binding")));
}
/*
* Cache.log.error("Attempt to make conflicting object binding! "+vobj+" id "
Object vobject = jv2vobj.remove(oldjvobject);
if (vobject == null)
{
- throw new Error(
- "IMPLEMENTATION ERROR: old jalview object is not bound ! ("
- + oldjvobject + ")");
+ throw new Error(MessageManager.formatMessage("error.implementation_error_old_jalview_object_not_bound", new String[]{oldjvobject.toString()}));
}
if (newjvobject != null)
{
tojalview = true;
if (jvobj != null && !(boundType.isAssignableFrom(jvobj.getClass())))
{
- throw new Error("Implementation Error: Vamsas Document Class "
- + vobj.getClass() + " should bind to a " + boundType
- + " (found a " + jvobj.getClass() + ")");
+ throw new Error(MessageManager.formatMessage("error.implementation_error_vamsas_doc_class_should_bind_to_type"
+ , new String[]{vobj.getClass().toString(),boundType.toString(),jvobj.getClass().toString()}));
}
dsReg.registerDsObj(this);
}
vobj = getjv2vObj(jvobj);
if (vobj != null && !(boundToType.isAssignableFrom(vobj.getClass())))
{
- throw new Error("Implementation Error: Jalview Class "
- + jvobj2.getClass() + " should bind to a " + boundToType
- + " (found a " + vobj.getClass() + ")");
+ throw new Error(MessageManager.formatMessage("error.implementation_error_vamsas_doc_class_should_bind_to_type"
+ , new String[]{jvobj2.getClass().toString(),boundToType.toString(),vobj.getClass().toString()}));
}
dsReg.registerDsObj(this);
}
import uk.ac.vamsas.objects.core.RangeType;
import uk.ac.vamsas.objects.core.Seg;
import jalview.io.VamsasAppDatastore;
+import jalview.util.MessageManager;
/**
* Enhances DatastoreItem objects with additional functions to do with RangeType
int[] se = null;
if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
{
- throw new Error(
- "Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");
+ throw new Error(MessageManager.getString("error.invalid_vamsas_rangetype_cannot_resolve_lists"));
}
if (dseta.getSegCount() > 0)
{
int[] se = null;
if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
{
- throw new Error(
- "Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");
+ throw new Error(MessageManager.getString("error.invalid_vamsas_rangetype_cannot_resolve_lists"));
}
if (dseta.getSegCount() > 0)
{
int[] se = null;
if (range.getSegCount() > 0 && range.getPosCount() > 0)
{
- throw new Error(
- "Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");
+ throw new Error(MessageManager.getString("error.invalid_vamsas_rangetype_cannot_resolve_lists"));
}
if (range.getSegCount() > 0)
{
{
if (ml == null)
{
- throw new Error(
- "Implementation error. MapList is null for initMapType.");
+ throw new Error(MessageManager.getString("error.implementation_error_maplist_is_null"));
}
maprange.setLocal(new Local());
maprange.setMapped(new Mapped());
}
});
removeRedundancyMenuItem.setText(MessageManager
- .getString("action.remove_redundancy"));
+ .getString("action.remove_redundancy").concat("..."));
removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
.getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
.getDefaultToolkit().getMenuShortcutKeyMask(), false));
autoIdWidth.setText(MessageManager
.getString("label.automatically_set_id_width"));
autoIdWidth
- .setToolTipText("<html>"
- + JvSwingUtils
- .wrapTooltip("Adjusts the width of the generated EPS or PNG file to ensure even the longest sequence ID or annotation label is displayed")
- + "</html>");
+ .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.adjusts_width_generated_eps_png")));
autoIdWidth.setBounds(new Rectangle(228, 96, 188, 23));
autoIdWidth.addActionListener(new ActionListener()
{
userIdWidthlabel.setText(MessageManager
.getString("label.figure_id_column_width"));
userIdWidth
- .setToolTipText("<html>"
- + JvSwingUtils
- .wrapTooltip("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>");
+ .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.manually_specify_width_left_column")));
userIdWidthlabel
- .setToolTipText("<html>"
- + JvSwingUtils
- .wrapTooltip("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>");
+ .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.manually_specify_width_left_column")));
userIdWidthlabel.setBounds(new Rectangle(236, 120, 168, 23));
userIdWidth.setFont(JvSwingUtils.getTextAreaFont());
userIdWidth.setText("");
// cpanel.setLayout(new FlowLayout());
hSeparable = new JCheckBox(MessageManager.getString("label.per_seq"));
hSeparable
- .setToolTipText("<html>"
- + JvSwingUtils
- .wrapTooltip("When checked, a job is created for every sequence in the current selection.")
- + "<html>");
+ .setToolTipText(JvSwingUtils
+ .wrapTooltip(false, MessageManager.getString("label.job_created_when_checked")));
hSeparable.addActionListener(new ActionListener()
{
vSeparable = new JCheckBox(
MessageManager.getString("label.result_vertically_separable"));
vSeparable
- .setToolTipText("<html>"
- + JvSwingUtils
- .wrapTooltip("When checked, a single job is created for the visible region and results"
- + " mapped back onto their location in the alignment. Otherwise, a job would be"
- + " created for every contiguous region visible in the alignment or current"
- + " selection (e.g. a multiple alignment).")
- + "</html>");
+ .setToolTipText(JvSwingUtils.wrapTooltip(false, MessageManager.getString("label.when_checked_job_visible_region_and_results")));
vSeparable.addActionListener(new ActionListener()
{
urldescPane.add(urldescVp, "span");
paste.add(urldescPane, "span");
urldescPane
- .setToolTipText("<html>"
- + JvSwingUtils
- .wrapTooltip("Flat file representation of this rest service using the Really Simple Bioinformatics Service formalism"));
+ .setToolTipText(JvSwingUtils.wrapTooltip(false, MessageManager.getString("label.flat_file_representation")));
parseRes = new JTextArea();
parseResVp = new JScrollPane();
parseWarnings.setBorder(new TitledBorder(MessageManager
.getString("label.parsing_errors")));
parseWarnings
- .setToolTipText("<html>"
- + JvSwingUtils
- .wrapTooltip("Results of parsing the RSBS representation")
- + "</html>");
+ .setToolTipText(JvSwingUtils.wrapTooltip(false, MessageManager.getString("label.result_of_parsing_rsbs")));
parseWarnings.add(parseResVp, "center");
parseRes.setEditable(false);
paste.add(parseWarnings, "span");
jLabel2.setText(MessageManager.getString("label.url"));
jLabel2.setBounds(new Rectangle(17, 37, 54, 27));
jLabel3.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
- jLabel3.setText("Use $SEQUENCE_ID$ or $SEQUENCE_ID=/<regex>/=$");
+ jLabel3.setText(MessageManager.getString("label.use_sequence_id_1"));
jLabel3.setBounds(new Rectangle(21, 72, 351, 15));
jLabel4.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
- jLabel4.setText("\nto embed sequence id in URL");
+ jLabel4.setText(MessageManager.getString("label.use_sequence_id_2"));
jLabel4.setBounds(new Rectangle(21, 93, 351, 15));
jPanel1.setBorder(BorderFactory.createEtchedBorder());
jPanel1.setLayout(null);
JOptionPane
.showInternalMessageDialog(
jalview.gui.Desktop.desktop,
- "Sequence URL must contain $SEQUENCE_ID$ or a regex $SEQUENCE_ID=/<regex>/=$",
- "URL not valid", JOptionPane.WARNING_MESSAGE);
+ MessageManager.getString("warn.url_must_contain"),
+ MessageManager.getString("label.invalid_url"), JOptionPane.WARNING_MESSAGE);
return false;
}
if (iter == maxIter)
{
- throw new Exception("Too many iterations in tqli (" + maxIter
- + ")");
+ throw new Exception(MessageManager.formatMessage("exception.matrix_too_many_iteration", new String[]{"tqli", Integer.valueOf(maxIter).toString()}));
}
else
{
if (iter == maxIter)
{
- throw new Exception("Too many iterations in tqli2 (max is "
- + maxIter + ")");
+ throw new Exception(MessageManager.formatMessage("exception.matrix_too_many_iteration", new String[]{"tqli2", Integer.valueOf(maxIter).toString()}));
}
else
{
//- Imported classes and packages -/
//---------------------------------/
+import jalview.util.MessageManager;
+
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
// check bounds for index
if (index < 0 || index >= this._alcodMapList.size())
{
- throw new IndexOutOfBoundsException("getAlcodMap: Index value '"
- + index + "' not in range [0.."
- + (this._alcodMapList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "getAlcodMap",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._alcodMapList.size() - 1)).toString()
+ }));
}
return (jalview.schemabinding.version2.AlcodMap) _alcodMapList
// check bounds for index
if (index < 0 || index >= this._alcodonList.size())
{
- throw new IndexOutOfBoundsException("getAlcodon: Index value '"
- + index + "' not in range [0.."
- + (this._alcodonList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "getAlcodon",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._alcodonList.size() - 1)).toString()
+ }));
}
return (jalview.schemabinding.version2.Alcodon) _alcodonList.get(index);
// check bounds for index
if (index < 0 || index >= this._alcodMapList.size())
{
- throw new IndexOutOfBoundsException("setAlcodMap: Index value '"
- + index + "' not in range [0.."
- + (this._alcodMapList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "setAlcodMap",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._alcodonList.size() - 1)).toString()
+ }));
}
this._alcodMapList.set(index, vAlcodMap);
// check bounds for index
if (index < 0 || index >= this._alcodonList.size())
{
- throw new IndexOutOfBoundsException("setAlcodon: Index value '"
- + index + "' not in range [0.."
- + (this._alcodonList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "setAlcodon",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._alcodonList.size() - 1)).toString()
+ }));
}
this._alcodonList.set(index, vAlcodon);
//- Imported classes and packages -/
//---------------------------------/
+import jalview.util.MessageManager;
+
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
// check bounds for index
if (index < 0 || index >= this._annotationElementList.size())
{
- throw new IndexOutOfBoundsException(
- "getAnnotationElement: Index value '" + index
- + "' not in range [0.."
- + (this._annotationElementList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "getAnnotationElement",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._annotationElementList.size() - 1)).toString()
+ }));
}
return (jalview.schemabinding.version2.AnnotationElement) _annotationElementList
// check bounds for index
if (index < 0 || index >= this._annotationElementList.size())
{
- throw new IndexOutOfBoundsException(
- "setAnnotationElement: Index value '" + index
- + "' not in range [0.."
- + (this._annotationElementList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "setAnnotationElement",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._annotationElementList.size() - 1)).toString()
+ }));
}
this._annotationElementList.set(index, vAnnotationElement);
//- Imported classes and packages -/
//---------------------------------/
+import jalview.util.MessageManager;
+
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
// check bounds for index
if (index < 0 || index >= this._otherDataList.size())
{
- throw new IndexOutOfBoundsException("getOtherData: Index value '"
- + index + "' not in range [0.."
- + (this._otherDataList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "getOtherData",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._otherDataList.size() - 1)).toString()
+ }));
}
return (jalview.schemabinding.version2.OtherData) _otherDataList
// check bounds for index
if (index < 0 || index >= this._otherDataList.size())
{
- throw new IndexOutOfBoundsException("setOtherData: Index value '"
- + index + "' not in range [0.."
- + (this._otherDataList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "setOtherData",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._otherDataList.size() - 1)).toString()
+ }));
}
this._otherDataList.set(index, vOtherData);
//- Imported classes and packages -/
//---------------------------------/
+import jalview.util.MessageManager;
+
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
// check bounds for index
if (index < 0 || index >= this._groupList.size())
{
- throw new IndexOutOfBoundsException("getGroup: Index value '" + index
- + "' not in range [0.." + (this._groupList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "getGroup",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._groupList.size() - 1)).toString()
+ }));
}
return (jalview.schemabinding.version2.Group) _groupList.get(index);
// check bounds for index
if (index < 0 || index >= this._settingList.size())
{
- throw new IndexOutOfBoundsException("getSetting: Index value '"
- + index + "' not in range [0.."
- + (this._settingList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "getSetting",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._settingList.size() - 1)).toString()
+ }));
}
return (jalview.schemabinding.version2.Setting) _settingList.get(index);
// check bounds for index
if (index < 0 || index >= this._groupList.size())
{
- throw new IndexOutOfBoundsException("setGroup: Index value '" + index
- + "' not in range [0.." + (this._groupList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "setGroup",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._groupList.size() - 1)).toString()
+ }));
}
this._groupList.set(index, vGroup);
// check bounds for index
if (index < 0 || index >= this._settingList.size())
{
- throw new IndexOutOfBoundsException("setSetting: Index value '"
- + index + "' not in range [0.."
