From: gmungoc Date: Wed, 6 Mar 2019 15:49:46 +0000 (+0000) Subject: JAL-3035 more das bits removed X-Git-Tag: Release_2_11_0~17^2~62^2 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=6d431e1a1f18894d35c9881fe5a45ffd6bfccf67;p=jalview.git JAL-3035 more das bits removed --- diff --git a/help/html/features/das.gif b/help/html/features/das.gif deleted file mode 100644 index 1f884cb..0000000 Binary files a/help/html/features/das.gif and /dev/null differ diff --git a/help/html/features/exportannot.gif b/help/html/features/exportannot.gif deleted file mode 100644 index 2133cc1..0000000 Binary files a/help/html/features/exportannot.gif and /dev/null differ diff --git a/help/html/features/search.gif b/help/html/features/search.gif deleted file mode 100755 index 1c0ffb0..0000000 Binary files a/help/html/features/search.gif and /dev/null differ diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties index ae5b0e7..a23bc00 100644 --- a/resources/lang/Messages.properties +++ b/resources/lang/Messages.properties @@ -118,10 +118,8 @@ action.select = Select action.new_view = New View action.close = Close action.add = Add -action.save_as_default = Save as default action.save_as = Save as... action.save = Save -action.cancel_fetch = Cancel Fetch action.change_font = Change Font action.change_font_tree_panel = Change Font (Tree Panel) action.colour = Colour @@ -140,7 +138,6 @@ 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.structures_manager = Structures Manager -label.nickname = Nickname: label.url = URL label.url\: = URL: label.input_file_url = Enter URL or Input File @@ -162,7 +159,6 @@ label.current_parameter_set_name = Current parameter set name: label.service_action = Service Action: label.post_url = POST URL: label.url_suffix = URL Suffix -label.sequence_source = Sequence Source label.per_seq = per Sequence label.result_vertically_separable = Results are vertically separable label.amend = Amend @@ -353,7 +349,6 @@ label.status = Status label.channels = Channels label.channel_title_item_count = {0} ({1}) label.blog_item_published_on_date = {0} {1} -label.select_das_service_from_table = Select a DAS service from the table to read a full description here. label.session_update = Session Update label.new_vamsas_session = New Vamsas Session action.load_vamsas_session = Load Vamsas Session... @@ -371,7 +366,6 @@ label.load_colours = Load Colours label.save_colours = Save Colours label.load_colours_tooltip = Load feature colours and filters from file label.save_colours_tooltip = Save feature colours and filters to file -label.fetch_das_features = Fetch DAS Features label.selected_database_to_fetch_from = Selected {0} database {1} to fetch from {2} label.database_param = Database: {0} label.example = Example @@ -409,9 +403,6 @@ label.couldnt_find_pdb_id_in_file = Couldn't find a PDB id in the file supplied. label.no_pdb_id_in_file = No PDB Id in File label.couldnt_read_pasted_text = Couldn't read the pasted text {0} label.error_parsing_text = Error parsing text -label.enter_local_das_source = Enter Nickname & URL of Local DAS Source -label.you_can_only_edit_or_remove_local_das_sources = You can only edit or remove local DAS Sources! -label.public_das_source = Public DAS source - not editable label.input_alignment_from_url = Input Alignment From URL label.input_alignment = Input Alignment label.couldnt_import_as_vamsas_session = Couldn't import {0} as a new vamsas session. @@ -428,8 +419,6 @@ label.invalid_url = Invalid URL ! label.error_loading_file = Error loading file label.problems_opening_file = Encountered problems opening {0}!! label.file_open_error = File open error -label.no_das_sources_selected_warn = No das sources were selected.\nPlease select some sources and\ntry again. -label.no_das_sources_selected_title = No DAS Sources Selected label.colour_scheme_exists_overwrite = Colour scheme {0} exists.\nContinue saving colour scheme as {1}?" label.duplicate_scheme_name = Duplicate scheme name label.jalview_new_questionnaire = There is a new Questionnaire available. Would you like to complete it now ?