From: darolmar Date: Tue, 23 Sep 2014 14:34:33 +0000 (+0200) Subject: JAL-1355 X-Git-Tag: Release_2_8_2b1^2~50^2~4 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=aced09c4feeaf3406269442c14e54abeeb4cad81;p=jalview.git JAL-1355 --- diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties index 8727627..5c0c9c5 100644 --- a/resources/lang/Messages.properties +++ b/resources/lang/Messages.properties @@ -58,7 +58,7 @@ action.by_id = by Id action.by_length = by Length action.by_group = by Group action.remove = Remove -action.remove_redundancy = Remove Redundancy... +action.remove_redundancy = Remove Redundancy action.pairwise_alignment = Pairwise Alignments... action.by_rna_helixes = by RNA Helices action.user_defined = User Defined... @@ -308,7 +308,7 @@ label.to_file = to File label.to_textbox = to Textbox label.jalview = Jalview label.csv_spreadsheet = CSV (Spreadsheet) -label.status = [Status] +label.status = Status label.channels = Channels label.channel_title_item_count = {0} ({1}) label.blog_item_published_on_date = {0} {1} @@ -455,8 +455,8 @@ label.settings_for_type = Settings for {0} label.view_full_application = View in Full Application label.load_associated_tree = Load Associated Tree ... label.load_features_annotations = Load Features/Annotations ... -label.export_features = Export Features ... -label.export_annotations = Export Annotations ... +label.export_features = Export Features +label.export_annotations = Export Annotations label.jalview_copy = Copy (Jalview Only) label.jalview_cut = Cut (Jalview Only) label.to_upper_case = To Upper Case @@ -647,7 +647,7 @@ label.edit_sequence_name_description = Edit Sequence Name/Description label.spaces_converted_to_backslashes = Spaces have been converted to _ label.no_spaces_allowed_sequence_name = No spaces allowed in Sequence Name label.select_outline_colour = Select Outline Colour -label.web_browser_not_found_unix = Unixers\: Couldn't find default web browser.\nAdd the full path to your browser in Preferences." +label.web_browser_not_found_unix = Unixers: Couldn't find default web browser.\nAdd the full path to your browser in Preferences." label.web_browser_not_found = Web browser not found label.select_pdb_file_for = Select a PDB file for {0} label.html = HTML @@ -806,7 +806,309 @@ label.set_proxy_settings = Please set up your proxy settings in the 'Connections label.proxy_authorization_failed = Proxy Authorization Failed label.internal_jalview_error = Internal Jalview Error label.secondary_structure_prediction_service_couldnt_be_located = The Secondary Structure Prediction Service named {0} at {1} couldn't be located. -label.service_called_is_not_msa_service = The Service called \n{0}\nis not a \nMultiple Sequence Alignment Service! +label.service_called_is_not_msa_service = The Service called \n{0}\nis not a \nMultiple Sequence Alignment Service\! label.msa_service_is_unknown = The Multiple Sequence Alignment Service named {0} is unknown -label.service_called_is_not_seq_search_service = The Service called \n{0}\nis not a \nSequence Search Service! +label.service_called_is_not_seq_search_service = The Service called \n{0}\nis not a \nSequence Search Service\! label.seq_search_service_is_unknown = The Sequence Search Service named {0} is unknown +label.feature_type = Feature Type +label.display = Display +label.service_url = Service URL +label.copied_sequences = Copied sequences +label.cut_sequences = Cut Sequences +label.conservation_colour_increment = Conservation Colour Increment ({0}) +label.percentage_identity_thereshold = Percentage Identity Thereshold ({0}) +label.error_unsupported_owwner_user_colour_scheme = Unsupported owner for User Colour scheme dialog +label.save_alignment_to_file = Save Alignment to file +label.save_features_to_file = Save Features to File +label.save_annotation_to_file = Save Annotation to File +label.no_features_on_alignment = No features found on alignment +label.save_pdb_file = Save PDB File +label.save_text_to_file = Save Text to File +label.save_state = Save State +label.restore_state = Restore State +label.saving_jalview_project = Saving jalview project {0} +label.loading_jalview_project = Loading jalview project {0} +label.save_vamsas_document_archive = Save Vamsas Document Archive +label.saving_vamsas_doc = Saving VAMSAS Document to {0} +label.load_feature_colours = Load Feature Colours +label.save_feature_colours = Save Feature Colour Scheme +label.dataset_for = {0} Dataset for {1} +label.select_startup_file = Select startup file +label.select_default_browser = Select default web browser +label.save_tree_as_newick = Save tree as newick file +label.create_eps_from_tree = Create EPS file from tree +label.create_png_from_tree = Create PNG image from tree +label.save_colour_scheme = Save colour scheme +label.edit_params_for = Edit parameters for {0} +label.choose_filename_for_param_file = Choose a filename for this parameter file +label.save_as_html = Save as HTML +label.recently_opened = Recently Opened +label.blasting_for_unidentified_sequence_jobs_running = BLASTing for unidentified sequences - {0} jobs running. +label.tree_from = Tree from {0} +label.webservice_job_title = {0} using {1} +label.select_visible_region_of = selected {0} region of {1} +label.visible = Visible +label.select_unselect_visible_regions_from = select and unselected {0} regions from {1} +label.visible_region_of = visible region of +label.webservice_job_title_on = {0} using {1} on {2} +label.updating_vamsas_session = Updating vamsas session +label.loading_file = Loading File: {0} +label.edit_params = Edit {0} +error.not_implemented = Not implemented +error.no_such_method_as_clone1_for = No such method as clone1 for {0} +error.null_from_clone1 = Null from clone1! +error.implementation_error_sortbyfeature = Implementation Error - sortByFeature method must be one of FEATURE_SCORE, FEATURE_LABEL or FEATURE_DENSITY. +error.not_yet_implemented = Not yet implemented +error.unknown_type_dna_or_pep = Unknown Type {0} - dna or pep are the only allowed values. +error.implementation_error_dont_know_thereshold_annotationcolourgradient = Implementation error: don't know about threshold setting for current AnnotationColourGradient. +error.implementation_error_embeddedpopup_not_null = Implementation error - embeddedPopup must be non-null +error.invalid_colour_for_mycheckbox = Invalid color for MyCheckBox +error.implementation_error_unrecognised_render_object_for_features_type = Implementation Error: Unrecognised render object {0} for features of type {1} +error.implementation_error_unsupported_feature_colour_object = Implementation error: Unsupported feature colour object. +error.invalid_separator_parameter = Invalid separator parameter - must be non-zero length +error.alignment_cigararray_not_implemented = Alignment(CigarArray) not yet implemented +error.weak_sequencei_equivalence_not_yet_implemented = Weak sequenceI equivalence not yet implemented. +error.implementation_error_can_only_make_alignmnet_from_cigararray = Implementation Error - can only make an alignment view from a CigarArray of sequences. +error.empty_view_cannot_be_updated = empty view cannot be updated. +error.mismatch_between_number_of_sequences_in_block = Mismatch between number of sequences in block {0} ({1}) and the original view ({2}) +error.padding_not_yet_implemented = Padding not yet implemented +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}) +error.unknown_seq_cigar_operation = Unknown SeqCigar operation '{0}' +error.implementation_bug_parse_cigar_string = Implementation bug in parseCigarString +error.implementation_error_invalid_operation_string = Implementation error. Invalid operation string. +error.invalid_range_string = Invalid range string (must be zero or positive number) +error.implementation_error_delete_range_out_of_bounds = Implementation Error: deleteRange out of bounds: start must be non-negative and less than end. +error.implementation_error = Implementation error +error.implementation_error_unknown_operation = Implementation Error! Unknown operation '{0}' +error.implementation_error_unexpected_null_from_get_sequence_and_deletions = Implementation Error - unexpected null from getSequenceAndDeletions +error.implementation_error_set_seq_null = Implementation Error - _setSeq(null,...) +error.implementation_error_s = Implementation Error: _s= {0} +error.implementation_error_seqcigar_possible = SeqCigar: Possible implementation error: sequence is longer than dataset sequence +error.implmentation_bug_seq_null = Implementation Bug. Null seq +error.implementation_bug_cigar_operation_list_range_list = Implementation Bug. Cigar Operation list!= range list +error.not_yet_implemented_cigar_object_from_cigar_string = NOT YET Implemented: Constructing a Cigar object from a cigar string and a gapped sequence. +error.implementation_bug_cigar_operation = Implementation Bug. Cigar Operation '{0}' '{1}' not one of '{2}', '{3}', or '{4}'. +error.implementation_error_for_new_cigar = Implementation error for new Cigar(SequenceI) +error.implementation_error_cigar_seq_no_operations = Implementation error: {0}'th sequence Cigar has no operations. +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 +error.implementation_error_no_pdbentry_from_index = Implementation error - no corresponding pdbentry (for index {0}) to add sequences mappings to +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 +error.not_implemented_remove = Remove: Not implemented +error.not_implemented_clone = Clone: Not implemented +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 +error.call_setprogressbar_before_registering_handler = call setProgressBar before registering the progress bar's handler. +label.cancelled_params = Cancelled {0} +error.implementation_error_cannot_show_view_alignment_frame = Implementation error: cannot show a view from another alignment in an AlignFrame. +error.implementation_error_dont_know_about_thereshold_setting = Implementation error: don't know about threshold setting for current AnnotationColourGradient. +error.eps_generation_not_implemented = EPS Generation not yet implemented +error.png_generation_not_implemented = PNG Generation not yet implemented +error.try_join_vamsas_session_another = Trying to join a vamsas session when another is already connected +error.invalid_vamsas_session_id = Invalid vamsas session id +error.implementation_error_cannot_create_groovyshell = Implementation Error. Cannot create groovyShell without Groovy on the classpath! +label.groovy_support_failed = Jalview Groovy Support Failed +label.couldnt_create_groovy_shell = Couldn't create the groovy Shell. Check the error log for the details of what went wrong. +error.unsupported_version_calcIdparam = Unsupported Version for calcIdparam {0} +error.implementation_error_cant_reorder_tree = Implementation Error: Can't reorder this tree. Not DefaultMutableTreeNode. +error.invalid_value_for_option = Invalid value {0} for option {1} +error.implementation_error_cannot_import_vamsas_doc = Implementation Error - cannot import existing vamsas document into an existing session, Yet! +label.vamsas_doc_couldnt_be_opened_as_new_session = VAMSAS Document could not be opened as a new session - please choose another +error.implementation_error_vamsas_operation_not_init = Impementation error! Vamsas Operations when client not initialised and connected +error.jalview_no_connected_vamsas_session = Jalview not connected to Vamsas session +error.implementation_error_cannot_recover_vamsas_object_mappings = IMPLEMENTATION ERROR: Cannot recover vamsas object mappings - no backup was made +error.setstatus_called_non_existent_job_pane = setStatus called for non-existent job pane {0} +error.implementation_error_cannot_find_marshaller_for_param_set =Implementation error: Can't find a marshaller for the parameter set +error.implementation_error_old_jalview_object_not_bound =IMPLEMENTATION ERROR: old jalview object is not bound ! ({0}) +error.implementation_error_vamsas_doc_class_should_bind_to_type = Implementation Error: Vamsas Document Class {0} should bind to a {1} (found a {2}) +error.implementation_error_jalview_class_should_bind_to_type = Implementation Error: Jalview Class {0} should bind to a {1} (found a {2}) +error.invalid_vamsas_rangetype_cannot_resolve_lists = Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice! +error.implementation_error_maplist_is_null = Implementation error. MapList is null for initMapType. +error.implementation_error_cannot_have_null_alignment = Implementation error: Cannot have null alignment property key +error.implementation_error_null_fileparse = Implementation error. Null FileParse in copy constructor +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. +error.implementation_error_cannot_duplicate_colour_scheme = Serious implementation error: cannot duplicate colourscheme {0} +error.implementation_error_structure_selection_manager_null = Implementation error. Structure selection manager's context is 'null' +exception.ssm_context_is_null = SSM context is null +error.idstring_seqstrings_only_one_per_sequence = idstrings and seqstrings contain one string each per sequence +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. +error.cannot_have_zero_length_vector_replacement_strings = Cannot have zero length vector of replacement strings - either 1 value or n values. +error.implementation_error_multiple_single_sequence_prediction_jobs_not_supported = Implementation Error! Multiple single sequence prediction jobs are not yet supported +error.implementation_error_invalid_msa_index_for_job =Implementation Error! Invalid msaIndex for JPredJob on parent MSA input object! +error.implementation_error_startjob_called = Implementation error - StartJob(JpredJob) called on {0} +error.multiple_jnet_subjob_merge_not_implemented = Multiple JNet subjob merging not yet implemented +label.job_never_ran = Job never ran - input returned to user. +error.implementation_error_minlen_must_be_greater_zero = Implementation error: minlen must be zero or more +error.implementation_error_msawbjob_called = Implementation error - StartJob(MsaWSJob) called on a WSJobInstance {0} +error.implementation_error_cannot_attach_ws_menu_entry = IMPLEMENTATION ERROR: cannot attach WS Menu Entry without service handle reference! +error.parameter_migration_not_implemented_yet = Parameter migration not implemented yet +error.implementation_error_cannot_set_jaba_option = Implementation error: cannot set Jaba Option to a value outside its allowed value range! +error.implementation_error_valuetype_doesnt_support_jabaws_type = IMPLEMENTATION ERROR: jalview.ws.params.ValueConstrainI.ValueType does not support the JABAWS type : {0} +error.cannot_create_jabaws_param_set = Cannot create a JabaWSParamSet from non-JabaWS parameters +error.cannot_set_arguments_to_jabaws_param_set = Cannot set arguments to a JabaWSParamSet that are not JabaWS arguments +error.implementation_error_runner_config_not_available = Implementation Error: Runner Config not available for a JABAWS service of type {0} ({1}) +error.implementation_error_cannot_handle_jaba_param = Implementation Error: Cannot handle Jaba parameter object {0} +error.implementation_error_attempt_to_delete_service_preset = Implementation error: Attempt to delete a service preset! +error.implementation_error_cannot_locate_oldname_presetname = Implementation error: Can't locate either oldname ({0}) or presetName ({1}in the datastore!" +error.implementation_error_jabaws_param_set_only_handled_by = Implementation error: JabaWsParamSets can only be handled by JabaParamStore +error.cannot_set_source_file_for = Cannot set source file for {0} +error.mismatch_service_instance_preset = Probable mismatch between service instance and preset! +error.cannot_set_params_for_ws_preset = Cannot set Parameters for a Jaba Web service's preset +error.implementation_error_can_only_instantiate_jaba_param_sets = Implementation error: Can only instantiate Jaba parameter sets +error.no_aacon_service_found = No AACon service found +error.implementation_error_couldnt_copy_value_constraint = Implementation error: could not copy ValueConstrain! +error.couldnt_encode_as_utf8 = Couldn't encode '{0}' as UTF-8. +error.tree_inputtype_not_yet_implemented = Tree InputType not yet implemented +error.implementation_error_need_to_have_httpresponse = Implementation Error: need to have an HttpResponse to process +error.dbrefsource_implementation_exception =DBRefSource Implementation Exception +error.implementation_error_dbinstance_must_implement_interface = Implmentation Error - getDbInstances must be given a class that implements jalview.ws.seqfetcher.DbSourceProxy (was given{0}) +error.implementation_error_must_init_dbsources =Implementation error. Must initialise dbSources +label.view_controller_toggled_marked = {0} {1} columns {2} containing features of type {3} across {4} sequence(s) +label.toggled = Toggled +label.marked = Marked +label.not = not +label.no_feature_of_type_found = No features of type {0} found. +label.submission_params = Submission {0} +label.empty_alignment_job = Empty Alignment Job +label.add_new_sbrs_service = Add a new Simple Bioinformatics Rest Service +label.edit_sbrs_entry = Edit Simple Bioinformatics Rest Service entry +label.pca_recalculating = Recalculating PCA +label.pca_calculating = Calculating PCA +label.select_foreground_colour = Choose foreground colour +label.select_colour_for_text = Select Colour for Text +label.adjunst_foreground_text_colour_thereshold = Adjust Foreground Text Colour Threshold +label.select_subtree_colour = Select Sub-Tree Colour +label.create_new_sequence_features = Create New Sequence Feature(s) +label.amend_delete_features = Amend/Delete Features for {0} +exception.out_of_bounds_for_file = Out of bounds for file: i={0}, Final Buffer: i0={1} iend={2} +exception.null_string_given_to_regex_search = Null String Given to Regex.search +exception.null_string_like_given_to_regex_search = Null StringLike Given to Regex.search +exception.null_string_given_to_regex_reverse_search = Null String Given to Regex.reverseSearch +exception.null_string_like_given_to_regex_reverse_search = Null StringLike Given to Regex.reverseSearch +exception.null_string_like_given_to_regex_search_from = Null String Given to Regex.searchFrom +exception.null_string_like_given_to_regex_search_region = Null String Given to Regex.searchRegion +exception.replace_null_regex_pointer = Replacer has null Regex pointer +exception.bad_pattern_to_regex_perl_code = bad pattern to Regex.perlCode: {0} +exception.no_stub_implementation_for_interface = There is no stub implementation for the interface: {0} +exception.cannot_set_endpoint_address_unknown_port = Cannot set Endpoint Address for Unknown Port {0} +exception.querying_matching_opening_parenthesis_for_non_closing_parenthesis = Querying matching opening parenthesis for non-closing parenthesis character {0} +exception.mismatched_unseen_closing_char = Mismatched (unseen) closing character {0} +exception.mismatched_closing_char = Mismatched closing character {0} +exception.mismatched_opening_char = Mismatched opening character {0} at {1} +exception.invalid_datasource_couldnt_obtain_reader = Invalid datasource. Could not obtain Reader +exception.index_value_not_in_range = {0}: Index value '{1}' not in range [0..