<p>
For more information, you might also want to take a look at the
documentation section of the Jalview website (<a
- href="http://www-test.jalview.org/about/documentation">http://www.jalview.org/about/documentation</a>).
+ href="http://www.jalview.org/about/documentation">http://www.jalview.org/about/documentation</a>).
</p>
<p>
If you are using the Jalview Desktop application and are looking for
Function, and Genetics</em> 43(2): 227-241. <a
href="http://www.ncbi.nlm.nih.gov/pubmed/12112692">PubMed</a>
or available on the <a
- href="http://valdarlab.unc.edu/publications.html">Valdar
+ href="http://valdarlab.unc.edu/publications">Valdar
Group publications page</a>), but the SMERFs score was developed later
and described by Manning et al. in 2008 (<a
href="http://www.biomedcentral.com/1471-2105/9/51">BMC
<ul>
<li><a href="http://www.clustal.org/omega">Clustal Omega</a> (version 1.2.4)</li>
<li><a href="http://www.clustal.org/clustal2">ClustalW</a> (version 2.1)</li>
- <li><a href="http://align.bmr.kyushu-u.ac.jp/mafft/software/">Mafft</a> (version 7.310)</li>
+ <li><a href="https://mafft.cbrc.jp/alignment/software/index.html">Mafft</a> (version 7.310)</li>
<li><a href="http://www.drive5.com/muscle">Muscle</a> (version 3.8.31)</li>
<li><a href="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html">T-coffee</a> (version 11.00.8cbe486)</li>
<li><a href="http://probcons.stanford.edu/">Probcons</a> (version 1.12)</li>
label.channels = Channels
label.channel_title_item_count = {0} ({1})
label.blog_item_published_on_date = {0} {1}
-label.session_update = Session Update
-label.new_vamsas_session = New Vamsas Session
-action.load_vamsas_session = Load Vamsas Session...
-action.save_vamsas_session = Save Vamsas Session
-label.select_vamsas_session_opened_as_new_vamsas_session= Select a vamsas session to be opened as a new vamsas session.
-label.open_saved_vamsas_session = Open a saved VAMSAS session
label.groovy_console = Groovy Console...
label.lineart = Lineart
label.dont_ask_me_again = Don't ask me again
label.error_parsing_text = Error parsing text
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.
label.vamsas_document_import_failed = Vamsas Document Import Failed
label.couldnt_locate = Couldn''t locate {0}
label.url_not_found = URL not found
label.new_sequence_url_link = New sequence URL link
-label.cannot_edit_annotations_in_wrapped_view = Cannot edit annotations in wrapped view
-label.wrapped_view_no_edit = Wrapped view - no edit
label.error_retrieving_data = Error Retrieving Data
label.user_colour_scheme_must_have_name = User colour scheme must have a name
label.no_name_colour_scheme = No name for colour scheme
label.fetch_embl_uniprot = Fetch from EMBL/EMBLCDS or Uniprot/PDB and any selected DAS sources
label.reset_min_max_colours_to_defaults = Reset min and max colours to defaults from user preferences.
label.align_structures_using_linked_alignment_views = Superpose structures using {0} selected alignment view(s)
-label.connect_to_session = Connect to session {0}
label.threshold_feature_display_by_score = Threshold the feature display by score.
label.threshold_feature_no_threshold = No Threshold
label.threshold_feature_above_threshold = Above Threshold
label.sequence_id_tooltip = Sequence ID Tooltip
label.no_services = <No Services>
label.select_copy_raw_html = Select this if you want to copy raw html
-label.share_data_vamsas_applications = Share data with other vamsas applications
-label.connect_to = Connect to
-label.join_existing_vamsas_session = Join an existing vamsas session
label.from_url = from URL
label.any_trees_calculated_or_loaded_alignment_automatically_sort = When selected, any trees calculated or loaded onto the alignment will automatically sort the alignment
label.sort_with_new_tree = Sort With New Tree
label.tools = Tools
label.fetch_sequences = Fetch Sequences
action.fetch_sequences = Fetch Sequences...
-label.stop_vamsas_session = Stop Vamsas Session
label.collect_garbage = Collect Garbage
label.show_memory_usage = Show Memory Usage
label.show_java_console = Show Java Console
label.save_state = Save State
label.restore_state = Restore State
label.saving_jalview_project = Saving jalview project {0}
-label.loading_jalview_project = Loading jalview project {0}
-label.save_vamsas_document_archive = Save Vamsas Document Archive
-label.saving_vamsas_doc = Saving VAMSAS Document to {0}
label.load_feature_colours = Load Feature Colours
label.save_feature_colours = Save Feature Colour Scheme
label.select_startup_file = Select startup file
label.select_unselect_visible_regions_from = select and unselected {0} regions from {1}
label.visible_region_of = visible region of
label.webservice_job_title_on = {0} using {1} on {2}
-label.updating_vamsas_session = Updating vamsas session
label.loading_file = Loading File: {0}
label.edit_params = Edit {0}
label.as_percentage = As Percentage
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_threshold_setting = Implementation error: don't know about threshold setting for current AnnotationColourGradient.
