From: Jim Procter Date: Thu, 25 Aug 2016 11:13:56 +0000 (+0100) Subject: Merge branch 'trailm' into trial_fixMakeCDSDBRefPropagation X-Git-Tag: Release_2_10_0~47^2~4^2~43^2~15 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=46c321b0c0f02adf71fe433c86ab6609e0872871;hp=cf3ca7be9551f368f038b88ca2c7ffae67539900;p=jalview.git Merge branch 'trailm' into trial_fixMakeCDSDBRefPropagation --- diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties index ac665e3..54181fe 100644 --- a/resources/lang/Messages.properties +++ b/resources/lang/Messages.properties @@ -38,7 +38,6 @@ action.cancel = Cancel action.create = Create action.update = Update action.delete = Delete -action.snapshot = Snapshot action.clear = Clear action.accept = Accept action.select_ddbb = --- Select Database --- @@ -121,7 +120,6 @@ action.save_as_default = Save as default action.save_as = Save as... action.save = Save action.cancel_fetch = Cancel Fetch -action.save_omit_hidden_columns = Save / Omit Hidden Regions action.change_font = Change Font action.change_font_tree_panel = Change Font (Tree Panel) action.colour = Colour @@ -137,21 +135,22 @@ action.show_group = Show Group action.fetch_db_references = Fetch DB References action.view_flanking_regions = Show flanking regions label.view_flanking_regions = Show sequence data either side of the subsequences involved in this alignment -label.str = Str: -label.seq = Seq: label.structures_manager = Structures Manager label.nickname = Nickname: label.url = URL: label.input_file_url = Enter URL or Input File -label.select_feature = Select feature: +label.select_feature = Select feature label.name = Name +label.name\: = Name: label.name_param = Name: {0} label.group = Group +label.group\: = Group: label.group_name = Group Name label.group_description = Group Description label.edit_group_name_description = Edit Group Name/Description label.colour = Colour: -label.description = Description: +label.description = Description +label.description\: = Description: label.start = Start: label.end = End: label.current_parameter_set_name = Current parameter set name: @@ -222,8 +221,8 @@ label.proteins = Proteins label.to_new_alignment = To New Alignment label.to_this_alignment = Add To This Alignment label.apply_colour_to_all_groups = Apply Colour To All Groups -label.modify_identity_thereshold = Modify Identity Threshold... -label.modify_conservation_thereshold = Modify Conservation Threshold... +label.modify_identity_threshold = Modify Identity Threshold... +label.modify_conservation_threshold = Modify Conservation Threshold... label.input_from_textbox = Input from textbox label.centre_column_labels = Centre column labels label.automatic_scrolling = Automatic Scrolling @@ -240,7 +239,6 @@ label.except_selected_sequences = All except selected sequences label.all_but_selected_region = All but Selected Region (Shift+Ctrl+H) label.selected_region = Selected Region label.all_sequences_columns = All Sequences and Columns -label.hide_insertions = Hide columns gapped for selection label.hide_selected_annotations = Hide selected annotations label.show_selected_annotations = Show selected annotations label.group_consensus = Group Consensus @@ -321,7 +319,6 @@ label.found_match_for = Found match for {0} label.font = Font: label.size = Size: label.style = Style: -label.enter_redundancy_threshold = Enter the redundancy threshold label.calculating = Calculating.... label.modify_conservation_visibility = Modify conservation visibility label.colour_residues_above_occurence = Colour residues above % occurence @@ -365,7 +362,6 @@ label.example = Example label.example_param = Example: {0} label.select_file_format_before_saving = You must select a file format before saving! label.file_format_not_specified = File format not specified -label.alignment_contains_hidden_columns = The Alignment contains hidden regions (hidden sequences/columns).\nDo you want to save only the visible alignment? label.couldnt_save_file = Couldn't save file: {0} label.error_saving_file = Error Saving File label.remove_from_default_list = Remove from default list? @@ -467,7 +463,6 @@ label.no_features_added_to_this_alignment = No Features added to this alignment! label.features_can_be_added_from_searches_1 = (Features can be added from searches or label.features_can_be_added_from_searches_2 = from Jalview / GFF features files) label.calculating_pca= Calculating PCA -label.reveal_columns = Reveal Columns label.jalview_cannot_open_file = Jalview can't open file label.jalview_applet = Jalview applet label.loading_data = Loading data @@ -475,7 +470,6 @@ label.memory_stats = Total Free Memory: {0} MB; Max Memory: {1} MB; {2} % label.calculating_tree = Calculating tree label.state_queueing = queuing label.state_running = running -label.state_complete = complete label.state_completed = finished label.state_job_cancelled = job cancelled!! label.state_job_error = job error! @@ -501,7 +495,6 @@ label.jmol_help = Jmol Help label.chimera_help = Chimera Help label.close_viewer = Close Viewer label.confirm_close_chimera = This will close Jalview''s connection to {0}.
Do you want to close the Chimera window as well? -label.chimera_help = Chimera Help label.all = All label.sort_by = Sort alignment by label.sort_by_score = Sort by Score @@ -521,15 +514,14 @@ label.reset_min_max_colours_to_defaults = Reset min and max colours to defaults label.align_structures_using_linked_alignment_views = Align structures using {0} linked alignment views label.connect_to_session = Connect to session {0} label.threshold_feature_display_by_score = Threshold the feature display by score. -label.threshold_feature_no_thereshold = No Threshold -label.threshold_feature_above_thereshold = Above Threshold -label.threshold_feature_below_thereshold = Below Threshold -label.adjust_thereshold = Adjust threshold +label.threshold_feature_no_threshold = No Threshold +label.threshold_feature_above_threshold = Above Threshold +label.threshold_feature_below_threshold = Below Threshold +label.adjust_threshold = Adjust threshold label.toggle_absolute_relative_display_threshold = Toggle between absolute and relative display threshold. label.display_features_same_type_different_label_using_different_colour = Display features of the same type with a different label using a different colour. (e.g. domain features) label.select_colour_minimum_value = Select Colour for Minimum Value label.select_colour_maximum_value = Select Colour for Maximum Value -label.open_new_jmol_view_with_all_structures_associated_current_selection_superimpose_using_alignment = Open a new structure viewer with all structures associated with the current selection and superimpose them using the alignment. label.open_url_param = Open URL {0} label.open_url_seqs_param = Open URL ({0}..) ({1} seqs) label.load_pdb_file_associate_with_sequence = Load a PDB file and associate it with sequence {0} @@ -584,8 +576,8 @@ label.histogram = Histogram label.logo = Logo label.non_positional_features = List Non-positional Features label.database_references = List Database References -label.share_selection_across_views = Share selection across views -label.scroll_highlighted_regions = Scroll to highlighted regions +#label.share_selection_across_views = Share selection across views +#label.scroll_highlighted_regions = Scroll to highlighted regions label.gap_symbol = Gap Symbol label.prot_alignment_colour = Protein Alignment Colour label.nuc_alignment_colour = Nucleotide Alignment Colour @@ -668,20 +660,12 @@ label.cut_paste = Cut'n'Paste label.adjusting_parameters_for_calculation = Adjusting parameters for existing Calculation label.2d_rna_structure_line = 2D RNA {0} (alignment) label.2d_rna_sequence_name = 2D RNA - {0} -label.edit_name_and_description_current_group = Edit name and description of current group. -label.view_structure_for = View structure for {0} -label.view_all_structures = View all {0} structures. -label.view_all_representative_structures = View all {0} representative structures. -label.open_new_jmol_view_with_all_representative_structures_associated_current_selection_superimpose_using_alignment = Opens a new structure viewer with all representative structures\nassociated with the current selection\nsuperimposed with the current alignment. -label.associate_structure_with_sequence = Associate Structure with Sequence +label.edit_name_and_description_current_group = Edit name and description of current group label.from_file = From File label.enter_pdb_id = Enter PDB Id (or pdbid:chaincode) -label.discover_pdb_ids = Discover PDB IDs label.text_colour = Text Colour action.set_text_colour = Text Colour... label.structure = Structure -label.view_structure = View Structure -label.view_protein_structure = View Protein Structure label.show_pdbstruct_dialog = 3D Structure Data... label.view_rna_structure = VARNA 2D Structure label.clustalx_colours = Clustalx colours @@ -709,7 +693,6 @@ label.translate_cDNA = Translate as cDNA label.reverse = Reverse label.reverse_complement = Reverse Complement label.linked_view_title = Linked CDS and protein view -label.align = Align label.extract_scores = Extract Scores label.get_cross_refs = Get Cross-References label.sort_alignment_new_tree = Sort Alignment With New Tree @@ -721,7 +704,6 @@ label.use_registry = Use Registry label.add_local_source = Add Local Source label.set_as_default = Set as Default label.show_labels = Show labels -label.background_colour = Background Colour action.background_colour = Background Colour... label.associate_nodes_with = Associate Nodes With label.jalview_pca_calculation = Jalview PCA Calculation @@ -814,7 +796,6 @@ label.services_at = Services at {0} label.rest_client_submit = {0} using {1} label.fetch_retrieve_from =Retrieve from {0} label.fetch_retrieve_from_all_sources = Retrieve from all {0} sources in {1}
First is :{2} -#label.feature_settings_click_drag = Click/drag feature types up or down to change render order.
Double click to select columns containing feature in alignment/current selection
Pressing Alt will select columns outside features rather than inside
Pressing Shift to modify current selection (rather than clear current selection)
Press CTRL or Command/Meta to toggle columns in/outside features
label.feature_settings_click_drag = Drag up or down to change render order.
Double click to select columns containing feature. label.transparency_tip = Adjust transparency to 'see through' feature colours. label.opt_and_params_further_details = see further details by right-clicking @@ -830,17 +811,10 @@ label.user_preset = User Preset label.service_preset = Service Preset label.run_with_preset = Run {0} with preset label.view_service_doc_url = View {1} -label.submit_sequence = Submit {0} {1} {2} {3} to
{4} action.by_title_param = By {0} -label.alignment = Alignment -label.secondary_structure_prediction = Secondary Structure Prediction -label.sequence_database_search = Sequence Database Search -label.analysis = Analysis -label.protein_disorder = Protein Disorder label.source_from_db_source = Sources from {0} label.from_msname = from {0} label.superpose_with = Superpose with -action.do = Do label.scale_label_to_column = Scale Label to Column label.add_new_row = Add New Row label.edit_label_description = Edit Label/Description @@ -884,7 +858,7 @@ 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 Threshold ({0}) +label.percentage_identity_threshold = Percentage Identity Threshold ({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 @@ -900,7 +874,6 @@ 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 @@ -928,15 +901,9 @@ 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.implementation_error_dont_know_threshold_annotationcolourgradient = Implementation error: don't know about threshold setting for current AnnotationColourGradient. 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 @@ -958,16 +925,14 @@ error.not_yet_implemented_cigar_object_from_cigar_string = NOT YET Implemented: 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.implementation_error_dont_know_about_threshold_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 @@ -986,7 +951,6 @@ error.setstatus_called_non_existent_job_pane = setStatus called for non-existent 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 @@ -1033,7 +997,6 @@ label.toggled = Toggled label.marked = Marked label.containing = containing label.not_containing = not containing -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 @@ -1043,7 +1006,7 @@ 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.adjunst_foreground_text_colour_threshold = 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} @@ -1063,7 +1026,6 @@ exception.mismatched_unseen_closing_char = Mismatched (unseen) closing character 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 @@ -1091,7 +1053,6 @@ 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}) @@ -1099,7 +1060,6 @@ 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} @@ -1108,8 +1068,6 @@ exception.interrupted_launching_browser = InterruptedException while launching b 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 @@ -1200,8 +1158,8 @@ label.edit_jabaws_url = Edit JABAWS URL label.add_jabaws_url = Add new JABAWS URL label.news_from_jalview = News from http://www.jalview.org label.cut_paste_alignmen_file = Cut & Paste Alignment File -label.enter_redundancy_thereshold = Enter the redundancy threshold -label.select_dark_light_set_thereshold = Select a dark and light text colour, then set the threshold to
switch between colours, based on background colour +label.enter_redundancy_threshold = Enter the redundancy threshold +label.select_dark_light_set_threshold = Select a dark and light text colour, then set the threshold to
switch between colours, based on background colour label.select_feature_colour = Select Feature Colour label.delete_all = Delete all sequences warn.delete_all = Deleting all sequences will close the alignment window.