{2}] +exception.unterminated_cigar_string = Unterminated cigar string +exception.unexpected_operation_cigar_string_pos = Unexpected operation '{0}' in cigar string (position {1} in '{2}' +exception.couldnt_parse_responde_from_annotated3d_server = Couldn't parse response from Annotate3d server +exception.application_test_npe = Application test: throwing an NullPointerException It should arrive at the console +exception.overwriting_vamsas_id_binding = Overwriting vamsas id binding +exception.overwriting_jalview_id_binding = Overwriting jalview id binding +error.implementation_error_unknown_file_format_string = Implementation error: Unknown file format string +exception.failed_to_resolve_gzip_stream = Failed to resolve GZIP stream +exception.problem_opening_file_also_tried = Problem opening {0} (also tried {1}) : {2} +exception.problem_opening_file = Problem opening {0} : {1} +exception.failed_to_read_data_from_source = Failed to read data from source: {0} +exception.no_init_source_stream = Unitialised Source Stream +exception.invalid_source_stream = Invalid Source Stream: {0} +error.implementation_error_reset_called_for_invalid_source = Implementation Error: Reset called for invalid source. +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}) +label.mapped = mapped +exception.jpredconcide_entry_has_unexpected_number_of_columns = JPredConcise: Entry ({0}) has an unexpected number of columns +exception.couldnt_parse_concise_annotation_for_prediction = Couldn't parse concise annotation for prediction profile.\n{0} +exception.newfile = NewickFile\: {0}\n +label.no_tree_read_in = No Tree read in +exception.rnaml_couldnt_access_datasource = Couldn't access datasource ({0}) +exception.ranml_couldnt_process_data = Couldn't process data as RNAML file ({0}) +exception.ranml_invalid_file = Invalid RNAML file ({0}) +exception.ranml_problem_parsing_data = Problem parsing data as RNAML ({0}) +exception.pfam_no_sequences_found = No sequences found (PFAM input) +exception.stockholm_invalid_format = This file is not in valid STOCKHOLM format: First line does not contain '# STOCKHOLM' +exception.couldnt_parse_sequence_line = Could not parse sequence line: {0} +exception.error_parsing_line = Error parsing {0} +exception.unknown_annotation_detected = Unknown annotation detected: {0} {1} +exception.couldnt_store_sequence_mappings = Couldn't store sequence mappings for {0} +exception.matrix_too_many_iteration = Too many iterations in {0} (max is {1}) +exception.browser_not_found = Exception in finding browser: {0} +exception.browser_unable_to_locate = Unable to locate browser: {0} +exception.invocation_target_exception_creating_aedesc = InvocationTargetException while creating AEDesc: {0} +exception.illegal_access_building_apple_evt= IllegalAccessException while building AppleEvent: {0} +exception.instantiation_creating_aedesc = InstantiationException while creating AEDesc: {0} +exception.unable_to_launch_url = Unable to launch URL: {0} +exception.unable_to_create_internet_config = Unable to create an Internet Config instance: {0} +exception.invocation_target_calling_url = InvocationTargetException while calling openURL: {0} +exception.illegal_access_calling_url = IllegalAccessException while calling openURL: {0} +exception.interrupted_launching_browser = InterruptedException while launching browser: {0} +exception.das_source_doesnt_support_sequence_command = Source {0} does not support the sequence command. +exception.invalid_das_source = Invalid das source: {0} +exception.ebiembl_retrieval_failed_on = EBI EMBL XML retrieval failed on {0}:{1} +label.no_embl_record_found = # No EMBL record retrieved for {0}:{1} +label.embl_successfully_parsed = # Successfully parsed the {0} queries into an Alignment +exception.no_pdb_records_for_chain = No PDB Records for {0} chain {1} +exception.unexpected_handling_rnaml_translation_for_pdb = Unexpected exception when handling RNAML translation of PDB data +exception.couldnt_recover_sequence_properties_for_alignment = Couldn't recover sequence properties for alignment +exception.unknown_format_for_file = Unknown format {0} for file \: \n{1} +label.remove_gaps = Remove Gaps +exception.couldnt_recover_sequence_props_for_jnet_query = Couldn't recover sequence properties for JNet Query sequence! +exception.server_timeout_try_later = Server timed out - try again later\n +exception.web_service_returned_null_try_later= Server at {0} returned null object, it probably cannot be contacted. Try again later. +exception.cannot_contact_service_endpoint_at = Cannot contact service endpoint at {0} +error.implementation_error_cannot_find_service_url_in_given_set = Implementation error: Cannot find service url in the given url set! +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}} +exception.jobsubmission_invalid_params_set = Invalid parameter set. Check Jalview implementation +exception.notvaliddata_group_contains_less_than_min_seqs = Group contains less than {0} sequences. +exception.outofmemory_loading_pdb_file = Out of memory loading PDB File +exception.eps_coudnt_write_output_file = Could not write to the output file: {0} +exception.eps_method_not_supported = Method not currently supported by EpsGraphics2D version {0} +exception.eps_unable_to_get_inverse_matrix = Unable to get inverse of matrix: {0} +warn.job_cannot_be_cancelled_close_window = This job cannot be cancelled.\nJust close the window. +warn.service_not_supported = Service not supported! +warn.input_is_too_big = Input is too big! +warn.invalid_job_param_set = Invalid job parameter set! +info.job_couldnt_be_run_server_doesnt_support_program = Job could not be run because the server doesn't support this program.\n{0} +info.job_couldnt_be_run_exceeded_hard_limit = Job could not be run because it exceeded a hard limit on the server.\n{0} +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 +info.no_jobs_ran = No jobs ran +info.failed_to_submit_prediction = Failed to submit the prediction:\n{0} {1} +info.invalid_jnet_job_result_data ={0}\n{1}\nInvalid JNet job result data!\n{2} +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 +info.alignment_object_method_notes = \nAlignment Object Method Notes\n +info.server_exception = \n{0} Server exception!\n{1} +status.processing_commandline_args = Processing commandline arguments... +status.das_features_being_retrived = DAS features being retrieved... +status.searching_for_sequences_from = Searching for sequences from {0} +status.finished_searching_for_sequences_from = Finished searching for sequences from {0} +label.eps_file = EPS file +label.png_image = PNG image +status.saving_file = Saving {0} +status.export_complete = Export complete. +status.fetching_pdb = Fetching PDB {0} +status.refreshing_news = Refreshing news +status.importing_vamsas_session_from = Importing VAMSAS session from {0} +status.opening_params = Opening {0} +status.waiting_sequence_database_fetchers_init = Waiting for Sequence Database Fetchers to initialise +status.init_sequence_database_fetchers = Initialising Sequence Database Fetchers +status.fetching_sequence_queries_from = Fetching {0} sequence queries from {1} +status.finshed_querying = Finished querying +status.parsing_results = Parsing results. +status.processing = Processing... +status.refreshing_web_service_menus = Refreshing Web Service Menus +status.collecting_job_results = Collecting job results. +status.fetching_das_sequence_features = Fetching DAS Sequence Features +status.no_das_sources_active = No DAS Sources Active +status.das_feature_fetching_cancelled = DAS Feature Fetching Cancelled +status.das_feature_fetching_complete = DAS Feature Fetching Complete +status.fetching_db_refs = Fetching db refs +label.font_doesnt_have_letters_defined = Font doesn't have letters defined\nso cannot be used\nwith alignment data +label.error_loading_file_params = Error loading file {0} +label.error_loading_jalview_file = Error loading Jalview file +warn.out_of_memory_when_action = Out of memory when {0}!!\nSee help files for increasing Java Virtual Machine memory. +warn.out_of_memory_loading_file = Out of memory loading file {0}!!\nSee help files for increasing Java Virtual Machine memory. +label.out_of_memory = Out of memory +label.invalid_id_column_width = Invalid ID Column width +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. +label.couldnt_create_sequence_fetcher = Couldn't create SequenceFetcher +warn.couldnt_create_sequence_fetcher_client = Could not create the sequence fetcher client. Check error logs for details. +warn.server_didnt_pass_validation = Service did not pass validation.\nCheck the Jalview Console for more details. +warn.url_must_contain = Sequence URL must contain $SEQUENCE_ID$ or a regex $SEQUENCE_ID=//=$ +info.validate_jabaws_server = Validate JabaWS Server ?\n(Look in console output for results) +label.test_server = Test Server? +info.you_want_jalview_to_find_uniprot_accessions = Do you want Jalview to find\nUniprot Accession ids for given sequence names? +label.find_uniprot_accession_ids = Find Uniprot Accession Ids \ No newline at end of file diff --git a/src/MCview/PDBViewer.java b/src/MCview/PDBViewer.java index eb214ac..b4cb80c 100755 --- a/src/MCview/PDBViewer.java +++ b/src/MCview/PDBViewer.java @@ -671,7 +671,7 @@ public class PDBViewer extends JInternalFrame implements Runnable 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); diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java index 302f3b2..e112b2a 100755 --- a/src/MCview/PDBfile.java +++ b/src/MCview/PDBfile.java @@ -240,7 +240,7 @@ 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) diff --git a/src/com/stevesoft/pat/Pattern.java b/src/com/stevesoft/pat/Pattern.java index 543391e..3a3462c 100755 --- a/src/com/stevesoft/pat/Pattern.java +++ b/src/com/stevesoft/pat/Pattern.java @@ -7,6 +7,8 @@ // package com.stevesoft.pat; +import jalview.util.MessageManager; + import java.util.*; /** @@ -259,7 +261,7 @@ public abstract class Pattern */ 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) @@ -272,7 +274,7 @@ public abstract class Pattern 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); diff --git a/src/com/stevesoft/pat/Regex.java b/src/com/stevesoft/pat/Regex.java index 04bb0da..861c33b 100755 --- a/src/com/stevesoft/pat/Regex.java +++ b/src/com/stevesoft/pat/Regex.java @@ -7,6 +7,8 @@ // package com.stevesoft.pat; +import jalview.util.MessageManager; + import java.io.*; import java.util.*; @@ -775,7 +777,7 @@ public class Regex extends RegRes implements FilenameFilter { 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()); } @@ -784,8 +786,7 @@ public class Regex extends RegRes implements FilenameFilter { 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()); } @@ -794,8 +795,7 @@ public class Regex extends RegRes implements FilenameFilter { 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()); } @@ -804,8 +804,7 @@ public class Regex extends RegRes implements FilenameFilter { 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()); } @@ -822,8 +821,7 @@ public class Regex extends RegRes implements FilenameFilter { 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()); } @@ -832,8 +830,7 @@ public class Regex extends RegRes implements FilenameFilter { 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()); } @@ -845,8 +842,7 @@ public class Regex extends RegRes implements FilenameFilter { 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); } diff --git a/src/com/stevesoft/pat/Replacer.java b/src/com/stevesoft/pat/Replacer.java index 062a548..b886f6a 100755 --- a/src/com/stevesoft/pat/Replacer.java +++ b/src/com/stevesoft/pat/Replacer.java @@ -7,6 +7,8 @@ // package com.stevesoft.pat; +import jalview.util.MessageManager; + import com.stevesoft.pat.wrap.*; /** Internally used class. */ @@ -178,7 +180,7 @@ public class Replacer 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)) { diff --git a/src/com/stevesoft/pat/Transformer.java b/src/com/stevesoft/pat/Transformer.java index d770f08..84a3a46 100755 --- a/src/com/stevesoft/pat/Transformer.java +++ b/src/com/stevesoft/pat/Transformer.java @@ -7,6 +7,8 @@ // package com.stevesoft.pat; +import jalview.util.MessageManager; + import com.stevesoft.pat.wrap.*; /** @@ -149,7 +151,7 @@ public class Transformer 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); } diff --git a/src/com/stevesoft/pat/wrap/RandomAccessFileWrap.java b/src/com/stevesoft/pat/wrap/RandomAccessFileWrap.java index b4d38dc..f5b61ab 100755 --- a/src/com/stevesoft/pat/wrap/RandomAccessFileWrap.java +++ b/src/com/stevesoft/pat/wrap/RandomAccessFileWrap.java @@ -7,6 +7,8 @@ // package com.stevesoft.pat.wrap; +import jalview.util.MessageManager; + import java.io.*; import com.stevesoft.pat.