-error.try_join_vamsas_session_another = Trying to join a vamsas session when another is already connected
-error.invalid_vamsas_session_id = Invalid vamsas session id
label.groovy_support_failed = Jalview Groovy Support Failed
label.couldnt_create_groovy_shell = Couldn't create the groovy Shell. Check the error log for the details of what went wrong.
error.unsupported_version_calcIdparam = Unsupported Version for calcIdparam {0}
error.invalid_value_for_option = Invalid value {0} for option {1}
error.implementation_error_cannot_import_vamsas_doc = Implementation Error - cannot import existing vamsas document into an existing session, Yet!
label.vamsas_doc_couldnt_be_opened_as_new_session = VAMSAS Document could not be opened as a new session - please choose another
-error.implementation_error_vamsas_operation_not_init = Impementation error! Vamsas Operations when client not initialised and connected
-error.jalview_no_connected_vamsas_session = Jalview not connected to Vamsas session
-error.implementation_error_cannot_recover_vamsas_object_mappings = IMPLEMENTATION ERROR: Cannot recover vamsas object mappings - no backup was made
error.setstatus_called_non_existent_job_pane = setStatus called for non-existent job pane {0}
error.implementation_error_cannot_find_marshaller_for_param_set =Implementation error: Can't find a marshaller for the parameter set
error.implementation_error_old_jalview_object_not_bound =IMPLEMENTATION ERROR: old jalview object is not bound ! ({0})
error.implementation_error_vamsas_doc_class_should_bind_to_type = Implementation Error: Vamsas Document Class {0} should bind to a {1} (found a {2})
error.invalid_vamsas_rangetype_cannot_resolve_lists = Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!
-error.implementation_error_maplist_is_null = Implementation error. MapList is null for initMapType.
error.implementation_error_cannot_have_null_alignment = Implementation error: Cannot have null alignment property key
error.implementation_error_null_fileparse = Implementation error. Null FileParse in copy constructor
-error.implementation_error_cannot_map_alignment_sequences = IMPLEMENTATION ERROR: Cannot map an alignment of sequences from different datasets into a single alignment in the vamsas document.
error.implementation_error_structure_selection_manager_null = Implementation error. Structure selection manager's context is 'null'
exception.ssm_context_is_null = SSM context is null
error.idstring_seqstrings_only_one_per_sequence = idstrings and seqstrings contain one string each per sequence
error.implementation_error_dbinstance_must_implement_interface = Implmentation Error - getDbInstances must be given a class that implements jalview.ws.seqfetcher.DbSourceProxy (was given{0})
error.implementation_error_must_init_dbsources =Implementation error. Must initialise dbSources
label.view_controller_toggled_marked = {0} {1} columns {2} features of type {3} across {4} sequence(s)
+label.no_highlighted_regions_marked = No highlighted regions marked
label.toggled = Toggled
label.marked = Marked
label.containing = containing
status.export_complete = {0} Export completed
status.fetching_pdb = Fetching PDB {0}
status.refreshing_news = Refreshing news
-status.importing_vamsas_session_from = Importing VAMSAS session from {0}
status.opening_params = Opening {0}
-status.waiting_sequence_database_fetchers_init = Waiting for Sequence Database Fetchers to initialise
-status.init_sequence_database_fetchers = Initialising Sequence Database Fetchers
status.fetching_sequence_queries_from = Fetching {0} sequence queries from {1}
status.finshed_querying = Finished querying
status.parsing_results = Parsing results.
status.colouring_structures = Colouring structures
label.font_doesnt_have_letters_defined = Font doesn't have letters defined\nso cannot be used\nwith alignment data
label.font_too_small = Font size is too small
-label.error_loading_file_params = Error loading file {0}
-label.error_loading_jalview_file = Error loading Jalview file
warn.out_of_memory_when_action = Out of memory when {0}\!\!\nSee help files for increasing Java Virtual Machine memory.
warn.out_of_memory_loading_file = Out of memory loading file {0}\!\!\nSee help files for increasing Java Virtual Machine memory.
label.out_of_memory = Out of memory
label.invalid_id_column_width = Invalid ID Column width
warn.user_defined_width_requirements = The user defined width for the\nannotation and sequence ID columns\nin exported figures must be\nat least 12 pixels wide.