Confirm deletion or Cancel. @@ -1222,28 +1180,23 @@ label.no_colour_selection_in_scheme = Please make a colour selection before appl label.no_colour_selection_warn = Error saving colour scheme label.open_split_window? = Would you like to open as a split window, with cDNA and protein linked? label.open_split_window = Open split window -label.no_mappings = No mappings found action.no = No action.yes = Yes label.for = for label.select_by_annotation = Select/Hide Columns by Annotation action.select_by_annotation = Select/Hide Columns by Annotation... label.threshold_filter = Threshold Filter -action.hide = Hide -action.select = Select label.alpha_helix = Alpha Helix label.beta_strand = Beta Strand label.turn = Turn label.select_all = Select All label.structures_filter = Structures Filter label.search_filter = Search Filter -label.description = Description label.include_description= Include Description action.back = Back label.hide_insertions = Hide Insertions label.mark_as_representative = Mark as representative label.open_jabaws_web_page = Open JABAWS web page -label.opens_the_jabaws_server_homepage = Opens the JABAWS server's homepage in web browser label.pdb_sequence_fetcher = PDB Sequence Fetcher label.result = result label.results = results @@ -1311,6 +1264,5 @@ status.obtaining_mapping_with_sifts = Obtaining mapping with SIFTS status.obtaining_mapping_with_nw_alignment = Obtaining mapping with NW alignment status.exporting_alignment_as_x_file = Exporting alignment as {0} file label.column = Column -label.sequence = Sequence label.cant_map_cds = Unable to map CDS to protein\nCDS missing or incomplete label.operation_failed = Operation failed diff --git a/resources/lang/Messages_es.properties b/resources/lang/Messages_es.properties index 92d4d78..45941c2 100644 --- a/resources/lang/Messages_es.properties +++ b/resources/lang/Messages_es.properties @@ -38,7 +38,6 @@ action.cancel = Cancelar action.create = Crear action.update = Actualizar action.delete = Borrar -action.snapshot = Imagen action.clear = Limpiar action.accept = Aceptar action.select_ddbb = --- Seleccionar base de datos --- @@ -118,7 +117,6 @@ action.save_as_default = Guardar como por defecto action.save_as = Guardar como action.save = Guardar action.cancel_fetch = Cancelar búsqueda -action.save_omit_hidden_columns = Guardar / Omitir las columnas ocultas action.change_font = Cambiar Fuente action.change_font_tree_panel = Cambiar fuente (panel del árbol) action.colour = Color @@ -134,21 +132,22 @@ action.show_group = Mostrar grupo action.fetch_db_references = Recuperar referencias a base de datos action.view_flanking_regions = Mostrar flancos label.view_flanking_regions = Mostrar los datos de la secuencia a ambos lados de las subsecuencias implicadas en este alineamiento -label.str = Str: -label.seq = Seq: label.structures_manager = Administrar estructuras label.nickname = Sobrenombre: label.url = URL: label.input_file_url = Introducir URL en el fichero de entrada -label.select_feature = Seleccionar función: -label.name = Nombre: +label.select_feature = Seleccionar característica +label.name = Nombre +label.name\: = Nombre: label.name_param = Nombre: {0} -label.group = Grupo: +label.group = Grupo +label.group\: = Grupo: label.group_name = Nombre del grupo label.group_description = Descripción del grupo label.edit_group_name_description = Editar nombre/descripción del grupo label.colour = Color: -label.description = Descripción: +label.description = Descripción +label.description\: = Descripción: label.start = Comenzar: label.end = Terminar: label.current_parameter_set_name = Nombre actual del conjunto de parámetros: @@ -208,8 +207,8 @@ label.nucleotide = Nucle label.to_new_alignment = A nuevo alineamiento label.to_this_alignment = Añadir a este alineamiento label.apply_colour_to_all_groups = Aplicar color a todos los grupos -label.modify_identity_thereshold = Modificar el umbral de identidad... -label.modify_conservation_thereshold = Modificar el umbral de conservación... +label.modify_identity_threshold = Modificar el umbral de identidad... +label.modify_conservation_threshold = Modificar el umbral de conservación... label.input_from_textbox = Introducir desde el cuadro de texto label.centre_column_labels = Centrar las etiquetas de las columnas label.automatic_scrolling = Desplazamiento automático @@ -217,7 +216,6 @@ label.documentation = Documentaci label.about = Acerca de... label.show_sequence_limits = Mostrar los límites de la secuencia label.feature_settings = Ajustar funciones... -label.sequence_features = Funciones de la secuencia label.all_columns = Todas las columnas label.all_sequences = Todas las secuencias label.selected_columns = Columnas seleccionadas @@ -291,7 +289,6 @@ label.found_match_for = Buscar coincidencia para {0} label.font = Fuente: label.size = Talla: label.style = Estilo: -label.enter_redundancy_threshold = Introducir el umbral de redundancia label.calculating = Calculando.... label.modify_conservation_visibility = Modificar la visibilidad de conservación label.colour_residues_above_occurence = Residuos de color por encima del % de aparición @@ -315,8 +312,6 @@ label.blog_item_published_on_date = {0} {1} label.select_das_service_from_table = Seleccionar servicio DAS de la tabla para leer una descripción completa aquí. label.session_update = Actualizar sesión label.new_vamsas_session = Nueva sesión Vamsas -label.load_vamsas_session = Cargar sesión Vamsas -label.save_vamsas_session = Guardar sesión Vamsas action.save_vamsas_session = Guardar Sesión Vamsas label.select_vamsas_session_opened_as_new_vamsas_session= Selecciones una sesión vamsas para abrirla como una nueva sesión. label.open_saved_vamsas_session = Abrir una sesión VAMSAS guardada @@ -336,7 +331,6 @@ label.example = Ejemplo label.example_param = Ejemplo: {0} label.select_file_format_before_saving = Debe seleccionar un formato de fichero antes de guardar! label.file_format_not_specified = Formato de fichero no especificado -label.alignment_contains_hidden_columns = El alineamiento contiene columnas ocultas.\nQuieres guardar s\u00F3lo el alineamiento visible? label.couldnt_save_file = No se pudo guardar el fichero: {0} label.error_saving_file = Error guardando el fichero label.remove_from_default_list = eliminar de la lista de defectuosos? @@ -436,7 +430,6 @@ label.no_features_added_to_this_alignment = No hay funciones asociadas a este al label.features_can_be_added_from_searches_1 = (Las funciones pueden ser añadidas de búsquedas o label.features_can_be_added_from_searches_2 = de ficheros de funciones Jalview / GFF) label.calculating_pca= Calculando PCA -label.reveal_columns = Mostrar Columnas label.jalview_cannot_open_file = Jalview no puede abrir el fichero label.jalview_applet = Aplicación Jalview label.loading_data = Cargando datos @@ -444,7 +437,6 @@ label.memory_stats = Memoria libre total: {0} MB; Memoria m label.calculating_tree = Calculando árbol label.state_queueing = En cola label.state_running = Procesando -label.state_complete = Completar label.state_completed = Finalizado label.state_job_cancelled = ¡Trabajo cancelado! label.state_job_error = Error del trabajo! @@ -458,8 +450,6 @@ label.load_associated_tree = Cargar label.load_features_annotations = Cargar características/anotaciones ... label.export_features = Exportar características... label.export_annotations = Exportar anotaciones ... -label.jalview_copy = Copiar (sólo Jalview) -label.jalview_cut = Cortar (sólo Jalview) label.to_upper_case = Pasar a mayúsculas label.to_lower_case = Pasar a minúsculas label.toggle_case = Alternar mayúsculas y minúsculas @@ -486,15 +476,14 @@ label.reset_min_max_colours_to_defaults = Reiniciar los colores min y max colour label.align_structures_using_linked_alignment_views = Alinear las estructuras utlizando las {0} vistas de alineamiento enlazadas label.connect_to_session = Conectar a la sesión {0} label.threshold_feature_display_by_score = Filtrar la característica mostrada por puntuación. -label.threshold_feature_no_thereshold = Sin umbral -label.threshold_feature_above_thereshold = Por encima del umbral -label.threshold_feature_below_thereshold = Por debajo del umbral -label.adjust_thereshold = Ajustar umbral +label.threshold_feature_no_threshold = Sin umbral +label.threshold_feature_above_threshold = Por encima del umbral +label.threshold_feature_below_threshold = Por debajo del umbral +label.adjust_threshold = Ajustar umbral label.toggle_absolute_relative_display_threshold = Cambiar entre mostrar el umbral absoluto y el relativo. label.display_features_same_type_different_label_using_different_colour = Mostrar las características del mismo tipo con una etiqueta diferente y empleando un color distinto (p.e. características del dominio) label.select_colour_minimum_value = Seleccionar el color para el valor mínimo label.select_colour_maximum_value = Seleccionar el color para el valor máximo -label.open_new_jmol_view_with_all_structures_associated_current_selection_superimpose_using_alignment = Abrir una nueva vista Jmol con todas las estructuras asociadas con la selección acxtual y superponer las utilizando el alineamiento. label.open_url_param = Abrir URL {0} label.open_url_seqs_param = Abrir URL ({0}..) ({1} secuencias) label.load_pdb_file_associate_with_sequence = Cargar un fichero PDB y asociarlo con la secuencia {0} @@ -545,10 +534,9 @@ label.histogram = Histograma label.logo = Logo label.non_positional_features = Características no posicionales label.database_references = Referencias a base de datos -label.share_selection_across_views = Compartir la selección en todas las vistas -label.scroll_highlighted_regions = Desplazarse hasta las regiones resaltadas +#label.share_selection_across_views = Compartir la selección en todas las vistas +#label.scroll_highlighted_regions = Desplazarse hasta las regiones resaltadas label.gap_symbol = Símbolo del hueco -label.alignment_colour = Color del alineamiento label.address = Dirección label.port = Puerto label.default_browser_unix = Navegador por defecto (Unix) @@ -627,18 +615,11 @@ label.cut_paste = Cortar y pegar label.adjusting_parameters_for_calculation = Ajustar los parámetros para el cálculo existente label.2d_rna_structure_line = 2D RNA {0} label.2d_rna_sequence_name = 2D RNA - {0} -label.edit_name_and_description_current_group = Editar el nombre y la descripción del grupo actual. -label.view_structure_for = Visualizar la estructura para {0} -label.view_all_structures = Visualizar todas las {0} estructuras. -label.view_all_representative_structures = Visualizar todas las {0} estructuras representativas. -label.open_new_jmol_view_with_all_representative_structures_associated_current_selection_superimpose_using_alignment = Abrir una nueva vista de Jmol con todas las estructuras representativas\nasociadas con la selecci\u00F3n actual\nsuperpuesta con el alineamiento actual. -label.associate_structure_with_sequence = Asociar estructura con la secuencia +label.edit_name_and_description_current_group = Editar el nombre y la descripción del grupo actual label.from_file = desde fichero label.enter_pdb_id = Introducir PDB Id -label.discover_pdb_ids = Buscar PDB ids label.text_colour = Color del texto label.structure = Estructura -label.view_structure = Visualizar estructura label.clustalx_colours = Colores de Clustalx label.above_identity_percentage = Sobre % identidad label.create_sequence_details_report_annotation_for = Anotación para {0} @@ -671,7 +652,6 @@ label.use_registry = Utilizar el registro label.add_local_source = Añadir fuente local label.set_as_default = Establecer por defecto label.show_labels = Mostrar etiquetas -label.background_colour = Color de fondo label.associate_nodes_with = Asociar nodos con label.jalview_pca_calculation = Cálculo del PCA por Jalview label.link_name = Nombre del enalce @@ -764,17 +744,10 @@ label.user_preset = Preselecci label.service_preset = Preselección del servicio label.run_with_preset = Ejecutar {0} con preselección label.view_service_doc_url = Visualizar {1} -label.submit_sequence = Enviar {0} {1} {2} {3} a
{4} action.by_title_param = por {0} -label.alignment = Alineamiento -label.secondary_structure_prediction = Predicción de la estructura secundaria -label.sequence_database_search = Búsqueda en base de datos de secuencias -label.analysis = Análisis -label.protein_disorder = Desorden en la proteína label.source_from_db_source = Fuentes de {0} label.from_msname = de {0} label.superpose_with = Superponer con... -action.do = Hacer label.scale_label_to_column = Ajustar la etiqueta a la columna label.add_new_row = Añadir nuevo fila label.edit_label_description = Editar etiqueta/descripción @@ -818,7 +791,7 @@ label.service_url = URL del servicio label.copied_sequences = Secuencias copiadas label.cut_sequences = Cortar secuencias label.conservation_colour_increment = Incremento de Conservación del Color ({0}) -label.percentage_identity_thereshold = Umbral del Porcentaje de Identidad ({0}) +label.percentage_identity_threshold = Umbral del Porcentaje de Identidad ({0}) label.error_unsupported_owwner_user_colour_scheme = Propietario no soportado para el diálogo del Esquema Cromático del Usuario label.save_alignment_to_file = Guardar Alineamiento en fichero label.save_features_to_file = Guardar Características en un fichero @@ -834,7 +807,6 @@ label.save_vamsas_document_archive = Guardar el archivo de documento Vamsas label.saving_vamsas_doc = Guardando el documento VAMSAS en {0} label.load_feature_colours = Cargar colores de características label.save_feature_colours = Guardar esquema cromático de características -label.dataset_for = {0} conjunto de datos para {1} label.select_startup_file = Seleccionar fichero de arranque label.select_default_browser = Seleccionar navegador web por defecto label.save_tree_as_newick = Guardar árbol como fichero newick @@ -862,15 +834,9 @@ error.null_from_clone1 = Nulo de clone1! error.implementation_error_sortbyfeature = Error de implementación - sortByFeature debe ser uno de FEATURE_SCORE, FEATURE_LABEL o FEATURE_DENSITY. error.not_yet_implemented = No se ha implementado todavía error.unknown_type_dna_or_pep = Tipo desconocido {0} - dna o pep son los únicos valores permitidos -error.implementation_error_dont_know_thereshold_annotationcolourgradient = Error de implementación: no se conoce el valor umbral para el AnnotationColourGradient