*; @@ -84,13 +86,16 @@ public class RandomAccessFileWrap implements StringLike { } - 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() diff --git a/src/ext/vamsas/IRegistryServiceLocator.java b/src/ext/vamsas/IRegistryServiceLocator.java index 6bd3af0..3473d4c 100755 --- a/src/ext/vamsas/IRegistryServiceLocator.java +++ b/src/ext/vamsas/IRegistryServiceLocator.java @@ -20,6 +20,8 @@ */ package ext.vamsas; +import jalview.util.MessageManager; + public class IRegistryServiceLocator extends org.apache.axis.client.Service implements ext.vamsas.IRegistryService { @@ -109,10 +111,7 @@ public class IRegistryServiceLocator extends org.apache.axis.client.Service { 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())})); } /** @@ -169,8 +168,7 @@ public class IRegistryServiceLocator extends org.apache.axis.client.Service } 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})); } } diff --git a/src/ext/vamsas/JpredServiceLocator.java b/src/ext/vamsas/JpredServiceLocator.java index 46566b9..79e9636 100755 --- a/src/ext/vamsas/JpredServiceLocator.java +++ b/src/ext/vamsas/JpredServiceLocator.java @@ -20,6 +20,8 @@ */ package ext.vamsas; +import jalview.util.MessageManager; + public class JpredServiceLocator extends org.apache.axis.client.Service implements ext.vamsas.JpredService { @@ -107,10 +109,7 @@ public class JpredServiceLocator extends org.apache.axis.client.Service { 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())})); } /** @@ -167,8 +166,7 @@ public class JpredServiceLocator extends org.apache.axis.client.Service } 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})); } } diff --git a/src/ext/vamsas/MuscleWSServiceLocator.java b/src/ext/vamsas/MuscleWSServiceLocator.java index a9ca1ed..9a580f8 100755 --- a/src/ext/vamsas/MuscleWSServiceLocator.java +++ b/src/ext/vamsas/MuscleWSServiceLocator.java @@ -20,6 +20,8 @@ */ package ext.vamsas; +import jalview.util.MessageManager; + public class MuscleWSServiceLocator extends org.apache.axis.client.Service implements ext.vamsas.MuscleWSService { @@ -115,10 +117,7 @@ public class MuscleWSServiceLocator extends org.apache.axis.client.Service 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())})); } /** @@ -177,8 +176,7 @@ public class MuscleWSServiceLocator extends org.apache.axis.client.Service } 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})); } } diff --git a/src/ext/vamsas/SeqSearchServiceLocator.java b/src/ext/vamsas/SeqSearchServiceLocator.java index cfe943c..75f46a3 100644 --- a/src/ext/vamsas/SeqSearchServiceLocator.java +++ b/src/ext/vamsas/SeqSearchServiceLocator.java @@ -20,6 +20,8 @@ */ package ext.vamsas; +import jalview.util.MessageManager; + public class SeqSearchServiceLocator extends org.apache.axis.client.Service implements ext.vamsas.SeqSearchServiceService { @@ -109,10 +111,7 @@ public class SeqSearchServiceLocator extends org.apache.axis.client.Service { 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())})); } /** @@ -169,8 +168,7 @@ public class SeqSearchServiceLocator extends org.apache.axis.client.Service } 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})); } } diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java index ab6fae8..4460985 100755 --- a/src/jalview/analysis/AlignSeq.java +++ b/src/jalview/analysis/AlignSeq.java @@ -410,8 +410,7 @@ public class AlignSeq 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})); } } diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java index a993e26..b7cfbbd 100755 --- a/src/jalview/analysis/AlignmentSorter.java +++ b/src/jalview/analysis/AlignmentSorter.java @@ -757,8 +757,7 @@ public class AlignmentSorter 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(); @@ -938,7 +937,7 @@ public class AlignmentSorter { if (method == FEATURE_LABEL) { - throw new Error("Not yet implemented."); + throw new Error(MessageManager.getString("error.not_yet_implemented")); } } if (lastSortByFeatureScore == null diff --git a/src/jalview/analysis/Rna.java b/src/jalview/analysis/Rna.java index 4c05ece..e4a0d76 100644 --- a/src/jalview/analysis/Rna.java +++ b/src/jalview/analysis/Rna.java @@ -35,6 +35,7 @@ import java.util.Vector; import jalview.analysis.SecStrConsensus.SimpleBP; import jalview.datamodel.SequenceFeature; +import jalview.util.MessageManager; public class Rna { @@ -85,9 +86,7 @@ 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); @@ -132,16 +131,14 @@ public class Rna 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 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(); @@ -154,8 +151,7 @@ public class Rna Stack 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; diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java index 64fed16..eba1200 100644 --- a/src/jalview/appletgui/APopupMenu.java +++ b/src/jalview/appletgui/APopupMenu.java @@ -559,7 +559,7 @@ public class APopupMenu extends java.awt.PopupMenu implements 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()), diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index cc1703c..f267858 100644 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -1763,14 +1763,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, 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); @@ -1805,7 +1805,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } // !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())); @@ -1855,7 +1855,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, /* * //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())); @@ -2780,10 +2780,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, 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")); @@ -3043,7 +3043,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, 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")); diff --git a/src/jalview/appletgui/AnnotationColourChooser.java b/src/jalview/appletgui/AnnotationColourChooser.java index f85a073..c7b7c6c 100644 --- a/src/jalview/appletgui/AnnotationColourChooser.java +++ b/src/jalview/appletgui/AnnotationColourChooser.java @@ -137,8 +137,7 @@ public class AnnotationColourChooser extends Panel implements 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()); diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java index bf82bca..42fbd70 100644 --- a/src/jalview/appletgui/AppletJmol.java +++ b/src/jalview/appletgui/AppletJmol.java @@ -139,7 +139,7 @@ public class AppletJmol extends EmbmenuFrame implements 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, @@ -315,8 +315,7 @@ public class AppletJmol extends EmbmenuFrame implements } 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); diff --git a/src/jalview/appletgui/EmbmenuFrame.java b/src/jalview/appletgui/EmbmenuFrame.java index 6c0d3a9..3757415 100644 --- a/src/jalview/appletgui/EmbmenuFrame.java +++ b/src/jalview/appletgui/EmbmenuFrame.java @@ -195,8 +195,7 @@ public class EmbmenuFrame extends Frame implements MouseListener { 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) { diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java index aef8e31..11ca86a 100644 --- a/src/jalview/appletgui/FeatureRenderer.java +++ b/src/jalview/appletgui/FeatureRenderer.java @@ -151,7 +151,7 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer } else { - throw new Error("Invalid color for MyCheckBox"); + throw new Error(MessageManager.getString("error.invalid_colour_for_mycheckbox")); } if (col != null) { @@ -901,8 +901,7 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer 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(),featureType})); } /** diff --git a/src/jalview/appletgui/FeatureSettings.java b/src/jalview/appletgui/FeatureSettings.java index f6e7772..cd11a35 100755 --- a/src/jalview/appletgui/FeatureSettings.java +++ b/src/jalview/appletgui/FeatureSettings.java @@ -592,8 +592,7 @@ public class FeatureSettings extends Panel implements ItemListener, } else { - throw new Error( - "Implementation error: Unsupported feature colour object."); + throw new Error(MessageManager.getString("error.implementation_error_unsupported_feature_colour_object")); } refreshTable(); } @@ -689,7 +688,7 @@ public class FeatureSettings extends Panel implements ItemListener, } else { - throw new Error("Invalid color for MyCheckBox"); + throw new Error(MessageManager.getString("error.invalid_colour_for_mycheckbox")); } if (col != null) { diff --git a/src/jalview/appletgui/RedundancyPanel.java b/src/jalview/appletgui/RedundancyPanel.java index f5e403f..216f45d 100644 --- a/src/jalview/appletgui/RedundancyPanel.java +++ b/src/jalview/appletgui/RedundancyPanel.java @@ -196,7 +196,7 @@ public class RedundancyPanel extends SliderPanel implements Runnable, } } - 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++) diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java index 5ba22b6..de4d979 100644 --- a/src/jalview/appletgui/SeqPanel.java +++ b/src/jalview/appletgui/SeqPanel.java @@ -31,6 +31,7 @@ import jalview.schemes.*; 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 @@ -945,15 +946,15 @@ public class SeqPanel extends Panel implements MouseMotionListener, 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) { @@ -961,7 +962,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, } if (editCommand == null) { - editCommand = new EditCommand("Edit " + label); + editCommand = new EditCommand(MessageManager.formatMessage("label.edit_params", new String[]{label})); } } diff --git a/src/jalview/appletgui/SliderPanel.java b/src/jalview/appletgui/SliderPanel.java index 14fab4e..220a7fb 100644 --- a/src/jalview/appletgui/SliderPanel.java +++ b/src/jalview/appletgui/SliderPanel.java @@ -59,8 +59,7 @@ public class SliderPanel extends Panel implements ActionListener, 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); @@ -114,7 +113,7 @@ public class SliderPanel extends Panel implements ActionListener, 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) { diff --git a/src/jalview/appletgui/UserDefinedColours.java b/src/jalview/appletgui/UserDefinedColours.java index 0b18688..afa6419 100644 --- a/src/jalview/appletgui/UserDefinedColours.java +++ b/src/jalview/appletgui/UserDefinedColours.java @@ -187,7 +187,7 @@ public class UserDefinedColours extends Panel implements ActionListener, 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); } @@ -206,7 +206,7 @@ public class UserDefinedColours extends Panel implements ActionListener, // // 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); diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index b6d6d3f..046d132 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -44,6 +44,7 @@ import java.util.*; import javax.swing.*; import jalview.gui.*; +import jalview.util.MessageManager; import jalview.util.Platform; /** @@ -340,7 +341,7 @@ public class Jalview { if (!headless) { - desktop.setProgressBar("Processing commandline arguments...", + desktop.setProgressBar(MessageManager.getString("status.processing_commandline_args"), progress = System.currentTimeMillis()); } System.out.println("Opening file: " + file); @@ -1058,7 +1059,7 @@ class FeatureFetcher 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); diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java index 4e02984..ef1e16e 100644 --- a/src/jalview/bin/JalviewLite.java +++ b/src/jalview/bin/JalviewLite.java @@ -1392,8 +1392,7 @@ public class JalviewLite extends Applet implements } else { - throw new Error( - "Invalid separator parameter - must be non-zero length"); + throw new Error(MessageManager.getString("error.invalid_separator_parameter")); } } int r = 255; diff --git a/src/jalview/binding/Annotation.java b/src/jalview/binding/Annotation.java index d1f28c0..463312f 100644 --- a/src/jalview/binding/Annotation.java +++ b/src/jalview/binding/Annotation.java @@ -24,6 +24,8 @@ package jalview.binding; //- Imported classes and packages -/ //---------------------------------/ +import jalview.util.MessageManager; + import org.exolab.castor.xml.Marshaller; import org.exolab.castor.xml.Unmarshaller; @@ -156,10 +158,11 @@ public class Annotation implements java.io.Serializable // 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 @@ -365,10 +368,11 @@ public class Annotation implements java.io.Serializable // 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); diff --git a/src/jalview/binding/FeatureSettings.java b/src/jalview/binding/FeatureSettings.java index 0564134..5cf43eb 100644 --- a/src/jalview/binding/FeatureSettings.java +++ b/src/jalview/binding/FeatureSettings.java @@ -24,6 +24,8 @@ package jalview.binding; //- Imported classes and packages -/ //---------------------------------/ +import jalview.util.MessageManager; + import org.exolab.castor.xml.Marshaller; import org.exolab.castor.xml.Unmarshaller; @@ -110,9 +112,11 @@ public class FeatureSettings implements java.io.Serializable // 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); @@ -243,9 +247,11 @@ public class FeatureSettings implements java.io.Serializable // 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); diff --git a/src/jalview/binding/JGroup.java b/src/jalview/binding/JGroup.java index 4a853ef..d2db3e8 100644 --- a/src/jalview/binding/JGroup.java +++ b/src/jalview/binding/JGroup.java @@ -24,6 +24,8 @@ package jalview.binding; //- Imported classes and packages -/ //---------------------------------/ +import jalview.util.MessageManager; + import org.exolab.castor.xml.Marshaller; import org.exolab.castor.xml.Unmarshaller; @@ -345,8 +347,11 @@ public class JGroup implements java.io.Serializable // 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(); @@ -704,8 +709,11 @@ public class JGroup implements java.io.Serializable // 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)); diff --git a/src/jalview/binding/JSeq.java b/src/jalview/binding/JSeq.java index 7b76f8a..7e2b7b1 100644 --- a/src/jalview/binding/JSeq.java +++ b/src/jalview/binding/JSeq.java @@ -24,6 +24,8 @@ package jalview.binding; //- Imported classes and packages -/ //---------------------------------/ +import jalview.util.MessageManager; + import org.exolab.castor.xml.Marshaller; import org.exolab.castor.xml.Unmarshaller; @@ -242,9 +244,11 @@ public class JSeq implements java.io.Serializable // 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); @@ -299,9 +303,11 @@ public class JSeq implements java.io.Serializable // 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); @@ -537,9 +543,11 @@ public class JSeq implements java.io.Serializable // 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); @@ -588,9 +596,11 @@ public class JSeq implements java.io.Serializable // 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); diff --git a/src/jalview/binding/JalviewModelSequence.java b/src/jalview/binding/JalviewModelSequence.java index d30ec14..97d68de 100644 --- a/src/jalview/binding/JalviewModelSequence.java +++ b/src/jalview/binding/JalviewModelSequence.java @@ -24,6 +24,8 @@ package jalview.binding; //- Imported classes and packages -/ //---------------------------------/ +import jalview.util.MessageManager; + import org.exolab.castor.xml.Marshaller; import org.exolab.castor.xml.Unmarshaller; @@ -299,9 +301,11 @@ public class JalviewModelSequence implements java.io.Serializable // 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); @@ -346,8 +350,11 @@ public class JalviewModelSequence implements java.io.Serializable // 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); @@ -392,8 +399,11 @@ public class JalviewModelSequence implements java.io.Serializable // 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); @@ -438,9 +448,11 @@ public class JalviewModelSequence implements java.io.Serializable // 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); @@ -486,9 +498,11 @@ public class JalviewModelSequence implements java.io.Serializable // 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); @@ -756,9 +770,11 @@ public class JalviewModelSequence implements java.io.Serializable // 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); @@ -794,8 +810,11 @@ public class JalviewModelSequence implements java.io.Serializable // 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); @@ -831,8 +850,11 @@ public class JalviewModelSequence implements java.io.Serializable // 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); @@ -869,9 +891,11 @@ public class JalviewModelSequence implements java.io.Serializable // 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); @@ -909,9 +933,11 @@ public class JalviewModelSequence implements java.io.Serializable // 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); diff --git a/src/jalview/binding/JalviewUserColours.java b/src/jalview/binding/JalviewUserColours.java index 7473bc7..8b70bcf 100644 --- a/src/jalview/binding/JalviewUserColours.java +++ b/src/jalview/binding/JalviewUserColours.java @@ -24,6 +24,8 @@ package jalview.binding; //- Imported classes and packages -/ //---------------------------------/ +import jalview.util.MessageManager; + import org.exolab.castor.xml.Marshaller; import org.exolab.castor.xml.Unmarshaller; @@ -120,9 +122,11 @@ public class JalviewUserColours implements java.io.Serializable // 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); @@ -274,9 +278,11 @@ public class JalviewUserColours implements java.io.Serializable // 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); diff --git a/src/jalview/binding/Pdbentry.java b/src/jalview/binding/Pdbentry.java index 2ee5c96..9b7c1cf 100644 --- a/src/jalview/binding/Pdbentry.java +++ b/src/jalview/binding/Pdbentry.java @@ -24,6 +24,8 @@ package jalview.binding; //- Imported classes and packages -/ //---------------------------------/ +import jalview.util.MessageManager; + import org.exolab.castor.xml.Marshaller; import org.exolab.castor.xml.Unmarshaller; @@ -131,9 +133,11 @@ public class Pdbentry implements java.io.Serializable // 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); @@ -286,9 +290,11 @@ public class Pdbentry implements java.io.Serializable // 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); diff --git a/src/jalview/binding/PdbentryItem.java b/src/jalview/binding/PdbentryItem.java index abd3fab..f24d281 100644 --- a/src/jalview/binding/PdbentryItem.java +++ b/src/jalview/binding/PdbentryItem.java @@ -20,6 +20,8 @@ */ package jalview.binding; +import jalview.util.MessageManager; + /** * Class PdbentryItem. * @@ -103,9 +105,11 @@ public class PdbentryItem implements java.io.Serializable // 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); @@ -182,9 +186,11 @@ public class PdbentryItem implements java.io.Serializable // 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); diff --git a/src/jalview/binding/SequenceSet.java b/src/jalview/binding/SequenceSet.java index 85b4889..59151c8 