-label.couldnt_create_sequence_fetcher = Couldn't create SequenceFetcher
-warn.couldnt_create_sequence_fetcher_client = Could not create the sequence fetcher client. Check error logs for details.
warn.server_didnt_pass_validation = Service did not pass validation.\nCheck the Jalview Console for more details.
warn.url_must_contain = Sequence URL must contain $SEQUENCE_ID$, $DB_ACCESSION$, or a regex
warn.urls_not_contacted = URLs that could not be contacted
option.autosearch = Autosearch
label.retrieve_ids = Retrieve IDs
label.display_settings_for = Display settings for {0} features
-label.simple = Simple
label.simple_colour = Simple Colour
label.colour_by_text = Colour by text
label.graduated_colour = Graduated Colour
label.append_to_filename = Append to filename (%n is replaced by the backup number)
label.append_to_filename_tooltip = %n in the text will be replaced by the backup number. The text will appear after the filename. See the summary box above.
label.index_digits = Number of digits to use for the backup number (%n)
-label.summary_of_backups_scheme = Summary of backup scheme
label.scheme_examples = Scheme examples
label.increment_index = Increase appended text numbers - newest file has largest number.
label.reverse_roll = "Roll" appended text numbers - newest backup file is always number 1.
label.keep_all_versions_description = Keep all previous versions of the file
label.rolled_backups_description = Keep the last nine versions of the file from _bak.1 (newest) to _bak.9 (oldest)
label.cancel_changes_description = Cancel changes made to your last saved Custom scheme
-label.previously_saved_scheme = Previously saved scheme
label.no_backup_files = NO BACKUP FILES
label.include_backup_files = Include backup files
label.cancel_changes = Cancel changes
label.warning_confirm_change_reverse = Warning!\nIf you change the increment/decrement of the backup filename number, without changing the suffix or number of digits,\nthis may cause loss of backup files created with the previous backup filename scheme.\nAre you sure you wish to do this?
label.change_increment_decrement = Change increment/decrement?
-label.was_previous = was {0}
label.newerdelete_replacement_line = Backup file\n''{0}''\t(modified {2}, size {4})\nis to be deleted and replaced by apparently older file\n''{1}''\t(modified {3}, size {5}).
label.confirm_deletion_or_rename = Confirm deletion of ''{0}'' or rename to ''{1}''?
label.newerdelete_line = Backup file\n''{0}''\t(modified {2}, size {4})\nis to be deleted but is newer than the oldest remaining backup file\n''{1}''\t(modified {3}, size {5}).
label.overview_window = Ventana resumen
label.none = Ninguno
label.above_identity_threshold = Por encima del umbral de identidad
-label.show_sequence_features = Mostrar las caracterÃsticas de las secuencias
+label.show_sequence_features = Mostrar las caracterÃsticas de secuencia
label.nucleotide = Nucleótido
label.to_new_alignment = A nuevo alineamiento
label.to_this_alignment = Añadir a este alineamiento
label.channels = Canales
label.channel_title_item_count = {0} ({1})
label.blog_item_published_on_date = {0} {1}
-label.session_update = Actualizar sesión
-label.new_vamsas_session = Nueva 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
label.groovy_console = Consola Groovy
label.lineart = Lineart
label.dont_ask_me_again = No volver a preguntar
label.error_parsing_text = Error analizando el texto
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.
label.vamsas_document_import_failed = Fallo en la importación del documento Vamsas
label.couldnt_locate = No se pudo localizar {0}
label.url_not_found = URL no encontrada
label.new_sequence_url_link = Enlace a una nueva secuencia URL
-label.cannot_edit_annotations_in_wrapped_view = No se pueden editar anotaciones en vista envolvente
-label.wrapped_view_no_edit = Vista envolvente - no editar
label.error_retrieving_data = Error en la recuperación de datos
label.user_colour_scheme_must_have_name = El esquema de colores del usuario debe tener un nombre
label.no_name_colour_scheme = No hay nombre para el esquema de colores
label.fetch_embl_uniprot = Recuperar de EMBL/EMBLCDS o Uniprot/PDB y de cualquier fuente DAS seleccionada
label.reset_min_max_colours_to_defaults = Reiniciar los colores min y max colours a los valores por defecto establecidos en las preferencias de usuario
label.align_structures_using_linked_alignment_views = Alinear las estructuras utilizando las {0} vista(s) de alineamiento enlazada(s)
-label.connect_to_session = Conectar a la sesión {0}
label.threshold_feature_display_by_score = Filtrar la caracterÃstica mostrada por puntuación.