actual. -error.implementation_error_embeddedpopup_not_null = Error de implementación - embeddedPopup debe ser no nulo. -error.invalid_colour_for_mycheckbox = Color no válido para MyCheckBox -error.implementation_error_unrecognised_render_object_for_features_type = Error de implementación: no se reconoce el objeto de representación {0} para las características de tipo {1} -error.implementation_error_unsupported_feature_colour_object = Error de implementación: objeto de color de características no soportado. +error.implementation_error_dont_know_threshold_annotationcolourgradient = Error de implementación: no se conoce el valor umbral para el AnnotationColourGradient actual. error.invalid_separator_parameter = Separador de parámetros no válido - debe tener longitud mayor que cero error.alignment_cigararray_not_implemented = Alignment(CigarArray) no se ha implementado todavía -error.weak_sequencei_equivalence_not_yet_implemented = Equivalencia débil sequenceI no se ha implementado todavía. -error.implementation_error_can_only_make_alignmnet_from_cigararray = Error de implementación - sólo se puede construir un vista de alineamiento a partir de una CigarArray de secuencias. error.empty_view_cannot_be_updated = una vista vacía no se puede actualizar. error.mismatch_between_number_of_sequences_in_block = No hay coincidencia entre el número de secuencias en el bloque {0} ({1}) y la vista original ({2}) error.padding_not_yet_implemented = El relleno no se ha implementado todavía @@ -892,16 +858,14 @@ error.not_yet_implemented_cigar_object_from_cigar_string = No implementado todav error.implementation_bug_cigar_operation = Bug de implementación. La operación Cigar {0} {1} no es ni {2}, ni {3} ni {4}. error.implementation_error_for_new_cigar = Error de implementación en new Cigar(SequenceI) error.implementation_error_cigar_seq_no_operations = Error de implementación: la {0}a secuencia Cigar no tiene operaciones. -error.implementation_error_jmol_getting_data = Error de implementación - Jmol parece estar todavía intentando recuperar sus datos - informe de ello en http://issues.jalview.org/browse/JAL-1016 error.implementation_error_no_pdbentry_from_index = Error de implementación - no existe la correspondiente entrada pdb (para el índice {0}) para añadir el mapeo de secuencias a error.jmol_version_not_compatible_with_jalview_version = La versión {0} de Jmol no es compatible con esta versión de Jalview. Informe de este problema en http://issues.jalview.org error.not_implemented_remove = Borrar: no implementado error.not_implemented_clone = Clonar: no implementado -error.implementation_error_chimera_getting_data = Error de implementación - Chimera parece estar todavía intentando recuperar sus datos - informe de ello en http://issues.jalview.org/browse/JAL-1016 error.call_setprogressbar_before_registering_handler = llamada a setProgressBar antes de registrar el manejador de la barra de estado label.cancelled_params = {0} cancelado error.implementation_error_cannot_show_view_alignment_frame = Error de implementación: no es posible mostrar una vista de otro alineamiento en un AlignFrame. -error.implementation_error_dont_know_about_thereshold_setting = Error de implementación: no se conoce la configuración del umbral para el AnnotationColourGradient actual. +error.implementation_error_dont_know_about_threshold_setting = Error de implementación: no se conoce la configuración del umbral para el AnnotationColourGradient actual. error.eps_generation_not_implemented = La generación de EPS no se ha implementado todavía error.png_generation_not_implemented = La generación de PNG no se ha implementado todavía error.try_join_vamsas_session_another = Tratando de establecer una sesión VAMSAS cuando ya había otra conectada @@ -920,7 +884,6 @@ error.setstatus_called_non_existent_job_pane = se lllamado a setStatus para el p error.implementation_error_cannot_find_marshaller_for_param_set =Error de implementación: no puede encontrar un marshaller para el conjunto de parámetros error.implementation_error_old_jalview_object_not_bound =Error de implementación: ¡el objeto Jalview antiguo no está enlazado! ({0}) error.implementation_error_vamsas_doc_class_should_bind_to_type = Error de implementación: la clase de documento VAMSAS {0} debe enlazar a {1} (pero se ha encontrado que lo está a {2}) -error.implementation_error_jalview_class_should_bind_to_type = Error de implementación: la clase Jalview {0} debe enlazar a {1} (pero se ha encontrado que lo está a {2}) error.invalid_vamsas_rangetype_cannot_resolve_lists = RangeType VAMSAS no válido - ¡no es posible resolver ambas listas de Pos y Seg con los valores elegidos! error.implementation_error_maplist_is_null = Error de implementación. MapList es nulo en initMapType. error.implementation_error_cannot_have_null_alignment = Error de implementación: no es posible tener una clave nula en el alineamiento @@ -967,7 +930,6 @@ label.toggled = Invertida label.marked = Marcada label.containing = conteniendo label.not_containing = no conteniendo -label.not = no label.no_feature_of_type_found = No se han encontrado características del tipo {0}. label.submission_params = Envío {0} label.empty_alignment_job = Trabajo de alineamiento vacío @@ -977,7 +939,7 @@ label.pca_recalculating = Recalculando PCA label.pca_calculating = Calculando PCA label.select_foreground_colour = Escoger color del primer plano label.select_colour_for_text = Seleccione el color del texto -label.adjunst_foreground_text_colour_thereshold = Ajustar el umbral del color del texto en primer plano +label.adjunst_foreground_text_colour_threshold = Ajustar el umbral del color del texto en primer plano label.select_subtree_colour = Seleccioanr el color del sub-árbol label.create_new_sequence_features = Crear nueva(s) característica(s) de secuencia label.amend_delete_features = Arrelgar/Borrar características de {0} @@ -997,7 +959,6 @@ exception.mismatched_unseen_closing_char = Discordancia (no vista) en el car exception.mismatched_closing_char = Carácter de cierre discordante {0} exception.mismatched_opening_char = Carácter de apertura discordante {0} en {1} exception.invalid_datasource_couldnt_obtain_reader = Fuente de datos no válida. No es posible obtener el Reader -exception.index_value_not_in_range = {0}: el valor del índice {1} en se encuentra en el rango [0..{2}] exception.unterminated_cigar_string = Cadena cigar sin terminar exception.unexpected_operation_cigar_string_pos = Operación no esperada {0} en una cadena cigar (posición {1} en {2}) exception.couldnt_parse_responde_from_annotated3d_server = No es posible parsear la respuesta procedente del servidor Annotate3d @@ -1025,7 +986,6 @@ exception.ranml_problem_parsing_data = Problema parseando los datos como RNAML ( exception.pfam_no_sequences_found = No se han encontrado secuencias (entrada PFAM) exception.stockholm_invalid_format = Este fichero no es tiene un formato STOCKHOLM válido: la primera línea no contiene '# STOCKHOLM' exception.couldnt_parse_sequence_line = No es posible parse la línea de secuencia: {0} -exception.error_parsing_line = Error parseando {0} exception.unknown_annotation_detected = Anotación desconocida detectada: {0} {1} exception.couldnt_store_sequence_mappings = No es posible almacenar los mapeos de secuencia para {0} exception.matrix_too_many_iteration = Demasiadas iteraciones en {0} (el máximo es {1}) @@ -1033,7 +993,6 @@ exception.browser_not_found = Excepci exception.browser_unable_to_locate = Imposible encontrar el navegador: {0} exception.invocation_target_exception_creating_aedesc = InvocationTargetException mientras se creaba AEDesc: {0} exception.illegal_access_building_apple_evt= IllegalAccessException mientras se construía AppleEvent: {0} -exception.instantiation_creating_aedesc = InstantiationException mientras se creaba AEDesc: {0} exception.unable_to_launch_url = Imposible lanzar la URL: {0} exception.unable_to_create_internet_config = Imposible crear una instancia de configuración de Internet: {0} exception.invocation_target_calling_url = InvocationTargetException mientras se invocaba openURL: {0} @@ -1042,8 +1001,6 @@ exception.interrupted_launching_browser = InterruptedException mientras se lanza exception.das_source_doesnt_support_sequence_command = La fuente {0} no soporta el comando sequence. exception.invalid_das_source = Fuente DAS no válida: {0} exception.ebiembl_retrieval_failed_on = La recuperación de datos EBI EMBL XML ha fallado en {0}:{1} -label.no_embl_record_found = # No se ha recuperado ningún registro EMBL de {0}:{1} -label.embl_successfully_parsed = # Se han parseado con éxito las consultas {0} en un alineamiento exception.no_pdb_records_for_chain = No se han encontrado registros {0} para la cadena {1} exception.unexpected_handling_rnaml_translation_for_pdb = Excepcion inesperada cuando se traducían a RNAML los datos PDB exception.couldnt_recover_sequence_properties_for_alignment = No es posible recuperar las propiedades de la secuencia para el alineamiento @@ -1125,8 +1082,8 @@ label.edit_jabaws_url = Editar JABAWS URL label.add_jabaws_url = Añadir nueva JABAWS URL label.news_from_jalview = Noticias de http://www.jalview.org label.cut_paste_alignmen_file = Cortar & Pegar fichero de alineamiento -label.enter_redundancy_thereshold = Introducir el umbral de redundancia -label.select_dark_light_set_thereshold = Seleccionar un color oscuro y un color claro para el texto y establecer el umbral en que
cambiar entre colores, basándose en el color de fondo +label.enter_redundancy_threshold = Introducir el umbral de redundancia +label.select_dark_light_set_threshold = Seleccionar un color oscuro y un color claro para el texto y establecer el umbral en que
cambiar entre colores, basándose en el color de fondo label.select_feature_colour = Seleccionar color de las características label.ignore_gaps_consensus = Ignorar huecos en el consenso label.show_group_histogram = Mostrar histograma de grupo @@ -1146,7 +1103,6 @@ action.feature_settings=Ajustes de caracter info.invalid_msa_notenough=No suficientes datos de sequencia para alinear label.result=resultado label.results=resultados -label.no_mappings=No hay mapeados encontrados label.struct_from_pdb=Procesar la estructura secundaria PDB label.hide_selected_annotations=Ocultar anotaciones seleccionados info.select_annotation_row=Seleccionar Fila de Anotaciones @@ -1170,7 +1126,6 @@ action.no=No action.yes=Sí label.export_settings=Exportar Ajustes label.linked_view_title=Vista vinculada de cDNA y proteína -label.view_protein_structure=Ver Estructura Proteica label.couldnt_read_data=No se pudo leer los datos status.opening_file=abriendo fichero label.except_selected_sequences=Todo excepto secuencias seleccionadas @@ -1215,7 +1170,6 @@ action.select_by_annotation=Seleccionar/Ocultar Columnas por Anotaci action.export_features=Exportar Características error.invalid_regex=Expresión regular inválida label.autoadd_temp=Añadir anotación factor de temperatura al alineamiento -tooltip.rnalifold_settings=Modificar la configuración de la predicción RNAAlifold. Úselo para ocultar o mostrar resultados del cálculo de RNA, o cambiar parámetros de el plegado de RNA. label.chimera_path_tip=Jalview intentará primero las rutas introducidas aquí, Y si no las rutas usuales de instalación label.structure_chooser=Selector de Estructuras label.structure_chooser_manual_association=Selector de Estructuras - asociación manual @@ -1231,9 +1185,7 @@ label.colour_with_chimera=Colorear con Chimera label.show_pdbstruct_dialog=Datos de Estructura 3D... label.hide_all=Ocultar todos label.invert=Invertir -label.pdb_sequence_getcher=Buscador de Secuencias PDB tooltip.aacon_settings=Cambiar ajustes para cálculos AACon -label.align=Alinear label.mark_as_representative=Marcar como representativa label.include_description=Incluir Descripción label.for=para @@ -1249,15 +1201,13 @@ info.associate_wit_sequence=Asociar con secuencia label.protein=Proteína warn.oneseq_msainput_selection=La selección actual sólo contiene una única secuencia. ¿Quieres enviar todas las secuencias para la alineación en su lugar? label.use_rnaview=Usar RNAView para estructura secondaria -label.opens_the_jabaws_server_homepage=Abre la página de inicio del servidor JABAWS en navegador label.search_all=Introducir uno o más valores de búsqueda separados por punto y coma ";" (Nota: buscará en toda la base de datos PDB) label.confirm_close_chimera=Cerrará la conexión de Jalview a {0}.
¿Quieres cerrar la ventana Chimera también? tooltip.rnalifold_calculations=Se calcularán predicciones de estructura secondaria de RNA para el alineaminento, y se actualizarán si se efectuan cambios -Calcular predicciónes de estructura secondaria para el alineamiento +tooltip.rnalifold_settings=Modificar la configuración de la predicción RNAAlifold. Úselo para ocultar o mostrar resultados del cálculo de RNA, o cambiar parámetros de el plegado de RNA. label.show_selected_annotations=Mostrar anotaciones seleccionadas status.colouring_chimera=Coloreando Chimera label.configure_displayed_columns=Configurar Columnas Mostradas -exception.pdb_server_error=Error desde el servidor PDB exception.resource_not_be_found=El recurso solicitado no se ha encontrado label.aacon_calculations=cálculos AACon label.pdb_web-service_error=Error de servicio web PDB @@ -1266,10 +1216,8 @@ label.chimera_path=Ruta de acceso a programa Chimera warn.delete_all=Borrar todas las secuencias cerrará la ventana del alineamiento.
Confirmar o Cancelar. label.select_all=Seleccionar Todos label.alpha_helix=Hélice Alfa -label.sequence_details_for=Detalles de secuencia para {0} label.chimera_help=Ayuda para Chimera label.find_tip=Buscar alineamiento, selección o IDs de secuencia para una subsecuencia (sin huecos) -exception.pdb_server_unreachable=Jalview no puede conectar con el servidor PDBE Solr.\nPor favor, asegúrese de que está conectado a Internet y vuelva a intentarlo. label.structure_viewer=Visualizador de estructura for defecto label.embbed_biojson=Incrustar BioJSON al exportar HTML label.transparency_tip=Ajustar la transparencia a "ver a través" los colores de las características. @@ -1282,7 +1230,6 @@ info.select_filter_option=Escoger Opci info.invalid_msa_input_mininfo=Necesita por lo menos dos secuencias con al menos 3 residuos cada una, sin regiones ocultas entre ellas. label.chimera_missing=Visualizador de estructura Chimera no encontrado.