\n @@ -622,7 +611,6 @@ label.visual = Visual label.connections = Connections label.output = Output label.editing = Editing -label.das_settings = DAS Settings label.web_services = Web Services label.right_click_to_edit_currently_selected_parameter = Right click to edit currently selected parameter. label.let_jmol_manage_structure_colours = Let Jmol manage structure colours @@ -638,10 +626,6 @@ label.delete_service_url = Delete Service URL label.details = Details label.options = Options label.parameters = Parameters -label.available_das_sources = Available DAS Sources -label.full_details = Full Details -label.authority = Authority -label.type = Type label.proxy_server = Proxy Server label.file_output = File Output label.select_input_type = Select input type @@ -710,9 +694,6 @@ label.sort_alignment_new_tree = Sort Alignment With New Tree label.add_sequences = Add Sequences label.new_window = New Window label.split_window = Split Window -label.refresh_available_sources = Refresh Available Sources -label.use_registry = Use Registry -label.add_local_source = Add Local Source label.set_as_default = Set as Default label.show_labels = Show labels action.background_colour = Background Colour... @@ -853,7 +834,6 @@ label.multiharmony = Multi-Harmony label.unable_start_web_service_analysis = Unable to start web service analysis label.job_couldnt_be_started_check_input = The Job couldn't be started. Please check your input, and the Jalview console for any warning messages. label.prompt_each_time = Prompt each time -label.use_source = Use Source label.couldnt_save_project = Couldn't save project label.error_whilst_saving_current_state_to = Error whilst saving current state to {0} label.error_whilst_loading_project_from = Error whilst loading project from {0} @@ -879,7 +859,6 @@ label.error_unsupported_owwner_user_colour_scheme = Unsupported owner for User C label.save_alignment_to_file = Save Alignment to file label.save_features_to_file = Save Features to File label.save_annotation_to_file = Save Annotation to File -label.no_features_on_alignment = No features found on alignment label.save_pdb_file = Save PDB File label.save_text_to_file = Save Text to File label.save_state = Save State @@ -1079,8 +1058,6 @@ exception.unable_to_create_internet_config = Unable to create an Internet Config exception.invocation_target_calling_url = InvocationTargetException while calling openURL: {0} exception.illegal_access_calling_url = IllegalAccessException while calling openURL: {0} exception.interrupted_launching_browser = InterruptedException while launching browser: {0} -exception.das_source_doesnt_support_sequence_command = Source {0} does not support the sequence command. -exception.invalid_das_source = Invalid das source: {0} exception.ebiembl_retrieval_failed_on = EBI EMBL XML retrieval failed on {0}:{1} 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 @@ -1135,10 +1112,6 @@ status.parsing_results = Parsing results. status.processing = Processing... status.refreshing_web_service_menus = Refreshing Web Service Menus status.collecting_job_results = Collecting job results. -status.fetching_das_sequence_features = Fetching DAS Sequence Features -status.no_das_sources_active = No DAS Sources Active -status.das_feature_fetching_cancelled = DAS Feature Fetching Cancelled -status.das_feature_fetching_complete = DAS Feature Fetching Complete status.fetching_db_refs = Fetching db refs status.loading_cached_pdb_entries = Loading Cached PDB Entries status.searching_for_pdb_structures = Searching for PDB Structures @@ -1161,8 +1134,6 @@ warn.urls_not_contacted = URLs that could not be contacted warn.urls_no_jaba = URLs without any JABA Services info.validate_jabaws_server = Validate JabaWS Server ?\n(Look in console output for results) label.test_server = Test Server? -info.you_want_jalview_to_find_uniprot_accessions = Do you want Jalview to find\nUniprot Accession ids for given sequence names? -label.find_uniprot_accession_ids = Find Uniprot Accession Ids label.new_sequence_fetcher = New Sequence Fetcher label.additional_sequence_fetcher = Additional Sequence Fetcher label.select_database_retrieval_source = Select Database Retrieval Source @@ -1299,7 +1270,6 @@ label.edit_sequence_url_link = Edit sequence URL link warn.name_cannot_be_duplicate = User-defined URL names must be unique and cannot be MIRIAM ids label.output_seq_details = Output Sequence Details to list all database references label.urllinks = Links -label.default_cache_size = Default Cache Size action.clear_cached_items = Clear Cached Items label.togglehidden = Show hidden regions label.quality_descr = Alignment Quality based on Blosum62 scores diff --git a/resources/lang/Messages_es.properties b/resources/lang/Messages_es.properties index 555977d..f04a139 100644 --- a/resources/lang/Messages_es.properties +++ b/resources/lang/Messages_es.properties @@ -115,10 +115,8 @@ action.select = Seleccionar action.new_view = Nueva vista action.close = Cerrar action.add = Añadir -action.save_as_default = Guardar como por defecto action.save_as = Guardar como action.save = Guardar -action.cancel_fetch = Cancelar búsqueda action.change_font = Cambiar Fuente action.change_font_tree_panel = Cambiar fuente (panel del árbol) action.colour = Color @@ -137,7 +135,6 @@ 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.structures_manager = Administrar estructuras -label.nickname = Sobrenombre: label.url\: = URL: label.url = URL label.input_file_url = Introducir URL en el fichero de entrada @@ -159,7 +156,6 @@ label.current_parameter_set_name = Nombre actual del conjunto de par label.service_action = Acción de servicio: label.post_url = POST URL: label.url_suffix = URL Sufijo -label.sequence_source = Fuente de la secuencia label.per_seq = por secuencia label.result_vertically_separable = Los resultados son separables verticalmente label.amend = Modificar @@ -322,7 +318,6 @@ label.status = [Estado] label.channels = Canales label.channel_title_item_count = {0} ({1}) 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 action.save_vamsas_session = Guardar Sesión Vamsas @@ -339,7 +334,6 @@ label.load_colours = Cargar colores label.save_colours = Guardar colores label.load_colours_tooltip = Cargar colores y filtros desde fichero label.save_colours_tooltip = Guardar colores y filtros en fichero -label.fetch_das_features = Recuperar funciones DAS label.selected_database_to_fetch_from = Seleccionada {0} Base de datos {1} para buscar de {2} label.database_param = Base de datos: {0} label.example = Ejemplo @@ -376,9 +370,6 @@ label.couldnt_find_pdb_id_in_file = No se pudo encontrar un Id PDB en el fichero label.no_pdb_id_in_file = No hay un Id PDB en el fichero label.couldnt_read_pasted_text = No se pudo leer el texto pegado {0} label.error_parsing_text = Error analizando el texto -label.enter_local_das_source = Intruduzca el Nickname & URL de la fuente DAS local -label.you_can_only_edit_or_remove_local_das_sources = Sólo puedes editar o eliminar fuentes DAS locales! -label.public_das_source = Fuente pública DAS - no editable label.input_alignment_from_url = Alineamiento de entrada desde URL label.input_alignment = Alineamiento de entrada label.couldnt_import_as_vamsas_session = No se pudo importar {0} como una nueva sesión Vamsas. @@ -395,8 +386,6 @@ label.invalid_url = URL Invalido! label.error_loading_file = Error al cargar el fichero label.problems_opening_file = Encontrados problemas al abrir el fichero {0}!! label.file_open_error = Error al abrir el fichero -label.no_das_sources_selected_warn = No han sido seleccionadas fuentes DAS.\nPor favor, seleccione algunas fuentes y\npruebe de nuevo. -label.no_das_sources_selected_title = No han sido seleccionadas fuentes DAS label.colour_scheme_exists_overwrite = El esquema de colores {0} ya existe.\nContinuar guardando el esquema de colores como {1}? label.duplicate_scheme_name = Duplicar nombre de esquema label.jalview_new_questionnaire = Hay un nuevo cuestionario disponible. Querr\u00EDa completarlo ahora ?\n @@ -577,7 +566,6 @@ label.visual = Visual label.connections = Conexiones label.output = Salida label.editing = Edición -label.das_settings = Configuración DAS label.web_services = Servicios web label.right_click_to_edit_currently_selected_parameter = Haga clic en el botón derecho para editar el parámetro seleccionado actualmente. label.let_jmol_manage_structure_colours = Permitir que Jmol gestione la estructuras cromáticas @@ -590,10 +578,6 @@ label.delete_service_url = Borrar la URL del servicio label.details = Detalles label.options = Opciones label.parameters = Paramétros -label.available_das_sources = Fuentes DAS disponibles -label.full_details = Detalles completos -label.authority = Autoridad -label.type = Tipo label.proxy_server = Servidor proxy label.file_output = Fichero de salida label.select_input_type = Seleccionar el tipo de entrada @@ -656,10 +640,6 @@ label.get_cross_refs = Obtener referencias cruzadas label.sort_alignment_new_tree = Alinear el alineamiento con el nuevo árbol label.add_sequences = Añadir secuencias label.new_window = Nueva ventana -label.refresh_available_sources = Refrescar las fuentes disponibles -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.associate_nodes_with = Asociar nodos con label.link_name = Nombre del enalce @@ -778,7 +758,6 @@ label.multiharmony = Multi-Harmony label.unable_start_web_service_analysis = No es posible iniciar el servicio web de análisis label.job_couldnt_be_started_check_input = El trabajo no puede arrancarse. Por favor, compruebe los parámetros de entrada y los mensajes de advertencia de la consola de Jalview. label.prompt_each_time = Preguntar siempre -label.use_source = Fuente label.couldnt_save_project = No es posible guardar el proyecto label.error_whilst_saving_current_state_to = Error mientras se guardaba el