- + (this._settingList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "setSetting",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._settingList.size() - 1)).toString()
+ }));
}
this._settingList.set(index, vSetting);
//- Imported classes and packages -/
//---------------------------------/
+import jalview.util.MessageManager;
+
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
// check bounds for index
if (index < 0 || index >= this._seqList.size())
{
- throw new IndexOutOfBoundsException("getSeq: Index value '" + index
- + "' not in range [0.." + (this._seqList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "getSeq",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._seqList.size() - 1)).toString()
+ }));
}
return (java.lang.String) _seqList.get(index);
// check bounds for index
if (index < 0 || index >= this._seqList.size())
{
- throw new IndexOutOfBoundsException("setSeq: Index value '" + index
- + "' not in range [0.." + (this._seqList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "setSeq",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._seqList.size() - 1)).toString()
+ }));
}
this._seqList.set(index, vSeq);
//- Imported classes and packages -/
//---------------------------------/
+import jalview.util.MessageManager;
+
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
// check bounds for index
if (index < 0 || index >= this._featuresList.size())
{
- throw new IndexOutOfBoundsException("getFeatures: Index value '"
- + index + "' not in range [0.."
- + (this._featuresList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "getFeatures",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._featuresList.size() - 1)).toString()
+ }));
}
return (jalview.schemabinding.version2.Features) _featuresList
// check bounds for index
if (index < 0 || index >= this._hiddenSequencesList.size())
{
- throw new IndexOutOfBoundsException(
- "getHiddenSequences: Index value '" + index
- + "' not in range [0.."
- + (this._hiddenSequencesList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "getHiddenSequences",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._hiddenSequencesList.size() - 1)).toString()
+ }));
}
return ((java.lang.Integer) _hiddenSequencesList.get(index)).intValue();
// check bounds for index
if (index < 0 || index >= this._pdbidsList.size())
{
- throw new IndexOutOfBoundsException("getPdbids: Index value '"
- + index + "' not in range [0.."
- + (this._pdbidsList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "getPdbids",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._pdbidsList.size() - 1)).toString()
+ }));
}
return (jalview.schemabinding.version2.Pdbids) _pdbidsList.get(index);
// check bounds for index
if (index < 0 || index >= this._featuresList.size())
{
- throw new IndexOutOfBoundsException("setFeatures: Index value '"
- + index + "' not in range [0.."
- + (this._featuresList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "setFeatures",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._featuresList.size() - 1)).toString()
+ }));
}
this._featuresList.set(index, vFeatures);
// check bounds for index
if (index < 0 || index >= this._hiddenSequencesList.size())
{
- throw new IndexOutOfBoundsException(
- "setHiddenSequences: Index value '" + index
- + "' not in range [0.."
- + (this._hiddenSequencesList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "setHiddenSequences",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._hiddenSequencesList.size() - 1)).toString()
+ }));
}
this._hiddenSequencesList.set(index, new java.lang.Integer(
// check bounds for index
if (index < 0 || index >= this._pdbidsList.size())
{
- throw new IndexOutOfBoundsException("setPdbids: Index value '"
- + index + "' not in range [0.."
- + (this._pdbidsList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "setPdbids",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._pdbidsList.size() - 1)).toString()
+ }));
}
this._pdbidsList.set(index, vPdbids);
//- Imported classes and packages -/
//---------------------------------/
+import jalview.util.MessageManager;
+
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
// check bounds for index
if (index < 0 || index >= this._JGroupList.size())
{
- throw new IndexOutOfBoundsException("getJGroup: Index value '"
- + index + "' not in range [0.."
- + (this._JGroupList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "getJGroup",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._JGroupList.size() - 1)).toString()
+ }));
}
return (jalview.schemabinding.version2.JGroup) _JGroupList.get(index);
// check bounds for index
if (index < 0 || index >= this._JSeqList.size())
{
- throw new IndexOutOfBoundsException("getJSeq: Index value '" + index
- + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "getJSeq",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._JSeqList.size() - 1)).toString()
+ }));
}
return (jalview.schemabinding.version2.JSeq) _JSeqList.get(index);
// check bounds for index
if (index < 0 || index >= this._treeList.size())
{
- throw new IndexOutOfBoundsException("getTree: Index value '" + index
- + "' not in range [0.." + (this._treeList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "getJgetTreeSeq",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._treeList.size() - 1)).toString()
+ }));
}
return (jalview.schemabinding.version2.Tree) _treeList.get(index);
// check bounds for index
if (index < 0 || index >= this._userColoursList.size())
{
- throw new IndexOutOfBoundsException("getUserColours: Index value '"
- + index + "' not in range [0.."
- + (this._userColoursList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "getUserColours",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._userColoursList.size() - 1)).toString()
+ }));
}
return (jalview.schemabinding.version2.UserColours) _userColoursList
// check bounds for index
if (index < 0 || index >= this._viewportList.size())
{
- throw new IndexOutOfBoundsException("getViewport: Index value '"
- + index + "' not in range [0.."
- + (this._viewportList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "getViewport",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._viewportList.size() - 1)).toString()
+ }));
}
return (jalview.schemabinding.version2.Viewport) _viewportList
// check bounds for index
if (index < 0 || index >= this._JGroupList.size())
{
- throw new IndexOutOfBoundsException("setJGroup: Index value '"
- + index + "' not in range [0.."
- + (this._JGroupList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "setJGroup",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._JGroupList.size() - 1)).toString()
+ }));
}
this._JGroupList.set(index, vJGroup);
// check bounds for index
if (index < 0 || index >= this._JSeqList.size())
{
- throw new IndexOutOfBoundsException("setJSeq: Index value '" + index
- + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "setJSeq",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._JSeqList.size() - 1)).toString()
+ }));
}
this._JSeqList.set(index, vJSeq);
// check bounds for index
if (index < 0 || index >= this._treeList.size())
{
- throw new IndexOutOfBoundsException("setTree: Index value '" + index
- + "' not in range [0.." + (this._treeList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "setTree",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._treeList.size() - 1)).toString()
+ }));
}
this._treeList.set(index, vTree);
// check bounds for index
if (index < 0 || index >= this._userColoursList.size())
{
- throw new IndexOutOfBoundsException("setUserColours: Index value '"
- + index + "' not in range [0.."
- + (this._userColoursList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "setUserColours",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._userColoursList.size() - 1)).toString()
+ }));
}
this._userColoursList.set(index, vUserColours);
// check bounds for index
if (index < 0 || index >= this._viewportList.size())
{
- throw new IndexOutOfBoundsException("setViewport: Index value '"
- + index + "' not in range [0.."
- + (this._viewportList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "setViewport",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._viewportList.size() - 1)).toString()
+ }));
}
this._viewportList.set(index, vViewport);
//- Imported classes and packages -/
//---------------------------------/
+import jalview.util.MessageManager;
+
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
// check bounds for index
if (index < 0 || index >= this._colourList.size())
{
- throw new IndexOutOfBoundsException("getColour: Index value '"
- + index + "' not in range [0.."
- + (this._colourList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "getColour",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._colourList.size() - 1)).toString()
+ }));
}
return (Colour) _colourList.get(index);
// check bounds for index
if (index < 0 || index >= this._colourList.size())
{
- throw new IndexOutOfBoundsException("setColour: Index value '"
- + index + "' not in range [0.."
- + (this._colourList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "setColour",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._colourList.size() - 1)).toString()
+ }));
}
this._colourList.set(index, vColour);
//- Imported classes and packages -/
//---------------------------------/
+import jalview.util.MessageManager;
+
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
// check bounds for index
if (index < 0 || index >= this._mapListFromList.size())
{
- throw new IndexOutOfBoundsException("getMapListFrom: Index value '"
- + index + "' not in range [0.."
- + (this._mapListFromList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "getMapListFrom",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._mapListFromList.size() - 1)).toString()
+ }));
}
return (jalview.schemabinding.version2.MapListFrom) _mapListFromList
// check bounds for index
if (index < 0 || index >= this._mapListToList.size())
{
- throw new IndexOutOfBoundsException("getMapListTo: Index value '"
- + index + "' not in range [0.."
- + (this._mapListToList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "getMapListTo",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._mapListToList.size() - 1)).toString()
+ }));
}
return (jalview.schemabinding.version2.MapListTo) _mapListToList
// check bounds for index
if (index < 0 || index >= this._mapListFromList.size())
{
- throw new IndexOutOfBoundsException("setMapListFrom: Index value '"
- + index + "' not in range [0.."
- + (this._mapListFromList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "setMapListFrom",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._mapListFromList.size() - 1)).toString()
+ }));
}
this._mapListFromList.set(index, vMapListFrom);
// check bounds for index
if (index < 0 || index >= this._mapListToList.size())
{
- throw new IndexOutOfBoundsException("setMapListTo: Index value '"
- + index + "' not in range [0.."
- + (this._mapListToList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "setMapListTo",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._mapListToList.size() - 1)).toString()
+ }));
}
this._mapListToList.set(index, vMapListTo);
//- Imported classes and packages -/
//---------------------------------/
+import jalview.util.MessageManager;
+
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
// check bounds for index
if (index < 0 || index >= this._items.size())
{
- throw new IndexOutOfBoundsException("getPdbentryItem: Index value '"
- + index + "' not in range [0.." + (this._items.size() - 1)
- + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "getPdbentryItem",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._items.size() - 1)).toString()
+ }));
}
return (jalview.schemabinding.version2.PdbentryItem) _items.get(index);
// check bounds for index
if (index < 0 || index >= this._items.size())
{
- throw new IndexOutOfBoundsException("setPdbentryItem: Index value '"
- + index + "' not in range [0.." + (this._items.size() - 1)
- + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "setPdbentryItem",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._items.size() - 1)).toString()
+ }));
}
this._items.set(index, vPdbentryItem);
*/
package jalview.schemabinding.version2;
+import jalview.util.MessageManager;
+
/**
* Class PdbentryItem.
*
// check bounds for index
if (index < 0 || index >= this._propertyList.size())
{
- throw new IndexOutOfBoundsException("getProperty: Index value '"
- + index + "' not in range [0.."
- + (this._propertyList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "getProperty",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._propertyList.size() - 1)).toString()
+ }));
}
return (jalview.schemabinding.version2.Property) _propertyList
// check bounds for index
if (index < 0 || index >= this._propertyList.size())
{
- throw new IndexOutOfBoundsException("setProperty: Index value '"
- + index + "' not in range [0.."
- + (this._propertyList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "setProperty",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._propertyList.size() - 1)).toString()
+ }));
}
this._propertyList.set(index, vProperty);
//- Imported classes and packages -/
//---------------------------------/
+import jalview.util.MessageManager;
+
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
// check bounds for index
if (index < 0 || index >= this._structureStateList.size())
{
- throw new IndexOutOfBoundsException(
- "getStructureState: Index value '" + index
- + "' not in range [0.."
- + (this._structureStateList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "getStructureState",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._structureStateList.size() - 1)).toString()
+ }));
}
return (jalview.schemabinding.version2.StructureState) _structureStateList
// check bounds for index
if (index < 0 || index >= this._structureStateList.size())
{
- throw new IndexOutOfBoundsException(
- "setStructureState: Index value '" + index
- + "' not in range [0.."
- + (this._structureStateList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "setStructureState",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._structureStateList.size() - 1)).toString()
+ }));
}
this._structureStateList.set(index, vStructureState);
//- Imported classes and packages -/
//---------------------------------/
+import jalview.util.MessageManager;
+
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
// check bounds for index
if (index < 0 || index >= this._DBRefList.size())
{
- throw new IndexOutOfBoundsException("getDBRef: Index value '" + index
- + "' not in range [0.." + (this._DBRefList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "getDBRef",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._DBRefList.size() - 1)).toString()
+ }));
}
return (jalview.schemabinding.version2.DBRef) _DBRefList.get(index);
// check bounds for index
if (index < 0 || index >= this._DBRefList.size())
{
- throw new IndexOutOfBoundsException("setDBRef: Index value '" + index
- + "' not in range [0.." + (this._DBRefList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "setDBRef",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._DBRefList.size() - 1)).toString()
+ }));
}
this._DBRefList.set(index, vDBRef);
//- Imported classes and packages -/
//---------------------------------/
+import jalview.util.MessageManager;
+
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
// check bounds for index
if (index < 0 || index >= this._alcodonFrameList.size())
{
- throw new IndexOutOfBoundsException("getAlcodonFrame: Index value '"
- + index + "' not in range [0.."
- + (this._alcodonFrameList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "getAlcodonFrame",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._alcodonFrameList.size() - 1)).toString()
+ }));
}
return (jalview.schemabinding.version2.AlcodonFrame) _alcodonFrameList
// check bounds for index
if (index < 0 || index >= this._annotationList.size())
{
- throw new IndexOutOfBoundsException("getAnnotation: Index value '"
- + index + "' not in range [0.."
- + (this._annotationList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "getAnnotation",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._alcodonFrameList.size() - 1)).toString()
+ }));
}
return (jalview.schemabinding.version2.Annotation) _annotationList
// check bounds for index
if (index < 0 || index >= this._sequenceList.size())
{
- throw new IndexOutOfBoundsException("getSequence: Index value '"
- + index + "' not in range [0.."