Por favor, introduzca la ruta de Chimera,
o descargar e instalar la UCSF Chimera. label.save_as_biojs_html=Guardar como HTML BioJs -exception.pdb_rest_service_no_longer_available=Servicios Rest PDB ya no están disponibles! exception.fts_server_unreachable=Jalview no puede conectar con el servidor {0}. \nPor favor asegúrese de que está conectado a Internet y vuelva a intentarlo. exception.outofmemory_loading_mmcif_file=Sin memoria al cargar el fichero mmCIF label.hide_columns_not_containing=Ocultar las columnas que no contengan @@ -1318,6 +1265,5 @@ status.fetching_dbrefs_for_sequences_without_valid_refs=Buscando referencias par status.obtaining_mapping_with_nw_alignment=Obteniendo mapeo por alineamiento Needleman y Wunsch status.exporting_alignment_as_x_file = Exportando alineamiento como fichero tipo {0} label.column = Columna -label.sequence = Secuencia label.cant_map_cds = No se pudo mapear CDS a proteína\nDatos CDS faltantes o incompletos label.operation_failed = Operación fallada diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java index c4e51b1..bed685a 100644 --- a/src/jalview/analysis/AlignmentUtils.java +++ b/src/jalview/analysis/AlignmentUtils.java @@ -22,7 +22,6 @@ package jalview.analysis; import static jalview.io.gff.GffConstants.CLINICAL_SIGNIFICANCE; -import jalview.api.DBRefEntryI; import jalview.datamodel.AlignedCodon; import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping; @@ -1682,6 +1681,10 @@ public class AlignmentUtils * its dataset sequence to the dataset */ cdsSeq = makeCdsSequence(dnaSeq.getDatasetSequence(), aMapping); + // cdsSeq has a name constructed as CDS| + // will be either the accession for the coding sequence, + // marked in the /via/ dbref to the protein product accession + // or it will be the original nucleotide accession. SequenceI cdsSeqDss = cdsSeq.createDatasetSequence(); cdsSeqs.add(cdsSeq); if (!dataset.getSequences().contains(cdsSeqDss)) @@ -1731,16 +1734,28 @@ public class AlignmentUtils * same source and accession, so need a different accession for * the CDS from the dna sequence */ - DBRefEntryI dnaRef = dnaDss.getSourceDBRef(); - if (dnaRef != null) - { - // assuming cds version same as dna ?!? - DBRefEntry proteinToCdsRef = new DBRefEntry(dnaRef.getSource(), - dnaRef.getVersion(), cdsSeq.getName()); - proteinToCdsRef.setMap(new Mapping(cdsSeqDss, cdsToProteinMap - .getInverse())); - proteinProduct.addDBRef(proteinToCdsRef); - } + // specific use case: + // Genomic contig ENSCHR:1, contains coding regions for ENSG01, + // ENSG02, ENSG03, with transcripts and products similarly named. + // cannot add distinct dbrefs mapping location on ENSCHR:1 to ENSG01 + // JBPNote: ?? can't actually create an example that demonstrates we + // need to + // synthesize an xref. + // TODO: merge conflicts from JAL-2154 branch and use PrimaryDBRefs() + // for (DBRefEntry primRef:dnaDss.getPrimaryDBRefs()) + // { + // creates a complementary cross-reference to the source sequence's + // primary reference. + + // // problem here is that the cross-reference is synthesized - + // cdsSeq.getName() may be like 'CDS|dnaaccession' or 'CDS|emblcdsacc' + // // assuming cds version same as dna ?!? + // DBRefEntry proteinToCdsRef = new DBRefEntry(dnaRef.getSource(), + // dnaRef.getVersion(), cdsSeq.getName()); + // proteinToCdsRef.setMap(new Mapping(cdsSeqDss, cdsToProteinMap + // .getInverse())); + // proteinProduct.addDBRef(proteinToCdsRef); + // } /* * transfer any features on dna that overlap the CDS diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java index ddfd7ff..c027742 100644 --- a/src/jalview/analysis/CrossRef.java +++ b/src/jalview/analysis/CrossRef.java @@ -742,14 +742,16 @@ public class CrossRef /* * and add a reverse DbRef with the inverse mapping */ - if (mapFrom.getDatasetSequence() != null - && mapFrom.getDatasetSequence().getSourceDBRef() != null) + if (mapFrom.getDatasetSequence() != null && false) + // && mapFrom.getDatasetSequence().getSourceDBRef() != null) { - DBRefEntry dbref = new DBRefEntry(mapFrom.getDatasetSequence() - .getSourceDBRef()); - dbref.setMap(new Mapping(mapFrom.getDatasetSequence(), mapping - .getInverse())); - mapTo.addDBRef(dbref); + // possible need to search primary references... except, why doesn't xref + // == getSourceDBRef ?? + // DBRefEntry dbref = new DBRefEntry(mapFrom.getDatasetSequence() + // .getSourceDBRef()); + // dbref.setMap(new Mapping(mapFrom.getDatasetSequence(), mapping + // .getInverse())); + // mapTo.addDBRef(dbref); } if (fromDna) diff --git a/src/jalview/api/DBRefEntryI.java b/src/jalview/api/DBRefEntryI.java index 32245b3..701acb6 100644 --- a/src/jalview/api/DBRefEntryI.java +++ b/src/jalview/api/DBRefEntryI.java @@ -70,4 +70,28 @@ public interface DBRefEntryI * @return */ public boolean updateFrom(DBRefEntryI otherEntry); + + /** + * Method to distinguish between direct and indirect database references + * + * primary references indicate the local sequence data directly corresponds + * with the database record. All other references are secondary. direct + * references indicate that part or all of the local sequence data can be + * mapped with another sequence, enabling annotation transfer. + * cross-references indicate the local sequence data can be corresponded to + * some other linear coordinate system via a transformation. + * + * This method is also sufficient to distinguish direct DBRefEntry mappings + * from other relationships - e.g. coding relationships (imply a 1:3/3:1 + * mapping), but not transcript relationships, which imply a (possibly + * non-contiguous) 1:1 mapping + * + * The only way a dbref's mappings can be fully verified is via the local + * sequence frame, so rather than use isPrimary directly, please use + * SequenceI.getPrimaryDbRefs() + * + * @return true if this reference provides a primary accession for the + * associated sequence object + */ + public boolean isPrimary(); } diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java index b6cc7c0..ec7cd25 100644 --- a/src/jalview/appletgui/APopupMenu.java +++ b/src/jalview/appletgui/APopupMenu.java @@ -964,7 +964,7 @@ public class APopupMenu extends java.awt.PopupMenu implements "label.represent_group_with", new Object[] { "" })); revealAll.setLabel(MessageManager.getString("action.reveal_all")); revealSeq.setLabel(MessageManager.getString("action.reveal_sequences")); - menu1.setLabel(MessageManager.getString("label.group") + ":"); + menu1.setLabel(MessageManager.getString("label.group:")); add(groupMenu); this.add(seqMenu); this.add(hideSeqs); diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index 849c05c..0312015 100644 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -3517,10 +3517,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, nucleotideColour.setLabel(MessageManager.getString("label.nucleotide")); nucleotideColour.addActionListener(this); modifyPID.setLabel(MessageManager - .getString("label.modify_identity_thereshold")); + .getString("label.modify_identity_threshold")); modifyPID.addActionListener(this); modifyConservation.setLabel(MessageManager - .getString("label.modify_conservation_thereshold")); + .getString("label.modify_conservation_threshold")); modifyConservation.addActionListener(this); annotationColour.setLabel(MessageManager .getString("action.by_annotation")); diff --git a/src/jalview/appletgui/AnnotationColourChooser.java b/src/jalview/appletgui/AnnotationColourChooser.java index 57b182c..5a9cd55 100644 --- a/src/jalview/appletgui/AnnotationColourChooser.java +++ b/src/jalview/appletgui/AnnotationColourChooser.java @@ -138,11 +138,11 @@ public class AnnotationColourChooser extends Panel implements } threshold.addItem(MessageManager - .getString("label.threshold_feature_no_thereshold")); + .getString("label.threshold_feature_no_threshold")); threshold.addItem(MessageManager - .getString("label.threshold_feature_above_thereshold")); + .getString("label.threshold_feature_above_threshold")); threshold.addItem(MessageManager - .getString("label.threshold_feature_below_thereshold")); + .getString("label.threshold_feature_below_threshold")); if (oldcs instanceof AnnotationColourGradient) { @@ -162,7 +162,7 @@ public class AnnotationColourChooser extends Panel implements default: throw new Error( MessageManager - .getString("error.implementation_error_dont_know_thereshold_annotationcolourgradient")); + .getString("error.implementation_error_dont_know_threshold_annotationcolourgradient")); } thresholdIsMin.setState(acg.thresholdIsMinMax); thresholdValue.setText("" + acg.getAnnotationThreshold()); diff --git a/src/jalview/appletgui/AnnotationRowFilter.java b/src/jalview/appletgui/AnnotationRowFilter.java index 4cb5ede..fc49de5 100644 --- a/src/jalview/appletgui/AnnotationRowFilter.java +++ b/src/jalview/appletgui/AnnotationRowFilter.java @@ -186,11 +186,11 @@ public abstract class AnnotationRowFilter extends Panel protected void populateThresholdComboBox(Choice threshold) { threshold.addItem(MessageManager - .getString("label.threshold_feature_no_thereshold")); + .getString("label.threshold_feature_no_threshold")); threshold.addItem(MessageManager - .getString("label.threshold_feature_above_thereshold")); + .getString("label.threshold_feature_above_threshold")); threshold.addItem(MessageManager - .getString("label.threshold_feature_below_thereshold")); + .getString("label.threshold_feature_below_threshold")); } public jalview.datamodel.AlignmentAnnotation getCurrentAnnotation() diff --git a/src/jalview/appletgui/FeatureColourChooser.java b/src/jalview/appletgui/FeatureColourChooser.java index 3c04ccd..0e85017 100644 --- a/src/jalview/appletgui/FeatureColourChooser.java +++ b/src/jalview/appletgui/FeatureColourChooser.java @@ -191,11 +191,11 @@ public class FeatureColourChooser extends Panel implements ActionListener, jPanel4.setBackground(Color.white); threshold.addItemListener(this); threshold.addItem(MessageManager - .getString("label.threshold_feature_no_thereshold")); + .getString("label.threshold_feature_no_threshold")); threshold.addItem(MessageManager - .getString("label.threshold_feature_above_thereshold")); + .getString("label.threshold_feature_above_threshold")); threshold.addItem(MessageManager - .getString("label.threshold_feature_below_thereshold")); + .getString("label.threshold_feature_below_threshold")); thresholdValue.addActionListener(this); slider.setBackground(Color.white); slider.setEnabled(false); diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java index 81d8ef5..82736d7 100644 --- a/src/jalview/appletgui/FeatureRenderer.java +++ b/src/jalview/appletgui/FeatureRenderer.java @@ -251,23 +251,24 @@ public class FeatureRenderer extends tmp = new Panel(); panel.add(tmp); - tmp.add(new Label("Name: ", Label.RIGHT)); + tmp.add(new Label(MessageManager.getString("label.name:"), Label.RIGHT)); tmp.add(name); tmp = new Panel(); panel.add(tmp); - tmp.add(new Label("Group: ", Label.RIGHT)); + tmp.add(new Label(MessageManager.getString("label.group:"), Label.RIGHT)); tmp.add(source); tmp = new Panel(); panel.add(tmp); - tmp.add(new Label("Colour: ", Label.RIGHT)); + tmp.add(new Label(MessageManager.getString("label.colour"), Label.RIGHT)); tmp.add(colourPanel); bigPanel.add(panel, BorderLayout.NORTH); panel = new Panel(); - panel.add(new Label("Description: ", Label.RIGHT)); + panel.add(new Label(MessageManager.getString("label.description:"), + Label.RIGHT)); panel.add(new ScrollPane().add(description)); if (!newFeatures) @@ -275,9 +276,11 @@ public class FeatureRenderer extends bigPanel.add(panel, BorderLayout.SOUTH); panel = new Panel(); - panel.add(new Label(" Start:", Label.RIGHT)); + panel.add(new Label(MessageManager.getString("label.start"), + Label.RIGHT)); panel.add(start); - panel.add(new Label(" End:", Label.RIGHT)); + panel.add(new Label(MessageManager.getString("label.end"), + Label.RIGHT)); panel.add(end); bigPanel.add(panel, BorderLayout.CENTER); } diff --git a/src/jalview/appletgui/ScalePanel.java b/src/jalview/appletgui/ScalePanel.java index 0f71818..d2c1693 100755 --- a/src/jalview/appletgui/ScalePanel.java +++ b/src/jalview/appletgui/ScalePanel.java @@ -409,22 +409,33 @@ public class ScalePanel extends Panel implements MouseMotionListener, // Fill the selected columns ColumnSelection cs = av.getColumnSelection(); - gg.setColor(new Color(220, 0, 0)); int avCharWidth = av.getCharWidth(); int avcharHeight = av.getCharHeight(); - for (int sel : cs.getSelected()) + if (cs != null) { - // TODO: JAL-2001 - provide a fast method to list visible selected in a - // given range - if (av.hasHiddenColumns()) + gg.setColor(new Color(220, 0, 0)); + boolean hasHiddenColumns = cs.hasHiddenColumns(); + for (int sel : cs.getSelected()) { - sel = av.getColumnSelection().findColumnPosition(sel); - } + // TODO: JAL-2001 - provide a fast method to list visible selected in a + // given range + if (hasHiddenColumns) + { + if (cs.isVisible(sel)) + { + sel = cs.findColumnPosition(sel); + } + else + { + continue; + } + } - if ((sel >= startx) && (sel <= endx)) - { - gg.fillRect((sel - startx) * avCharWidth, 0, avCharWidth, - getSize().height); + if ((sel >= startx) && (sel <= endx)) + { + gg.fillRect((sel - startx) * avCharWidth, 0, avCharWidth, + getSize().height); + } } } @@ -471,12 +482,10 @@ public