100644 --- a/src/jalview/binding/SequenceSet.java +++ b/src/jalview/binding/SequenceSet.java @@ -24,6 +24,8 @@ package jalview.binding; //- Imported classes and packages -/ //---------------------------------/ +import jalview.util.MessageManager; + import org.exolab.castor.xml.Marshaller; import org.exolab.castor.xml.Unmarshaller; @@ -186,9 +188,11 @@ public class SequenceSet implements java.io.Serializable // 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); @@ -244,9 +248,11 @@ public class SequenceSet implements java.io.Serializable // 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); @@ -441,9 +447,11 @@ public class SequenceSet implements java.io.Serializable // 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); @@ -492,9 +500,11 @@ public class SequenceSet implements java.io.Serializable // 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); diff --git a/src/jalview/binding/VAMSAS.java b/src/jalview/binding/VAMSAS.java index 0d1f789..bd4ea40 100644 --- a/src/jalview/binding/VAMSAS.java +++ b/src/jalview/binding/VAMSAS.java @@ -24,6 +24,8 @@ package jalview.binding; //- Imported classes and packages -/ //---------------------------------/ +import jalview.util.MessageManager; + import org.exolab.castor.xml.Marshaller; import org.exolab.castor.xml.Unmarshaller; @@ -195,9 +197,11 @@ public class VAMSAS implements java.io.Serializable // 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); @@ -242,9 +246,11 @@ public class VAMSAS implements java.io.Serializable // 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); @@ -289,8 +295,11 @@ public class VAMSAS implements java.io.Serializable // 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); @@ -482,9 +491,11 @@ public class VAMSAS implements java.io.Serializable // 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); @@ -520,9 +531,11 @@ public class VAMSAS implements java.io.Serializable // 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); @@ -558,8 +571,11 @@ public class VAMSAS implements java.io.Serializable // 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); diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java index 077f9cd..dbc3524 100644 --- a/src/jalview/controller/AlignViewController.java +++ b/src/jalview/controller/AlignViewController.java @@ -35,6 +35,7 @@ import jalview.datamodel.SequenceCollectionI; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; +import jalview.util.MessageManager; public class AlignViewController implements AlignViewControllerI { @@ -276,16 +277,17 @@ 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(); diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java index ad7cdd2..98abfe2 100755 --- a/src/jalview/datamodel/Alignment.java +++ b/src/jalview/datamodel/Alignment.java @@ -112,7 +112,7 @@ public class Alignment implements AlignmentI */ 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); } diff --git a/src/jalview/datamodel/AlignmentOrder.java b/src/jalview/datamodel/AlignmentOrder.java index c0f9ab4..a17881e 100755 --- a/src/jalview/datamodel/AlignmentOrder.java +++ b/src/jalview/datamodel/AlignmentOrder.java @@ -20,6 +20,8 @@ */ package jalview.datamodel; +import jalview.util.MessageManager; + import java.util.*; public class AlignmentOrder @@ -217,7 +219,7 @@ 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 { @@ -284,7 +286,7 @@ 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 { diff --git a/src/jalview/datamodel/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java index 6c4cfae..efb7c4a 100644 --- a/src/jalview/datamodel/AlignmentView.java +++ b/src/jalview/datamodel/AlignmentView.java @@ -20,6 +20,7 @@ */ package jalview.datamodel; +import jalview.util.MessageManager; import jalview.util.ShiftList; import java.io.PrintStream; @@ -241,8 +242,7 @@ public class AlignmentView { 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(); @@ -652,7 +652,7 @@ public class AlignmentView { 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) { @@ -682,11 +682,7 @@ public class AlignmentView 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. @@ -839,7 +835,7 @@ public class AlignmentView else { // place gaps. - throw new Error("Padding not yet implemented."); + throw new Error(MessageManager.getString("error.padding_not_yet_implemented")); } } } @@ -852,9 +848,7 @@ public class AlignmentView { 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) { diff --git a/src/jalview/datamodel/CigarBase.java b/src/jalview/datamodel/CigarBase.java index 69826b6..d0ead87 100644 --- a/src/jalview/datamodel/CigarBase.java +++ b/src/jalview/datamodel/CigarBase.java @@ -20,6 +20,8 @@ */ package jalview.datamodel; +import jalview.util.MessageManager; + import java.util.*; public abstract class CigarBase @@ -144,7 +146,7 @@ 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) @@ -223,7 +225,7 @@ public abstract class CigarBase } 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 { @@ -232,7 +234,7 @@ public abstract class CigarBase 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') { @@ -244,9 +246,11 @@ public abstract class CigarBase } 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[] @@ -269,7 +273,7 @@ public abstract class CigarBase } 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) { @@ -277,8 +281,7 @@ public abstract class CigarBase } 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) @@ -390,8 +393,7 @@ public abstract class CigarBase } 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. @@ -463,10 +465,9 @@ public abstract class CigarBase } 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 diff --git a/src/jalview/datamodel/SeqCigar.java b/src/jalview/datamodel/SeqCigar.java index ffe152b..8441609 100644 --- a/src/jalview/datamodel/SeqCigar.java +++ b/src/jalview/datamodel/SeqCigar.java @@ -93,8 +93,7 @@ public class SeqCigar extends CigarSimple 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], @@ -142,11 +141,11 @@ public class SeqCigar extends CigarSimple 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()) @@ -212,8 +211,7 @@ public class SeqCigar extends CigarSimple // 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(); } @@ -237,12 +235,11 @@ public class SeqCigar extends CigarSimple 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) @@ -252,17 +249,14 @@ public class SeqCigar extends CigarSimple 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]; @@ -276,8 +270,7 @@ public class SeqCigar extends CigarSimple 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")); } } } @@ -384,7 +377,7 @@ public class SeqCigar extends CigarSimple 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 @@ -406,7 +399,7 @@ public class SeqCigar extends CigarSimple 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 @@ -461,8 +454,7 @@ public class SeqCigar extends CigarSimple // 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 diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java index cadb205..9187912 100644 --- a/src/jalview/ext/jmol/JalviewJmolBinding.java +++ b/src/jalview/ext/jmol/JalviewJmolBinding.java @@ -36,6 +36,7 @@ import jalview.structure.StructureListener; 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; @@ -412,8 +413,7 @@ public abstract class JalviewJmolBinding extends SequenceStructureBindingModel i // 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++) @@ -1574,9 +1574,7 @@ public abstract class JalviewJmolBinding extends SequenceStructureBindingModel i { 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(); diff --git a/src/jalview/ext/jmol/PDBFileWithJmol.java b/src/jalview/ext/jmol/PDBFileWithJmol.java index 9672268..847453f 100644 --- a/src/jalview/ext/jmol/PDBFileWithJmol.java +++ b/src/jalview/ext/jmol/PDBFileWithJmol.java @@ -42,6 +42,7 @@ import jalview.datamodel.Sequence; import jalview.datamodel.SequenceI; import jalview.io.AlignFile; import jalview.io.FileParse; +import jalview.util.MessageManager; /** * Import and process PDB files with Jmol @@ -95,10 +96,7 @@ public class PDBFileWithJmol extends AlignFile implements 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); } } diff --git a/src/jalview/ext/paradise/Annotate3D.java b/src/jalview/ext/paradise/Annotate3D.java index 4842033..3930fc0 100644 --- a/src/jalview/ext/paradise/Annotate3D.java +++ b/src/jalview/ext/paradise/Annotate3D.java @@ -20,6 +20,7 @@ */ package jalview.ext.paradise; +import jalview.util.MessageManager; import jalview.ws.HttpClientUtils; import java.io.IOException; @@ -189,14 +190,14 @@ public class Annotate3D @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 @@ -217,8 +218,7 @@ public class Annotate3D }; } 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); } } diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java index 11aa5c0..a39f355 100644 --- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java +++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java @@ -36,6 +36,7 @@ import jalview.structure.StructureListener; 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; @@ -476,8 +477,7 @@ public abstract class JalviewChimeraBinding extends // 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++) @@ -1350,9 +1350,7 @@ public abstract class JalviewChimeraBinding extends { 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(); diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 0a686d2..6346870 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -819,8 +819,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { 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)); @@ -836,10 +835,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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); @@ -1002,7 +998,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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); @@ -1947,7 +1943,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // ///// // 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 @@ -2206,7 +2202,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /* * //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())); @@ -2610,7 +2606,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, boolean addFirstIndex = false; if (viewTitle == null || viewTitle.trim().length() == 0) { - viewTitle = "View"; + viewTitle = MessageManager.getString("action.view"); addFirstIndex = true; } else @@ -4602,7 +4598,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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 @@ -4656,7 +4652,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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); } @@ -5687,8 +5683,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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 diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index 134019d..cdac5b4 100644 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -34,6 +34,7 @@ import jalview.datamodel.*; import jalview.jbgui.*; import jalview.schemes.*; import jalview.structure.StructureSelectionManager; +import jalview.util.MessageManager; /** * DOCUMENT ME! @@ -1119,9 +1120,7 @@ public class AlignmentPanel extends GAlignmentPanel implements .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 { @@ -1208,7 +1207,7 @@ public class AlignmentPanel extends GAlignmentPanel implements { if (alignFrame != null && !headless) { - alignFrame.setProgressBar("Export complete.", progress); + alignFrame.setProgressBar(MessageManager.getString("status.export_complete"), progress); } } } diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java index 39f3a13..7226eb0 100644 --- a/src/jalview/gui/AnnotationColourChooser.java +++ b/src/jalview/gui/AnnotationColourChooser.java @@ -168,8 +168,7 @@ public class AnnotationColourChooser extends JPanel 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()); @@ -472,7 +471,7 @@ public class AnnotationColourChooser extends JPanel 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); @@ -484,7 +483,7 @@ public class AnnotationColourChooser extends JPanel 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); diff --git a/src/jalview/gui/AnnotationExporter.java b/src/jalview/gui/AnnotationExporter.java index 0975d24..315c3e2 100644 --- a/src/jalview/gui/AnnotationExporter.java +++ b/src/jalview/gui/AnnotationExporter.java @@ -75,7 +75,7 @@ public class AnnotationExporter extends JPanel this.ap = ap; features = true; CSVFormat.setVisible(false); - frame.setTitle("Export Features"); + frame.setTitle(MessageManager.getString("label.export_features")); } public void exportAnnotations(AlignmentPanel ap, @@ -89,7 +89,7 @@ public class AnnotationExporter extends JPanel 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) @@ -98,15 +98,15 @@ public class AnnotationExporter extends JPanel 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()) @@ -153,7 +153,7 @@ public class AnnotationExporter extends JPanel 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()) diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java index 4036347..30253bf 100755 --- a/src/jalview/gui/AnnotationPanel.java +++ b/src/jalview/gui/AnnotationPanel.java @@ -307,7 +307,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, 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++) { diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java index bab8a2d..998db4b 100644 --- a/src/jalview/gui/AppJmol.java +++ b/src/jalview/gui/AppJmol.java @@ -731,7 +731,7 @@ public class AppJmol extends GStructureViewer implements Runnable, 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 { @@ -747,7 +747,7 @@ public class AppJmol extends GStructureViewer implements Runnable, } if (progressBar != null) { - progressBar.setProgressBar("Finished.", hdl); + progressBar.setProgressBar(MessageManager.getString("label.state_completed"), hdl); } if (pdbseq != null) { @@ -891,7 +891,7 @@ public class AppJmol extends GStructureViewer implements Runnable, 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); @@ -1096,7 +1096,7 @@ public class AppJmol extends GStructureViewer implements Runnable, 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); diff --git a/src/jalview/gui/BlogReader.java b/src/jalview/gui/BlogReader.java index 0935d9f..c7835a5 100644 --- a/src/jalview/gui/BlogReader.java +++ b/src/jalview/gui/BlogReader.java @@ -440,7 +440,7 @@ public class BlogReader extends JPanel 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() { diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java index cf04ae8..236d094 100644 --- a/src/jalview/gui/ChimeraViewFrame.java +++ b/src/jalview/gui/ChimeraViewFrame.java @@ -698,7 +698,7 @@ public class ChimeraViewFrame extends GStructureViewer implements Runnable, 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 { @@ -714,7 +714,7 @@ public class ChimeraViewFrame extends GStructureViewer implements Runnable, } if (progressBar != null) { - progressBar.setProgressBar("Finished.", hdl); + progressBar.setProgressBar(MessageManager.getString("label.state_completed"), hdl); } if (pdbseq != null) { @@ -866,7 +866,7 @@ public class ChimeraViewFrame extends GStructureViewer implements Runnable, 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); @@ -928,7 +928,7 @@ public class ChimeraViewFrame extends GStructureViewer implements Runnable, */ public void eps_actionPerformed(ActionEvent e) { - throw new Error("EPS Generation not yet implemented."); + throw new Error(MessageManager.getString("error.eps_generation_not_implemented")); } /** @@ -939,7 +939,7 @@ public class ChimeraViewFrame extends GStructureViewer implements Runnable, */ 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) @@ -1044,7 +1044,7 @@ public class ChimeraViewFrame extends GStructureViewer implements Runnable, 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); diff --git a/src/jalview/gui/Console.java b/src/jalview/gui/Console.java index 5f06bad..ea7e539 100644 --- a/src/jalview/gui/Console.java +++ b/src/jalview/gui/Console.java @@ -501,8 +501,7 @@ public class Console extends WindowAdapter implements WindowListener, } 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")); } } diff --git a/src/jalview/gui/CutAndPasteHtmlTransfer.java b/src/jalview/gui/CutAndPasteHtmlTransfer.java index 74297bb..7fd091f 100644 --- a/src/jalview/gui/CutAndPasteHtmlTransfer.java +++ b/src/jalview/gui/CutAndPasteHtmlTransfer.java @@ -141,7 +141,7 @@ public class CutAndPasteHtmlTransfer extends GCutAndPasteHtmlTransfer 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); diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java index 7f8d289..0c22b14 100644 --- a/src/jalview/gui/CutAndPasteTransfer.java +++ b/src/jalview/gui/CutAndPasteTransfer.java @@ -100,7 +100,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer 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); diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java index 772a5d7..a3cec98 100644 --- a/src/jalview/gui/Desktop.java +++ b/src/jalview/gui/Desktop.java @@ -452,7 +452,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements 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(); @@ -1012,7 +1012,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements 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; @@ -1386,7 +1386,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements { "Jalview Project" }, "Jalview Project"); chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle("Save State"); + chooser.setDialogTitle(MessageManager.getString("label.save_state")); int value = chooser.showSaveDialog(this); @@ -1399,7 +1399,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements 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()); @@ -1443,7 +1443,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements { "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); @@ -1456,7 +1456,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements { public void run() { - setProgressBar("loading jalview project " + choice, + setProgressBar(MessageManager.formatMessage("label.loading_jalview_project", new String[]{choice}), choice.hashCode()); try { @@ -1491,8 +1491,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements { if (fileLoadingCount == 0) { - fileLoadingPanels.add(addProgressPanel("Loading File: " + fileName - + " ")); + fileLoadingPanels.add(addProgressPanel(MessageManager.formatMessage("label.loading_file", new String[]{fileName}))); } fileLoadingCount++; } @@ -1730,7 +1729,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements 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")); @@ -1823,22 +1822,22 @@ public class Desktop extends jalview.jbgui.GDesktop implements 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(); } @@ -1847,12 +1846,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements { 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(); @@ -1999,15 +1997,14 @@ public class Desktop extends jalview.jbgui.GDesktop implements { "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; @@ -2059,7 +2056,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements } if (b) { - vamUpdate = this.addProgressPanel("Updating vamsas session"); + vamUpdate = this.addProgressPanel(MessageManager.getString("label.updating_vamsas_session")); } vamsasStart.setVisible(!b); vamsasStop.setVisible(!b); @@ -2290,8 +2287,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements // 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 { @@ -2313,8 +2309,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements .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); } } @@ -2365,8 +2361,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements { 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)); @@ -2381,10 +2376,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements 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); @@ -2646,7 +2638,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements { 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) @@ -2654,9 +2646,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements 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(); diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java index eb64dee..b04aa85 100644 --- a/src/jalview/gui/FeatureRenderer.java +++ b/src/jalview/gui/FeatureRenderer.java @@ -940,8 +940,7 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer 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})); } /** @@ -965,8 +964,7 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer 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) @@ -1218,12 +1216,12 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer { "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(); diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java index 08c4ef2..577012b 100644 --- a/src/jalview/gui/FeatureSettings.java +++ b/src/jalview/gui/FeatureSettings.java @@ -646,7 +646,7 @@ public class FeatureSettings extends JPanel { "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); @@ -744,7 +744,7 @@ public class FeatureSettings extends JPanel { "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); @@ -1380,7 +1380,7 @@ public class FeatureSettings extends JPanel } private String[] columnNames = - { "Feature Type", "Colour", "Display" }; + { MessageManager.getString("label.feature_type"), MessageManager.getString("action.colour"), MessageManager.getString("label.display") }; private Object[][] data; diff --git a/src/jalview/gui/FontChooser.java b/src/jalview/gui/FontChooser.java index cda6c46..b6116d9 100755 --- a/src/jalview/gui/FontChooser.java +++ b/src/jalview/gui/FontChooser.java @@ -226,8 +226,8 @@ public class FontChooser extends GFontChooser 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) diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java index ee779f7..7f6ac85 100755 --- a/src/jalview/gui/IdPanel.java +++ b/src/jalview/gui/IdPanel.java @@ -226,9 +226,8 @@ public class IdPanel extends JPanel implements MouseListener, 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(); } diff --git a/src/jalview/gui/JDatabaseTree.java b/src/jalview/gui/JDatabaseTree.java index 43f5333..279662a 100644 --- a/src/jalview/gui/JDatabaseTree.java +++ b/src/jalview/gui/JDatabaseTree.java @@ -219,8 +219,7 @@ public class JDatabaseTree extends JalviewDialog implements KeyListener } 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); diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java index f3bc42e..105209f 100644 --- a/src/jalview/gui/Jalview2XML.java +++ b/src/jalview/gui/Jalview2XML.java @@ -40,6 +40,7 @@ import jalview.datamodel.AlignmentI; 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; @@ -437,7 +438,7 @@ public class Jalview2XML 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"; @@ -1502,8 +1503,7 @@ public class Jalview2XML return false; } } - throw new Error("Unsupported Version for calcIdparam " - + calcIdParam.toString()); + throw new Error(MessageManager.formatMessage("error.unsupported_version_calcIdparam", new String[]{calcIdParam.toString()})); } /** diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java index 2e3b236..946181c 100755 --- a/src/jalview/gui/Jalview2XML_V1.java +++ b/src/jalview/gui/Jalview2XML_V1.java @@ -160,7 +160,7 @@ public class Jalview2XML_V1 { 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); } }); diff --git a/src/jalview/gui/OOMWarning.java b/src/jalview/gui/OOMWarning.java index 8a61757..a9347eb 100644 --- a/src/jalview/gui/OOMWarning.java +++ b/src/jalview/gui/OOMWarning.java @@ -20,6 +20,8 @@ */ package jalview.gui; +import jalview.util.MessageManager; + import java.awt.Component; public class OOMWarning implements Runnable @@ -78,11 +80,8 @@ 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; diff --git a/src/jalview/gui/OptsAndParamsPage.java b/src/jalview/gui/OptsAndParamsPage.java index b3ef1ed..4a9b580 100644 --- a/src/jalview/gui/OptsAndParamsPage.java +++ b/src/jalview/gui/OptsAndParamsPage.java @@ -855,7 +855,7 @@ public class OptsAndParamsPage } else { - throw new Error("Invalid value " + string + " for option " + option); + throw new Error(MessageManager.formatMessage("error.invalid_value_for_option", new String[]{string,option})); } } diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java index 04e8556..3483cc4 100644 --- a/src/jalview/gui/PCAPanel.java +++ b/src/jalview/gui/PCAPanel.java @@ -151,7 +151,7 @@ public class PCAPanel extends GPCAPanel implements Runnable, 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) @@ -168,11 +168,11 @@ public class PCAPanel extends GPCAPanel implements Runnable, { 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 @@ -666,8 +666,7 @@ public class PCAPanel extends GPCAPanel implements Runnable, { 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)); @@ -683,10 +682,7 @@ public class PCAPanel extends GPCAPanel implements Runnable, 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); diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java index b5c27c6..e44915d 100755 --- a/src/jalview/gui/Preferences.java +++ b/src/jalview/gui/Preferences.java @@ -509,7 +509,7 @@ public class Preferences extends GPreferences { "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); @@ -651,7 +651,7 @@ public class Preferences extends GPreferences 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); @@ -687,7 +687,7 @@ public class Preferences extends GPreferences 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); @@ -698,7 +698,7 @@ public class Preferences extends GPreferences 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); @@ -726,8 +726,8 @@ public class Preferences extends GPreferences 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(""); } diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java index 5adfae9..91f2450 100755 --- a/src/jalview/gui/RedundancyPanel.java +++ b/src/jalview/gui/RedundancyPanel.java @@ -228,7 +228,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable } } - 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++) diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index bf5ea93..02c6c16 100644 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -949,7 +949,7 @@ public class SeqPanel extends JPanel implements MouseListener, message.append("Edit group:"); if (editCommand == null) { - editCommand = new EditCommand("Edit Group"); + editCommand = new EditCommand(MessageManager.getString("action.edit_group")); } } else @@ -962,7 +962,7 @@ public class SeqPanel extends JPanel implements MouseListener, } if (editCommand == null) { - editCommand = new EditCommand("Edit " + label); + editCommand = new EditCommand(MessageManager.formatMessage("label.edit_params", new String[]{label})); } } diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java index b2bf35f..4506eaa 100755 --- a/src/jalview/gui/SequenceFetcher.java +++ b/src/jalview/gui/SequenceFetcher.java @@ -78,7 +78,7 @@ public class SequenceFetcher extends JPanel implements Runnable 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 @@ -97,7 +97,7 @@ public class SequenceFetcher extends JPanel implements Runnable if (guiWindow != null) { guiWindow.setProgressBar( - "Waiting for Sequence Database Fetchers to initialise", + MessageManager.getString("status.waiting_sequence_database_fetchers_init"), Thread.currentThread().hashCode()); } } @@ -115,7 +115,7 @@ public class SequenceFetcher extends JPanel implements Runnable */ 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(); @@ -124,7 +124,7 @@ public class SequenceFetcher extends JPanel implements Runnable 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 @@ -161,8 +161,8 @@ public class SequenceFetcher extends JPanel implements Runnable 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); } }); @@ -494,8 +494,7 @@ public class SequenceFetcher extends JPanel implements Runnable 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) @@ -693,11 +692,11 @@ public class SequenceFetcher extends JPanel implements Runnable 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) { diff --git a/src/jalview/gui/SliderPanel.java b/src/jalview/gui/SliderPanel.java index 48f09f8..81b3bd3 100755 --- a/src/jalview/gui/SliderPanel.java +++ b/src/jalview/gui/SliderPanel.java @@ -136,8 +136,7 @@ public class SliderPanel extends GSliderPanel 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) { @@ -213,7 +212,7 @@ public class SliderPanel extends GSliderPanel 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) { diff --git a/src/jalview/gui/TextColourChooser.java b/src/jalview/gui/TextColourChooser.java index dc705b2..bb2f295 100644 --- a/src/jalview/gui/TextColourChooser.java +++ b/src/jalview/gui/TextColourChooser.java @@ -81,7 +81,7 @@ public class TextColourChooser 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); @@ -95,7 +95,7 @@ public class TextColourChooser 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); @@ -113,7 +113,7 @@ public class TextColourChooser }); 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); diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java index e188177..c5650f5 100755 --- a/src/jalview/gui/TreeCanvas.java +++ b/src/jalview/gui/TreeCanvas.java @@ -757,7 +757,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, 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); diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java index cf49608..ee0bfaf 100755 --- a/src/jalview/gui/TreePanel.java +++ b/src/jalview/gui/TreePanel.java @@ -399,7 +399,7 @@ public class TreePanel extends GTreePanel 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); @@ -695,7 +695,7 @@ public class TreePanel extends GTreePanel { "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); @@ -742,7 +742,7 @@ public class TreePanel extends GTreePanel { "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); diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java index f719d27..a16fdc7 100755 --- a/src/jalview/gui/UserDefinedColours.java +++ b/src/jalview/gui/UserDefinedColours.java @@ -746,7 +746,7 @@ public class UserDefinedColours extends GUserDefinedColours implements { "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); diff --git a/src/jalview/gui/VamsasApplication.java b/src/jalview/gui/VamsasApplication.java index b789040..77a7693 100644 --- a/src/jalview/gui/VamsasApplication.java +++ b/src/jalview/gui/VamsasApplication.java @@ -31,6 +31,7 @@ import jalview.structure.SelectionSource; import jalview.structure.StructureSelectionManager; import jalview.structure.VamsasListener; import jalview.structure.VamsasSource; +import jalview.util.MessageManager; import java.beans.PropertyChangeEvent; import java.beans.PropertyChangeListener; @@ -155,8 +156,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource { 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 { @@ -176,8 +176,8 @@ public class VamsasApplication implements SelectionSource, VamsasSource .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); } @@ -263,8 +263,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource { 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(); @@ -348,7 +347,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource 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 { @@ -716,8 +715,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource 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(); diff --git a/src/jalview/gui/WebserviceInfo.java b/src/jalview/gui/WebserviceInfo.java index 2afec55..8dcf72a 100644 --- a/src/jalview/gui/WebserviceInfo.java +++ b/src/jalview/gui/WebserviceInfo.java @@ -356,8 +356,7 @@ public class WebserviceInfo extends GWebserviceInfo implements { 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) { @@ -651,8 +650,8 @@ public class WebserviceInfo extends GWebserviceInfo implements // 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 { @@ -912,8 +911,7 @@ public class WebserviceInfo extends GWebserviceInfo implements { 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)); @@ -929,10 +927,7 @@ public class WebserviceInfo extends GWebserviceInfo implements 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); diff --git a/src/jalview/gui/WsJobParameters.java b/src/jalview/gui/WsJobParameters.java index c81e8c8..23645df 100644 --- a/src/jalview/gui/WsJobParameters.java +++ b/src/jalview/gui/WsJobParameters.java @@ -218,7 +218,7 @@ public class WsJobParameters extends JPanel implements ItemListener, 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( diff --git a/src/jalview/gui/WsParamSetManager.java b/src/jalview/gui/WsParamSetManager.java index dec4745..3322d6a 100644 --- a/src/jalview/gui/WsParamSetManager.java +++ b/src/jalview/gui/WsParamSetManager.java @@ -178,8 +178,7 @@ public class WsParamSetManager implements ParamManager } 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) { @@ -189,7 +188,7 @@ public class WsParamSetManager implements ParamManager { "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) diff --git a/src/jalview/gui/WsPreferences.java b/src/jalview/gui/WsPreferences.java index a85ebbf..1a5b9f8 100644 --- a/src/jalview/gui/WsPreferences.java +++ b/src/jalview/gui/WsPreferences.java @@ -125,7 +125,7 @@ public class WsPreferences extends GWsPreferences } wsList.setModel(new WsUrlTableModel(tdat)); - wsList.getColumn("Status").setMinWidth(10); + wsList.getColumn(MessageManager.getString("label.status")).setMinWidth(10); } private class JabaWSStatusRenderer extends JPanel implements @@ -184,6 +184,8 @@ public class WsPreferences extends GWsPreferences { private Object[][] data; + private String[] columnNames = new String[] + { MessageManager.getString("label.service_url"), MessageManager.getString("label.status") }; public WsUrlTableModel(Object[][] tdat) { @@ -199,11 +201,7 @@ public class WsPreferences extends GWsPreferences @Override public String getColumnName(int column) { - if (column == 1) - { - return "Status"; - } - return "Service URL"; + return columnNames[column]; } @Override @@ -302,7 +300,7 @@ public class WsPreferences extends GWsPreferences 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)) { @@ -320,7 +318,7 @@ public class WsPreferences extends GWsPreferences { 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) { @@ -484,8 +482,8 @@ public class WsPreferences extends GWsPreferences 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)) @@ -497,7 +495,7 @@ public class WsPreferences extends GWsPreferences JOptionPane .showInternalMessageDialog( Desktop.desktop, - "Service did not pass validation.