- + (this._sequenceList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "getSequence",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._sequenceList.size() - 1)).toString()
+ }));
}
return (jalview.schemabinding.version2.Sequence) _sequenceList
// check bounds for index
if (index < 0 || index >= this._sequenceSetPropertiesList.size())
{
- throw new IndexOutOfBoundsException(
- "getSequenceSetProperties: Index value '" + index
- + "' not in range [0.."
- + (this._sequenceSetPropertiesList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "getSequenceSetProperties",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._sequenceSetPropertiesList.size() - 1)).toString()
+ }));
}
return (jalview.schemabinding.version2.SequenceSetProperties) _sequenceSetPropertiesList
// check bounds for index
if (index < 0 || index >= this._alcodonFrameList.size())
{
- throw new IndexOutOfBoundsException("setAlcodonFrame: Index value '"
- + index + "' not in range [0.."
- + (this._alcodonFrameList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "setAlcodonFrame",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._alcodonFrameList.size() - 1)).toString()
+ }));
}
this._alcodonFrameList.set(index, vAlcodonFrame);
// check bounds for index
if (index < 0 || index >= this._annotationList.size())
{
- throw new IndexOutOfBoundsException("setAnnotation: Index value '"
- + index + "' not in range [0.."
- + (this._annotationList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "setAnnotation",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._annotationList.size() - 1)).toString()
+ }));
}
this._annotationList.set(index, vAnnotation);
// check bounds for index
if (index < 0 || index >= this._sequenceList.size())
{
- throw new IndexOutOfBoundsException("setSequence: Index value '"
- + index + "' not in range [0.."
- + (this._sequenceList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "setSequence",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._sequenceList.size() - 1)).toString()
+ }));
}
this._sequenceList.set(index, vSequence);
// check bounds for index
if (index < 0 || index >= this._sequenceSetPropertiesList.size())
{
- throw new IndexOutOfBoundsException(
- "setSequenceSetProperties: Index value '" + index
- + "' not in range [0.."
- + (this._sequenceSetPropertiesList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "setSequenceSetProperties",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._sequenceSetPropertiesList.size() - 1)).toString()
+ }));
}
this._sequenceSetPropertiesList.set(index, vSequenceSetProperties);
//- Imported classes and packages -/
//---------------------------------/
+import jalview.util.MessageManager;
+
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
// check bounds for index
if (index < 0 || index >= this._sequenceSetList.size())
{
- throw new IndexOutOfBoundsException("getSequenceSet: Index value '"
- + index + "' not in range [0.."
- + (this._sequenceSetList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "getSequenceSet",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._sequenceSetList.size() - 1)).toString()
+ }));
}
return (jalview.schemabinding.version2.SequenceSet) _sequenceSetList
// check bounds for index
if (index < 0 || index >= this._treeList.size())
{
- throw new IndexOutOfBoundsException("getTree: Index value '" + index
- + "' not in range [0.." + (this._treeList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "getTree",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._treeList.size() - 1)).toString()
+ }));
}
return (java.lang.String) _treeList.get(index);
// check bounds for index
if (index < 0 || index >= this._sequenceSetList.size())
{
- throw new IndexOutOfBoundsException("setSequenceSet: Index value '"
- + index + "' not in range [0.."
- + (this._sequenceSetList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "setSequenceSet",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._sequenceSetList.size() - 1)).toString()
+ }));
}
this._sequenceSetList.set(index, vSequenceSet);
// check bounds for index
if (index < 0 || index >= this._treeList.size())
{
- throw new IndexOutOfBoundsException("setTree: Index value '" + index
- + "' not in range [0.." + (this._treeList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "setTree",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._treeList.size() - 1)).toString()
+ }));
}
this._treeList.set(index, vTree);
//- Imported classes and packages -/
//---------------------------------/
+import jalview.util.MessageManager;
+
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
// check bounds for index
if (index < 0 || index >= this._calcIdParamList.size())
{
- throw new IndexOutOfBoundsException("getCalcIdParam: Index value '"
- + index + "' not in range [0.."
- + (this._calcIdParamList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "getCalcIdParam",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._calcIdParamList.size() - 1)).toString()
+ }));
}
return (jalview.schemabinding.version2.CalcIdParam) _calcIdParamList
// check bounds for index
if (index < 0 || index >= this._hiddenColumnsList.size())
{
- throw new IndexOutOfBoundsException("getHiddenColumns: Index value '"
- + index + "' not in range [0.."
- + (this._hiddenColumnsList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "getHiddenColumns",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._hiddenColumnsList.size() - 1)).toString()
+ }));
}
return (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList
// check bounds for index
if (index < 0 || index >= this._calcIdParamList.size())
{
- throw new IndexOutOfBoundsException("setCalcIdParam: Index value '"
- + index + "' not in range [0.."
- + (this._calcIdParamList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "setCalcIdParam",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._calcIdParamList.size() - 1)).toString()
+ }));
}
this._calcIdParamList.set(index, vCalcIdParam);
// check bounds for index
if (index < 0 || index >= this._hiddenColumnsList.size())
{
- throw new IndexOutOfBoundsException("setHiddenColumns: Index value '"
- + index + "' not in range [0.."
- + (this._hiddenColumnsList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "setHiddenColumns",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._hiddenColumnsList.size() - 1)).toString()
+ }));
}
this._hiddenColumnsList.set(index, vHiddenColumns);
//- Imported classes and packages -/
//---------------------------------/
+import jalview.util.MessageManager;
+
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
// check bounds for index
if (index < 0 || index >= this._serviceURLList.size())
{
- throw new IndexOutOfBoundsException("getServiceURL: Index value '"
- + index + "' not in range [0.."
- + (this._serviceURLList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "getServiceURL",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._serviceURLList.size() - 1)).toString()
+ }));
}
return (java.lang.String) _serviceURLList.get(index);
// check bounds for index
if (index < 0 || index >= this._serviceURLList.size())
{
- throw new IndexOutOfBoundsException("setServiceURL: Index value '"
- + index + "' not in range [0.."
- + (this._serviceURLList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "setServiceURL",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._serviceURLList.size() - 1)).toString()
+ }));
}
this._serviceURLList.set(index, vServiceURL);
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
import java.awt.Color;
import java.util.Hashtable;
return getClass().newInstance();
} catch (Exception q)
{
- throw new Error(
- "Serious implementation error: cannot duplicate colourscheme "
- + getClass().getName(), q);
+ throw new Error(MessageManager.formatMessage("error.implementation_error_cannot_duplicate_colour_scheme", new String[]{getClass().getName()}), q);
}
}
}
import jalview.api.AlignmentViewPanel;
import jalview.api.StructureSelectionManagerProvider;
import jalview.datamodel.*;
+import jalview.util.MessageManager;
public class StructureSelectionManager
{
{
if (instances != null)
{
- throw new Error(
- "Implementation error. Structure selection manager's context is 'null'",
- new NullPointerException("SSM context is null"));
+ throw new Error(MessageManager.getString("error.implementation_error_structure_selection_manager_null"),
+ new NullPointerException(MessageManager.getString("exception.ssm_context_is_null")));
}
else
{
} catch (InterruptedException ie)
{
}
- throw new NullPointerException(
- "Application test: throwing an NullPointerException It should arrive at the console");
+ throw new NullPointerException(MessageManager.getString("exception.application_test_npe"));
}
}
{
if (!loadedWithoutErrors)
{
- throw new IOException("Exception in finding browser: " + errorMessage);
+ throw new IOException(MessageManager.formatMessage("exception.browser_not_found", new String[]{errorMessage}));
}
Object browser = locateBrowser();
if (browser == null)
{
- throw new IOException("Unable to locate browser: " + errorMessage);
+ throw new IOException(MessageManager.formatMessage("exception.browser_unable_to_locate", new String[]{errorMessage}));
}
switch (jvm)
{});
} catch (InvocationTargetException ite)
{
- throw new IOException(
- "InvocationTargetException while creating AEDesc: "
- + ite.getMessage());
+ throw new IOException(MessageManager.formatMessage("exception.invocation_target_exception_creating_aedesc", new String[]{ite.getMessage()}));
} catch (IllegalAccessException iae)
{
- throw new IOException(
- "IllegalAccessException while building AppleEvent: "
- + iae.getMessage());
+ throw new IOException(MessageManager.formatMessage("exception.illegal_access_building_apple_evt", new String[]{iae.getMessage()}));
} catch (InstantiationException ie)
{
- throw new IOException(
- "InstantiationException while creating AEDesc: "
- + ie.getMessage());
+ throw new IOException(MessageManager.formatMessage("exception.illegal_access_building_apple_evt", new String[]{ie.getMessage()}));
} finally
{
aeDesc = null; // Encourage it to get disposed if it was created
}
else
{
- throw new IOException("Unable to launch URL: " + result);
+ throw new IOException(MessageManager.formatMessage("exception.unable_to_launch_url", new String[]{Integer.valueOf(result).toString()}));
}
}
else
{
- throw new IOException(
- "Unable to create an Internet Config instance: " + result);
+ throw new IOException(MessageManager.formatMessage("exception.unable_to_create_internet_config", new String[]{Integer.valueOf(result).toString()}));
}
break;
{ url });
} catch (InvocationTargetException ite)
{
- throw new IOException(
- "InvocationTargetException while calling openURL: "
- + ite.getMessage());
+ throw new IOException(MessageManager.formatMessage("exception.invocation_target_calling_url", new String[]{ite.getMessage()}));
} catch (IllegalAccessException iae)
{
- throw new IOException(
- "IllegalAccessException while calling openURL: "
- + iae.getMessage());
+ throw new IOException(MessageManager.formatMessage("exception.illegal_access_calling_url", new String[]{iae.getMessage()}));
}
break;
process.exitValue();
} catch (InterruptedException ie)
{
- throw new IOException(
- "InterruptedException while launching browser: "
- + ie.getMessage());
+ throw new IOException(MessageManager.formatMessage("exception.interrupted_launching_browser", new String[]{ie.getMessage()}));
}
break;
}
} catch (InterruptedException ie)
{
- throw new IOException(
- "InterruptedException while launching browser: "
- + ie.getMessage());
+ throw new IOException(MessageManager.formatMessage("exception.interrupted_launching_browser", new String[]{ie.getMessage()}));
}
break;
// check for chaincode and mapping
// PFAM style stockhom PDB citation
com.stevesoft.pat.Regex r = new com.stevesoft.pat.Regex(
- "([0-9][0-9A-Za-z]{3})\\s*(.?)\\s*;([0-9]+)-([0-9]+)");
+ "([0-9][0-9A-Za-z]{3})\\s*(.?)\\s*;\\s*([0-9]+)-([0-9]+)");
if (r.search(acn.trim()))
{
String pdbid = r.stringMatched(1);
String chaincode = r.stringMatched(2);
+ if (chaincode==null)
+ {
+ chaincode = " ";
+ }
String mapstart = r.stringMatched(3);
String mapend = r.stringMatched(4);
if (chaincode.equals(" "))
ref = new DBRefEntry(locsrc, version, pdbid + chaincode);
PDBEntry pdbr = new PDBEntry();
pdbr.setId(pdbid);
+ pdbr.setProperty(new Hashtable());
pdbr.getProperty().put("CHAIN", chaincode);
seq.addPDBId(pdbr);
+ } else {
+ System.err.println("Malformed PDB DR line:"+acn);
}
}
else
{ dsstring });
if (idstrings.length != seqstrings.length)
{
- throw new Error(
- "idstrings and seqstrings contain one string each per sequence.");
+ throw new Error(MessageManager.getString("error.idstring_seqstrings_only_one_per_sequence"));
}
return rstrings;
}
{
if (maxs != idseq[i].length)
{
- throw new Error(
- "Cannot have mixed length replacement vectors. Replacement vector for "
- + (mtch[i]) + " is " + idseq[i].length
- + " strings long, and have already seen a "
- + maxs + " length vector.");
+ throw new Error(MessageManager.formatMessage("error.cannot_have_mixed_length_replacement_vectors",
+ new String[]{(mtch[i]), Integer.valueOf(idseq[i].length).toString(),Integer.valueOf(maxs).toString()}));
}
}
}
else
{
- throw new Error(
- "Cannot have zero length vector of replacement strings - either 1 value or n values.");
+ throw new Error(MessageManager.getString("error.cannot_have_zero_length_vector_replacement_strings"));
}
}
// iterate through input, collating segments to be inserted into url
import jalview.gui.AlignFrame;
import jalview.gui.WebserviceInfo;
import jalview.gui.FeatureRenderer.FeatureRendererSettings;
+import jalview.util.MessageManager;
public abstract class AWSThread extends Thread
{
} catch (Exception ex)
{
// Deal with Transaction exceptions
- wsInfo.appendProgressText(jobs[j].jobnum, "\n" + WebServiceName
- + " Server exception!\n" + ex.getMessage());
+ wsInfo.appendProgressText(jobs[j].jobnum,
+ MessageManager.formatMessage("info.server_exception", new String[]{WebServiceName,ex.getMessage()}));
// always output the exception's stack trace to the log
Cache.log.warn(WebServiceName + " job(" + jobs[j].jobnum
+ ") Server exception.");
Cache.log
.debug("WebServiceJob poll loop finished with no jobs created.");
wsInfo.setStatus(wsInfo.STATE_STOPPED_ERROR);
- wsInfo.appendProgressText("No jobs ran.");
+ wsInfo.appendProgressText(MessageManager.getString("info.no_jobs_ran"));
wsInfo.setFinishedNoResults();
}
}
{
if (dbSources == null)
{
- throw new Error("Implementation error. Must initialise dbSources");
+ throw new Error(MessageManager.getString("error.implementation_error_must_init_dbsources"));
}
running = true;
long startTime = System.currentTimeMillis();
- af.setProgressBar("Fetching db refs", startTime);
+ af.setProgressBar(MessageManager.getString("status.fetching_db_refs"), startTime);
try
{
if (Cache.getDefault("DBREFFETCH_USEPICR", false))
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
import jalview.gui.FeatureSettings;
+import jalview.util.MessageManager;
import jalview.util.UrlLink;
import jalview.ws.dbsources.das.api.DasSourceRegistryI;
import jalview.ws.dbsources.das.api.jalviewSourceI;
reply = JOptionPane
.showInternalConfirmDialog(
Desktop.desktop,
- "Do you want Jalview to find\n"
- + "Uniprot Accession ids for given sequence names?",
- "Find Uniprot Accession Ids",
+ MessageManager.getString("info.you_want_jalview_to_find_uniprot_accessions"),
+ MessageManager.getString("label.find_uniprot_accession_ids"),
JOptionPane.YES_NO_OPTION,
JOptionPane.QUESTION_MESSAGE);
}
startTime = System.currentTimeMillis();
if (af != null)
{
- af.setProgressBar("Fetching DAS Sequence Features", startTime);
+ af.setProgressBar(MessageManager.getString("status.fetching_das_sequence_features"), startTime);
}
if (sourceRegistry == null)
{
if (af != null)
{
- af.setProgressBar("No DAS Sources Active", startTime);
+ af.setProgressBar(MessageManager.getString("status.no_das_sources_active"), startTime);
}
if (getFeatSettings() != null)
{
{
if (af != null)
{
- af.setProgressBar("DAS Feature Fetching Cancelled", startTime);
+ af.setProgressBar(MessageManager.getString("status.das_feature_fetching_cancelled"), startTime);
}
cancelled = true;
}
if (!cancelled && af != null)
{
// only update the progress bar if we've completed the fetch normally
- af.setProgressBar("DAS Feature Fetching Complete", startTime);
+ af.setProgressBar(MessageManager.getString("status.das_feature_fetching_complete"), startTime);
}
if (af != null && af.featureSettings != null)
import jalview.gui.Desktop;
import jalview.gui.JvSwingUtils;
import jalview.util.GroupUrlLink;
+import jalview.util.MessageManager;
import jalview.util.GroupUrlLink.UrlStringTooLongException;
import java.awt.Component;
{
dbname = "";
}
- item.setToolTipText("<html>"
- + JvSwingUtils.wrapTooltip("Submit " + i + " " + dbname + " "
- + (seqsorids ? "sequence" : "sequence id")
- + (i > 1 ? "s" : "")
-
- + " to<br/>" + descr) + "</html>");
+ item.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.submit_sequence", new String[]{Integer.valueOf(i).toString(), dbname, (seqsorids ? "sequence" : "sequence id"), (i > 1 ? "s" : "")})));
item.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
JOptionPane
.showInternalMessageDialog(
Desktop.desktop,
- "Unixers: Couldn't find default web browser."