class ScalePanel extends Panel implements MouseMotionListener, if (av.getShowHiddenMarkers()) { int widthx = 1 + endx - startx; - for (int i = 0; i < av.getColumnSelection().getHiddenColumns() - .size(); i++) + for (int i = 0; i < cs.getHiddenColumns().size(); i++) { - res = av.getColumnSelection().findHiddenRegionPosition(i) - - startx; + res = cs.findHiddenRegionPosition(i) - startx; if (res < 0 || res > widthx) { diff --git a/src/jalview/appletgui/SliderPanel.java b/src/jalview/appletgui/SliderPanel.java index 2fc15d0..2c53c08 100644 --- a/src/jalview/appletgui/SliderPanel.java +++ b/src/jalview/appletgui/SliderPanel.java @@ -132,7 +132,7 @@ public class SliderPanel extends Panel implements ActionListener, pid.cs = cs; } PIDSlider.setTitle(MessageManager - .formatMessage("label.percentage_identity_thereshold", + .formatMessage("label.percentage_identity_threshold", new String[] { source })); if (ap.av.getAlignment().getGroups() != null) diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java index 82c8d38..f508bc3 100644 --- a/src/jalview/controller/AlignViewController.java +++ b/src/jalview/controller/AlignViewController.java @@ -194,13 +194,13 @@ public class AlignViewController implements AlignViewControllerI avcg.setStatus(MessageManager.formatMessage( "label.view_controller_toggled_marked", new String[] { - MessageManager.getString(toggle ? "label.toggled" - : "label.marked"), + toggle ? MessageManager.getString("label.toggled") + : MessageManager.getString("label.marked"), String.valueOf(columnCount), - MessageManager - .getString(invert ? "label.not_containing" - : "label.containing"), featureType, - Integer.valueOf(nseq).toString() })); + invert ? MessageManager + .getString("label.not_containing") + : MessageManager.getString("label.containing"), + featureType, Integer.valueOf(nseq).toString() })); return true; } } diff --git a/src/jalview/datamodel/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java index fa72e80..9db9f38 100644 --- a/src/jalview/datamodel/AlignmentView.java +++ b/src/jalview/datamodel/AlignmentView.java @@ -277,8 +277,7 @@ public class AlignmentView if (!seqcigararray.isSeqCigarArray()) { throw new Error( - MessageManager - .getString("error.implementation_error_can_only_make_alignmnet_from_cigararray")); + "Implementation Error - can only make an alignment view from a CigarArray of sequences."); } // contigs = seqcigararray.applyDeletions(); contigs = seqcigararray.getDeletedRegions(); diff --git a/src/jalview/datamodel/DBRefEntry.java b/src/jalview/datamodel/DBRefEntry.java index a641b1b..11e77d8 100755 --- a/src/jalview/datamodel/DBRefEntry.java +++ b/src/jalview/datamodel/DBRefEntry.java @@ -22,9 +22,12 @@ package jalview.datamodel; import jalview.api.DBRefEntryI; +import java.util.Arrays; + public class DBRefEntry implements DBRefEntryI { String source = "", version = "", accessionId = ""; + /** * maps from associated sequence to the database sequence's coordinate system */ @@ -35,7 +38,6 @@ public class DBRefEntry implements DBRefEntryI } - public DBRefEntry(String source, String version, String accessionId) { this(source, version, accessionId, null); @@ -138,7 +140,8 @@ public class DBRefEntry implements DBRefEntryI String otherAccession = other.getAccessionId(); if ((accessionId == null && otherAccession != null) || (accessionId != null && otherAccession == null) - || (accessionId != null && !accessionId.equalsIgnoreCase(otherAccession))) + || (accessionId != null && !accessionId + .equalsIgnoreCase(otherAccession))) { return false; } @@ -148,7 +151,7 @@ public class DBRefEntry implements DBRefEntryI * otherwise the versions have to match */ String otherVersion = other.getVersion(); - + if ((version == null || version.equals("0") || version.endsWith(":0")) && otherVersion != null) { @@ -223,28 +226,24 @@ public class DBRefEntry implements DBRefEntryI return accessionId; } - @Override public void setAccessionId(String accessionId) { this.accessionId = accessionId; } - @Override public void setSource(String source) { this.source = source; } - @Override public void setVersion(String version) { this.version = version; } - @Override public Mapping getMap() { @@ -280,4 +279,53 @@ public class DBRefEntry implements DBRefEntryI { return getSrcAccString(); } + + @Override + public boolean isPrimary() + { + /* + * if a map is present, unless it is 1:1 and has no SequenceI mate, it cannot be a primary reference. + */ + if (map != null) + { + if (map.getTo() != null) + { + return false; + } + if (map.getMap().getFromRatio() != map.getMap().getToRatio() + || map.getMap().getFromRatio() != 1) + { + return false; + } + // check map is really 1:1, no shifts allowed. + if (map.getMap().getFromHighest() != map.getMap().getToHighest() + && map.getMap().getFromLowest() != map.getMap().getToLowest() + && !Arrays.equals( + map.getMap().getFromRanges().toArray(new int[0][]), + map.getMap().getToRanges().toArray(new int[0][]))) + { + return false; + } + } + if (version == null) + { + // no version string implies the reference has not been verified at all. + return false; + } + // tricky - this test really needs to search the sequence's set of dbrefs to + // see if there is a primary reference that derived this reference. + String ucv = version.toUpperCase(); + for (String primsrc : Arrays.asList(DBRefSource.allSources())) + { + if (ucv.startsWith(primsrc.toUpperCase())) + { + // by convention, many secondary references inherit the primary + // reference's + // source string as a prefix for any version information from the + // secondary reference. + return false; + } + } + return true; + } } diff --git a/src/jalview/datamodel/DBRefSource.java b/src/jalview/datamodel/DBRefSource.java index fba9211..064764c 100755 --- a/src/jalview/datamodel/DBRefSource.java +++ b/src/jalview/datamodel/DBRefSource.java @@ -20,6 +20,10 @@ */ package jalview.datamodel; +import java.lang.reflect.Field; +import java.util.ArrayList; +import java.util.List; + /** * Defines internal constants for unambiguous annotation of DbRefEntry source * strings and describing the data retrieved from external database sources (see @@ -36,12 +40,12 @@ public class DBRefSource /** * UNIPROT Accession Number */ - public static String UNIPROT = "UNIPROT"; + public static final String UNIPROT = "UNIPROT"; /** * UNIPROT Entry Name */ - public static String UP_NAME = "UNIPROT_NAME".toUpperCase(); + public static final String UP_NAME = "UNIPROT_NAME".toUpperCase(); /** * Uniprot Knowledgebase/TrEMBL as served from EMBL protein products. @@ -54,27 +58,27 @@ public class DBRefSource /** * PDB Entry Code */ - public static String PDB = "PDB"; + public static final String PDB = "PDB"; /** * EMBL ID */ - public static String EMBL = "EMBL"; + public static final String EMBL = "EMBL"; /** * EMBLCDS ID */ - public static String EMBLCDS = "EMBLCDS"; + public static final String EMBLCDS = "EMBLCDS"; /** * PFAM ID */ - public static String PFAM = "PFAM"; + public static final String PFAM = "PFAM"; /** * RFAM ID */ - public static String RFAM = "RFAM"; + public static final String RFAM = "RFAM"; /** * GeneDB ID @@ -98,4 +102,23 @@ public class DBRefSource public static final String[] PROTEINDBS = { UNIPROT, PDB, UNIPROTKB, EMBLCDSProduct, ENSEMBL }; // Ensembl ENSP* entries are protein + + public static String[] allSources() + { + List src = new ArrayList(); + for (Field f : DBRefSource.class.getFields()) + { + if (String.class.equals(f.getType())) + { + try + { + src.add((String) f.get(null)); + } catch (Exception x) + { + x.printStackTrace(); + } + } + } + return src.toArray(new String[0]); + } } diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java index 88f4308..620bcc1 100755 --- a/src/jalview/datamodel/Sequence.java +++ b/src/jalview/datamodel/Sequence.java @@ -22,6 +22,8 @@ package jalview.datamodel; import jalview.analysis.AlignSeq; import jalview.api.DBRefEntryI; +import jalview.util.DBRefUtils; +import jalview.util.MapList; import jalview.util.StringUtils; import java.util.ArrayList; @@ -235,8 +237,6 @@ public class Sequence extends ASequence implements SequenceI seq.getEnd()); } description = seq.getDescription(); - sourceDBRef = seq.getSourceDBRef() == null ? null : new DBRefEntry( - seq.getSourceDBRef()); if (seq != datasetSequence) { setDatasetSequence(seq.getDatasetSequence()); @@ -1395,12 +1395,15 @@ public class Sequence extends ASequence implements SequenceI @Override public PDBEntry getPDBEntry(String pdbIdStr) { - if (getDatasetSequence() == null - || getDatasetSequence().getAllPDBEntries() == null) + if (getDatasetSequence() != null) + { + return getDatasetSequence().getPDBEntry(pdbIdStr); + } + if (pdbIds == null) { return null; } - List entries = getDatasetSequence().getAllPDBEntries(); + List entries = getAllPDBEntries(); for (PDBEntry entry : entries) { if (entry.getId().equalsIgnoreCase(pdbIdStr)) @@ -1411,16 +1414,59 @@ public class Sequence extends ASequence implements SequenceI return null; } - @Override - public void setSourceDBRef(DBRefEntryI dbRef) - { - this.sourceDBRef = dbRef; - } @Override - public DBRefEntryI getSourceDBRef() + public List getPrimaryDBRefs() { - return this.sourceDBRef; + if (datasetSequence!=null) + { + return datasetSequence.getPrimaryDBRefs(); + } + if (dbrefs==null || dbrefs.length==0) + { + return Arrays.asList(new DBRefEntry[0]); + } + synchronized (dbrefs) + { + List primaries = new ArrayList(); + DBRefEntry tmp[] = new DBRefEntry[1], res[] = null; + for (DBRefEntry ref : dbrefs) + { + if (!ref.isPrimary()) + { + continue; + } + if (ref.hasMap()) + { + MapList mp = ref.getMap().getMap(); + if (mp.getFromLowest() > start || mp.getFromHighest() < end) + { + // map only involves a subsequence, so cannot be primary + continue; + } + } + // whilst it looks like it is a primary ref, we also sanity check type + if (DBRefUtils.getCanonicalName(DBRefSource.PDB).equals( + DBRefUtils.getCanonicalName(ref.getSource()))) + { + // PDB dbrefs imply there should be a PDBEntry associated + if (getPDBEntry(ref.getAccessionId()) != null) + { + primaries.add(ref); + } + continue; + } + // check standard protein or dna sources + tmp[0] = ref; + res = DBRefUtils.selectDbRefs(!isProtein(), tmp); + if (res != null && res[0] == tmp[0]) + { + primaries.add(ref); + continue; + } + } + return primaries; + } } } diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java index 45a767c..ec7520b 100755 --- a/src/jalview/datamodel/SequenceI.java +++ b/src/jalview/datamodel/SequenceI.java @@ -20,8 +20,6 @@ */ package jalview.datamodel; -import jalview.api.DBRefEntryI; - import java.util.List; import java.util.Vector; @@ -443,21 +441,14 @@ public interface SequenceI extends ASequenceI */ public PDBEntry getPDBEntry(String pdbId); - /** - * Set the distinct source database, and accession number from which a - * sequence and its start-end data were derived from. This is very important - * for SIFTS mappings and must be set prior to performing SIFTS mapping. - * - * @param dbRef - * the source dbRef for the sequence - */ - public void setSourceDBRef(DBRefEntryI dbRef); /** - * Get the distinct source database, and accession number from which a - * sequence and its start-end data were derived from. + * Get all primary database/accessions for this sequence's data. These + * DBRefEntry are expected to resolve to a valid record in the associated + * external database, either directly or via a provided 1:1 Mapping. * - * @return + * @return just the primary references (if any) for this sequence, or an empty + * list */ - public DBRefEntryI getSourceDBRef(); + public List getPrimaryDBRefs(); } diff --git a/src/jalview/datamodel/xdb/embl/EmblEntry.java b/src/jalview/datamodel/xdb/embl/EmblEntry.java index 06e929d..3ba36ca 100644 --- a/src/jalview/datamodel/xdb/embl/EmblEntry.java +++ b/src/jalview/datamodel/xdb/embl/EmblEntry.java @@ -195,7 +195,6 @@ public class EmblEntry DBRefEntry retrievedref = new DBRefEntry(sourceDb, getSequenceVersion(), accession); dna.addDBRef(retrievedref); - dna.setSourceDBRef(retrievedref); // add map to indicate the sequence is a valid coordinate frame for the // dbref retrievedref.setMap(new Mapping(null, new int[] { 1, dna.getLength() }, @@ -504,7 +503,6 @@ public class EmblEntry dnaToProteinMapping.setTo(proteinSeq); dnaToProteinMapping.setMappedFromId(proteinId); proteinSeq.addDBRef(proteinDbRef); - proteinSeq.setSourceDBRef(proteinDbRef); ref.setMap(dnaToProteinMapping); } hasUniprotDbref = true; @@ -549,7 +547,6 @@ public class EmblEntry DBRefSource.EMBLCDSProduct, getSequenceVersion(), proteinId); } product.addDBRef(proteinToEmblProteinRef); - product.setSourceDBRef(proteinToEmblProteinRef); if (dnaToProteinMapping != null && dnaToProteinMapping.getTo() != null) diff --git a/src/jalview/ext/ensembl/EnsemblSeqProxy.java b/src/jalview/ext/ensembl/EnsemblSeqProxy.java index 31552af..e44b610 100644 --- a/src/jalview/ext/ensembl/EnsemblSeqProxy.java +++ b/src/jalview/ext/ensembl/EnsemblSeqProxy.java @@ -276,8 +276,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient { // clunky: ensure Uniprot xref if we have one is on mapped sequence SequenceI ds = proteinSeq.getDatasetSequence(); - ds.setSourceDBRef(proteinSeq.getSourceDBRef()); - + // TODO: Verify ensp primary ref is on