label.threshold_feature_no_threshold = Sin umbral
label.threshold_feature_above_threshold = Por encima del umbral
label.sequence_id_tooltip = Ayuda del ID de la secuencia
label.no_services = <Sin Servicios>
label.select_copy_raw_html = Seleccione esta opción si desea copiar el html en bruto
-label.share_data_vamsas_applications = Compartir datos con otras aplicaciones vamsas
-label.connect_to = Conectar a
-label.join_existing_vamsas_session = Unirse a una sesión vamsas existente
label.from_url = desde una URL
label.any_trees_calculated_or_loaded_alignment_automatically_sort = Cuando está habilitado, cualquier árbol calculado o cargado en el alineamiento lo ordenará
label.sort_with_new_tree = Ordenar con el nuevo árbol
label.preferences = Preferencias
label.tools = Herramientas
label.fetch_sequences = Recuperar secuencia(s)
-label.stop_vamsas_session = Parar sesión vamsas
label.collect_garbage = Recolector de basura
label.show_memory_usage = Mostrar uso de memoria
label.show_java_console = Mostrar consola de Java
label.generating_features_for_params = Generando caracterÃsticas de - {0}
label.generating_annotations_for_params = Generando anotaciones de - {0}
label.varna_params = VARNA - {0}
-label.sequence_feature_settings = Configuración de las caracterÃsticas de la secuencia
+label.sequence_feature_settings = Configuración de las caracterÃsticas de secuencia
+label.sequence_feature_settings_for = Configuración de las caracterÃsticas de secuencia para {0}
+label.sequence_feature_settings_for_view = Configuración de las caracterÃsticas de secuencia para vista "{0}"
+label.sequence_feature_settings_for_CDS_and_Protein = Configuración de las caracterÃsticas de secuencia para CDS y ProteÃna
+action.undo_changes_to_feature_settings = Deshacer todos los cambios no aplicados
+action.undo_changes_to_feature_settings_and_close_the_dialog = Deshacer cambios pendientes, cerrar diálogo
label.pairwise_aligned_sequences = Secuencias alineadas a pares
label.original_data_for_params = Datos originales de {0}
label.points_for_params = Puntos de {0}
label.save_state = Guardar estado
label.restore_state = Restaurar estado
label.saving_jalview_project = Guardando el proyecto de Jalview {0}
-label.loading_jalview_project = Cargando el proyecto de Jalview {0}
-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 caracterÃsticas
label.save_feature_colours = Guardar esquema cromático de caracterÃsticas
label.select_startup_file = Seleccionar fichero de arranque
label.select_unselect_visible_regions_from = seleccionada y deseleccionadas {0} regiones de {1}
label.visible_region_of = región visible de
label.webservice_job_title_on = {0} usando {1} de {2}
-label.updating_vamsas_session = Actualizando sesión VAMSAS
label.loading_file = Cargando fichero: {0}
label.edit_params = Editar {0}
label.as_percentage = Como Porcentaje
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_threshold_setting = Error de implementación: no se conoce la configuración del umbral para el AnnotationColourGradient actual.
-error.try_join_vamsas_session_another = Tratando de establecer una sesión VAMSAS cuando ya habÃa otra conectada
-error.invalid_vamsas_session_id = Identificador de sesión VAMSAS no válido
label.groovy_support_failed = El soporte Groovy de Jalview ha fallado
label.couldnt_create_groovy_shell = No es posible crear el shell de Groovy. Compruebe el fichero de log para conocer los detalles.
error.unsupported_version_calcIdparam = Versión no soportada de {0}
error.invalid_value_for_option = Valor no válido de {0} para la opción {1}
error.implementation_error_cannot_import_vamsas_doc = Error de implementación - todavÃa no es posible importar el documento VAMSAS existente en una sesión existente.
label.vamsas_doc_couldnt_be_opened_as_new_session = El documento VAMSAS no ha podido abrirse como una nueva sesión. Por favor, escoja otra.
-error.implementation_error_vamsas_operation_not_init = ¡Error de implementación! Operaciones VAMSAS cuando el cliente no estaba inicializado ni conectado
-error.jalview_no_connected_vamsas_session = Jalview está conectado a una sesión VAMSAS
-error.implementation_error_cannot_recover_vamsas_object_mappings = Error de implementación: no es posible recuperar los mapeos del objeto VAMSAS - no se ha hecho ningún backup
error.setstatus_called_non_existent_job_pane = se lllamado a setStatus para el panel de trabajo {0} no existente
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.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
error.implementation_error_null_fileparse = Error de implementación. FileParse nulo en el construictor de copia
-error.implementation_error_cannot_map_alignment_sequences = Error de implementación: no es posible maper un alineamiento de secuencias desde distintos conjuntos de datos en un único alineamiento en el documento VAMSAS.
error.implementation_error_structure_selection_manager_null = Error de implementación. El contexto structure selection manager's es nulo
exception.ssm_context_is_null = El contexto SSM es nulo
error.idstring_seqstrings_only_one_per_sequence = idstrings y seqstrings contienen una cadena por cada secuencia
error.implementation_error_dbinstance_must_implement_interface = Error de Implementación- getDbInstances debe recibir una clase que implemente jalview.ws.seqfetcher.DbSourceProxy (recibió {0})
error.implementation_error_must_init_dbsources =Error de implementación. Debe inicializar dbSources
label.view_controller_toggled_marked = {0} {1} columnas {2} caracterÃsticas del tipo {3} en {4} secuencia(s)
+label.no_highlighted_regions_marked = No hay regiones resaltadas marcadas
label.toggled = Invertida
label.marked = Marcada
label.containing = conteniendo
status.export_complete = Exportación completada
status.fetching_pdb = Recuperando PDB {0}
status.refreshing_news = Refrescando noticias
-status.importing_vamsas_session_from = Importando sesión VAMSAS de {0}
status.opening_params = Abriendo {0}
-status.waiting_sequence_database_fetchers_init = Esperando inicialización de los recuperadores de bases de datos de secuencias
-status.init_sequence_database_fetchers = Inicializando recuperadores de bases de datos de secuencias
status.fetching_sequence_queries_from = Recuperando {0} consultas de secuencias de {1}
status.finshed_querying = Consulta finalizada
status.parsing_results = Parseando resultados.