- + "\nAdd the full path to your browser in Preferences.",
- "Web browser not found", JOptionPane.WARNING_MESSAGE);
+ MessageManager.getString("label.web_browser_not_found_unix"),
+ MessageManager.getString("label.web_browser_not_found"), JOptionPane.WARNING_MESSAGE);
ex.printStackTrace();
}
// menu appears asap
// sequence only URLs
// ID/regex match URLs
- JMenu groupLinksMenu = new JMenu("Group Link");
+ JMenu groupLinksMenu = new JMenu(MessageManager.getString("action.group_link"));
String[][] idandseqs = GroupUrlLink.formStrings(seqs);
Hashtable commonDbrefs = new Hashtable();
for (int sq = 0; sq < seqs.length; sq++)
// three types of url that might be
// created.
wflinkMenus = new JMenu[]
- { null, new JMenu("IDS"), new JMenu("Sequences"),
- new JMenu("IDS and Sequences") };
+ { null, new JMenu(MessageManager.getString("action.ids")), new JMenu(MessageManager.getString("action.sequences")),
+ new JMenu(MessageManager.getString("action.ids_sequences")) };
gurlMenus.put(label, wflinkMenus);
}
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.datamodel.xdb.embl.EmblEntry;
+import jalview.util.MessageManager;
import jalview.ws.ebi.EBIFetchClient;
import java.io.File;
} catch (Exception e)
{
stopQuery();
- throw new Exception("EBI EMBL XML retrieval failed on "
- + emprefx.toLowerCase() + ":" + query.trim(), e);
+ throw new Exception(MessageManager.formatMessage("exception.ebiembl_retrieval_failed_on", new String[]{emprefx.toLowerCase(),query.trim()}), e);
}
return getEmblSequenceRecords(emprefx, query, reply);
}
}
else
{
- result.append("# No EMBL record retrieved for "
- + emprefx.toLowerCase() + ":" + query.trim());
+ result.append(MessageManager.formatMessage("label.no_embl_record_found", new String[]{emprefx.toLowerCase(),query.trim()}));
}
}
if (efile != null)
if (seqs != null && seqs.length > 0)
{
al = new Alignment(seqs);
- result.append("# Successfully parsed the " + emprefx
- + " queries into an Alignment");
+ result.append(MessageManager.formatMessage("label.embl_successfully_parsed", new String[]{emprefx}));
results = result;
}
stopQuery();
package jalview.ws.dbsources;
import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.AlignmentI;
import jalview.io.FormatAdapter;
+import jalview.util.MessageManager;
import jalview.ws.ebi.EBIFetchClient;
import jalview.ws.seqfetcher.DbSourceProxy;
for (SequenceI pdbcs : toremove)
{
pdbfile.deleteSequence(pdbcs);
+ if (pdbcs.getAnnotation()!=null)
+ {
+ for (AlignmentAnnotation aa: pdbcs.getAnnotation())
+ {
+ pdbfile.deleteAnnotation(aa);
+ }
+ }
}
}
if (pdbfile == null || pdbfile.getHeight() < 1)
{
- throw new Exception("No PDB Records for " + id + " chain "
- + ((chain == null) ? "' '" : chain));
+ throw new Exception(MessageManager.formatMessage("exception.no_pdb_records_for_chain", new String[]{id, ((chain == null) ? "' '" : chain)}));
}
} catch (Exception ex) // Problem parsing PDB file
import com.stevesoft.pat.Regex;
+import jalview.util.MessageManager;
import jalview.ws.dbsources.das.api.jalviewSourceI;
import jalview.ws.seqfetcher.*;
import jalview.bin.Cache;
if (!(jsrc = new JalviewSource(source, connprops, false))
.isSequenceSource())
{
- throw new Exception("Source " + source.getTitle()
- + " does not support the sequence command.");
+ throw new Exception(MessageManager.formatMessage("exception.das_source_doesnt_support_sequence_command", new String[]{source.getTitle()}));
}
this.tier = 1 + ((jsrc.isLocal() || jsrc.isReferenceSource()) ? 0 : 1);
this.source = source;
import org.biodas.jdas.schema.sources.SOURCE;
import org.biodas.jdas.schema.sources.VERSION;
+import jalview.util.MessageManager;
import jalview.ws.dbsources.das.api.jalviewSourceI;
import jalview.ws.seqfetcher.DbSourceProxy;
int p = cap.getQueryUri().lastIndexOf(capname);
if (p < -1)
{
- throw new Exception("Invalid das source: " + source.getUri());
+ throw new Exception(MessageManager.formatMessage("exception.invalid_das_source", new String[]{source.getUri()}));
}
if (cap.getQueryUri().charAt(p) == '/')
{
*/
package jalview.ws.ebi;
+import jalview.util.MessageManager;
+
import java.io.BufferedInputStream;
import java.io.BufferedReader;
import java.io.File;
public String[] getSupportedDBs()
{
// TODO - implement rest call for dbfetch getSupportedDBs
- throw new Error("Not yet implemented");
+ throw new Error(MessageManager.getString("error.not_yet_implemented"));
}
/**
public String[] getSupportedFormats()
{
// TODO - implement rest call for dbfetch getSupportedFormats
- throw new Error("Not yet implemented");
+ throw new Error(MessageManager.getString("error.not_yet_implemented"));
}
/**
public String[] getSupportedStyles()
{
// TODO - implement rest call for dbfetch getSupportedStyles
- throw new Error("Not yet implemented");
+ throw new Error(MessageManager.getString("error.not_yet_implemented"));
}
public File fetchDataAsFile(String ids, String f, String s)
import jalview.io.FileParse;
import jalview.io.FormatAdapter;
import jalview.io.InputStreamParser;
+import jalview.util.MessageManager;
import java.io.BufferedReader;
import java.io.FileReader;
}
else
{
- throw new IOException(
- "Unexpected exception when handling RNAML translation of PDB data",
+ throw new IOException(MessageManager.getString("exception.unexpected_handling_rnaml_translation_for_pdb"),
x);
}
}
*/
package jalview.ws.jws1;
+import jalview.util.MessageManager;
+
import java.util.*;
import javax.swing.*;
"Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment "
+ "with high accuracy and high throughput, Nucleic Acids Research 32(5), 1792-97.",
"http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS",
- "Muscle Multiple Protein Sequence Alignment"),
+ MessageManager.getString("label.muscle_multiple_protein_sequence_alignment")),
new ServiceHandle(
"MsaWS",
"Katoh, K., K. Kuma, K., Toh, H., and Miyata, T. (2005) "
+ "\"MAFFT version 5: improvement in accuracy of multiple sequence alignment.\""
+ " Nucleic Acids Research, 33 511-518",
"http://www.compbio.dundee.ac.uk/JalviewWS/services/MafftWS",
- "MAFFT Multiple Sequence Alignment"),
+ MessageManager.getString("label.mafft_multiple_sequence_alignment")),
new ServiceHandle(
"MsaWS",
"Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple"
+ " sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice."
+ " Nucleic Acids Research, 22 4673-4680",
"http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS",
- "ClustalW Multiple Sequence Alignment"),
+ MessageManager.getString("label.clustalw_multiple_sequence_alignment")),
new ServiceHandle(
"SecStrPred",
"Cole C., Barber J. D., Barton G.J (2008) "
JOptionPane
.showMessageDialog(
jalview.gui.Desktop.desktop,
- "Please set up your proxy settings in the 'Connections' tab of the Preferences window",
- "Proxy Authorization Failed",
+ MessageManager.getString("label.set_proxy_settings"),
+ MessageManager.getString("label.proxy_authorization_failed"),
JOptionPane.WARNING_MESSAGE);
}
}
import jalview.bin.*;
import jalview.datamodel.*;
import jalview.gui.*;
+import jalview.util.MessageManager;
public class JPredClient extends WS1Client
{
{
if (!msa && msf.length > 1)
{
- throw new Error(
- "Implementation Error! Multiple single sequence prediction jobs are not yet supported.");
+ throw new Error(MessageManager.getString("error.implementation_error_multiple_single_sequence_prediction_jobs_not_supported"));
}
String altitle = getPredictionName(WebServiceName) + " for "
private WebserviceInfo setWebService()
{
WebServiceName = "JNetWS";
- WebServiceJobTitle = "JNet secondary structure prediction";
+ WebServiceJobTitle = MessageManager.getString("label.jnet_secondary_structure_prediction");
WebServiceReference = "\"Cuff J. A and Barton G.J (2000) Application of "
+ "multiple sequence alignment profiles to improve protein secondary structure prediction, "
+ "Proteins 40:502-511\".";
} catch (Exception ex)
{
JOptionPane.showMessageDialog(Desktop.desktop,
- "The Secondary Structure Prediction Service named "
- + WebServiceName + " at " + WsURL
- + " couldn't be located.", "Internal Jalview Error",
+ MessageManager.formatMessage("label.secondary_structure_prediction_service_couldnt_be_located", new String[]{WebServiceName,WsURL}),
+ MessageManager.getString("label.internal_jalview_error"),
JOptionPane.WARNING_MESSAGE);
- wsInfo.setProgressText("Serious! " + WebServiceName
- + " Service location failed\nfor URL :" + WsURL + "\n"
+ wsInfo.setProgressText(MessageManager.formatMessage("label.secondary_structure_prediction_service_couldnt_be_located", new String[]{WebServiceName,WsURL})
+ + "\n"
+ ex.getMessage());
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
if (!jalview.analysis.SeqsetUtils.deuniquify(
(Hashtable) SequenceInfo, sqs))
{
- throw (new Exception(
- "Couldn't recover sequence properties for alignment."));
+ throw (new Exception(MessageManager.getString("exception.couldnt_recover_sequence_properties_for_alignment")));
}
}
FirstSeq = 0;
}
else
{
- throw (new Exception("Unknown format " + format
- + " for file : \n" + result.getAligfile()));
+ throw (new Exception(MessageManager.formatMessage("exception.unknown_format_for_file", new String[]{format,result.getAligfile()})));
}
}
else
.getAlignmentAndColumnSelection(gc))[0];
if (this.msaIndex >= sqs.length)
{
- throw new Error(
- "Implementation Error! Invalid msaIndex for JPredJob on parent MSA input object!");
+ throw new Error(MessageManager.getString("error.implementation_error_invalid_msa_index_for_job"));
}
// ///
// Uses RemoveGapsCommand
// ///
- new jalview.commands.RemoveGapsCommand("Remove Gaps",
+ new jalview.commands.RemoveGapsCommand(MessageManager.getString("label.remove_gaps"),
new SequenceI[]
{ sqs[msaIndex] }, currentView);
if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(
al.getSequenceAt(FirstSeq), SequenceInfo))
{
- throw (new Exception(
- "Couldn't recover sequence properties for JNet Query sequence!"));
+ throw (new Exception(MessageManager.getString("exception.couldnt_recover_sequence_props_for_jnet_query")));
}
else
{
{
if (!(j instanceof JPredJob))
{
- throw new Error(
- "Implementation error - StartJob(JpredJob) called on "
- + j.getClass());
+ throw new Error(MessageManager.formatMessage("error.implementation_error_startjob_called", new String[]{j.getClass().toString()}));
}
try
{
{
job.result = (vamsas.objects.simple.Result) new JpredResult();
job.result.setInvalid(true);
- job.result.setStatus("Submission " + job.getJobId());
+ job.result.setStatus(MessageManager.formatMessage("label.submission_params", new String[]{job.getJobId().toString()}));
throw new Exception(job.getJobId());
}
else
}
else
{
- throw new Exception("Server timed out - try again later\n");
+ throw new Exception(MessageManager.getString("exception.server_timeout_try_later"));
}
} catch (Exception e)
{
{
wsInfo.setStatus(j.getJobnum(), WebserviceInfo.STATE_STOPPED_ERROR);
// JBPNote - this could be a popup informing the user of the problem.