\nCheck the Jalview Console for more details."); + MessageManager.getString("warn.server_didnt_pass_validation")); } } else @@ -603,7 +601,7 @@ public class WsPreferences extends GWsPreferences 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) { diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java index c3c86d6..f73e250 100755 --- a/src/jalview/io/AlignFile.java +++ b/src/jalview/io/AlignFile.java @@ -24,6 +24,7 @@ import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceI; +import jalview.util.MessageManager; import java.io.IOException; import java.util.Enumeration; @@ -196,8 +197,7 @@ public abstract class AlignFile extends FileParse { 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) { diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java index 3f9a425..67559b9 100755 --- a/src/jalview/io/AppletFormatAdapter.java +++ b/src/jalview/io/AppletFormatAdapter.java @@ -501,8 +501,7 @@ public class AppletFormatAdapter 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); diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java index 4ec464a..0f94efa 100755 --- a/src/jalview/io/FileLoader.java +++ b/src/jalview/io/FileLoader.java @@ -417,11 +417,8 @@ public class FileLoader implements Runnable 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); } }); diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java index d20b468..4b8caec 100755 --- a/src/jalview/io/FileParse.java +++ b/src/jalview/io/FileParse.java @@ -20,6 +20,8 @@ */ package jalview.io; +import jalview.util.MessageManager; + import java.io.*; import java.net.*; import java.util.zip.GZIPInputStream; @@ -94,8 +96,7 @@ public class FileParse { 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; @@ -208,7 +209,7 @@ public class FileParse { 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; } @@ -263,14 +264,12 @@ public class FileParse { 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})); } } } @@ -345,8 +344,7 @@ public class FileParse 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); @@ -366,7 +364,7 @@ public class FileParse } else { - throw new IOException("Unitialised Source Stream"); + throw new IOException(MessageManager.getString("exception.no_init_source_stream")); } } @@ -374,7 +372,7 @@ public class FileParse { 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() @@ -406,8 +404,7 @@ public class FileParse } else { - throw new IOException( - "Implementation Error: Reset called for invalid source."); + throw new IOException(MessageManager.getString("error.implementation_error_reset_called_for_invalid_source")); } } diff --git a/src/jalview/io/HTMLOutput.java b/src/jalview/io/HTMLOutput.java index ac7f5b3..50b07e4 100755 --- a/src/jalview/io/HTMLOutput.java +++ b/src/jalview/io/HTMLOutput.java @@ -53,7 +53,7 @@ public class HTMLOutput { "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); diff --git a/src/jalview/io/JPredFile.java b/src/jalview/io/JPredFile.java index 0b3cd13..ca74f2c 100755 --- a/src/jalview/io/JPredFile.java +++ b/src/jalview/io/JPredFile.java @@ -29,6 +29,7 @@ import java.io.*; 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 @@ -293,9 +294,7 @@ public class JPredFile extends AlignFile 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() @@ -319,9 +318,7 @@ public class JPredFile extends AlignFile } 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; diff --git a/src/jalview/io/JalviewFileChooser.java b/src/jalview/io/JalviewFileChooser.java index 90e3229..470fd89 100755 --- a/src/jalview/io/JalviewFileChooser.java +++ b/src/jalview/io/JalviewFileChooser.java @@ -271,7 +271,7 @@ public class JalviewFileChooser extends JFileChooser } }); - 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)); diff --git a/src/jalview/io/JnetAnnotationMaker.java b/src/jalview/io/JnetAnnotationMaker.java index dabd8ca..5c95a3f 100755 --- a/src/jalview/io/JnetAnnotationMaker.java +++ b/src/jalview/io/JnetAnnotationMaker.java @@ -21,6 +21,7 @@ package jalview.io; import jalview.datamodel.*; +import jalview.util.MessageManager; public class JnetAnnotationMaker { @@ -60,13 +61,12 @@ 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; diff --git a/src/jalview/io/NewickFile.java b/src/jalview/io/NewickFile.java index 9c91c13..f2a29ea 100755 --- a/src/jalview/io/NewickFile.java +++ b/src/jalview/io/NewickFile.java @@ -30,6 +30,7 @@ import java.io.*; 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 @@ -611,11 +612,11 @@ public class NewickFile extends FileParse 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()) diff --git a/src/jalview/io/PfamFile.java b/src/jalview/io/PfamFile.java index 361b47f..7d4baa2 100755 --- a/src/jalview/io/PfamFile.java +++ b/src/jalview/io/PfamFile.java @@ -100,7 +100,7 @@ public class PfamFile extends AlignFile 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++) diff --git a/src/jalview/io/RnamlFile.java b/src/jalview/io/RnamlFile.java index 2b9a7b0..d366edc 100644 --- a/src/jalview/io/RnamlFile.java +++ b/src/jalview/io/RnamlFile.java @@ -31,6 +31,7 @@ import jalview.datamodel.AlignmentAnnotation; 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; @@ -97,24 +98,21 @@ public class RnamlFile extends AlignFile _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); } } diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java index 9d21a40..0a18be0 100644 --- a/src/jalview/io/StockholmFile.java +++ b/src/jalview/io/StockholmFile.java @@ -33,6 +33,7 @@ import jalview.datamodel.Sequence; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; import jalview.util.Format; +import jalview.util.MessageManager; import java.io.BufferedReader; import java.io.FileReader; @@ -197,8 +198,7 @@ public class StockholmFile extends AlignFile 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 { @@ -416,7 +416,7 @@ public class StockholmFile extends AlignFile 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) @@ -528,7 +528,7 @@ public class StockholmFile extends AlignFile } else { - throw new IOException("Error parsing " + line); + throw new IOException(MessageManager.formatMessage("exception.error_parsing_line", new String[]{line})); } } else if (annType.equals("GC")) @@ -653,8 +653,7 @@ public class StockholmFile extends AlignFile } else { - throw new IOException("Unknown annotation detected: " + annType - + " " + annContent); + throw new IOException(MessageManager.formatMessage("exception.unknown_annotation_detected", new String[]{annType,annContent})); } } } diff --git a/src/jalview/io/VamsasAppDatastore.java b/src/jalview/io/VamsasAppDatastore.java index 6472dd3..6293a1b 100644 --- a/src/jalview/io/VamsasAppDatastore.java +++ b/src/jalview/io/VamsasAppDatastore.java @@ -33,6 +33,8 @@ import jalview.io.vamsas.Datasetsequence; 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; @@ -222,8 +224,7 @@ public class VamsasAppDatastore { 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())) @@ -310,8 +311,7 @@ public class VamsasAppDatastore 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 } @@ -1473,9 +1473,7 @@ public class VamsasAppDatastore { // 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) { @@ -2417,8 +2415,7 @@ public class VamsasAppDatastore 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) { @@ -2476,8 +2473,7 @@ public class VamsasAppDatastore 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) { @@ -2733,8 +2729,7 @@ public class VamsasAppDatastore } } 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); } } diff --git a/src/jalview/io/WSWUBlastClient.java b/src/jalview/io/WSWUBlastClient.java index cc5fbed..871c6d5 100755 --- a/src/jalview/io/WSWUBlastClient.java +++ b/src/jalview/io/WSWUBlastClient.java @@ -208,8 +208,7 @@ public class WSWUBlastClient 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[]{jobsRunning})); } catch (Exception ex) { } diff --git a/src/jalview/io/vamsas/DatastoreItem.java b/src/jalview/io/vamsas/DatastoreItem.java index 74c5bd1..2a070e8 100644 --- a/src/jalview/io/vamsas/DatastoreItem.java +++ b/src/jalview/io/vamsas/DatastoreItem.java @@ -22,6 +22,7 @@ package jalview.io.vamsas; import jalview.bin.Cache; import jalview.io.VamsasAppDatastore; +import jalview.util.MessageManager; import java.util.Enumeration; import java.util.Hashtable; @@ -131,16 +132,14 @@ public abstract class DatastoreItem { 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 " @@ -190,9 +189,7 @@ public abstract class DatastoreItem 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) { @@ -231,9 +228,8 @@ public abstract class DatastoreItem 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); } @@ -259,9 +255,8 @@ public abstract class DatastoreItem 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); } diff --git a/src/jalview/io/vamsas/Rangetype.java b/src/jalview/io/vamsas/Rangetype.java index a2b5ff4..3cc977f 100644 --- a/src/jalview/io/vamsas/Rangetype.java +++ b/src/jalview/io/vamsas/Rangetype.java @@ -29,6 +29,7 @@ import uk.ac.vamsas.objects.core.Mapped; 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 @@ -75,8 +76,7 @@ public abstract class Rangetype extends DatastoreItem 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) { @@ -134,8 +134,7 @@ public abstract class Rangetype extends DatastoreItem 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) { @@ -182,8 +181,7 @@ public abstract class Rangetype extends DatastoreItem 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) { @@ -299,8 +297,7 @@ public abstract class Rangetype extends DatastoreItem { 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()); diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index d3154c7..e122f21 100755 --- a/src/jalview/jbgui/GAlignFrame.java +++ b/src/jalview/jbgui/GAlignFrame.java @@ -799,7 +799,7 @@ public class GAlignFrame extends JInternalFrame } }); 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)); diff --git a/src/jalview/jbgui/GSequenceLink.java b/src/jalview/jbgui/GSequenceLink.java index ca0f5ee..3e6f91a 100755 --- a/src/jalview/jbgui/GSequenceLink.java +++ b/src/jalview/jbgui/GSequenceLink.java @@ -121,8 +121,8 @@ public class GSequenceLink extends Panel JOptionPane .showInternalMessageDialog( jalview.gui.Desktop.desktop, - "Sequence URL must contain $SEQUENCE_ID$ or a regex $SEQUENCE_ID=//=$", - "URL not valid", JOptionPane.WARNING_MESSAGE); + MessageManager.getString("warn.url_must_contain"), + MessageManager.getString("label.invalid_url"), JOptionPane.WARNING_MESSAGE); return false; } diff --git a/src/jalview/math/Matrix.java b/src/jalview/math/Matrix.java index 036d16a..acd83a8 100755 --- a/src/jalview/math/Matrix.java +++ b/src/jalview/math/Matrix.java @@ -403,8 +403,7 @@ public class Matrix 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 { @@ -653,8 +652,7 @@ public class Matrix 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 { diff --git a/src/jalview/schemabinding/version2/AlcodonFrame.java b/src/jalview/schemabinding/version2/AlcodonFrame.java index a0e1ea1..c7d2f17 100644 --- a/src/jalview/schemabinding/version2/AlcodonFrame.java +++ b/src/jalview/schemabinding/version2/AlcodonFrame.java @@ -24,6 +24,8 @@ package jalview.schemabinding.version2; //- Imported classes and packages -/ //---------------------------------/ +import jalview.util.MessageManager; + import org.exolab.castor.xml.Marshaller; import org.exolab.castor.xml.Unmarshaller; @@ -159,9 +161,11 @@ public class AlcodonFrame implements java.io.Serializable // 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 @@ -209,9 +213,11 @@ public class AlcodonFrame implements java.io.Serializable // 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); @@ -378,9 +384,11 @@ public class AlcodonFrame implements java.io.Serializable // 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); @@ -418,9 +426,11 @@ public class AlcodonFrame implements java.io.Serializable // 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); diff --git a/src/jalview/schemabinding/version2/Annotation.java b/src/jalview/schemabinding/version2/Annotation.java index f5cd880..0741387 100644 --- a/src/jalview/schemabinding/version2/Annotation.java +++ b/src/jalview/schemabinding/version2/Annotation.java @@ -24,6 +24,8 @@ package jalview.schemabinding.version2; //- Imported classes and packages -/ //---------------------------------/ +import jalview.util.MessageManager; + import org.exolab.castor.xml.Marshaller; import org.exolab.castor.xml.Unmarshaller; @@ -373,10 +375,11 @@ public class Annotation implements java.io.Serializable // 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 @@ -935,10 +938,11 @@ public class Annotation implements java.io.Serializable // 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); diff --git a/src/jalview/schemabinding/version2/Feature.java b/src/jalview/schemabinding/version2/Feature.java index 3bc1a9e..bbc5f67 100644 --- a/src/jalview/schemabinding/version2/Feature.java +++ b/src/jalview/schemabinding/version2/Feature.java @@ -24,6 +24,8 @@ package jalview.schemabinding.version2; //- Imported classes and packages -/ //---------------------------------/ +import jalview.util.MessageManager; + import org.exolab.castor.xml.Marshaller; import org.exolab.castor.xml.Unmarshaller; @@ -224,9 +226,11 @@ public class Feature implements java.io.Serializable // 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 @@ -467,9 +471,11 @@ public class Feature implements java.io.Serializable // 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); diff --git a/src/jalview/schemabinding/version2/FeatureSettings.java b/src/jalview/schemabinding/version2/FeatureSettings.java index 8c40929..14d9844 100644 --- a/src/jalview/schemabinding/version2/FeatureSettings.java +++ b/src/jalview/schemabinding/version2/FeatureSettings.java @@ -24,6 +24,8 @@ package jalview.schemabinding.version2; //- Imported classes and packages -/ //---------------------------------/ +import jalview.util.MessageManager; + import org.exolab.castor.xml.Marshaller; import org.exolab.castor.xml.Unmarshaller; @@ -158,8 +160,11 @@ public class FeatureSettings implements java.io.Serializable // 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); @@ -206,9 +211,11 @@ public class FeatureSettings implements java.io.Serializable // 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); @@ -374,8 +381,11 @@ public class FeatureSettings implements java.io.Serializable // 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); @@ -413,9 +423,11 @@ public class FeatureSettings implements java.io.Serializable // 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); diff --git a/src/jalview/schemabinding/version2/JGroup.java b/src/jalview/schemabinding/version2/JGroup.java index b909250..3a8dab2 100644 --- a/src/jalview/schemabinding/version2/JGroup.java +++ b/src/jalview/schemabinding/version2/JGroup.java @@ -24,6 +24,8 @@ package jalview.schemabinding.version2; //- Imported classes and packages -/ //---------------------------------/ +import jalview.util.MessageManager; + import org.exolab.castor.xml.Marshaller; import org.exolab.castor.xml.Unmarshaller; @@ -535,8 +537,11 @@ public class JGroup implements java.io.Serializable // 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); @@ -1131,8 +1136,11 @@ public class JGroup implements java.io.Serializable // 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); diff --git a/src/jalview/schemabinding/version2/JSeq.java b/src/jalview/schemabinding/version2/JSeq.java index 52aed9a..31a128e 100644 --- a/src/jalview/schemabinding/version2/JSeq.java +++ b/src/jalview/schemabinding/version2/JSeq.java @@ -24,6 +24,8 @@ package jalview.schemabinding.version2; //- Imported classes and packages -/ //---------------------------------/ +import jalview.util.MessageManager; + import org.exolab.castor.xml.Marshaller; import org.exolab.castor.xml.Unmarshaller; @@ -296,9 +298,11 @@ public class JSeq implements java.io.Serializable // 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 @@ -355,10 +359,11 @@ public class JSeq implements java.io.Serializable // 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(); @@ -417,9 +422,11 @@ public class JSeq implements java.io.Serializable // 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); @@ -702,9 +709,11 @@ public class JSeq implements java.io.Serializable // 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); @@ -753,10 +762,11 @@ public class JSeq