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
-label.error_loading_file_params = Error cargando el fichero {0}
-label.error_loading_jalview_file = Error cargando el fichero Jalview
warn.out_of_memory_when_action = Sin memoria al {0}\!\!\nConsulte los ficheros de ayuda para ajustar la memoria de la m\u00E1quina virtual de Java.
warn.out_of_memory_loading_file = Sin memoria al cargar el fichero {0}\!\!\nConsulte los ficheros de ayuda para ajustar la memoria de la m\u00E1quina virtual de Java.
label.out_of_memory = Sin memoria
label.invalid_id_column_width = Identificador de anchura de columna no válido
warn.user_defined_width_requirements = La anchura definida por el usuario para la \nlas columnas de anotaci\u00F3n e identificador de secuencias\nen figuras exportadas debe ser\na, al menos, de 12 p\u00EDxels
-label.couldnt_create_sequence_fetcher = No es posible crear SequenceFetcher
-warn.couldnt_create_sequence_fetcher_client = No es posible crear el cliente de recuperador de secuencias. Comprueba el fichero de log para más detalles.
warn.server_didnt_pass_validation = El servicio no ha pasado la validaci\u00F3n.\nCompruebe la consola de Jalview para m\u00E1s detalles.
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.rnalifold_settings=Cambiar ajustes RNAAliFold...
label.sort_ann_by=Ordenar anotaciones por
info.enter_search_text_here=Introducir texto de búsqueda aquÃ
-action.load_vamsas_session=Cargar Sesión Vamsas...
label.show_all_al_annotations=Mostrar anotaciones relacionadas con el alineamiento
label.hide_all_al_annotations=Ocultar anotaciones relacionadas con el alineamiento
label.show_all_seq_annotations=Mostrar anotaciones relacionadas con las secuencias
action.annotations=Anotaciones
label.nuc_alignment_colour=Color del Alineamiento NucleotÃdico
label.copy_format_from=Copiar formato de
-label.create_chimera_attributes = Escribir caracterÃsticas de Jalview
-label.create_chimera_attributes_tip = Establecer atributos en Chimera para caracterÃsticas visibles
+label.create_viewer_attributes = Escribir caracterÃsticas de Jalview
+label.create_viewer_attributes_tip = Establecer atributos de residuos para caracterÃsticas visibles
label.attributes_set = {0} valores de atributos establecidos en Chimera
label.open_split_window=Abrir ventana dividida
label.open_split_window?=¿Quieres abrir ventana dividida, con cDNA y proteÃna vinculadas?
label.prot_alignment_colour=Color del Alineamiento Proteico
info.associate_wit_sequence=Asociar con secuencia
label.protein=ProteÃna
+label.CDS=CDS
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.search_all=Introducir uno o más valores de búsqueda separados por punto y coma ";" (Nota: buscará en toda la base de datos PDB)
exception.outofmemory_loading_mmcif_file=Sin memoria al cargar el fichero mmCIF
label.hide_columns_not_containing=Ocultar las columnas que no contengan
label.pdb_sequence_fetcher=Recuperador de secuencias PDB
-status.waiting_for_user_to_select_output_file=Esperando que el usuario seleccione el fichero {0}
action.prev_page=<<
status.cancelled_image_export_operation=Operación de exportación {0} cancelada
label.couldnt_run_groovy_script=No se ha podido ejecutar el script Groovy
option.autosearch = Auto búsqueda
label.retrieve_ids = Recuperar IDs
label.display_settings_for = Visualización de caracterÃsticas {0}
-label.simple = Simple
label.simple_colour = Color simple
label.colour_by_text = Colorear por texto
label.graduated_colour = Color graduado
label.append_to_filename = Adjuntar texto (%n es reemplazado por el número de respaldo)
label.append_to_filename_tooltip = %n en el texto será reemplazado por el número de respaldo. El texto será después del nombre del archivo. Vea el cuadro de resumen arriba.
label.index_digits = Número de dÃgitos a utilizar para el número de respaldo.
-label.summary_of_backups_scheme = Resumen del esquema de copias de seguridad
label.scheme_examples = Ejemplos de esquema
label.increment_index = Aumente los números de texto adjuntos: el archivo más nuevo tiene el número más grande
label.reverse_roll = Ciclos de texto adjuntos: el respaldo más reciente es siempre el número 1
label.keep_all_versions_description = Mantener todas las versiones anteriores del archivo
label.rolled_backups_description = Mantenga las últimas nueve versiones del archivo desde _bak.1 (más reciente) a _bak.9 (más antigua)
label.cancel_changes_description = Cancelar los cambios realizados en su último esquema personalizado guardado
-label.previously_saved_scheme = Esquema previamente guardado
label.no_backup_files = NO ARCHIVOS DE RESPALDOS
label.include_backup_files = Incluir archivos de respaldos
label.cancel_changes = Cancelar cambios
label.warning_confirm_change_reverse = ¡Advertencia!\nSi cambia el incremento/decremento del número de archivos de respaldos, sin cambiar el sufijo o número de dÃgitos,\nesto puede causar la pérdida de los archivos de respaldos creados con el esquema anterior de nombre de archivo de respaldos.\n¿Está seguro de que desea hacer esto?
label.change_increment_decrement = ¿Cambiar de incremento/decremento?