- wsInfo.appendProgressText(j.getJobnum(),
- "Failed to submit the prediction:\n" + e.getMessage()
- + wsInfo.getProgressText());
+ wsInfo.appendProgressText(j.getJobnum(), MessageManager.formatMessage("info.failed_to_submit_prediction", new String[]{e.getMessage(),wsInfo.getProgressText()}));
jalview.bin.Cache.log.debug(
"Failed Submission of job " + j.getJobnum(), e);
else
{
// do merge with other job results
- throw new Error(
- "Multiple JNet subjob merging not yet implemented.");
+ throw new Error(MessageManager.getString("error.multiple_jnet_subjob_merge_not_implemented"));
}
} catch (Exception e)
{
"JNet Client: JPred Annotation Parse Error", e);
wsInfo.setStatus(j.getJobnum(),
WebserviceInfo.STATE_STOPPED_ERROR);
- wsInfo.appendProgressText(j.getJobnum(), OutputHeader + "\n"
- + j.result.getStatus()
- + "\nInvalid JNet job result data!\n" + e.getMessage());
+ wsInfo.appendProgressText(j.getJobnum(), MessageManager.formatMessage("info.invalid_jnet_job_result_data", new String[]{OutputHeader.toString(),j.result.getStatus(), e.getMessage() }));
j.result.setBroken(true);
}
}
public void cancelJob()
{
- throw new Error("Implementation error!");
+ throw new Error(MessageManager.getString("error.implementation_error"));
}
public boolean canMergeResults()
import ext.vamsas.*;
import jalview.datamodel.*;
import jalview.gui.*;
+import jalview.util.MessageManager;
/**
* DOCUMENT ME!
JOptionPane
.showMessageDialog(
Desktop.desktop,
- "The Service called \n"
- + sh.getName()
- + "\nis not a \nMultiple Sequence Alignment Service !",
- "Internal Jalview Error", JOptionPane.WARNING_MESSAGE);
+ MessageManager.formatMessage("label.service_called_is_not_msa_service", new String[]{sh.getName()}),
+ MessageManager.getString("label.internal_jalview_error"), JOptionPane.WARNING_MESSAGE);
return;
}
{
JOptionPane.showMessageDialog(
Desktop.desktop,
- "The Multiple Sequence Alignment Service named "
- + sh.getName() + " is unknown",
- "Internal Jalview Error", JOptionPane.WARNING_MESSAGE);
+ MessageManager.formatMessage("label.msa_service_is_unknown", new String[]{sh.getName()}),
+ MessageManager.getString("label.internal_jalview_error"), JOptionPane.WARNING_MESSAGE);
return;
}
import jalview.bin.*;
import jalview.datamodel.*;
import jalview.gui.*;
+import jalview.util.MessageManager;
import jalview.ws.AWsJob;
import jalview.ws.JobStateSummary;
import jalview.ws.WSClientI;
subjobComplete = true;
result = new MsaResult();
result.setFinished(true);
- result.setStatus("Job never ran - input returned to user.");
+ result.setStatus(MessageManager.getString("label.job_never_ran"));
}
}
int nseqs = 0;
if (minlen < 0)
{
- throw new Error(
- "Implementation error: minlen must be zero or more.");
+ throw new Error(MessageManager.getString("error.implementation_error_minlen_must_be_greater_zero"));
}
for (int i = 0; i < seqs.length; i++)
{
{
if (!(job instanceof MsaWSJob))
{
- throw new Error("StartJob(MsaWSJob) called on a WSJobInstance "
- + job.getClass());
+ throw new Error(MessageManager.formatMessage("error.implementation_error_msawbjob_called", new String[]{job.getClass().toString()}));
}
MsaWSJob j = (MsaWSJob) job;
if (j.isSubmitted())
j.setSubmitted(true);
j.result = new MsaResult();
j.result.setFinished(true);
- j.result.setStatus("Empty Alignment Job");
+ j.result.setStatus(MessageManager.getString("label.empty_alignment_job"));
((MsaResult) j.result).setMsa(null);
}
try
{
if (jobsubmit == null)
{
- throw new Exception(
- "Server at "
- + WsUrl
- + " returned null object, it probably cannot be contacted. Try again later ?");
+ throw new Exception(MessageManager.formatMessage("exception.web_service_returned_null_try_later", new String[]{WsUrl}));
}
throw new Exception(jobsubmit.getJobId());
WebserviceInfo.STATE_STOPPED_SERVERERROR);
wsInfo.appendProgressText(
j.getJobnum(),
- "Failed to submit sequences for alignment.\n"
- + "It is most likely that there is a problem with the server.\n"
- + "Just close the window\n");
+ MessageManager.getString("info.failed_to_submit_sequences_for_alignment"));
// e.printStackTrace(); // TODO: JBPNote DEBUG
}
if (valign != null)
{
wsInfo.appendProgressText(jobs[j].getJobnum(),
- "\nAlignment Object Method Notes\n");
+ MessageManager.getString("info.alignment_object_method_notes"));
String[] lines = valign.getMethod();
for (int line = 0; line < lines.length; line++)
{
import ext.vamsas.*;
import jalview.datamodel.*;
import jalview.gui.*;
+import jalview.util.MessageManager;
/**
* DOCUMENT ME!
if (!sh.getAbstractName().equals(this.getServiceActionKey()))
{
JOptionPane.showMessageDialog(Desktop.desktop,
- "The Service called \n" + sh.getName()
- + "\nis not a \nSequence Search Service !",
- "Internal Jalview Error", JOptionPane.WARNING_MESSAGE);
+ MessageManager.formatMessage("label.service_called_is_not_seq_search_service", new String[]{sh.getName()}),
+ MessageManager.getString("label.internal_jalview_error"), JOptionPane.WARNING_MESSAGE);
return;
}
if ((wsInfo = setWebService(sh)) == null)
{
JOptionPane.showMessageDialog(Desktop.desktop,
- "The Sequence Search Service named " + sh.getName()
- + " is unknown", "Internal Jalview Error",
+ MessageManager.formatMessage("label.seq_search_service_is_unknown", new String[]{sh.getName()}),
+ MessageManager.getString("label.internal_jalview_error"),
JOptionPane.WARNING_MESSAGE);
return;
}
if (!locateWebService())
{
- throw new Exception("Cannot contact service endpoint at " + WsURL);
+ throw new Exception(MessageManager.formatMessage("exception.cannot_contact_service_endpoint_at", new String[]{WsURL}));
}
String database = server.getDatabase();
if (database == null)
import jalview.datamodel.*;
import jalview.gui.*;
import jalview.io.NewickFile;
+import jalview.util.MessageManager;
import jalview.ws.AWsJob;
import jalview.ws.JobStateSummary;
import jalview.ws.WSClientI;
subjobComplete = true;
result = new MsaResult();
result.setFinished(true);
- result.setStatus("Job never ran - input returned to user.");
+ result.setStatus(MessageManager.getString("label.job_never_ran"));
}
}
int nseqs = 0;
if (minlen < 0)
{
- throw new Error(
- "Implementation error: minlen must be zero or more.");
+ throw new Error(MessageManager.getString("error.implementation_error_minlen_must_be_greater_zero"));
}
for (int i = 0; i < seqs.length; i++)
{
{
if (!(job instanceof SeqSearchWSJob))
{
- throw new Error("StartJob(MsaWSJob) called on a WSJobInstance "
- + job.getClass());
+ throw new Error(MessageManager.formatMessage("error.implementation_error_msawbjob_called", new String[]{job.getClass().toString()}));
}
SeqSearchWSJob j = (SeqSearchWSJob) job;
if (j.isSubmitted())
j.setSubmitted(true);
j.result = new MsaResult();
j.result.setFinished(true);
- j.result.setStatus("Empty Alignment Job");
+ j.result.setStatus(MessageManager.getString("label.empty_alignment_job"));
((MsaResult) j.result).setMsa(null);
}
try
{
if (jobsubmit == null)
{
- throw new Exception(
- "Server at "
- + WsUrl
- + " returned null object, it probably cannot be contacted. Try again later ?");
+ throw new Exception(MessageManager.formatMessage("exception.web_service_returned_null_try_later", new String[]{WsUrl}));
}
throw new Exception(jobsubmit.getJobId());
WebserviceInfo.STATE_STOPPED_SERVERERROR);
wsInfo.appendProgressText(
j.getJobnum(),
- "Failed to submit sequences for alignment.\n"
- + "It is most likely that there is a problem with the server.\n"
- + "Just close the window\n");
+ MessageManager.getString("info.failed_to_submit_sequences_for_alignment"));
// e.printStackTrace(); // TODO: JBPNote DEBUG
}
if (valign != null)
{
wsInfo.appendProgressText(jobs[j].getJobnum(),
- "\nAlignment Object Method Notes\n");
+ MessageManager.getString("info.alignment_object_method_notes"));
String[] lines = valign.getMethod();
for (int line = 0; line < lines.length; line++)
{
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
if (nf != null)
{
- af.ShowNewickTree(nf, "Tree from " + this.alTitle);
+ af.ShowNewickTree(nf, MessageManager.formatMessage("label.tree_from", new String[]{this.alTitle}));
}
// initialise with same renderer settings as in parent alignframe.