estado a {0} label.error_whilst_loading_project_from = Error cargando el proyecto desde {0} @@ -804,7 +783,6 @@ label.error_unsupported_owwner_user_colour_scheme = Propietario no soportado par label.save_alignment_to_file = Guardar Alineamiento en fichero label.save_features_to_file = Guardar Características en un fichero label.save_annotation_to_file = Guardar Anotación en un fichero -label.no_features_on_alignment = No se han encontrado características en el alineamiento label.save_pdb_file = Guardar fichero PDB label.save_text_to_file = Guardar Texto en un fichero label.save_state = Guardar estado @@ -1004,8 +982,6 @@ exception.unable_to_create_internet_config = Imposible crear una instancia de co exception.invocation_target_calling_url = InvocationTargetException mientras se invocaba openURL: {0} exception.illegal_access_calling_url = IllegalAccessException mientras se invocaba openURL: {0} exception.interrupted_launching_browser = InterruptedException mientras se lanzaba el navegador: {0} -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} 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 @@ -1057,10 +1033,6 @@ status.parsing_results = Parseando resultados. status.processing = Procesando... status.refreshing_web_service_menus = Refrescando los menús de servicios web status.collecting_job_results = Recolectando los resultados de los trabajos. -status.fetching_das_sequence_features = Recuperando las características DAS de las secuencias -status.no_das_sources_active = No existe ninguna fuente DAS activa -status.das_feature_fetching_cancelled = Recuperación de características DAS cancelada -status.das_feature_fetching_complete = Recuperación de características DAS completada status.fetching_db_refs = Recuperando db refs label.font_doesnt_have_letters_defined = La fuente no tiene letras definidas\npor lo que no puede emplease\ncon datos de alineamientos label.font_too_small = Tamaño de la letra es demasiado pequeña @@ -1077,8 +1049,6 @@ warn.server_didnt_pass_validation = El servicio no ha pasado la validaci\u00F3n. warn.url_must_contain = La URL de la secuencia debe contener $SEQUENCE_ID$, $DB_ACCESSION$ o un regex info.validate_jabaws_server = \u00BFValidar el servidor JabaWS?\n(Consulte la consola de salida para obtener los resultados) label.test_server = ¿Probar servidor? -info.you_want_jalview_to_find_uniprot_accessions = \u00BFDesea que Jalview encuentre\nUniprot Accession ids para los nombres de secuencias dados? -label.find_uniprot_accession_ids = Buscar Uniprot Accession Ids label.new_sequence_fetcher = Añadir recuperador de secuencias label.additional_sequence_fetcher = Recuperador de secuencia adicional label.select_database_retrieval_source = Seleccionar fuente de recuperación de bases de datos @@ -1300,7 +1270,6 @@ label.edit_sequence_url_link = Editar link de secuencia URL warn.name_cannot_be_duplicate = Los nombres URL definidos por el usuario deben ser únicos y no pueden ser ids de MIRIAM label.output_seq_details = Seleccionar Detalles de la secuencia para ver todas label.urllinks = Enlaces -label.default_cache_size = Tamaño del caché por defecto action.clear_cached_items = Borrar elementos en caché label.quality_descr = Calidad de alineamiento basándose en puntuación Blosum62 label.conservation_descr = Conservación del alineamiento total menos de {0}% huecos diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index cd7d1af..c7738da 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -828,9 +828,6 @@ public class Jalview // (quote the 'PROPERTY=VALUE' pair to ensure spaces are // passed in correctly)" + "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n" - + "-dasserver nickname=URL\tAdd and enable a das server with given nickname\n\t\t\t(alphanumeric or underscores only) for retrieval of features for all alignments.\n" - + "\t\t\tSources that also support the sequence command may be specified by prepending the URL with sequence:\n" - + "\t\t\t e.g. sequence:http://localdas.somewhere.org/das/source)\n" + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n" // + // "-vdoc vamsas-document\tImport vamsas document into new diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java index 061e70c..5dbb6c4 100644 --- a/src/jalview/ws/DBRefFetcher.java +++ b/src/jalview/ws/DBRefFetcher.java @@ -754,8 +754,6 @@ public class DBRefFetcher implements Runnable // and remove it from the rest // TODO: decide if we should remove annotated sequence from set sdataset.remove(sequence); - // TODO: should we make a note of sequences that have received new DB - // ids, so we can query all enabled DAS servers for them ? } } return modified;