-label.was_previous = era {0}
label.newerdelete_replacement_line = El archivo de respaldo\n''{0}''\t(modificado {2}, tamaño {4})\nserá borrado y reemplazarse por un archivo aparentemente más antiguo\n''{1}''\t(modificado {3}, tamaño {5}).
label.confirm_deletion_or_rename = Confirmar borrar ''{0}'', o cambiar el nombre a ''{1}''?
label.newerdelete_line = El archivo de respaldo\n''{0}''\t(modificado {2}, tamaño {4})\nserá borrado pero es mas nuevo que el archivo de respaldo restante más antiguo\n''{1}''\t(modified {3}, size {5}).
BLOSUM62Colour.setName(JalviewColourScheme.Blosum62.toString());
BLOSUM62Colour.addItemListener(this);
PIDColour.setLabel(
- MessageManager.getString("label.colourScheme_%_identity"));
+ MessageManager.getString("label.colourScheme_%identity"));
PIDColour.setName(JalviewColourScheme.PID.toString());
PIDColour.addItemListener(this);
zappoColour
.setName(JalviewColourScheme.Hydrophobic.toString());
hydrophobicityColour.addItemListener(this);
helixColour.setLabel(MessageManager
- .getString("label.colourScheme_helix_propensity"));
+ .getString("label.colourScheme_helixpropensity"));
helixColour.setName(JalviewColourScheme.Helix.toString());
helixColour.addItemListener(this);
strandColour.setLabel(MessageManager
- .getString("label.colourScheme_strand_propensity"));
+ .getString("label.colourScheme_strandpropensity"));
strandColour.setName(JalviewColourScheme.Strand.toString());
strandColour.addItemListener(this);
turnColour.setLabel(
- MessageManager.getString("label.colourScheme_turn_propensity"));
+ MessageManager.getString("label.colourScheme_turnpropensity"));
turnColour.setName(JalviewColourScheme.Turn.toString());
turnColour.addItemListener(this);
buriedColour.setLabel(
- MessageManager.getString("label.colourScheme_buried_index"));
+ MessageManager.getString("label.colourScheme_buriedindex"));
buriedColour.setName(JalviewColourScheme.Buried.toString());
buriedColour.addItemListener(this);
nucleotideColour.setLabel(
MessageManager.getString("label.colourScheme_hydrophobic"));
hydrophobicityColour.addActionListener(this);
helixColour.setLabel(MessageManager
- .getString("label.colourScheme_helix_propensity"));
+ .getString("label.colourScheme_helixpropensity"));
helixColour.addActionListener(this);
strandColour.setLabel(MessageManager
- .getString("label.colourScheme_strand_propensity"));
+ .getString("label.colourScheme_strandpropensity"));
strandColour.addActionListener(this);
turnColour.setLabel(
- MessageManager.getString("label.colourScheme_turn_propensity"));
+ MessageManager.getString("label.colourScheme_turnpropensity"));
turnColour.addActionListener(this);
buriedColour.setLabel(
- MessageManager.getString("label.colourScheme_buried_index"));
+ MessageManager.getString("label.colourScheme_buriedindex"));
buriedColour.addActionListener(this);
purinePyrimidineColour.setLabel(MessageManager
.getString("label.colourScheme_purine/pyrimidine"));
// .getString("label.rna_interaction"));
// RNAInteractionColour.addActionListener(this);
RNAHelixColour.setLabel(
- MessageManager.getString("label.colourScheme_rna_helices"));
+ MessageManager.getString("label.colourScheme_rnahelices"));
RNAHelixColour.addActionListener(this);
userDefinedColour
.setLabel(MessageManager.getString("action.user_defined"));
userDefinedColour.addActionListener(this);
PIDColour.setLabel(
- MessageManager.getString("label.colourScheme_%_identity"));
+ MessageManager.getString("label.colourScheme_%identity"));
PIDColour.addActionListener(this);
BLOSUM62Colour.setLabel(
MessageManager.getString("label.colourScheme_blosum62"));
BLOSUM62Colour.addActionListener(this);
tcoffeeColour.setLabel(
- MessageManager.getString("label.colourScheme_t-coffee_scores"));
+ MessageManager.getString("label.colourScheme_t-coffeescores"));
// it will be enabled only if a score file is provided
tcoffeeColour.setEnabled(false);
tcoffeeColour.addActionListener(this);
MessageManager.getString("label.colourScheme_hydrophobic"));
MenuItem helix = new MenuItem(
- MessageManager.getString("label.colourScheme_helix_propensity"));
+ MessageManager.getString("label.colourScheme_helixpropensity"));
MenuItem strand = new MenuItem(
- MessageManager.getString("label.colourScheme_strand_propensity"));
+ MessageManager.getString("label.colourScheme_strandpropensity"));