af.getFeatureRenderer().transferSettings(this.featureSettings);
import jalview.gui.AlignFrame;
import jalview.gui.WebserviceInfo;
+import jalview.util.MessageManager;
import jalview.ws.WSClient;
import jalview.ws.WSMenuEntryProviderI;
{
if (serviceHandle == null)
{
- throw new Error(
- "IMPLEMENTATION ERROR: cannot attach WS Menu Entry without service handle reference!");
+ throw new Error(MessageManager.getString("error.implementation_error_cannot_attach_ws_menu_entry"));
}
attachWSMenuEntry(wsmenu, serviceHandle, alignFrame);
}
import compbio.metadata.PresetManager;
import compbio.metadata.RunnerConfig;
+import jalview.util.MessageManager;
import jalview.ws.jws2.dm.JabaOption;
import jalview.ws.jws2.dm.JabaParameter;
import jalview.ws.jws2.dm.JabaWsParamSet;
}
if (narg == null)
{
- throw new Error(
- "Implementation Error: Cannot handle Jaba parameter object "
- + rg.getClass());
+ throw new Error(MessageManager.formatMessage("error.implementation_error_cannot_handle_jaba_param", new String[]{rg.getClass().toString()}));
}
else
{
.getOption() : null;
if (narg == null)
{
- throw new Error(
- "Implementation Error: Cannot handle Jaba parameter object "
- + rg.getClass());
+ throw new Error(MessageManager.formatMessage("error.implementation_error_cannot_handle_jaba_param", new String[]{rg.getClass().toString()}));
}
else
{
}
if (servicePresets.containsKey(name))
{
- throw new Error(
- "Implementation error: Attempt to delete a service preset!");
+ throw new Error(MessageManager.getString("error.implementation_error_attempt_to_delete_service_preset"));
}
}
: getPreset(presetName));
if (jps == null)
{
- throw new Error("Implementation error: Can't locate either oldname ("
- + oldName + ") or presetName (" + presetName
- + "in the datastore!");
+ throw new Error(MessageManager.formatMessage("error.implementation_error_cannot_locate_oldname_presetname", new String[]{oldName,presetName}));
}
jps.setName(presetName);
jps.setDescription(text);
{
if (!involves(urls))
{
- throw new IOException(
- "Implementation error: Cannot find service url in the given url set!");
+ throw new IOException(MessageManager.getString("error.implementation_error_cannot_find_service_url_in_given_set"));
}
JabaWsParamSet wsp = new JabaWsParamSet();
{
if (!involves(pset.getApplicableUrls()))
{
- throw new IOException(
- "Implementation error: Cannot find service url in the given url set for this service parameter store ("
- + service.getUri() + ") !");
-
+ throw new IOException(MessageManager.formatMessage("error.implementation_error_cannot_find_service_url_in_given_set_param_store", new String[]{service.getUri()}));
}
if (!(pset instanceof JabaWsParamSet))
{
- throw new Error(
- "Implementation error: JabaWsParamSets can only be handled by JabaParamStore");
+ throw new Error(MessageManager.getString("error.implementation_error_jabaws_param_set_only_handled_by"));
}
StringBuffer rslt = new StringBuffer();
*/
package jalview.ws.jws2;
+import jalview.util.MessageManager;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.params.ArgumentI;
import jalview.ws.params.WsParamSetI;
@Override
public void setSourceFile(String newfile)
{
- throw new Error("Cannot set source file for " + getClass());
+ throw new Error(MessageManager.formatMessage("error.cannot_set_source_file_for", new String[]{getClass().toString()}));
}
@Override
} catch (Exception e)
{
e.printStackTrace();
- throw new Error(
- "Probable mismatch between service instance and preset!");
+ throw new Error(MessageManager.getString("error.mismatch_service_instance_preset"));
}
}
@Override
public void setArguments(List<ArgumentI> args)
{
- throw new Error("Cannot set Parameters for a Jaba Web service's preset");
+ throw new Error(MessageManager.getString("error.cannot_set_params_for_ws_preset"));
}
}
import jalview.datamodel.Annotation;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
+import jalview.util.MessageManager;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.params.WsParamSetI;
rslt = aaservice.customAnalize(seqs, getJabaArguments());
} catch (WrongParameterException x)
{
- throw new JobSubmissionException(
- "Invalid parameter set. Check Jalview implementation.", x);
+ throw new JobSubmissionException(MessageManager.getString("exception.jobsubmission_invalid_params_set"), x);
}
}
import jalview.datamodel.Annotation;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
+import jalview.util.MessageManager;
import jalview.workers.AlignCalcWorker;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.params.WsParamSetI;
rslt = msaservice.customAlign(seqs, getJabaArguments());
} catch (WrongParameterException x)
{
- throw new JobSubmissionException(
- "Invalid parameter set. Check Jalview implementation.", x);
-
+ throw new JobSubmissionException(MessageManager.getString("exception.jobsubmission_invalid_params_set"), x);
}
}
return rslt;
* arguments. for (Argument opt : arguments) { newargs.add(opt); } }
* paramset = newargs; } else {
*/
- throw new Error(
- "Implementation error: Can only instantiate Jaba parameter sets.");
+ throw new Error(MessageManager.getString("error.implementation_error_can_only_instantiate_jaba_param_sets"));
}
}
else
final JCheckBoxMenuItem aaConEnabled = new JCheckBoxMenuItem(
aaui.getAAconToggle());
- aaConEnabled.setToolTipText("<html><p>"
- + JvSwingUtils.wrapTooltip(aaui.getAAconToggleTooltip()
- + "</p>") + "</html>");
+ aaConEnabled.setToolTipText(JvSwingUtils.wrapTooltip(true, aaui.getAAconToggleTooltip()));
aaConEnabled.addActionListener(new ActionListener()
{
@Override
wsmenu.add(aaConEnabled);
final JMenuItem modifyParams = new JMenuItem(aaui.getAAeditSettings());
modifyParams.setToolTipText("<html><p>"
- + JvSwingUtils.wrapTooltip(aaui.getAAeditSettingsTooltip()
+ + JvSwingUtils.wrapTooltip(false, aaui.getAAeditSettingsTooltip()
+ "</p>") + "</html>");
modifyParams.addActionListener(new ActionListener()
{
{
// TODO raise dialog box explaining error, and/or open the JABA
// preferences menu.
- throw new Error("No AACon service found.");
+ throw new Error(MessageManager.getString("error.no_aacon_service_found"));
}
return new AAConSettings(true, service, null, null);
}
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
import jalview.gui.JvSwingUtils;
+import jalview.util.MessageManager;
import jalview.ws.WSMenuEntryProviderI;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.params.ParamDatastoreI;
}
});
hitm.setToolTipText(JvSwingUtils
- .wrapTooltip("Opens the JABAWS server's homepage in web browser"));
+ .wrapTooltip(false, MessageManager.getString("label.open_jabaws_web_page ")));
service.attachWSMenuEntry(atpoint, alignFrame);
if (alternates.containsKey(service.serviceType))
{
- atpoint.add(hitm = new JMenu("Switch server"));
+ atpoint.add(hitm = new JMenu(MessageManager.getString("label.switch_server")));
hitm.setToolTipText(JvSwingUtils
- .wrapTooltip("Choose a server for running this service"));
+ .wrapTooltip(false, MessageManager.getString("label.choose_jabaws_server")));
for (final Jws2Instance sv : alternates.get(service.serviceType))
{
JMenuItem itm;
atpoint = JvSwingUtils.findOrCreateMenu(atpoint, host);
if (atpoint.getToolTipText() == null)
{
- atpoint.setToolTipText("Services at " + host);
+ atpoint.setToolTipText(MessageManager.formatMessage("label.services_at", new String[]{host}));
}
}
if (bytype)
}
});
hitm.setToolTipText(JvSwingUtils
- .wrapTooltip("Opens the JABAWS server's homepage in web browser"));
+ .wrapTooltip(true, MessageManager.getString("label.open_jabaws_web_page")));
lasthostFor.put(service.action, host);
}
hostLabels.add(host + service.serviceType
JOptionPane
.showMessageDialog(
Desktop.desktop,
- "The Service called \n"
- + sh.serviceType
- + "\nis not a \nMultiple Sequence Alignment Service !",
- "Internal Jalview Error", JOptionPane.WARNING_MESSAGE);
+ MessageManager.formatMessage("label.service_called_is_not_msa_service", new String[]{sh.serviceType}),
+ MessageManager.getString("label.internal_jalview_error"), JOptionPane.WARNING_MESSAGE);
return;
}
if ((wsInfo = setWebService(sh, false)) == null)
{
JOptionPane.showMessageDialog(Desktop.desktop,
- "The Multiple Sequence Alignment Service named "
- + sh.serviceType + " is unknown",
- "Internal Jalview Error", JOptionPane.WARNING_MESSAGE);
+ MessageManager.formatMessage("label.msa_service_is_unknown", new String[]{sh.serviceType}),
+ MessageManager.getString("label.internal_jalview_error"), JOptionPane.WARNING_MESSAGE);
return;
}
for (final WsParamSetI preset : presets)
{
final JMenuItem methodR = new JMenuItem(preset.getName());
- methodR.setToolTipText("<html><p>"
- + JvSwingUtils.wrapTooltip("<strong>"
- + (preset.isModifiable() ? "User Preset"
- : "Service Preset") + "</strong><br/>"
- + preset.getDescription() + "</p>") + "</html>");
+ methodR.setToolTipText(JvSwingUtils.wrapTooltip(true, "<p><strong>"
+ + (preset.isModifiable() ? MessageManager.getString("label.user_preset")
+ : MessageManager.getString("label.service_preset")) + "</strong><br/>"
+ + preset.getDescription() + "</p>"));
methodR.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
import jalview.bin.*;
import jalview.datamodel.*;
import jalview.gui.*;
+import jalview.util.MessageManager;
import jalview.ws.AWsJob;
import jalview.ws.WSClientI;
import jalview.ws.JobStateSummary;
int nseqs = 0;
if (minlen < 0)
{
- throw new Error(
- "Implementation error: minlen must be zero or more.");
+ throw new Error(MessageManager.getString("error.implementation_error_minlen_must_be_greater_zero"));
}
for (int i = 0; i < seqs.length; i++)
{
// boiler plate template
if (!(job instanceof MsaWSJob))
{
- throw new Error("StartJob(MsaWSJob) called on a WSJobInstance "
- + job.getClass());
+ throw new Error(MessageManager.formatMessage("error.implementation_error_msawbjob_called", new String[]{job.getClass().toString()}));
}
MsaWSJob j = (MsaWSJob) job;
if (j.isSubmitted())
{
// special case - selection consisted entirely of empty sequences...
j.setjobStatus(JobStatus.FINISHED);
- j.setStatus("Empty Alignment Job");
+ j.setStatus(MessageManager.getString("label.empty_alignment_job"));
}
try
{
}
else
{
- throw new Exception(
- "Server at "
- + WsUrl
- + " returned null string for job id, it probably cannot be contacted. Try again later ?");
+ throw new Exception(MessageManager.formatMessage("exception.web_service_returned_null_try_later", new String[]{WsUrl}));
}
} catch (compbio.metadata.UnsupportedRuntimeException _lex)
{
lex = _lex;
- wsInfo.appendProgressText("Job could not be run because the server doesn't support this program.\n"
- + _lex.getMessage());
- wsInfo.warnUser(_lex.getMessage(), "Service not supported!");
+ wsInfo.appendProgressText(MessageManager.formatMessage("info.job_couldnt_be_run_server_doesnt_support_program", new String[]{_lex.getMessage()}));
+ wsInfo.warnUser(_lex.getMessage(), MessageManager.getString("warn.service_not_supported"));
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
wsInfo.setStatus(j.getJobnum(),
WebserviceInfo.STATE_STOPPED_SERVERERROR);
} catch (compbio.metadata.LimitExceededException _lex)
{
lex = _lex;
- wsInfo.appendProgressText("Job could not be run because it exceeded a hard limit on the server.\n"
- + _lex.getMessage());
- wsInfo.warnUser(_lex.getMessage(), "Input is too big!");
+ wsInfo.appendProgressText(MessageManager.formatMessage("info.job_couldnt_be_run_exceeded_hard_limit", new String[]{_lex.getMessage()}));
+ wsInfo.warnUser(_lex.getMessage(), MessageManager.getString("warn.input_is_too_big"));
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
wsInfo.setStatus(j.getJobnum(), WebserviceInfo.STATE_STOPPED_ERROR);
} catch (compbio.metadata.WrongParameterException _lex)
{
lex = _lex;
- wsInfo.warnUser(_lex.getMessage(), "Invalid job parameter set!");
- wsInfo.appendProgressText("Job could not be run because some of the parameter settings are not supported by the server.\n"
- + _lex.getMessage()
- + "\nPlease check to make sure you have used the correct parameter set for this service!\n");
+ wsInfo.warnUser(_lex.getMessage(), MessageManager.getString("warn.invalid_job_param_set"));
+ wsInfo.appendProgressText(MessageManager.formatMessage("info.job_couldnt_be_run_incorrect_param_setting", new String[]{_lex.getMessage()}));
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
wsInfo.setStatus(j.getJobnum(), WebserviceInfo.STATE_STOPPED_ERROR);
} catch (Error e)
j.setAllowedServerExceptions(0);
wsInfo.appendProgressText(j.getJobnum(),
- "Failed to submit sequences for alignment.\n"
- + "Just close the window\n");
+ MessageManager.getString("info.failed_to_submit_sequences_for_alignment"));
}
}
}
public void parseResult()
{
long progbar = System.currentTimeMillis();
- wsInfo.setProgressBar("Collecting job results.", progbar);
+ wsInfo.setProgressBar(MessageManager.getString("status.collecting_job_results"), progbar);
int results = 0; // number of result sets received
JobStateSummary finalState = new JobStateSummary();
try
*/
package jalview.ws.jws2;
+import jalview.util.MessageManager;
+
import java.net.MalformedURLException;
import java.util.ArrayList;
import java.util.HashSet;
} catch (Exception e)
{
e.printStackTrace();
- throw new Error(
- "Implementation error: could not copy ValueConstrain!");
+ throw new Error(MessageManager.getString("error.implementation_error_couldnt_copy_value_constraint"));
}
}
} catch (Exception x)
{
x.printStackTrace();
- throw new Error("Implementation error", x);
+ throw new Error(MessageManager.getString("error.implementation_error"), x);
}
alignFrame.getViewport().getCalcManager().registerWorker(worker);
alignFrame.getViewport().getCalcManager().startWorker(worker);
List<WsParamSetI> presets = service.getParamStore().getPresets();
if (presets != null && presets.size() > 0)
{
- JMenu presetlist = new JMenu("Run " + calcName + "with preset");
+ JMenu presetlist = new JMenu(MessageManager.formatMessage("label.run_with_preset", new String[]{calcName}));
for (final WsParamSetI preset : presets)
{
final JMenuItem methodR = new JMenuItem(preset.getName());
- methodR.setToolTipText("<html><p>"
- + JvSwingUtils.wrapTooltip("<strong>"
- + (preset.isModifiable() ? "User Preset"
- : "Service Preset") + "</strong><br/>"
- + preset.getDescription() + "</p>") + "</html>");
+ methodR.setToolTipText(JvSwingUtils.wrapTooltip(true, "<strong>"
+ + (preset.isModifiable() ? MessageManager.getString("label.user_preset")
+ : MessageManager.getString("label.service_preset")) + "</strong><br/>"
+ + preset.getDescription()));
methodR.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
Desktop.instance.showUrl(service.docUrl);
}
});
- annotservice.setToolTipText("<html>"
- + JvSwingUtils.wrapTooltip("View <a href=\""
- + service.docUrl + "\">" + service.docUrl + "</a>")
- + "</html>");
+ annotservice.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.view_service_doc_url", new String[]{service.docUrl,service.docUrl})));
wsmenu.add(annotservice);
}
}
import compbio.metadata.Argument;
import compbio.metadata.Option;
+import jalview.util.MessageManager;
import jalview.ws.jws2.JabaParamStore;
import jalview.ws.jws2.JabaPreset;
import jalview.ws.jws2.ParameterUtils;
return;
}
// Try even harder to migrate arguments.