proteinSeq.getDatasetSequence() Mapping map = new Mapping(ds, mapList); DBRefEntry dbr = new DBRefEntry(getDbSource(), getEnsemblDataVersion(), proteinSeq.getName(), map); @@ -322,7 +321,6 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient DBRefEntry self = new DBRefEntry(getDbSource(), getEnsemblDataVersion(), seq.getName()); seq.addDBRef(self); - seq.setSourceDBRef(self); } /** @@ -382,7 +380,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient { DBRefEntry dbref = DBRefUtils.parseToDbRef(sq, getDbSource(), getEnsemblDataVersion(), name); - sq.setSourceDBRef(dbref); + sq.addDBRef(dbref); } } if (alignment == null) diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 84edb4e..dd8fb7a 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -844,8 +844,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, showGroupConservation.setEnabled(!nucleotide); rnahelicesColour.setEnabled(nucleotide); purinePyrimidineColour.setEnabled(nucleotide); - showComplementMenuItem.setText(MessageManager - .getString(nucleotide ? "label.protein" : "label.nucleotide")); + showComplementMenuItem.setText(nucleotide ? MessageManager + .getString("label.protein") : MessageManager + .getString("label.nucleotide")); setColourSelected(jalview.bin.Cache.getDefault( nucleotide ? Preferences.DEFAULT_COLOUR_NUC : Preferences.DEFAULT_COLOUR_PROT, "None")); @@ -3214,30 +3215,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } /** - * Set or clear 'Show Sequence Features' - * - * @param evt - * DOCUMENT ME! - */ - @Override - public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt) - { - viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight - .isSelected()); - if (viewport.isShowSequenceFeaturesHeight()) - { - // ensure we're actually displaying features - viewport.setShowSequenceFeatures(true); - showSeqFeatures.setSelected(true); - } - alignPanel.paintAlignment(true); - if (alignPanel.getOverviewPanel() != null) - { - alignPanel.getOverviewPanel().updateOverviewImage(); - } - } - - /** * Action on toggle of the 'Show annotations' menu item. This shows or hides * the annotations panel as a whole. * @@ -4462,22 +4439,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // object broker mechanism. final Vector wsmenu = new Vector(); final IProgressIndicator af = me; + + /* + * do not i18n these strings - they are hard-coded in class + * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and + * SequenceAnnotationWSClient.initSequenceAnnotationWSClient() + */ final JMenu msawsmenu = new JMenu("Alignment"); final JMenu secstrmenu = new JMenu( "Secondary Structure Prediction"); final JMenu seqsrchmenu = new JMenu("Sequence Database Search"); final JMenu analymenu = new JMenu("Analysis"); final JMenu dismenu = new JMenu("Protein Disorder"); - // final JMenu msawsmenu = new - // JMenu(MessageManager.getString("label.alignment")); - // final JMenu secstrmenu = new - // JMenu(MessageManager.getString("label.secondary_structure_prediction")); - // final JMenu seqsrchmenu = new - // JMenu(MessageManager.getString("label.sequence_database_search")); - // final JMenu analymenu = new - // JMenu(MessageManager.getString("label.analysis")); - // final JMenu dismenu = new - // JMenu(MessageManager.getString("label.protein_disorder")); // JAL-940 - only show secondary structure prediction services from // the legacy server if (// Cache.getDefault("SHOW_JWS1_SERVICES", true) diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java index b1a4fee..62e05d0 100644 --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@ -507,17 +507,6 @@ public class AlignViewport extends AlignmentViewport implements /** * DOCUMENT ME! * - * @return DOCUMENT ME! - */ - @Override - public ColumnSelection getColumnSelection() - { - return colSel; - } - - /** - * DOCUMENT ME! - * * @param tree * DOCUMENT ME! */ diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java index 19eed27..93c9a6b 100644 --- a/src/jalview/gui/AnnotationColourChooser.java +++ b/src/jalview/gui/AnnotationColourChooser.java @@ -141,7 +141,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter default: throw new Error( MessageManager - .getString("error.implementation_error_dont_know_about_thereshold_setting")); + .getString("error.implementation_error_dont_know_about_threshold_setting")); } thresholdIsMin.setSelected(acg.thresholdIsMinMax); thresholdValue.setText("" + acg.getAnnotationThreshold()); diff --git a/src/jalview/gui/AnnotationRowFilter.java b/src/jalview/gui/AnnotationRowFilter.java index 17298ba..f0bea60 100644 --- a/src/jalview/gui/AnnotationRowFilter.java +++ b/src/jalview/gui/AnnotationRowFilter.java @@ -257,11 +257,11 @@ public abstract class AnnotationRowFilter extends JPanel protected void populateThresholdComboBox(JComboBox threshold) { threshold.addItem(MessageManager - .getString("label.threshold_feature_no_thereshold")); + .getString("label.threshold_feature_no_threshold")); threshold.addItem(MessageManager - .getString("label.threshold_feature_above_thereshold")); + .getString("label.threshold_feature_above_threshold")); threshold.addItem(MessageManager - .getString("label.threshold_feature_below_thereshold")); + .getString("label.threshold_feature_below_threshold")); } protected void seqAssociated_actionPerformed(ActionEvent arg0, diff --git a/src/jalview/gui/CrossRefAction.java b/src/jalview/gui/CrossRefAction.java index f0b0891..32af226 100644 --- a/src/jalview/gui/CrossRefAction.java +++ b/src/jalview/gui/CrossRefAction.java @@ -192,8 +192,9 @@ public class CrossRefAction implements Runnable { newFrame.hideFeatureColumns(SequenceOntologyI.EXON, false); } - String newtitle = String.format("%s %s %s", MessageManager - .getString(dna ? "label.proteins" : "label.nucleotides"), + String newtitle = String.format("%s %s %s", + dna ? MessageManager.getString("label.proteins") + : MessageManager.getString("label.nucleotides"), MessageManager.getString("label.for"), alignFrame.getTitle()); newFrame.setTitle(newtitle); diff --git a/src/jalview/gui/DasSourceBrowser.java b/src/jalview/gui/DasSourceBrowser.java index b176672..e677084 100644 --- a/src/jalview/gui/DasSourceBrowser.java +++ b/src/jalview/gui/DasSourceBrowser.java @@ -448,7 +448,7 @@ public class DasSourceBrowser extends GDasSourceBrowser implements seqs.setSelected(seqsrc); JPanel panel = new JPanel(new BorderLayout()); JPanel pane12 = new JPanel(new BorderLayout()); - pane12.add(new JLabel(MessageManager.getString("label.name")), + pane12.add(new JLabel(MessageManager.getString("label.name:")), BorderLayout.CENTER); pane12.add(nametf, BorderLayout.EAST); panel.add(pane12, BorderLayout.NORTH); diff --git a/src/jalview/gui/FeatureColourChooser.java b/src/jalview/gui/FeatureColourChooser.java index 79217ea..5594e1a 100644 --- a/src/jalview/gui/FeatureColourChooser.java +++ b/src/jalview/gui/FeatureColourChooser.java @@ -242,11 +242,11 @@ public class FeatureColourChooser extends JalviewDialog threshold.setToolTipText(MessageManager .getString("label.threshold_feature_display_by_score")); threshold.addItem(MessageManager - .getString("label.threshold_feature_no_thereshold")); // index 0 + .getString("label.threshold_feature_no_threshold")); // index 0 threshold.addItem(MessageManager - .getString("label.threshold_feature_above_thereshold")); // index 1 + .getString("label.threshold_feature_above_threshold")); // index 1 threshold.addItem(MessageManager - .getString("label.threshold_feature_below_thereshold")); // index 2 + .getString("label.threshold_feature_below_threshold")); // index 2 jPanel3.setLayout(flowLayout2); thresholdValue.addActionListener(new ActionListener() { @@ -263,7 +263,7 @@ public class FeatureColourChooser extends JalviewDialog slider.setOpaque(false); slider.setPreferredSize(new Dimension(100, 32)); slider.setToolTipText(MessageManager - .getString("label.adjust_thereshold")); + .getString("label.adjust_threshold")); thresholdValue.setEnabled(false); thresholdValue.setColumns(7); jPanel3.setBackground(Color.white); diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java index 727c13b..426ea32 100644 --- a/src/jalview/gui/FeatureRenderer.java +++ b/src/jalview/gui/FeatureRenderer.java @@ -173,7 +173,8 @@ public class FeatureRenderer extends { panel = new JPanel(new GridLayout(4, 1)); tmp = new JPanel(); - tmp.add(new JLabel(MessageManager.getString("label.select_feature"))); + tmp.add(new JLabel(MessageManager.getString("label.select_feature") + + ":")); overlaps = new JComboBox(); for (int i = 0; i < features.length; i++) { @@ -224,12 +225,13 @@ public class FeatureRenderer extends tmp = new JPanel(); panel.add(tmp); - tmp.add(new JLabel(MessageManager.getString("label.name"), JLabel.RIGHT)); + tmp.add(new JLabel(MessageManager.getString("label.name:"), + JLabel.RIGHT)); tmp.add(name); tmp = new JPanel(); panel.add(tmp); - tmp.add(new JLabel(MessageManager.getString("label.group") + ":", + tmp.add(new JLabel(MessageManager.getString("label.group:"), JLabel.RIGHT)); tmp.add(source); @@ -248,7 +250,7 @@ public class FeatureRenderer extends bigPanel.add(panel, BorderLayout.NORTH); panel = new JPanel(); - panel.add(new JLabel(MessageManager.getString("label.description"), + panel.add(new JLabel(MessageManager.getString("label.description:"), JLabel.RIGHT)); description.setFont(JvSwingUtils.getTextAreaFont()); description.setLineWrap(true); diff --git a/src/jalview/gui/FontChooser.java b/src/jalview/gui/FontChooser.java index 535196e..1f6c068 100755 --- a/src/jalview/gui/FontChooser.java +++ b/src/jalview/gui/FontChooser.java @@ -157,6 +157,7 @@ public class FontChooser extends GFontChooser init = false; } + @Override public void smoothFont_actionPerformed(ActionEvent e) { ap.av.antiAlias = smoothFont.isSelected(); @@ -170,6 +171,7 @@ public class FontChooser extends GFontChooser * @param e * DOCUMENT ME! */ + @Override protected void ok_actionPerformed(ActionEvent e) { try @@ -194,6 +196,7 @@ public class FontChooser extends GFontChooser * @param e * DOCUMENT ME! */ + @Override protected void cancel_actionPerformed(ActionEvent e) { if (ap != null) @@ -247,10 +250,10 @@ public class FontChooser extends GFontChooser double iw = iBounds.getWidth(); if (mw < 1 || iw < 1) { - final String messageKey = iBounds.getHeight() < 1 ? "label.font_doesnt_have_letters_defined" - : "label.font_too_small"; - JOptionPane.showInternalMessageDialog(this, - MessageManager.getString(messageKey), + String message = iBounds.getHeight() < 1 ? MessageManager + .getString("label.font_doesnt_have_letters_defined") + : MessageManager.getString("label.font_too_small"); + JOptionPane.showInternalMessageDialog(this, message, MessageManager.getString("label.invalid_font"), JOptionPane.WARNING_MESSAGE); /* @@ -301,6 +304,7 @@ public class FontChooser extends GFontChooser * @param e * DOCUMENT ME! */ + @Override protected void fontName_actionPerformed(ActionEvent e) { if (init) @@ -317,6 +321,7 @@ public class FontChooser extends GFontChooser * @param e * DOCUMENT ME! */ + @Override protected void fontSize_actionPerformed(ActionEvent e) { if (init) @@ -333,6 +338,7 @@ public class FontChooser extends GFontChooser * @param e * DOCUMENT ME! */ + @Override protected void fontStyle_actionPerformed(ActionEvent e) { if (init) @@ -349,6 +355,7 @@ public class FontChooser extends GFontChooser * * @param e */ + @Override public void defaultButton_actionPerformed(ActionEvent e) { Cache.setProperty("FONT_NAME", fontName.getSelectedItem().toString()); diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java index 2b09eb6..51d247d 100644 --- a/src/jalview/gui/PCAPanel.java +++ b/src/jalview/gui/PCAPanel.java @@ -140,8 +140,8 @@ public class PCAPanel extends GPCAPanel implements Runnable, { // create an entry for this score matrix for use in PCA JCheckBoxMenuItem jm = new JCheckBoxMenuItem(); - jm.setText(MessageManager - .getStringOrReturn("label.score_model", sm)); + jm.setText(MessageManager.getStringOrReturn("label.score_model_", + sm)); jm.setSelected(pcaModel.getScore_matrix().equals(sm)); if ((ResidueProperties.scoreMatrices.get(sm).isDNA() && ResidueProperties.scoreMatrices .get(sm).isProtein()) diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 569fcec..d28dc60 100644 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -476,8 +476,6 @@ public class PopupMenu extends JPopupMenu if (sg != null && sg.getSize() > 0) { - groupName.setText(MessageManager.formatMessage("label.name_param", - new Object[] { sg.getName() })); groupName.setText(MessageManager .getString("label.edit_name_and_description_current_group")); @@ -1097,7 +1095,6 @@ public class PopupMenu extends JPopupMenu */ private void jbInit() throws Exception { - groupMenu.setText(MessageManager.getString("label.group")); groupMenu.setText(MessageManager.getString("label.selection")); groupName.setText(MessageManager.getString("label.name")); groupName.addActionListener(new java.awt.event.ActionListener() diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java index 7fb0593..a9d2690 100755 --- a/src/jalview/gui/RedundancyPanel.java +++ b/src/jalview/gui/RedundancyPanel.java @@ -172,7 +172,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable progress = null; label.setText(MessageManager - .getString("label.enter_redundancy_thereshold")); + .getString("label.enter_redundancy_threshold")); slider.setVisible(true); applyButton.setEnabled(true); valueField.setVisible(true); diff --git a/src/jalview/gui/SliderPanel.java b/src/jalview/gui/SliderPanel.java index e1e70dc..c3fec4f 100755 --- a/src/jalview/gui/SliderPanel.java +++ b/src/jalview/gui/SliderPanel.java @@ -220,7 +220,7 @@ public class SliderPanel extends GSliderPanel } PIDSlider.setTitle(MessageManager - .formatMessage("label.percentage_identity_thereshold", + .formatMessage("label.percentage_identity_threshold", new String[] { source })); if (ap.av.getAlignment().getGroups() != null) diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index 13fa460..b2cc70f 100644 --- a/src/jalview/gui/StructureChooser.java +++ b/src/jalview/gui/StructureChooser.java @@ -867,7 +867,7 @@ public class StructureChooser extends GStructureChooser implements ArrayList seqsWithoutSourceDBRef = new ArrayList(); for (SequenceI seq : sequences) { - if (seq.getSourceDBRef() == null && seq.getDBRefs() == null) + if (seq.getPrimaryDBRefs().size() == 0) { seqsWithoutSourceDBRef.add(seq); continue; diff --git a/src/jalview/gui/TextColourChooser.java b/src/jalview/gui/TextColourChooser.java index f1c6768..39d9c1d 100644 --- a/src/jalview/gui/TextColourChooser.java +++ b/src/jalview/gui/TextColourChooser.java @@ -81,7 +81,7 @@ public class TextColourChooser new JLabel( "" + MessageManager - .getString("label.select_dark_light_set_thereshold") + .getString("label.select_dark_light_set_threshold") + ""), BorderLayout.NORTH); panel.add(col1); panel.add(slider); @@ -133,7 +133,7 @@ public class TextColourChooser ap, bigpanel, MessageManager - .getString("label.adjunst_foreground_text_colour_thereshold"), + .getString("label.adjunst_foreground_text_colour_threshold"), JOptionPane.OK_CANCEL_OPTION, JOptionPane.QUESTION_MESSAGE, null, null, null); diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java index 23c4d21..ab80ffa 100644 --- a/src/jalview/io/StockholmFile.java +++ b/src/jalview/io/StockholmFile.java @@ -101,6 +101,7 @@ public class StockholmFile extends AlignFile super(source); } + @Override public void initData() { super.initData(); @@ -178,6 +179,7 @@ public class StockholmFile extends AlignFile * @throws IOException * If there is an error with the input file */ + @Override public void parse() throws IOException { StringBuffer treeString = new StringBuffer(); @@ -533,8 +535,7 @@ public class StockholmFile extends AlignFile } else { - // throw new IOException(MessageManager.formatMessage( - // "exception.error_parsing_line", new String[] { line })); + // throw new IOException("Error parsing " + line); System.err.println(">> missing annotation: " + line); } } @@ -1106,6 +1107,7 @@ public class StockholmFile extends AlignFile return seq; } + @Override public String print() { out = new StringBuffer(); diff --git a/src/jalview/io/StructureFile.java b/src/jalview/io/StructureFile.java index fc0e207..f095383 100644 --- a/src/jalview/io/StructureFile.java +++ b/src/jalview/io/StructureFile.java @@ -117,7 +117,9 @@ public abstract class StructureFile extends AlignFile DBRefEntry sourceDBRef = new DBRefEntry(); sourceDBRef.setAccessionId(getId()); sourceDBRef.setSource(DBRefSource.PDB); - pdbSequence.setSourceDBRef(sourceDBRef); + // TODO: specify version for 'PDB' database ref if it is read from a file. + // TODO: decide if jalview.io should be creating primary refs! + sourceDBRef.setVersion(""); pdbSequence.addPDBId(entry); pdbSequence.addDBRef(sourceDBRef); SequenceI chainseq = pdbSequence; diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index b2eb094..d7def6b 100755 --- a/src/jalview/jbgui/GAlignFrame.java +++ b/src/jalview/jbgui/GAlignFrame.java @@ -136,8 +136,6 @@ public class GAlignFrame extends JInternalFrame public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem(); - public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem(); - JMenuItem copy = new JMenuItem(); JMenuItem cut = new JMenuItem(); @@ -1591,7 +1589,7 @@ public class GAlignFrame extends JInternalFrame }); JMenuItem modifyPID = new JMenuItem( - MessageManager.getString("label.modify_identity_thereshold")); + MessageManager.getString("label.modify_identity_threshold")); modifyPID.addActionListener(new ActionListener() { @Override @@ -1601,7 +1599,7 @@ public class GAlignFrame extends JInternalFrame } }); modifyConservation.setText(MessageManager - .getString("label.modify_conservation_thereshold")); + .getString("label.modify_conservation_threshold")); modifyConservation.addActionListener(new ActionListener() { @Override @@ -2520,13 +2518,6 @@ public class GAlignFrame extends JInternalFrame } - protected void showSeqFeaturesHeight_actionPerformed( - ActionEvent actionEvent) - { - // TODO Auto-generated method stub - - } - protected void justifyRightMenuItem_actionPerformed(ActionEvent e) { // TODO Auto-generated method stub diff --git a/src/jalview/renderer/ScaleRenderer.java b/src/jalview/renderer/ScaleRenderer.java index 164c7c7..6940f22 100644 --- a/src/jalview/renderer/ScaleRenderer.java +++ b/src/jalview/renderer/ScaleRenderer.java @@ -34,7 +34,7 @@ import java.util.List; */ public class ScaleRenderer { - public class ScaleMark + public final class ScaleMark { public final boolean major; diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java index be042e6..182a48f 100644 --- a/src/jalview/structure/StructureSelectionManager.java +++ b/src/jalview/structure/StructureSelectionManager.java @@ -502,7 +502,7 @@ public class StructureSelectionManager } ArrayList seqToStrucMapping = new ArrayList(); - if (isMapUsingSIFTs) + if (isMapUsingSIFTs && seq.isProtein()) { setProgressBar(null); setProgressBar(MessageManager @@ -585,6 +585,20 @@ public class StructureSelectionManager return "cif".equalsIgnoreCase(fileExt); } + /** + * retrieve a mapping for seq from SIFTs using associated DBRefEntry for + * uniprot or PDB + * + * @param seq + * @param pdbFile + * @param targetChainId + * @param pdb + * @param maxChain + * @param sqmpping + * @param maxAlignseq + * @return + * @throws SiftsException + */ private StructureMapping getStructureMapping(SequenceI seq, String pdbFile, String targetChainId, StructureFile pdb, PDBChain maxChain, jalview.datamodel.Mapping sqmpping, diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java index 3ba0e34..6213568 100644 --- a/src/jalview/ws/DBRefFetcher.java +++ b/src/jalview/ws/DBRefFetcher.java @@ -622,33 +622,43 @@ public class DBRefFetcher implements Runnable final int sequenceStart = sequence.getStart(); if (absStart == -1) { - // Is local sequence contained in dataset sequence? + // couldn't find local sequence in sequence from database, so check if + // the database sequence is a subsequence of local sequence absStart = nonGapped.indexOf(entrySeq); if (absStart == -1) - { // verification failed. + { + // verification failed. couldn't find any relationship between + // entrySeq and local sequence messages.append(sequence.getName() + " SEQUENCE NOT %100 MATCH \n"); continue; } + /* + * found match for the whole of the database sequence within the local + * sequence's reference frame. + */ transferred = true; sbuffer.append(sequence.getName() + " HAS " + absStart + " PREFIXED RESIDUES COMPARED TO " + dbSource + "\n"); - // - // + " - ANY SEQUENCE FEATURES" - // + " HAVE BEEN ADJUSTED ACCORDINGLY \n"); - // absStart = 0; - // create valid mapping between matching region of local sequence and - // the mapped sequence + + /* + * So create a mapping to the external entry from the matching region of + * the local sequence, and leave local start/end untouched. + */ mp = new Mapping(null, new int[] { sequenceStart + absStart, sequenceStart + absStart + entrySeq.length() - 1 }, new int[] { entry.getStart(), entry.getStart() + entrySeq.length() - 1 }, 1, 1); - updateRefFrame = false; // mapping is based on current start/end so - // don't modify start and end + updateRefFrame = false; } else { + /* + * found a match for the local sequence within sequence from + * the external database + */ transferred = true; + // update start and end of local sequence to place it in entry's // reference frame. // apply identity map map from whole of local sequence to matching @@ -660,10 +670,14 @@ public class DBRefFetcher implements Runnable // absStart+sequence.getStart()+entrySeq.length()-1}, // new int[] { entry.getStart(), entry.getEnd() }, 1, 1); // relocate local features for updated start + if (updateRefFrame) { if (sequence.getSequenceFeatures() != null) { + /* + * relocate existing sequence features by offset + */ SequenceFeature[] sf = sequence.getSequenceFeatures(); int start = sequenceStart; int end = sequence.getEnd(); @@ -686,7 +700,7 @@ public class DBRefFetcher implements Runnable System.out.println("Adding dbrefs to " + sequence.getName() + " from " + dbSource + " sequence : " + entry.getName()); sequence.transferAnnotation(entry, mp); - // unknownSequences.remove(sequence); + absStart += entry.getStart(); int absEnd = absStart + nonGapped.length() - 1; if (!trimDatasetSeqs) diff --git a/src/jalview/ws/SequenceFetcher.java b/src/jalview/ws/SequenceFetcher.java index 65179a2..37946b1 100644 --- a/src/jalview/ws/SequenceFetcher.java +++ b/src/jalview/ws/SequenceFetcher.java @@ -27,10 +27,8 @@ import jalview.ws.dbsources.EmblSource; import jalview.ws.dbsources.Pdb; import jalview.ws.dbsources.PfamFull; import jalview.ws.dbsources.PfamSeed; -import jalview.ws.dbsources.RfamFull; import jalview.ws.dbsources.RfamSeed; import jalview.ws.dbsources.Uniprot; -import jalview.ws.dbsources.UniprotName; import jalview.ws.dbsources.das.api.jalviewSourceI; import jalview.ws.seqfetcher.ASequenceFetcher; import jalview.ws.seqfetcher.DbSourceProxy; @@ -62,11 +60,11 @@ public class SequenceFetcher extends ASequenceFetcher addDBRefSourceImpl(EmblSource.class); addDBRefSourceImpl(EmblCdsSource.class); addDBRefSourceImpl(Uniprot.class); - addDBRefSourceImpl(UniprotName.class); addDBRefSourceImpl(Pdb.class); addDBRefSourceImpl(PfamFull.class); addDBRefSourceImpl(PfamSeed.class); addDBRefSourceImpl(RfamSeed.class); + if (addDas) { registerDasSequenceSources(); diff --git a/src/jalview/ws/dbsources/Uniprot.java b/src/jalview/ws/dbsources/Uniprot.java index 8cc0ce4..81b4caf 100644 --- a/src/jalview/ws/dbsources/Uniprot.java +++ b/src/jalview/ws/dbsources/Uniprot.java @@ -205,10 +205,10 @@ public class Uniprot extends DbSourceProxyImpl { DBRefEntry dbRef = new DBRefEntry(DBRefSource.UNIPROT, dbVersion, accessionId); + + // mark dbRef as a primary reference for this sequence dbRefs.add(dbRef); } - sequence.setSourceDBRef((dbRefs != null && dbRefs.size() > 0) ? dbRefs - .get(0) : null); Vector onlyPdbEntries = new Vector(); for (PDBEntry pdb : entry.getDbReference()) diff --git a/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java index 6c94723..0ab6e7d 100644 --- a/src/jalview/ws/sifts/SiftsClient.java +++ b/src/jalview/ws/sifts/SiftsClient.java @@ -323,41 +323,28 @@ public class SiftsClient implements SiftsClientI public DBRefEntryI getValidSourceDBRef(SequenceI seq) throws SiftsException { - DBRefEntryI sourceDBRef = null; - sourceDBRef = seq.getSourceDBRef(); - if (sourceDBRef != null && isValidDBRefEntry(sourceDBRef)) + DBRefEntry[] dbRefs = seq.getDBRefs(); + if (dbRefs == null || dbRefs.length < 1) { - return sourceDBRef; + throw new SiftsException( + "Source DBRef could not be determined. DBRefs might not have been retrieved."); } - else + + for (DBRefEntryI dbRef : dbRefs) { - DBRefEntry[] dbRefs = seq.getDBRefs(); - if (dbRefs == null || dbRefs.length < 1) + if (dbRef == null || dbRef.getAccessionId() == null + || dbRef.getSource() == null) { - throw new SiftsException( - "Source DBRef could not be determined. DBRefs might not have been retrieved."); + continue; } - - for (DBRefEntryI dbRef : dbRefs) + if (isValidDBRefEntry(dbRef) + && dbRef.isPrimary() + && (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT) || dbRef + .getSource().equalsIgnoreCase(DBRefSource.PDB))) { - if (dbRef == null || dbRef.getAccessionId() == null - || dbRef.getSource() == null) - { - continue; - } - if (isFoundInSiftsEntry(dbRef.getAccessionId()) - && (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT) || dbRef - .getSource().equalsIgnoreCase(DBRefSource.PDB))) - { - seq.setSourceDBRef(dbRef); - return dbRef; - } + return dbRef; } } - if (sourceDBRef != null && isValidDBRefEntry(sourceDBRef)) - { - return sourceDBRef; - } throw new SiftsException("Could not get source DB Ref"); } @@ -440,7 +427,7 @@ public class SiftsClient implements SiftsClientI String originalSeq = AlignSeq.extractGaps( jalview.util.Comparison.GapChars, seq.getSequenceAsString()); HashMap mapping = new HashMap(); - DBRefEntryI sourceDBRef = seq.getSourceDBRef(); + DBRefEntryI sourceDBRef; sourceDBRef = getValidSourceDBRef(seq); // TODO ensure sequence start/end is in the same coordinate system and // consistent with the choosen sourceDBRef diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java index 2ec2e18..a0ce475 100644 --- a/test/jalview/analysis/AlignmentUtilsTests.java +++ b/test/jalview/analysis/AlignmentUtilsTests.java @@ -997,9 +997,11 @@ public class AlignmentUtilsTests * sequence from the dna contig sequences */ DBRefEntry dbref = new