MenuItem turn = new MenuItem(
- MessageManager.getString("label.colourScheme_turn_propensity"));
+ MessageManager.getString("label.colourScheme_turnpropensity"));
MenuItem buried = new MenuItem(
- MessageManager.getString("label.colourScheme_buried_index"));
+ MessageManager.getString("label.colourScheme_buriedindex"));
MenuItem purinepyrimidine = new MenuItem(
MessageManager.getString("label.colourScheme_purine/pyrimidine"));
}
else
{
- avcg.setStatus(MessageManager
- .formatMessage("No highlighted regions marked"));
+ avcg.setStatus(MessageManager.getString("label.no_highlighted_regions_marked"));
if (!extendCurrent)
{
cs.clear();
*/
package jalview.fts.core;
-import jalview.fts.api.FTSDataColumnI;
-import jalview.fts.api.FTSDataColumnI.FTSDataColumnGroupI;
-import jalview.fts.api.FTSRestClientI;
-import jalview.util.MessageManager;
-
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.util.Collection;
import java.util.Objects;
+import jalview.fts.api.FTSDataColumnI;
+import jalview.fts.api.FTSDataColumnI.FTSDataColumnGroupI;
+import jalview.fts.api.FTSRestClientI;
+
/**
* Base class providing implementation for common methods defined in
* FTSRestClientI
break;
case 410:
- message = MessageManager.formatMessage(
- service + " rest services no longer available!");
+ message = service + " rest services no longer available!";
break;
case 403:
case 404:
pos);
if (mf != null)
{
- unshownFeatures = seqARep.appendFeatures(tooltipText,
+ unshownFeatures += seqARep.appendFeatures(tooltipText,
pos, mf, fr2, MAX_TOOLTIP_LENGTH);
}
}
{
if (!inSession())
{
- throw new Error(MessageManager.getString(
- "error.implementation_error_vamsas_operation_not_init"));
+ throw new Error(
+ "Implementation error! Vamsas Operations when client not initialised and connected");
}
addDocumentUpdateHandler();
addStoreDocumentHandler();
{
if (!inSession())
{
- throw new Error(MessageManager
- .getString("error.jalview_no_connected_vamsas_session"));
+ throw new Error("Jalview not connected to Vamsas session");
}
Cache.log.info("Jalview disconnecting from the Vamsas Session.");
try
return;
}
- throw new Error(MessageManager.getString(
- "error.implementation_error_cannot_recover_vamsas_object_mappings"));
+ throw new Error(
+ "IMPLEMENTATION ERROR: Cannot recover vamsas object mappings - no backup was made");
}
jv2vobj.clear();
Iterator el = _backup_jv2vobj.entrySet().iterator();
if (vbound.getV_parent() != null
&& dataset != vbound.getV_parent())
{
- throw new Error(MessageManager.getString(
- "error.implementation_error_cannot_map_alignment_sequences"));
- // This occurs because the dataset for the alignment we are
- // trying to
+ throw new Error(
+ "IMPLEMENTATION ERROR: Cannot map an alignment of sequences from different datasets into a single alignment in the vamsas document.");
}
}
}
{
if (ml == null)
{
- throw new Error(MessageManager
- .getString("error.implementation_error_maplist_is_null"));
+ throw new Error(
+ "Implementation error. MapList is null for initMapType.");
}
maprange.setLocal(new Local());
maprange.setMapped(new Mapped());
* RuntimeException throwable by htsjdk
*/
String msg = String.format("Error reading VCF for %s:%d-%d: %s ",
- map.chromosome, vcfStart, vcfEnd);
+ map.chromosome, vcfStart, vcfEnd,e.getLocalizedMessage());
Cache.log.error(msg);
}
}
taylor.setLabel(MessageManager.getString("label.colourScheme_taylor"));
taylor.addActionListener(this);
helix.setLabel(MessageManager
- .getString("label.colourScheme_helix_propensity"));
+ .getString("label.colourScheme_helixpropensity"));
helix.addActionListener(this);
strand.setLabel(MessageManager
- .getString("label.colourScheme_strand_propensity"));
+ .getString("label.colourScheme_strandpropensity"));
strand.addActionListener(this);
turn.setLabel(
- MessageManager.getString("label.colourScheme_turn_propensity"));
+ MessageManager.getString("label.colourScheme_turnpropensity"));
turn.addActionListener(this);
buried.setLabel(
- MessageManager.getString("label.colourScheme_buried_index"));
+ MessageManager.getString("label.colourScheme_buriedindex"));
buried.addActionListener(this);
user.setLabel(MessageManager.getString("action.user_defined"));
user.addActionListener(this);
+
/*
* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ The Jalview Authors
import java.io.FileReader;