- throw new Error("Parameter migration not implemented yet");
+ throw new Error(MessageManager.getString("error.parameter_migration_not_implemented_yet"));
}
}
*/
package jalview.ws.jws2.dm;
+import jalview.util.MessageManager;
import jalview.ws.jws2.ParameterUtils;
import jalview.ws.params.OptionI;
} catch (Exception e)
{
e.printStackTrace();
- throw new Error(
- "Implementation error: cannot set Jaba Option to a value outside its allowed value range!");
+ throw new Error(MessageManager.getString("error.implementation_error_cannot_set_jaba_option"));
}
}
import compbio.metadata.ValueConstrain;
+import jalview.util.MessageManager;
import jalview.ws.params.ValueConstrainI;
public class JabaValueConstrain implements ValueConstrainI
{
return ValueType.Integer;
}
- throw new Error(
- "IMPLEMENTATION ERROR: jalview.ws.params.ValueConstrainI.ValueType does not support the JABAWS type :"
- + vc.toString());
+ throw new Error(MessageManager.formatMessage("error.implementation_error_valuetype_doesnt_support_jabaws_type", new String[]{vc.toString()}));
}
@Override
import compbio.metadata.Option;
+import jalview.util.MessageManager;
import jalview.ws.jws2.JabaParamStore;
import jalview.ws.params.ArgumentI;
import jalview.ws.params.WsParamSetI;
{
if (!allJaba(jobParams))
{
- throw new Error(
- "Cannot create a JabaWSParamSet from non-JabaWS parameters");
+ throw new Error(MessageManager.getString("error.cannot_create_jabaws_param_set"));
}
else
{
{
if (!allJaba(args))
{
- throw new Error(
- "Cannot set arguments to a JabaWSParamSet that are not JabaWS arguments");
+ throw new Error(MessageManager.getString("error.cannot_set_arguments_to_jabaws_param_set"));
}
jabaArguments = new ArrayList<Option>();
for (ArgumentI rg : args)
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
+import jalview.util.MessageManager;
import jalview.ws.jws2.JabaParamStore;
import jalview.ws.jws2.MsaWSClient;
import jalview.ws.jws2.SequenceAnnotationWSClient;
{
return ((SequenceAnnotation) service).getRunnerOptions();
}
- throw new Error(
- "Implementation Error: Runner Config not available for a JABAWS service of type "
- + serviceType + " (" + service.getClass() + ")");
+ throw new Error(MessageManager.formatMessage("error.implementation_error_runner_config_not_available", new String[]{serviceType,service.getClass().toString()}));
}
@Override
import jalview.io.packed.ParsePackedSet;
import jalview.io.packed.SimpleDataProvider;
import jalview.io.packed.DataProvider.JvDataType;
+import jalview.util.MessageManager;
import jalview.ws.io.mime.JalviewMimeContentHandler;
import java.io.BufferedReader;
if (en == null)
{
- throw new Error(
- "Implementation Error: need to have an HttpResponse to process.");
+ throw new Error(MessageManager.getString("error.implementation_error_need_to_have_httpresponse"));
}
jalview.io.packed.JalviewDataset ds = restJob.newJalviewDataset();
// Decide how we deal with content.
import jalview.gui.Desktop;
import jalview.gui.WebserviceInfo;
import jalview.io.packed.DataProvider.JvDataType;
+import jalview.util.MessageManager;
import jalview.ws.WSClient;
import jalview.ws.WSClientI;
import jalview.ws.WSMenuEntryProviderI;
public void setWebserviceInfo(boolean headless)
{
- WebServiceJobTitle = service.details.Action + " using "
- + service.details.Name;
+ WebServiceJobTitle = MessageManager.formatMessage("label.webservice_job_title", new String[]{service.details.Action,service.details.Name});
WebServiceName = service.details.Name;
WebServiceReference = "No reference - go to url for more info";
if (service.details.description != null)
final AlignFrame alignFrame)
{
JMenuItem submit = new JMenuItem(service.details.Name);
- submit.setToolTipText(service.details.Action + " using "
- + service.details.Name);
+ submit.setToolTipText(MessageManager.formatMessage("label.rest_client_submit", new String[]{service.details.Action,service.details.Name}));
submit.addActionListener(new ActionListener()
{
_input = new AlignmentView(av.getAlignment(),
av.getColumnSelection(), av.getSelectionGroup(),
av.hasHiddenColumns(), true, true);
- viewTitle = "selected "
- + (av.hasHiddenColumns() ? "visible" : "")
- + " region of " + af.getTitle();
+ viewTitle = MessageManager.formatMessage("label.select_visible_region_of", new String[]{(av.hasHiddenColumns() ? MessageManager.getString("label.visible") : ""),af.getTitle()});
}
else
{
av.getColumnSelection(), av.getSelectionGroup(),
av.hasHiddenColumns(), false, true);
}
- viewTitle = "select and unselected "
- + (av.hasHiddenColumns() ? "visible" : "")
- + " regions from " + af.getTitle();
+ viewTitle = MessageManager.formatMessage("label.select_unselect_visible_regions_from", new String[]{(av.hasHiddenColumns() ? MessageManager.getString("label.visible") : ""),af.getTitle()});
}
else
{
_input = new AlignmentView(av.getAlignment(),
av.getColumnSelection(), av.getSelectionGroup(),
av.hasHiddenColumns(), true, true);
- viewTitle = "selected " + (av.hasHiddenColumns() ? "visible" : "")
- + " region of " + af.getTitle();
+ viewTitle = MessageManager.formatMessage("label.select_visible_region_of", new String[]{(av.hasHiddenColumns() ? MessageManager.getString("label.visible") : ""),af.getTitle()});
}
}
else
_input = new AlignmentView(av.getAlignment(),
av.getColumnSelection(), null, av.hasHiddenColumns(), false,
true);
- viewTitle = "" + (av.hasHiddenColumns() ? "visible region of " : "")
+ viewTitle = "" + (av.hasHiddenColumns() ? (new StringBuffer(" ").append(MessageManager.getString("label.visible_region_of")).toString()) : "")
+ af.getTitle();
}
.showMessageDialog(
Desktop.desktop,
(jobsthread.hasWarnings() ? jobsthread.getWarnings()
- : "The Job couldn't be started. Please check your input, and the Jalview console for any warning messages."),
- "Unable to start web service analysis",
+ : MessageManager.getString("label.job_couldnt_be_started_check_input")),
+ MessageManager.getString("label.unable_start_web_service_analysis"),
JOptionPane.WARNING_MESSAGE);
}
}
public static RestClient makeShmmrRestClient()
{
- String action = "Analysis", description = "Sequence Harmony and Multi-Relief (Brandt et al. 2010)", name = "Multi-Harmony";
+ String action = "Analysis", description = "Sequence Harmony and Multi-Relief (Brandt et al. 2010)", name = MessageManager.getString("label.multiharmony");
Hashtable<String, InputType> iparams = new Hashtable<String, InputType>();
jalview.ws.rest.params.JobConstant toolp;
// toolp = new jalview.ws.rest.JobConstant("tool","jalview");
import jalview.io.NewickFile;
import jalview.io.packed.JalviewDataset;
import jalview.io.packed.JalviewDataset.AlignmentSet;
+import jalview.util.MessageManager;
import jalview.ws.AWSThread;
import jalview.ws.AWsJob;
destAls.add(destAl);
destColsel.add(destCs);
resultDest.add(AddDataTo.newAlignment);
- throw new Error("Impl. Error! TODO: ");
+ throw new Error(MessageManager.getString("error.implementation_error")+"TODO: ");
}
}
/**
{
AlignmentI destal;
ColumnSelection destcs;
- String alTitle = restClient.service.details.Action + " using "
- + restClient.service.details.Name + " on "
- + restClient.viewTitle;
+ String alTitle = MessageManager.formatMessage("label.webservice_job_title_on", new String[]{restClient.service.details.Action,restClient.service.details.Name,restClient.viewTitle});
switch (action)
{
case newAlignment:
*/
package jalview.ws.rest.params;
+import jalview.util.MessageManager;
import jalview.ws.params.OptionI;
import jalview.ws.rest.InputType;
import jalview.ws.rest.NoValidInputDataException;
prm.add(URLEncoder.encode(value, "UTF-8"));
} catch (UnsupportedEncodingException ex)
{
- throw new Error("Couldn't encode '" + value + "' as UTF-8.", ex);
+ throw new Error(MessageManager.formatMessage("error.couldnt_encode_as_utf8", new String[]{value}), ex);
}
}
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
import jalview.ws.params.OptionI;
import jalview.ws.params.simple.IntegerParameter;
import jalview.ws.params.simple.Option;
{
if (sg.getSize() < minsize)
{
- throw new NoValidInputDataException("Group contains less than "
- + minsize + " sequences.");
+ throw new NoValidInputDataException(MessageManager.formatMessage("exception.notvaliddata_group_contains_less_than_min_seqs", new String[]{Integer.valueOf(minsize).toString()}));
}
// TODO: refactor to sequenceGroup for efficiency -
// getAlignmentRowInterval(AlignmentI al)
*/
package jalview.ws.rest.params;
+import jalview.util.MessageManager;
import jalview.ws.params.OptionI;
import jalview.ws.rest.InputType;
import jalview.ws.rest.RestJob;
/*
* rj.getTreeForInput(token); return new StringBody(new )
*/
- throw new Error("Tree InputType not yet implemented");
+ throw new Error(MessageManager.getString("error.tree_inputtype_not_yet_implemented"));
// return null;
}
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.SequenceI;
import jalview.util.DBRefUtils;
+import jalview.util.MessageManager;
import java.util.ArrayList;
import java.util.Enumeration;
} catch (Exception e)
{
// Serious problems if this happens.