implements java.io.Serializable // 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( @@ -806,9 +816,11 @@ public class JSeq implements java.io.Serializable // 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); diff --git a/src/jalview/schemabinding/version2/JalviewModelSequence.java b/src/jalview/schemabinding/version2/JalviewModelSequence.java index b40ab80..790a1ca 100644 --- a/src/jalview/schemabinding/version2/JalviewModelSequence.java +++ b/src/jalview/schemabinding/version2/JalviewModelSequence.java @@ -24,6 +24,8 @@ package jalview.schemabinding.version2; //- Imported classes and packages -/ //---------------------------------/ +import jalview.util.MessageManager; + import org.exolab.castor.xml.Marshaller; import org.exolab.castor.xml.Unmarshaller; @@ -309,9 +311,11 @@ public class JalviewModelSequence implements java.io.Serializable // 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); @@ -358,8 +362,11 @@ public class JalviewModelSequence implements java.io.Serializable // 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); @@ -406,8 +413,11 @@ public class JalviewModelSequence implements java.io.Serializable // 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); @@ -454,9 +464,11 @@ public class JalviewModelSequence implements java.io.Serializable // 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 @@ -504,9 +516,11 @@ public class JalviewModelSequence implements java.io.Serializable // 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 @@ -781,9 +795,11 @@ public class JalviewModelSequence implements java.io.Serializable // 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); @@ -821,8 +837,11 @@ public class JalviewModelSequence implements java.io.Serializable // 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); @@ -859,8 +878,11 @@ public class JalviewModelSequence implements java.io.Serializable // 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); @@ -897,9 +919,11 @@ public class JalviewModelSequence implements java.io.Serializable // 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); @@ -937,9 +961,11 @@ public class JalviewModelSequence implements java.io.Serializable // 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); diff --git a/src/jalview/schemabinding/version2/JalviewUserColours.java b/src/jalview/schemabinding/version2/JalviewUserColours.java index 49f428a..e6ced25 100644 --- a/src/jalview/schemabinding/version2/JalviewUserColours.java +++ b/src/jalview/schemabinding/version2/JalviewUserColours.java @@ -24,6 +24,8 @@ package jalview.schemabinding.version2; //- Imported classes and packages -/ //---------------------------------/ +import jalview.util.MessageManager; + import org.exolab.castor.xml.Marshaller; import org.exolab.castor.xml.Unmarshaller; @@ -120,9 +122,11 @@ public class JalviewUserColours implements java.io.Serializable // 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); @@ -274,9 +278,11 @@ public class JalviewUserColours implements java.io.Serializable // 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); diff --git a/src/jalview/schemabinding/version2/MapListType.java b/src/jalview/schemabinding/version2/MapListType.java index a43e797..32e8ce2 100644 --- a/src/jalview/schemabinding/version2/MapListType.java +++ b/src/jalview/schemabinding/version2/MapListType.java @@ -24,6 +24,8 @@ package jalview.schemabinding.version2; //- Imported classes and packages -/ //---------------------------------/ +import jalview.util.MessageManager; + import org.exolab.castor.xml.Marshaller; import org.exolab.castor.xml.Unmarshaller; @@ -220,9 +222,11 @@ public class MapListType implements java.io.Serializable // 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 @@ -270,9 +274,11 @@ public class MapListType implements java.io.Serializable // 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 @@ -492,9 +498,11 @@ public class MapListType implements java.io.Serializable // 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); @@ -532,9 +540,11 @@ public class MapListType implements java.io.Serializable // 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); diff --git a/src/jalview/schemabinding/version2/Pdbentry.java b/src/jalview/schemabinding/version2/Pdbentry.java index 8644745..a558e12 100644 --- a/src/jalview/schemabinding/version2/Pdbentry.java +++ b/src/jalview/schemabinding/version2/Pdbentry.java @@ -24,6 +24,8 @@ package jalview.schemabinding.version2; //- Imported classes and packages -/ //---------------------------------/ +import jalview.util.MessageManager; + import org.exolab.castor.xml.Marshaller; import org.exolab.castor.xml.Unmarshaller; @@ -148,9 +150,11 @@ public class Pdbentry implements java.io.Serializable // 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); @@ -316,9 +320,11 @@ public class Pdbentry implements java.io.Serializable // 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); diff --git a/src/jalview/schemabinding/version2/PdbentryItem.java b/src/jalview/schemabinding/version2/PdbentryItem.java index 20bbac8..b1bbf11 100644 --- a/src/jalview/schemabinding/version2/PdbentryItem.java +++ b/src/jalview/schemabinding/version2/PdbentryItem.java @@ -20,6 +20,8 @@ */ package jalview.schemabinding.version2; +import jalview.util.MessageManager; + /** * Class PdbentryItem. * @@ -106,9 +108,11 @@ public class PdbentryItem implements java.io.Serializable // 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 @@ -189,9 +193,11 @@ public class PdbentryItem implements java.io.Serializable // 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); diff --git a/src/jalview/schemabinding/version2/Pdbids.java b/src/jalview/schemabinding/version2/Pdbids.java index b491cf0..bf700f9 100644 --- a/src/jalview/schemabinding/version2/Pdbids.java +++ b/src/jalview/schemabinding/version2/Pdbids.java @@ -24,6 +24,8 @@ package jalview.schemabinding.version2; //- Imported classes and packages -/ //---------------------------------/ +import jalview.util.MessageManager; + import org.exolab.castor.xml.Marshaller; import org.exolab.castor.xml.Unmarshaller; @@ -115,10 +117,11 @@ public class Pdbids extends jalview.schemabinding.version2.Pdbentry // 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 @@ -255,10 +258,11 @@ public class Pdbids extends jalview.schemabinding.version2.Pdbentry // 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); diff --git a/src/jalview/schemabinding/version2/Sequence.java b/src/jalview/schemabinding/version2/Sequence.java index 4ada896..54f2e30 100644 --- a/src/jalview/schemabinding/version2/Sequence.java +++ b/src/jalview/schemabinding/version2/Sequence.java @@ -24,6 +24,8 @@ package jalview.schemabinding.version2; //- Imported classes and packages -/ //---------------------------------/ +import jalview.util.MessageManager; + import org.exolab.castor.xml.Marshaller; import org.exolab.castor.xml.Unmarshaller; @@ -120,8 +122,11 @@ public class Sequence extends jalview.schemabinding.version2.SequenceType // 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); @@ -267,8 +272,11 @@ public class Sequence extends jalview.schemabinding.version2.SequenceType // 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); diff --git a/src/jalview/schemabinding/version2/SequenceSet.java b/src/jalview/schemabinding/version2/SequenceSet.java index fe146fa..d058ad5 100644 --- a/src/jalview/schemabinding/version2/SequenceSet.java +++ b/src/jalview/schemabinding/version2/SequenceSet.java @@ -24,6 +24,8 @@ package jalview.schemabinding.version2; //- Imported classes and packages -/ //---------------------------------/ +import jalview.util.MessageManager; + import org.exolab.castor.xml.Marshaller; import org.exolab.castor.xml.Unmarshaller; @@ -264,9 +266,11 @@ public class SequenceSet implements java.io.Serializable // 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 @@ -314,9 +318,11 @@ public class SequenceSet implements java.io.Serializable // 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 @@ -387,9 +393,11 @@ public class SequenceSet implements java.io.Serializable // 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 @@ -438,10 +446,11 @@ public class SequenceSet implements java.io.Serializable // 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 @@ -677,9 +686,11 @@ public class SequenceSet implements java.io.Serializable // 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); @@ -717,9 +728,11 @@ public class SequenceSet implements java.io.Serializable // 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); @@ -782,9 +795,11 @@ public class SequenceSet implements java.io.Serializable // 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); @@ -823,10 +838,11 @@ public class SequenceSet implements java.io.Serializable // 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); diff --git a/src/jalview/schemabinding/version2/VAMSAS.java b/src/jalview/schemabinding/version2/VAMSAS.java index 2a7d463..7f0c216 100644 --- a/src/jalview/schemabinding/version2/VAMSAS.java +++ b/src/jalview/schemabinding/version2/VAMSAS.java @@ -24,6 +24,8 @@ package jalview.schemabinding.version2; //- Imported classes and packages -/ //---------------------------------/ +import jalview.util.MessageManager; + import org.exolab.castor.xml.Marshaller; import org.exolab.castor.xml.Unmarshaller; @@ -156,9 +158,11 @@ public class VAMSAS implements java.io.Serializable // 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 @@ -205,8 +209,11 @@ public class VAMSAS implements java.io.Serializable // 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); @@ -370,9 +377,11 @@ public class VAMSAS implements java.io.Serializable // 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); @@ -409,8 +418,11 @@ public class VAMSAS implements java.io.Serializable // 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); diff --git a/src/jalview/schemabinding/version2/Viewport.java b/src/jalview/schemabinding/version2/Viewport.java index 03bd2a9..1faf480 100644 --- a/src/jalview/schemabinding/version2/Viewport.java +++ b/src/jalview/schemabinding/version2/Viewport.java @@ -24,6 +24,8 @@ package jalview.schemabinding.version2; //- Imported classes and packages -/ //---------------------------------/ +import jalview.util.MessageManager; + import org.exolab.castor.xml.Marshaller; import org.exolab.castor.xml.Unmarshaller; @@ -845,9 +847,11 @@ public class Viewport implements java.io.Serializable // 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 @@ -995,9 +999,11 @@ public class Viewport implements java.io.Serializable // 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 @@ -2121,9 +2127,11 @@ public class Viewport implements java.io.Serializable // 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); @@ -2280,9 +2288,11 @@ public class Viewport implements java.io.Serializable // 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); diff --git a/src/jalview/schemabinding/version2/WebServiceParameterSet.java b/src/jalview/schemabinding/version2/WebServiceParameterSet.java index 0cf7c49..822a175 100644 --- a/src/jalview/schemabinding/version2/WebServiceParameterSet.java +++ b/src/jalview/schemabinding/version2/WebServiceParameterSet.java @@ -24,6 +24,8 @@ package jalview.schemabinding.version2; //- Imported classes and packages -/ //---------------------------------/ +import jalview.util.MessageManager; + import org.exolab.castor.xml.Marshaller; import org.exolab.castor.xml.Unmarshaller; @@ -183,9 +185,11 @@ public class WebServiceParameterSet implements java.io.Serializable // 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); @@ -373,9 +377,11 @@ public class WebServiceParameterSet implements java.io.Serializable // 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); diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java index 609e741..47b8fbd 100755 --- a/src/jalview/schemes/ResidueColourScheme.java +++ b/src/jalview/schemes/ResidueColourScheme.java @@ -25,6 +25,7 @@ import jalview.analysis.Conservation; import jalview.datamodel.AnnotatedCollectionI; import jalview.datamodel.SequenceCollectionI; import jalview.datamodel.SequenceI; +import jalview.util.MessageManager; import java.awt.Color; import java.util.Hashtable; @@ -323,9 +324,7 @@ public class ResidueColourScheme implements ColourSchemeI 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); } } } diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java index c0c559a..73a5905 100644 --- a/src/jalview/structure/StructureSelectionManager.java +++ b/src/jalview/structure/StructureSelectionManager.java @@ -28,6 +28,7 @@ import jalview.analysis.*; import jalview.api.AlignmentViewPanel; import jalview.api.StructureSelectionManagerProvider; import jalview.datamodel.*; +import jalview.util.MessageManager; public class StructureSelectionManager { @@ -68,9 +69,8 @@ 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 { diff --git a/src/jalview/util/AWTConsole.java b/src/jalview/util/AWTConsole.java index 9aaa307..871b480 100644 --- a/src/jalview/util/AWTConsole.java +++ b/src/jalview/util/AWTConsole.java @@ -223,8 +223,7 @@ public class AWTConsole extends WindowAdapter implements WindowListener, } 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")); } } diff --git a/src/jalview/util/BrowserLauncher.java b/src/jalview/util/BrowserLauncher.java index a0f9523..60e2fed 100755 --- a/src/jalview/util/BrowserLauncher.java +++ b/src/jalview/util/BrowserLauncher.java @@ -702,14 +702,14 @@ public class BrowserLauncher { 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) @@ -728,19 +728,13 @@ public class BrowserLauncher {}); } 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 @@ -778,13 +772,12 @@ public class BrowserLauncher } 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; @@ -797,14 +790,10 @@ public class BrowserLauncher { 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; @@ -829,9 +818,7 @@ public class BrowserLauncher 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; @@ -870,9 +857,7 @@ public class BrowserLauncher } } 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; diff --git a/src/jalview/util/GroupUrlLink.java b/src/jalview/util/GroupUrlLink.java index ea3f69f..e8af4cd 100644 --- a/src/jalview/util/GroupUrlLink.java +++ b/src/jalview/util/GroupUrlLink.java @@ -396,8 +396,7 @@ public class GroupUrlLink { 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; } @@ -487,18 +486,14 @@ public class GroupUrlLink { 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 diff --git a/src/jalview/ws/AWSThread.java b/src/jalview/ws/AWSThread.java index 7ab1781..edb56a9 100644 --- a/src/jalview/ws/AWSThread.java +++ b/src/jalview/ws/AWSThread.java @@ -29,6 +29,7 @@ import jalview.datamodel.SequenceI; import jalview.gui.AlignFrame; import jalview.gui.WebserviceInfo; import jalview.gui.FeatureRenderer.FeatureRendererSettings; +import jalview.util.MessageManager; public abstract class AWSThread extends Thread { @@ -123,8 +124,8 @@ 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."); @@ -189,7 +190,7 @@ public abstract class AWSThread extends Thread 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(); } } diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java index ebf3a7d..f5789ea 100644 --- a/src/jalview/ws/DBRefFetcher.java +++ b/src/jalview/ws/DBRefFetcher.java @@ -283,11 +283,11 @@ public class DBRefFetcher implements Runnable { 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)) diff --git a/src/jalview/ws/DasSequenceFeatureFetcher.java b/src/jalview/ws/DasSequenceFeatureFetcher.java index ff715ba..8a7bcbc 100644 --- a/src/jalview/ws/DasSequenceFeatureFetcher.java +++ b/src/jalview/ws/DasSequenceFeatureFetcher.java @@ -27,6 +27,7 @@ import jalview.datamodel.SequenceI; 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; @@ -204,9 +205,8 @@ public class DasSequenceFeatureFetcher 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); } @@ -264,7 +264,7 @@ public class DasSequenceFeatureFetcher 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) { @@ -537,7 +537,7 @@ public class DasSequenceFeatureFetcher if (af != null) { - af.setProgressBar("No DAS Sources Active", startTime); + af.setProgressBar(MessageManager.getString("status.no_das_sources_active"), startTime); } if (getFeatSettings() != null) { @@ -567,7 +567,7 @@ public class DasSequenceFeatureFetcher { if (af != null) { - af.setProgressBar("DAS Feature Fetching Cancelled", startTime); + af.setProgressBar(MessageManager.getString("status.das_feature_fetching_cancelled"), startTime); } cancelled = true; } @@ -582,7 +582,7 @@ public class DasSequenceFeatureFetcher 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) diff --git a/src/jalview/ws/EnfinEnvision2OneWay.java b/src/jalview/ws/EnfinEnvision2OneWay.java index d2e55c4..83dae2c 100644 --- a/src/jalview/ws/EnfinEnvision2OneWay.java +++ b/src/jalview/ws/EnfinEnvision2OneWay.java @@ -376,9 +376,8 @@ public class EnfinEnvision2OneWay extends DefaultHandler implements 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(); } diff --git a/src/jalview/ws/dbsources/EmblXmlSource.java b/src/jalview/ws/dbsources/EmblXmlSource.java index ee8eb79..ec5c62d 100644 --- a/src/jalview/ws/dbsources/EmblXmlSource.java +++ b/src/jalview/ws/dbsources/EmblXmlSource.java @@ -24,6 +24,7 @@ import jalview.datamodel.Alignment; 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; @@ -65,8 +66,7 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy } 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); } @@ -98,8 +98,7 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy } 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) @@ -153,8 +152,7 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy 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(); diff --git a/src/jalview/ws/dbsources/Pdb.java b/src/jalview/ws/dbsources/Pdb.java index 1c6c015..a352de6 100644 --- a/src/jalview/ws/dbsources/Pdb.java +++ b/src/jalview/ws/dbsources/Pdb.java @@ -37,6 +37,7 @@ import com.stevesoft.pat.Regex; import jalview.datamodel.AlignmentI; import jalview.io.FormatAdapter; +import jalview.util.MessageManager; import jalview.ws.ebi.EBIFetchClient; import jalview.ws.seqfetcher.DbSourceProxy; @@ -197,8 +198,7 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy 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 diff --git a/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java b/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java index b9d778b..cb5705e 100644 --- a/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java +++ b/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java @@ -39,6 +39,7 @@ import org.biodas.jdas.schema.sources.VERSION; import com.stevesoft.pat.Regex; +import jalview.util.MessageManager; import jalview.ws.dbsources.das.api.jalviewSourceI; import jalview.ws.seqfetcher.