import java.io.IOException;
import java.util.HashSet;
+import java.util.Iterator;
import java.util.Properties;
import java.util.Set;
import java.util.TreeSet;
*/
private void doMain(String srcPath) throws IOException
{
- System.out.println("Scanning " + srcPath
- + " for calls to MessageManager\n");
+ System.out.println(
+ "Scanning " + srcPath + " for calls to MessageManager\n");
+
sourcePath = srcPath;
loadMessages();
File dir = new File(srcPath);
*/
private void reportResults()
{
- System.out.println("\nScanned " + javaCount + " source files");
System.out.println(
- "Messages.properties has " + messages.size()
- + " keys");
+ "\nMessages.properties has " + messages.size() + " keys");
+ System.out.println("Scanned " + javaCount + " source files\n");
+
if (!invalidKeys.isEmpty())
{
System.out.println("Found " + invalidKeys.size()
- + " possibly invalid parameter call"
+ + " possibly invalid unmatched key(s) in source code"
+ (invalidKeys.size() > 1 ? "s" : ""));
}
- System.out.println("Keys not found, assumed constructed dynamically:");
+ System.out.println(
+ "Keys not found in source code, assumed constructed dynamically:");
int dynamicCount = 0;
for (String key : messageKeys)
{
if (dynamicCount < messageKeys.size())
{
System.out.println((messageKeys.size() - dynamicCount)
- + " keys not found, possibly unused");
+ + " key(s) not found, possibly unused, or used indirectly (check code manually!)");
for (String key : messageKeys)
{
if (!isDynamic(key))
}
}
System.out
- .println("(Run i18nAnt.xml to compare other message bundles)");
+ .println("\nRun i18nAnt.xml to compare other message bundles");
}
/**
* @param lineNo
* @param line
*/
- private void inspectSourceLines(String path, int lineNo, String line)
+ private void inspectSourceLines(String path, int lineNo,
+ final String line)
{
- String lineNos = String
- .format("%d-%d", lineNo, lineNo + bufferSize
- - 1);
+ String lineNos = String.format("%d-%d", lineNo,
+ lineNo + bufferSize - 1);
for (String method : METHODS)
{
int pos = line.indexOf(method);
if (METHOD3 == method)
{
- System.out.println(String.format("Dynamic key at %s line %s %s",
- path.substring(sourcePath.length()), lineNos, line));
String key = messageKey.substring(1, messageKey.length() - 1);
- dynamicKeys.add(key);
+ if (!dynamicKeys.contains(key))
+ {
+// System.out.println(String.format(
+// "Dynamic key \"" + key + "\" at %s line %s %s",
+// path.substring(sourcePath.length()), lineNos, line));
+ dynamicKeys.add(key);
+ }
continue;
}
if (!(STRING_PATTERN.matcher(messageKey).matches()))
{
- System.out.println(String.format("Dynamic key at %s line %s %s",
- path.substring(sourcePath.length()), lineNos, line));
+// System.out.println(String.format("Dynamic key at %s line %s %s",
+// path.substring(sourcePath.length()), lineNos, line));
continue;
}
if (!this.messages.containsKey(messageKey))
{
- System.out.println(String.format(
- "Unmatched key '%s' at line %s of %s", messageKey, lineNos,
- path.substring(sourcePath.length())));
if (!invalidKeys.contains(messageKey))
{
+ // report each key the first time found only
+ System.out.println(String.format(
+ "Unmatched key '%s' at line %s of %s", messageKey,
+ lineNos, path.substring(sourcePath.length())));
invalidKeys.add(messageKey);
}
}
messageKeys.remove(messageKey);
}
+
+ /*
+ * and a brute force scan for _any_ as yet unseen message key, to catch the
+ * cases where it is in a variable or a condition
+ */
+ if (line.contains("\""))
+ {
+ Iterator<String> it = messageKeys.iterator();
+ while (it.hasNext())
+ {
+ if (line.contains(it.next()))
+ {
+ it.remove(); // remove as 'seen'
+ }
+ }
+ }
}
/**
*/
int commaPos = key.indexOf(",");
int bracePos = key.indexOf(")");
- int endPos = commaPos == -1 ? bracePos : (bracePos == -1 ? commaPos
- : Math.min(commaPos, bracePos));
+ int endPos = commaPos == -1 ? bracePos
+ : (bracePos == -1 ? commaPos : Math.min(commaPos, bracePos));
if (endPos == -1 && key.length() > 1 && key.endsWith("\""))
{
endPos = key.length();
void loadMessages() throws IOException
{
messages = new Properties();
- FileReader reader = new FileReader(new File(sourcePath,
- "../resources/lang/Messages.properties"));
+ FileReader reader = new FileReader(
+ new File(sourcePath, "../resources/lang/Messages.properties"));
messages.load(reader);
reader.close();