- throw new Error("DBRefSource Implementation Exception", e);
+ throw new Error(MessageManager.getString("error.dbrefsource_implementation_exception"), e);
}
addDbRefSourceImpl(proxy);
}
{
if (!jalview.ws.seqfetcher.DbSourceProxy.class.isAssignableFrom(class1))
{
- throw new Error(
- "Implmentation Error - getDbInstances must be given a class that implements jalview.ws.seqfetcher.DbSourceProxy (was given '"
- + class1 + "')");
+ throw new Error(MessageManager.formatMessage("error.implementation_error_dbinstance_must_implement_interface", new String[]{class1.toString()}));
}
if (FETCHABLEDBS == null)
{
*/
package org.jibble.epsgraphics;
+import jalview.util.MessageManager;
+
import java.io.*;
import java.util.*;
_bufferedWriter.write(line + "\n");
} catch (IOException e)
{
- throw new EpsException("Could not write to the output file: " + e);
+ throw new EpsException(MessageManager.formatMessage("exception.eps_coudnt_write_output_file", new String[]{e.getMessage()}));
}
}
*/
package org.jibble.epsgraphics;
+import jalview.util.MessageManager;
+
import java.io.*;
import java.text.*;
import java.util.*;
*/
private void methodNotSupported()
{
- EpsException e = new EpsException(
- "Method not currently supported by EpsGraphics2D version "
- + VERSION);
+ EpsException e = new EpsException(MessageManager.formatMessage("exception.eps_method_not_supported", new String[]{VERSION}));
e.printStackTrace(System.err);
}
return t.createTransformedShape(_clip);
} catch (Exception e)
{
- throw new EpsException("Unable to get inverse of matrix: "
- + _transform);
+ throw new EpsException(MessageManager.formatMessage("exception.eps_unable_to_get_inverse_matrix", new String[]{_transform.toString()}));
}
}
}
matrix = matrix.createInverse();
} catch (Exception e)
{
- throw new EpsException("Unable to get inverse of matrix: " + matrix);
+ throw new EpsException(MessageManager.formatMessage("exception.eps_unable_to_get_inverse_matrix", new String[]{matrix.toString()}));
}
matrix.scale(1, -1);
matrix.getMatrix(m);
*/
package uk.ac.ebi.www;
+import jalview.util.MessageManager;
+
public class WSWUBlastServiceLocator extends org.apache.axis.client.Service
implements uk.ac.ebi.www.WSWUBlastService
{
{
throw new javax.xml.rpc.ServiceException(t);
}
- throw new javax.xml.rpc.ServiceException(
- "There is no stub implementation for the interface: "
- + (serviceEndpointInterface == null ? "null"
- : serviceEndpointInterface.getName()));
+ throw new javax.xml.rpc.ServiceException(MessageManager.formatMessage("exception.no_stub_implementation_for_interface", new String[]{(serviceEndpointInterface == null ? "null": serviceEndpointInterface.getName())}));
}
/**
*/
package uk.ac.ebi.www.picr.AccessionMappingService;
+import jalview.util.MessageManager;
+
public class AccessionMapperServiceLocator extends
org.apache.axis.client.Service implements
uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperService
{
throw new javax.xml.rpc.ServiceException(t);
}
- throw new javax.xml.rpc.ServiceException(
- "There is no stub implementation for the interface: "
- + (serviceEndpointInterface == null ? "null"
- : serviceEndpointInterface.getName()));
+ throw new javax.xml.rpc.ServiceException(MessageManager.formatMessage("exception.no_stub_implementation_for_interface", new String[]{(serviceEndpointInterface == null ? "null": serviceEndpointInterface.getName())}));
}
/**
}
else
{ // Unknown Port Name
- throw new javax.xml.rpc.ServiceException(
- " Cannot set Endpoint Address for Unknown Port" + portName);
+ throw new javax.xml.rpc.ServiceException(MessageManager.formatMessage("exception.cannot_set_endpoint_address_unknown_port", new String[]{portName}));
}
}
public class PDBFileWithJmolTest
{
String[] testFile = new String[]
- { "./examples/1GAQ.txt" }; // , "./examples/DNMT1_MOUSE.pdb" };
+ { "./examples/1GAQ.txt" }; // ,
+
+ // "./examples/DNMT1_MOUSE.pdb"
+ // };
@Test
- public void testAlignmentLoader() throws Exception
- {
- for (String f:testFile) {
+ public void testAlignmentLoader() throws Exception
+ {
+ for (String f : testFile)
+ {
FileLoader fl = new jalview.io.FileLoader(false);
- AlignFrame af = fl.LoadFileWaitTillLoaded(f, AppletFormatAdapter.FILE);
+ AlignFrame af = fl
+ .LoadFileWaitTillLoaded(f, AppletFormatAdapter.FILE);
validateSecStrRows(af.getViewport().getAlignment());
}
- }
+ }
+
@Test
public void testFileParser() throws Exception
{
private void validateSecStrRows(AlignmentI al)
{
-
if (!al.isNucleotide())
{
for (SequenceI asq : al.getSequences())
{
SequenceI sq = asq;
- while (sq.getDatasetSequence()!=null && sq.getAnnotation()==null)
+ boolean hasDs = false;
+ while (sq.getDatasetSequence() != null
+ && sq.getAnnotation() == null)
{
- sq = asq.getDatasetSequence();
+ sq = sq.getDatasetSequence();
+ hasDs = true;
+ }
+ checkFirstAAIsAssoc(sq);
+ if (hasDs)
+ {
+ // also verify if alignment sequence has annotation on it
+ // that is correctly mapped
+ checkFirstAAIsAssoc(asq);
}
- assertTrue(
- "No secondary structure assigned for protein sequence.",
- sq.getAnnotation() != null
- && sq.getAnnotation().length >= 1
- && sq.getAnnotation()[0].hasIcons);
- assertTrue(
- "Secondary structure not associated for sequence "
- + sq.getName(),
- sq.getAnnotation()[0].sequenceRef == sq);
}
}
}
+
+ private void checkFirstAAIsAssoc(SequenceI sq)
+ {
+ assertTrue("No secondary structure assigned for protein sequence.",
+ sq.getAnnotation() != null && sq.getAnnotation().length >= 1
+ && sq.getAnnotation()[0].hasIcons);
+ assertTrue(
+ "Secondary structure not associated for sequence "
+ + sq.getName(), sq.getAnnotation()[0].sequenceRef == sq);
+ }
}
--- /dev/null
+>1PHT
+YQYRALYDYKKEREEDIDLHLGDILTVNKGSLVALGFSDGQEARPEEI--
+--------GWLNGYNETTGERGDFPGTYVEYIG
+>1BB9
+FKVQAQHDYTATDTDELQLKAGDVVLVIP-------FQNP----EEQDEG
+WLMGVKESDWNQHK-ELEKCRGVFPENFTERVQ
+>1UHC
+QVYFAVYTFKARNPNELSVSANQKLKILE-------FKDV----TGNT--
+--------EWWLAE--VNGKKGYVPSNYIRKTE
+>1YCS
+GVIYALWDYEPQNDDELPMKEGDCMTIIH-------REDE----D-EI--
+--------EWWWA--RLNDKEGYVPRNLLGLYP
+>1OOT
+PKAVALYSFAGEESGDLPFRKGDVITILKK-------S------DSQN--
+--------DWWTG--RVNGREGIFPANYVE-LV
+>1ABO
+NLFVALYDFVASGDNTLSITKGEKLRVLG-------YNH-------NG--
+--------EWCEAQ--TKNGQGWVPSNYITPVN
+>1FYN
+TLFVALYDYEARTEDDLSFHKGEKFQILN-------SS--------EG--
+--------DWWEARSLTTGETGYIPSNYVAPVD
+>1QCF
+IIVVALYDYEAIHHEDLSFQKGDQMVVLE-------E---------SG--
+--------EWWKARSLATRKEGYIPSNYVARVD
\ No newline at end of file
-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.ws;
-
-import static org.junit.Assert.*;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SequenceI;
-import jalview.ws.seqfetcher.DbSourceProxy;
-
-import java.util.List;
-
-import org.junit.Before;
-import org.junit.Test;
-
-public class PDBSequenceFetcherTest
-{
-
- SequenceFetcher sf;
-
- @Before
- public void setUp() throws Exception
- {
- sf = new SequenceFetcher(false);
- }
-
- @Test
- public void testPdbPerChainRetrieve() throws Exception
- {
- List<DbSourceProxy> sps = sf.getSourceProxy("PDB");
- AlignmentI response = sps.get(0).getSequenceRecords("1QIPA");
- assertTrue(response != null);
- assertTrue(response.getHeight() == 1);
- }
-
- @Test
- public void testRnaSeqRetrieve() throws Exception
- {
- List<DbSourceProxy> sps = sf.getSourceProxy("PDB");
- AlignmentI response = sps.get(0).getSequenceRecords("2GIS");
- assertTrue(response != null);
- assertTrue(response.getHeight() == 1);
- for (SequenceI sq : response.getSequences())
- {
- assertTrue("No annotation transfered to sequence.",
- sq.getAnnotation().length > 0);
- assertTrue("No PDBEntry on sequence.", sq.getPDBId().size() > 0);
- assertTrue("No RNA annotation on sequence.", sq.getRNA() != null);
- }
- }
-
-}
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)\r
+ * Copyright (C) 2014 The Jalview Authors\r
+ * \r
+ * This file is part of Jalview.\r
+ * \r
+ * Jalview is free software: you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License \r
+ * as published by the Free Software Foundation, either version 3\r
+ * of the License, or (at your option) any later version.\r
+ * \r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License\r
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
+ * The Jalview Authors are detailed in the 'AUTHORS' file.\r
+ */\r
+package jalview.ws;\r
+\r
+import static org.junit.Assert.*;\r
+import jalview.datamodel.AlignmentI;\r
+import jalview.datamodel.SequenceI;\r
+import jalview.ws.seqfetcher.DbSourceProxy;\r
+\r
+import java.util.List;\r
+\r
+import org.junit.Before;\r
+import org.junit.Test;\r
+\r
+public class PDBSequenceFetcherTest\r
+{\r
+\r
+ SequenceFetcher sf;\r
+\r
+ @Before\r
+ public void setUp() throws Exception\r
+ {\r
+ sf = new SequenceFetcher(false);\r
+ }\r
+\r
+ @Test\r
+ public void testRnaSeqRetrieve() throws Exception\r
+ {\r
+ List<DbSourceProxy> sps = sf.getSourceProxy("PDB");\r
+ AlignmentI response = sps.get(0).getSequenceRecords("2GIS");\r
+ assertTrue(response != null);\r
+ assertTrue(response.getHeight() == 1);\r
+ for (SequenceI sq : response.getSequences())\r
+ {\r
+ assertTrue("No annotation transfered to sequence.",\r
+ sq.getAnnotation().length > 0);\r
+ assertTrue("No PDBEntry on sequence.", sq.getPDBId().size() > 0);\r
+ assertTrue("No RNA annotation on sequence.", sq.getRNA() != null);\r
+ }\r
+ }\r
+\r
+}\r
import static org.junit.Assert.*;
import jalview.gui.WsJobParameters;
+import jalview.util.MessageManager;
import jalview.ws.jabaws.JalviewJabawsTestUtils;
import jalview.ws.jws2.JabaPreset;
import jalview.ws.jws2.Jws2Discoverer;
}
WsJobParameters pgui = new WsJobParameters(lastserv,
new JabaPreset(lastserv, pr));
- JFrame jf = new JFrame("Parameters for "
- + lastserv.getActionText());
+ JFrame jf = new JFrame(MessageManager.formatMessage("label.ws_parameters_for", new String[]{lastserv.getActionText()}));
JPanel cont = new JPanel(new BorderLayout());
pgui.validate();
cont.setPreferredSize(pgui.getPreferredSize());
--- /dev/null
+package jalview.ws.jabaws;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.fail;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.function.Consumer;
+
+import org.junit.Test;
+
+import compbio.data.msa.MsaWS;
+import compbio.data.msa.RegistryWS;
+import compbio.data.sequence.FastaSequence;
+import compbio.metadata.JobStatus;
+import compbio.ws.client.Jws2Client;
+import compbio.ws.client.Services;
+
+public class MinJabawsClientTests {
+
+ /**
+ * simple test for the benefit of JAL-1338
+ * @throws Exception
+ */
+ @SuppressWarnings("rawtypes")
+ @Test
+ public void msaTest() throws Exception {
+ String url;
+ RegistryWS registry = Jws2Client
+ .connectToRegistry(url = "http://www.compbio.dundee.ac.uk/jabaws");
+ if (registry != null) {
+
+ MsaWS msaservice = null;
+ for (Services service : registry.getSupportedServices()) {
+ if (service.equals(Services.ClustalOWS)) {
+ msaservice = (MsaWS) Jws2Client.connect(url, service);
+ if (msaservice != null) {
+ break;
+ }
+ }
+ }
+ if (msaservice == null) {
+ fail("couldn't find a clustalO service on the public registry");
+ }
+ FastaSequence fsq = new FastaSequence("seqA",
+ "SESESESESESESESSESESSESESESESESESESESESEEEEEESSESESESESSSSESESESESESESE");
+ List<FastaSequence> iseqs = new ArrayList<FastaSequence>();
+ for (int i = 0; i < 9; i++) {
+ iseqs.add(new FastaSequence(fsq.getId() + i, fsq.getSequence()
+ + fsq.getSequence().substring(i + 3, i + 3 + i)));
+ }
+
+ String jobid = msaservice.align(iseqs);
+ if (jobid != null) {
+ JobStatus js = null;
+ do {
+ try {
+ Thread.sleep(500);
+ } catch (InterruptedException q) {
+ }
+ ;
+ js = msaservice.getJobStatus(jobid);
+ } while (!js.equals(JobStatus.FAILED)
+ && !js.equals(JobStatus.CANCELLED)
+ && !js.equals(JobStatus.FINISHED));
+ assertEquals("Trial alignment failed. State was " + js.name(),
+ js, JobStatus.FINISHED);
+ assertEquals(
+ "Mismatch in number of input and result sequences - assume alignment service wasn't interacted with correctly",
+ msaservice.getResult(jobid).getSequences().size(),
+ iseqs.size());
+ msaservice.getResult(jobid).getSequences()
+ .forEach(new Consumer<FastaSequence>() {
+ @Override
+ public void accept(FastaSequence t) {
+ System.out.println(">"+t.getId());
+ System.out.println(t.getFormattedFasta());
+ }
+ });
+ }
+
+ }
+ }
+}
git://source.jalview.org / jalview.git / commitdiff