*; import jalview.bin.Cache; @@ -100,8 +101,7 @@ public class DasSequenceSource extends DbSourceProxyImpl implements 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; diff --git a/src/jalview/ws/dbsources/das/datamodel/JalviewSource.java b/src/jalview/ws/dbsources/das/datamodel/JalviewSource.java index d260b9e..c994fd5 100644 --- a/src/jalview/ws/dbsources/das/datamodel/JalviewSource.java +++ b/src/jalview/ws/dbsources/das/datamodel/JalviewSource.java @@ -37,6 +37,7 @@ import org.biodas.jdas.schema.sources.PROP; 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; @@ -346,7 +347,7 @@ public class JalviewSource implements jalviewSourceI 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) == '/') { diff --git a/src/jalview/ws/ebi/EBIFetchClient.java b/src/jalview/ws/ebi/EBIFetchClient.java index f5f9190..fe9e28f 100644 --- a/src/jalview/ws/ebi/EBIFetchClient.java +++ b/src/jalview/ws/ebi/EBIFetchClient.java @@ -20,6 +20,8 @@ */ package jalview.ws.ebi; +import jalview.util.MessageManager; + import java.io.BufferedInputStream; import java.io.BufferedReader; import java.io.File; @@ -56,7 +58,7 @@ public class EBIFetchClient 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")); } /** @@ -67,7 +69,7 @@ public class EBIFetchClient 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")); } /** @@ -78,7 +80,7 @@ public class EBIFetchClient 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) diff --git a/src/jalview/ws/jws1/Annotate3D.java b/src/jalview/ws/jws1/Annotate3D.java index 465c5fc..4502b39 100644 --- a/src/jalview/ws/jws1/Annotate3D.java +++ b/src/jalview/ws/jws1/Annotate3D.java @@ -25,6 +25,7 @@ import jalview.datamodel.AlignmentI; import jalview.io.FileParse; import jalview.io.FormatAdapter; import jalview.io.InputStreamParser; +import jalview.util.MessageManager; import java.io.BufferedReader; import java.io.FileReader; @@ -105,8 +106,7 @@ public class Annotate3D } 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); } } diff --git a/src/jalview/ws/jws1/JPredClient.java b/src/jalview/ws/jws1/JPredClient.java index f1d3e43..1a96464 100644 --- a/src/jalview/ws/jws1/JPredClient.java +++ b/src/jalview/ws/jws1/JPredClient.java @@ -144,8 +144,7 @@ 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 " @@ -285,7 +284,7 @@ public class JPredClient extends WS1Client 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\"."; diff --git a/src/jalview/ws/jws1/JPredThread.java b/src/jalview/ws/jws1/JPredThread.java index 6531bbf..85969fc 100644 --- a/src/jalview/ws/jws1/JPredThread.java +++ b/src/jalview/ws/jws1/JPredThread.java @@ -140,8 +140,7 @@ class JPredThread extends JWS1Thread implements WSClientI 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; @@ -153,8 +152,7 @@ class JPredThread extends JWS1Thread implements WSClientI } 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 @@ -168,14 +166,13 @@ class JPredThread extends JWS1Thread implements WSClientI .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); @@ -186,8 +183,7 @@ class JPredThread extends JWS1Thread implements WSClientI 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 { @@ -357,9 +353,7 @@ class JPredThread extends JWS1Thread implements WSClientI { 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 { @@ -380,7 +374,7 @@ class JPredThread extends JWS1Thread implements WSClientI { 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 @@ -392,7 +386,7 @@ class JPredThread extends JWS1Thread implements WSClientI } else { - throw new Exception("Server timed out - try again later\n"); + throw new Exception(MessageManager.getString("exception.server_timeout_try_later")); } } catch (Exception e) { @@ -416,9 +410,7 @@ class JPredThread extends JWS1Thread implements WSClientI { 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); @@ -508,8 +500,7 @@ class JPredThread extends JWS1Thread implements WSClientI 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) { @@ -517,9 +508,7 @@ class JPredThread extends JWS1Thread implements WSClientI "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); } } @@ -587,7 +576,7 @@ class JPredThread extends JWS1Thread implements WSClientI public void cancelJob() { - throw new Error("Implementation error!"); + throw new Error(MessageManager.getString("error.implementation_error")); } public boolean canMergeResults() diff --git a/src/jalview/ws/jws1/MsaWSThread.java b/src/jalview/ws/jws1/MsaWSThread.java index 2d111ca..a6ba751 100644 --- a/src/jalview/ws/jws1/MsaWSThread.java +++ b/src/jalview/ws/jws1/MsaWSThread.java @@ -26,6 +26,7 @@ import jalview.analysis.*; 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; @@ -63,7 +64,7 @@ class MsaWSThread extends JWS1Thread implements 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")); } } @@ -86,8 +87,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI 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++) { @@ -431,8 +431,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI { 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()) @@ -450,7 +449,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI 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 @@ -468,10 +467,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI { 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()); @@ -491,9 +487,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI 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 } @@ -539,7 +533,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI 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++) { diff --git a/src/jalview/ws/jws1/SeqSearchWSClient.java b/src/jalview/ws/jws1/SeqSearchWSClient.java index 3a4bbd4..c1935b4 100644 --- a/src/jalview/ws/jws1/SeqSearchWSClient.java +++ b/src/jalview/ws/jws1/SeqSearchWSClient.java @@ -208,7 +208,7 @@ public class SeqSearchWSClient extends WS1Client } 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) diff --git a/src/jalview/ws/jws1/SeqSearchWSThread.java b/src/jalview/ws/jws1/SeqSearchWSThread.java index b9d38fe..7c2ea49 100644 --- a/src/jalview/ws/jws1/SeqSearchWSThread.java +++ b/src/jalview/ws/jws1/SeqSearchWSThread.java @@ -27,6 +27,7 @@ import jalview.bin.*; 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; @@ -61,7 +62,7 @@ class SeqSearchWSThread extends JWS1Thread implements 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")); } } @@ -84,8 +85,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI 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++) { @@ -446,8 +446,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI { 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()) @@ -465,7 +464,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI 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 @@ -484,10 +483,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI { 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()); @@ -507,9 +503,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI 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 } @@ -548,7 +542,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI 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++) { @@ -648,7 +642,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI 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); diff --git a/src/jalview/ws/jws1/WS1Client.java b/src/jalview/ws/jws1/WS1Client.java index 4d1af4c..210e520 100644 --- a/src/jalview/ws/jws1/WS1Client.java +++ b/src/jalview/ws/jws1/WS1Client.java @@ -22,6 +22,7 @@ package jalview.ws.jws1; import jalview.gui.AlignFrame; import jalview.gui.WebserviceInfo; +import jalview.util.MessageManager; import jalview.ws.WSClient; import jalview.ws.WSMenuEntryProviderI; @@ -109,8 +110,7 @@ public abstract class WS1Client extends WSClient implements { 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); } diff --git a/src/jalview/ws/jws2/JabaParamStore.java b/src/jalview/ws/jws2/JabaParamStore.java index 65f939a..7c0eabd 100644 --- a/src/jalview/ws/jws2/JabaParamStore.java +++ b/src/jalview/ws/jws2/JabaParamStore.java @@ -35,6 +35,7 @@ import compbio.metadata.Preset; 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; @@ -166,9 +167,7 @@ public class JabaParamStore implements ParamDatastoreI } 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 { @@ -203,9 +202,7 @@ public class JabaParamStore implements ParamDatastoreI .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 { @@ -243,8 +240,7 @@ public class JabaParamStore implements ParamDatastoreI } 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")); } } @@ -270,9 +266,7 @@ public class JabaParamStore implements ParamDatastoreI : 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); @@ -322,8 +316,7 @@ public class JabaParamStore implements ParamDatastoreI { 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(); @@ -348,15 +341,11 @@ public class JabaParamStore implements ParamDatastoreI { 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(); diff --git a/src/jalview/ws/jws2/JabaPreset.java b/src/jalview/ws/jws2/JabaPreset.java index 7d7f4f0..c47c63a 100644 --- a/src/jalview/ws/jws2/JabaPreset.java +++ b/src/jalview/ws/jws2/JabaPreset.java @@ -20,6 +20,7 @@ */ package jalview.ws.jws2; +import jalview.util.MessageManager; import jalview.ws.jws2.jabaws2.Jws2Instance; import jalview.ws.params.ArgumentI; import jalview.ws.params.WsParamSetI; @@ -74,7 +75,7 @@ public class JabaPreset implements 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 @@ -87,14 +88,13 @@ public class JabaPreset implements WsParamSetI } 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 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")); } } diff --git a/src/jalview/ws/jws2/JabawsCalcWorker.java b/src/jalview/ws/jws2/JabawsCalcWorker.java index afb46e9..e966886 100644 --- a/src/jalview/ws/jws2/JabawsCalcWorker.java +++ b/src/jalview/ws/jws2/JabawsCalcWorker.java @@ -24,6 +24,7 @@ import jalview.datamodel.AlignmentAnnotation; 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; @@ -114,8 +115,7 @@ public abstract class JabawsCalcWorker extends AbstractJabaCalcWorker 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); } } diff --git a/src/jalview/ws/jws2/JabawsMsaInterfaceAlignCalcWorker.java b/src/jalview/ws/jws2/JabawsMsaInterfaceAlignCalcWorker.java index 1f0d92c..3f0e47d 100644 --- a/src/jalview/ws/jws2/JabawsMsaInterfaceAlignCalcWorker.java +++ b/src/jalview/ws/jws2/JabawsMsaInterfaceAlignCalcWorker.java @@ -40,6 +40,7 @@ import jalview.datamodel.AlignmentAnnotation; 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; @@ -129,9 +130,7 @@ public abstract class JabawsMsaInterfaceAlignCalcWorker extends AbstractJabaCalc 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; diff --git a/src/jalview/ws/jws2/Jws2Client.java b/src/jalview/ws/jws2/Jws2Client.java index b2b676f..4f6e8f6 100644 --- a/src/jalview/ws/jws2/Jws2Client.java +++ b/src/jalview/ws/jws2/Jws2Client.java @@ -77,8 +77,7 @@ public abstract class Jws2Client extends jalview.ws.WSClient * 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 @@ -410,7 +409,7 @@ public abstract class Jws2Client extends jalview.ws.WSClient { // 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); } diff --git a/src/jalview/ws/jws2/MsaWSThread.java b/src/jalview/ws/jws2/MsaWSThread.java index f40c250..0d0f047 100644 --- a/src/jalview/ws/jws2/MsaWSThread.java +++ b/src/jalview/ws/jws2/MsaWSThread.java @@ -32,6 +32,7 @@ import jalview.analysis.*; 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; @@ -109,8 +110,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI 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++) { @@ -625,8 +625,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI // 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()) @@ -644,7 +643,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI { // 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 { @@ -672,35 +671,28 @@ class MsaWSThread extends AWS2Thread implements WSClientI } 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) @@ -734,8 +726,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI 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")); } } } @@ -743,7 +734,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI 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 diff --git a/src/jalview/ws/jws2/ParameterUtils.java b/src/jalview/ws/jws2/ParameterUtils.java index e2bfbbd..e44fa6a 100644 --- a/src/jalview/ws/jws2/ParameterUtils.java +++ b/src/jalview/ws/jws2/ParameterUtils.java @@ -181,8 +181,7 @@ public class ParameterUtils } 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")); } } diff --git a/src/jalview/ws/jws2/SequenceAnnotationWSClient.java b/src/jalview/ws/jws2/SequenceAnnotationWSClient.java index 77a7a67..2138473 100644 --- a/src/jalview/ws/jws2/SequenceAnnotationWSClient.java +++ b/src/jalview/ws/jws2/SequenceAnnotationWSClient.java @@ -106,7 +106,7 @@ public class SequenceAnnotationWSClient extends Jws2Client } 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); diff --git a/src/jalview/ws/jws2/dm/AAConSettings.java b/src/jalview/ws/jws2/dm/AAConSettings.java index 28a6955..8ce4639 100644 --- a/src/jalview/ws/jws2/dm/AAConSettings.java +++ b/src/jalview/ws/jws2/dm/AAConSettings.java @@ -92,7 +92,7 @@ public class AAConSettings extends jalview.ws.params.AutoCalcSetting 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")); } } diff --git a/src/jalview/ws/jws2/dm/JabaOption.java b/src/jalview/ws/jws2/dm/JabaOption.java index f29b6ed..995af35 100644 --- a/src/jalview/ws/jws2/dm/JabaOption.java +++ b/src/jalview/ws/jws2/dm/JabaOption.java @@ -20,6 +20,7 @@ */ package jalview.ws.jws2.dm; +import jalview.util.MessageManager; import jalview.ws.jws2.ParameterUtils; import jalview.ws.params.OptionI; @@ -94,8 +95,7 @@ public class JabaOption implements 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")); } } diff --git a/src/jalview/ws/jws2/dm/JabaValueConstrain.java b/src/jalview/ws/jws2/dm/JabaValueConstrain.java index f57abde..920b73e 100644 --- a/src/jalview/ws/jws2/dm/JabaValueConstrain.java +++ b/src/jalview/ws/jws2/dm/JabaValueConstrain.java @@ -22,6 +22,7 @@ package jalview.ws.jws2.dm; import compbio.metadata.ValueConstrain; +import jalview.util.MessageManager; import jalview.ws.params.ValueConstrainI; public class JabaValueConstrain implements ValueConstrainI @@ -45,9 +46,7 @@ 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 diff --git a/src/jalview/ws/jws2/dm/JabaWsParamSet.java b/src/jalview/ws/jws2/dm/JabaWsParamSet.java index 7a67f6e..d6d1d5c 100644 --- a/src/jalview/ws/jws2/dm/JabaWsParamSet.java +++ b/src/jalview/ws/jws2/dm/JabaWsParamSet.java @@ -25,6 +25,7 @@ import java.util.List; import compbio.metadata.Option; +import jalview.util.MessageManager; import jalview.ws.jws2.JabaParamStore; import jalview.ws.params.ArgumentI; import jalview.ws.params.WsParamSetI; @@ -53,8 +54,7 @@ public class JabaWsParamSet implements 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 { @@ -177,8 +177,7 @@ public class JabaWsParamSet implements WsParamSetI { 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