DBRefEntry("ENSEMBL", "0", "dna1"); - dna1.getDatasetSequence().setSourceDBRef(dbref); + dna1.getDatasetSequence().addDBRef(dbref); + org.testng.Assert.assertEquals(dbref, dna1.getPrimaryDBRefs().get(0)); dbref = new DBRefEntry("ENSEMBL", "0", "dna2"); - dna2.getDatasetSequence().setSourceDBRef(dbref); + dna2.getDatasetSequence().addDBRef(dbref); + org.testng.Assert.assertEquals(dbref, dna2.getPrimaryDBRefs().get(0)); /* * CDS sequences are 'discovered' from dna-to-protein mappings on the alignment @@ -1071,6 +1073,7 @@ public class AlignmentUtilsTests * verify peptide has added a dbref with reverse mapping to CDS */ assertNotNull(pep1.getDBRefs()); + // FIXME pep1.getDBRefs() is 1 - is that the correct behaviour ? assertEquals(2, pep1.getDBRefs().length); dbref = pep1.getDBRefs()[1]; assertEquals("ENSEMBL", dbref.getSource()); diff --git a/test/jalview/datamodel/DBRefEntryTest.java b/test/jalview/datamodel/DBRefEntryTest.java index ae6dcda..09d9df1 100644 --- a/test/jalview/datamodel/DBRefEntryTest.java +++ b/test/jalview/datamodel/DBRefEntryTest.java @@ -138,4 +138,62 @@ public class DBRefEntryTest assertFalse(ref1.updateFrom(ref2)); assertEquals("10", ref1.getVersion()); } + + @Test(groups = { "Functional" }) + public void testIsPrimary() + { + DBRefEntry dbr = new DBRefEntry(DBRefSource.UNIPROT, "", "Q12345"); + assertTrue(dbr.isPrimary()); + /* + * 1:1 mapping + */ + dbr.setMap(new Mapping(null, new int[] { 1, 3 }, new int[] { 1, 3 }, 1, + 1)); + assertTrue(dbr.isPrimary()); + /* + * Version string is prefixed with another dbref source string (fail) + */ + dbr.setVersion(DBRefSource.EMBL + ":0"); + assertFalse(dbr.isPrimary()); + + /* + * Version string is alphanumeric + */ + dbr.setVersion("0.1.b"); + assertTrue(dbr.isPrimary()); + + /* + * 1:1 mapping with shift (fail) + */ + dbr.setMap(new Mapping(null, new int[] { 1, 3 }, new int[] { 2, 4 }, 1, + 1)); + assertFalse(dbr.isPrimary()); + + /* + * 1:1 mapping and sequenceRef (fail) + */ + dbr.setMap(new Mapping(new Sequence("foo", "ASDF"), new int[] { 1, 3 }, + new int[] { 1, 3 }, 1, 1)); + assertFalse(dbr.isPrimary()); + + /* + * 1:3 mapping (fail) + */ + dbr.setMap(new Mapping(null, new int[] { 1, 3 }, new int[] { 1, 3 }, 1, + 3)); + assertFalse(dbr.isPrimary()); + /* + * 2:2 mapping with shift (expected fail, but maybe use case for a pass) + */ + dbr.setMap(new Mapping(null, new int[] { 1, 3 }, new int[] { 1, 3 }, 2, + 2)); + assertFalse(dbr.isPrimary()); + + /* + * Version string is prefixed with another dbref source string + */ + dbr.setVersion(DBRefSource.EMBL + ":0"); + assertFalse(dbr.isPrimary()); + + } } diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java index cfc4cbb..fcd24dd 100644 --- a/test/jalview/datamodel/SequenceTest.java +++ b/test/jalview/datamodel/SequenceTest.java @@ -438,36 +438,54 @@ public class SequenceTest sq.setDescription("Test sequence description.."); sq.setVamsasId("TestVamsasId"); - sq.setSourceDBRef(new DBRefEntry("PDB", "version0", "1TST")); + sq.addDBRef(new DBRefEntry("PDB", "version0", "1TST")); - sq.addDBRef(new DBRefEntry("PDB", "version1", "1Tst")); - sq.addDBRef(new DBRefEntry("PDB", "version2", "2Tst")); - sq.addDBRef(new DBRefEntry("PDB", "version3", "3Tst")); - sq.addDBRef(new DBRefEntry("PDB", "version4", "4Tst")); + sq.addDBRef(new DBRefEntry("PDB", "version1", "1PDB")); + sq.addDBRef(new DBRefEntry("PDB", "version2", "2PDB")); + sq.addDBRef(new DBRefEntry("PDB", "version3", "3PDB")); + sq.addDBRef(new DBRefEntry("PDB", "version4", "4PDB")); sq.addPDBId(new PDBEntry("1PDB", "A", Type.PDB, "filePath/test1")); sq.addPDBId(new PDBEntry("1PDB", "B", Type.PDB, "filePath/test1")); sq.addPDBId(new PDBEntry("2PDB", "A", Type.MMCIF, "filePath/test2")); sq.addPDBId(new PDBEntry("2PDB", "B", Type.MMCIF, "filePath/test2")); + + DBRefEntry pdb1pdb = new DBRefEntry("PDB", "version1", "1PDB"); + DBRefEntry pdb2pdb = new DBRefEntry("PDB", "version1", "2PDB"); + List primRefs = Arrays.asList(new DBRefEntry[] { pdb1pdb, + pdb2pdb }); + sq.getDatasetSequence().addDBRef(pdb1pdb); + sq.getDatasetSequence().addDBRef(pdb2pdb); sq.getDatasetSequence().addDBRef( - new DBRefEntry("PDB", "version1", "1Tst")); - sq.getDatasetSequence().addDBRef( - new DBRefEntry("PDB", "version2", "2Tst")); - sq.getDatasetSequence().addDBRef( - new DBRefEntry("PDB", "version3", "3Tst")); + new DBRefEntry("PDB", "version3", "3PDB")); sq.getDatasetSequence().addDBRef( - new DBRefEntry("PDB", "version4", "4Tst")); - - sq.getDatasetSequence().addPDBId( - new PDBEntry("1PDB", "A", Type.PDB, "filePath/test1")); - sq.getDatasetSequence().addPDBId( - new PDBEntry("1PDB", "B", Type.PDB, "filePath/test1")); + new DBRefEntry("PDB", "version4", "4PDB")); + + PDBEntry pdbe1a=new PDBEntry("1PDB", "A", Type.PDB, "filePath/test1"); + PDBEntry pdbe1b = new PDBEntry("1PDB", "B", Type.PDB, "filePath/test1"); + PDBEntry pdbe2a=new PDBEntry("2PDB", "A", Type.MMCIF, "filePath/test2"); + PDBEntry pdbe2b = new PDBEntry("2PDB", "B", Type.MMCIF, "filePath/test2"); sq.getDatasetSequence().addPDBId( - new PDBEntry("2PDB", "A", Type.MMCIF, "filePath/test2")); + pdbe1a); sq.getDatasetSequence().addPDBId( - new PDBEntry("2PDB", "B", Type.MMCIF, "filePath/test2")); + pdbe1b); + sq.getDatasetSequence().addPDBId(pdbe2a); + sq.getDatasetSequence().addPDBId(pdbe2b); + + /* + * test we added pdb entries to the dataset sequence + */ + Assert.assertEquals(sq.getDatasetSequence().getAllPDBEntries(), Arrays + .asList(new PDBEntry[] { pdbe1a, pdbe1b, pdbe2a, pdbe2b }), + "PDB Entries were not found on dataset sequence."); + /* + * we should recover a pdb entry that is on the dataset sequence via PDBEntry + */ + Assert.assertEquals(pdbe1a, + sq.getDatasetSequence().getPDBEntry("1PDB"), + "PDB Entry '1PDB' not found on dataset sequence via getPDBEntry."); ArrayList annotsList = new ArrayList(); System.out.println(">>>>>> " + sq.getSequenceAsString().length()); annotsList.add(new Annotation("A", "A", 'X', 0.1f)); @@ -479,7 +497,7 @@ public class SequenceTest new AlignmentAnnotation("Test annot", "Test annot description", annots)); Assert.assertEquals(sq.getDescription(), "Test sequence description.."); - Assert.assertEquals(sq.getDBRefs().length, 4); + Assert.assertEquals(sq.getDBRefs().length, 5); Assert.assertEquals(sq.getAllPDBEntries().size(), 4); Assert.assertNotNull(sq.getAnnotation()); Assert.assertEquals(sq.getAnnotation()[0].annotations.length, 2); @@ -492,7 +510,7 @@ public class SequenceTest Assert.assertEquals(derived.getDescription(), "Test sequence description.."); - Assert.assertEquals(derived.getDBRefs().length, 4); + Assert.assertEquals(derived.getDBRefs().length, 4); // come from dataset Assert.assertEquals(derived.getAllPDBEntries().size(), 4); Assert.assertNotNull(derived.getAnnotation()); Assert.assertEquals(derived.getAnnotation()[0].annotations.length, 2); @@ -510,6 +528,17 @@ public class SequenceTest assertNotNull(sq.getSequenceFeatures()); assertArrayEquals(sq.getSequenceFeatures(), derived.getSequenceFeatures()); + + /* + * verify we have primary db refs *just* for PDB IDs with associated + * PDBEntry objects + */ + + assertEquals(primRefs, sq.getPrimaryDBRefs()); + assertEquals(primRefs, sq.getDatasetSequence().getPrimaryDBRefs()); + + assertEquals(sq.getPrimaryDBRefs(), derived.getPrimaryDBRefs()); + } /** diff --git a/test/jalview/datamodel/xdb/embl/EmblEntryTest.java b/test/jalview/datamodel/xdb/embl/EmblEntryTest.java index 4b71417..abe5099 100644 --- a/test/jalview/datamodel/xdb/embl/EmblEntryTest.java +++ b/test/jalview/datamodel/xdb/embl/EmblEntryTest.java @@ -128,6 +128,7 @@ public class EmblEntryTest assertEquals(5, dbrefs.length); assertEquals(DBRefSource.EMBL, dbrefs[0].getSource()); assertEquals("CAA30420.1", dbrefs[0].getAccessionId()); + // TODO: verify getPrimaryDBRefs() for peptide products assertEquals(cds1Map.getInverse(), dbrefs[0].getMap().getMap()); assertEquals(DBRefSource.EMBLCDS, dbrefs[1].getSource()); assertEquals("CAA30420.1", dbrefs[1].getAccessionId()); diff --git a/utils/MessageBundleChecker.java b/utils/MessageBundleChecker.java index 7850eb5..9d322df 100644 --- a/utils/MessageBundleChecker.java +++ b/utils/MessageBundleChecker.java @@ -5,6 +5,7 @@ import java.io.IOException; import java.util.HashSet; import java.util.Properties; import java.util.TreeSet; +import java.util.regex.Pattern; /** * This class scans Java source files for calls to MessageManager and reports @@ -22,18 +23,32 @@ import java.util.TreeSet; public class MessageBundleChecker { /* + * regex ^"[^"]*"$ + * opening quote, closing quote, no quotes in between + */ + static Pattern STRING_PATTERN = Pattern.compile("^\"[^\"]*\"$"); + + /* * number of text lines to read at a time in order to parse * code that is split over several lines */ static int bufferSize = 3; + /* + * resource bundle key is arg0 for these methods + */ static final String METHOD1 = "MessageManager.getString("; - static final String METHOD2 = "MessageManager.getStringOrReturn("; + static final String METHOD2 = "MessageManager.formatMessage("; - static final String METHOD3 = "MessageManager.formatMessage("; + static final String METHOD3 = "MessageManager.getStringOrReturn("; - static final String[] METHODS = { METHOD1, METHOD2, METHOD3 }; + /* + * resource bundle key is arg1 for this method + */ + static final String JVINIT = "JvSwingUtils.jvInitComponent("; + + static final String[] METHODS = { METHOD1, METHOD2, METHOD3, JVINIT }; /* * root of the Java source folders we want to scan @@ -123,7 +138,7 @@ public class MessageBundleChecker + " possibly invalid parameter calls"); System.out.println(messageKeys.size() - + " keys not found, possibly unused"); + + " keys not found, either unused or constructed dynamically"); for (String key : messageKeys) { System.out.println(" " + key); @@ -169,6 +184,14 @@ public class MessageBundleChecker } javaCount++; + /* + * skip class with designed dynamic lookup call + */ + if (path.endsWith("gui/JvSwingUtils.java")) + { + return; + } + String[] lines = new String[bufferSize]; BufferedReader br = new BufferedReader(new FileReader(f)); for (int i = 0; i < bufferSize; i++) @@ -231,30 +254,61 @@ public class MessageBundleChecker { continue; } - String methodArgs = combined.substring(pos + method.length()); + + /* + * extract what follows the opening bracket of the method call + */ + String methodArgs = combined.substring(pos + method.length()).trim(); if ("".equals(methodArgs)) { /* - * continues on next line - catch in the next read loop iteration + * arguments are on next line - catch in the next read loop iteration */ continue; } - if (!methodArgs.startsWith("\"")) + if (methodArgs.indexOf(",") == -1 && methodArgs.indexOf(")") == -1) { - System.out.println(String.format( - "Possible dynamic key at %s line %s %s", + /* + * arguments continue on next line - catch in the next read loop iteration + */ + continue; + } + + if (JVINIT == method && methodArgs.indexOf(",") == -1) + { + /* + * not interested in 1-arg calls to jvInitComponent + */ + continue; + } + + if (METHOD3 == method) + { + System.out.println(String.format("Dynamic key at %s line %s %s", path.substring(sourcePath.length()), lineNos, combined)); continue; } - methodArgs = methodArgs.substring(1); - int quotePos = methodArgs.indexOf("\""); - if (quotePos == -1) + + String messageKey = getMessageKey(method, methodArgs); + if (messageKey == null) { System.out.println(String.format("Trouble parsing %s line %s %s", path.substring(sourcePath.length()), lineNos, combined)); continue; } - String messageKey = methodArgs.substring(0, quotePos); + + if (!(STRING_PATTERN.matcher(messageKey).matches())) + { + System.out.println(String.format("Dynamic key at %s line %s %s", + path.substring(sourcePath.length()), lineNos, combined)); + continue; + } + + /* + * strip leading and trailing quote + */ + messageKey = messageKey.substring(1, messageKey.length() - 1); + if (!this.messages.containsKey(messageKey)) { System.out.println(String.format( @@ -269,6 +323,47 @@ public class MessageBundleChecker } } + /** + * Helper method to parse out the resource bundle key parameter of a method + * call + * + * @param method + * @param methodArgs + * the rest of the source line starting with arguments to method + * @return + */ + private String getMessageKey(String method, String methodArgs) + { + String key = methodArgs; + + /* + * locate second argument if calling jvInitComponent() + */ + if (method == JVINIT) + { + int commaLoc = methodArgs.indexOf(","); + if (commaLoc == -1) + { + return null; + } + key = key.substring(commaLoc + 1).trim(); + } + + /* + * take up to next comma or ) or end of line + */ + int commaPos = key.indexOf(","); + int bracePos = key.indexOf(")"); + int endPos = commaPos == -1 ? bracePos : (bracePos == -1 ? commaPos + : Math.min(commaPos, bracePos)); + if (endPos == -1 && key.length() > 1 && key.endsWith("\"")) + { + endPos = key.length(); + } + + return endPos == -1 ? null : key.substring(0, endPos); + } + private String combineLines(String[] lines) { String combined = ""; diff --git a/utils/i18nAnt.xml b/utils/i18nAnt.xml index 47c404e..01973d2 100755 --- a/utils/i18nAnt.xml +++ b/utils/i18nAnt.xml @@ -19,8 +19,7 @@ var logger = project.getBuildListeners( ).firstElement( ); logger.setMessageOutputLevel( 1 ); - - + @@ -29,15 +28,28 @@ + + + + + + + + + + + + + + + - + - -