action.close_all = Close all
action.load_project = Load Project
action.save_project = Save Project
+ action.save_project_as = Save Project as...
action.quit = Quit
action.expand_views = Expand Views
action.gather_views = Gather Views
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
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
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
label.average_distance_identity = Average Distance Using % Identity
label.neighbour_joining_identity = Neighbour Joining Using % Identity
label.choose_calculation = Choose Calculation
- label.treecalc_title = {0} Using {1}
+ label.calc_title = {0} Using {1}
label.tree_calc_av = Average Distance
label.tree_calc_nj = Neighbour Joining
- label.select_score_model = Select score model
label.score_model_pid = % Identity
label.score_model_blosum62 = BLOSUM62
label.score_model_pam250 = PAM 250
label.occupancy = Occupancy
# delete Clustal - use FileFormat name instead
label.clustal = Clustal
- # label.colourScheme_<schemeName> as in JalviewColourScheme
+ # label.colourScheme_<schemeName> as in JalviewColourScheme, spaces removed
label.colourScheme_clustal = Clustalx
label.colourScheme_blosum62 = BLOSUM62 Score
- label.colourScheme_%_identity = Percentage Identity
+ label.colourScheme_%identity = Percentage Identity
label.colourScheme_zappo = Zappo
label.colourScheme_taylor = Taylor
label.colourScheme_hydrophobic = Hydrophobicity
- label.colourScheme_helix_propensity = Helix Propensity
- label.colourScheme_strand_propensity = Strand Propensity
- label.colourScheme_turn_propensity = Turn Propensity
- label.colourScheme_buried_index = Buried Index
+ label.colourScheme_helixpropensity = Helix Propensity
+ label.colourScheme_strandpropensity = Strand Propensity
+ label.colourScheme_turnpropensity = Turn Propensity
+ label.colourScheme_buriedindex = Buried Index
label.colourScheme_purine/pyrimidine = Purine/Pyrimidine
label.colourScheme_nucleotide = Nucleotide
- label.colourScheme_t-coffee_scores = T-Coffee Scores
- label.colourScheme_rna_helices = By RNA Helices
+ label.colourScheme_t-coffeescores = T-Coffee Scores
+ label.colourScheme_rnahelices = By RNA Helices
+ label.colourScheme_sequenceid = Sequence ID Colour
label.blc = BLC
label.fasta = Fasta
label.msf = MSF
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.</font></html>
label.session_update = Session Update
label.new_vamsas_session = New Vamsas Session
action.load_vamsas_session = Load Vamsas Session...
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
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.
label.vamsas_document_import_failed = Vamsas Document Import Failed
- label.couldnt_locate = Couldn't locate {0}
+ label.couldnt_locate = Could not 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.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
label.create_sequence_feature = Create Sequence Feature...
label.edit_sequence = Edit Sequence
label.edit_sequences = Edit Sequences
+ label.insert_gap = Insert 1 gap
+ label.insert_gaps = Insert {0} gaps
+ label.delete_gap = Delete 1 gap
+ label.delete_gaps = Delete {0} gaps
label.sequence_details = Sequence Details
label.jmol_help = Jmol Help
label.chimera_help = Chimera Help
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
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
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...
label.view_and_change_parameters_before_running_calculation = View and change parameters before running calculation
label.view_documentation = View documentation
label.select_return_type = Select return type
- label.translation_of_params = Translation of {0}
+ label.translation_of_params = Translation of {0} (Table {1})
label.features_for_params = Features for - {0}
label.annotations_for_params = Annotations for - {0}
label.generating_features_for_params = Generating features for - {0}
label.fetch_retrieve_from =Retrieve from {0}</html>
label.fetch_retrieve_from_all_sources = Retrieve from all {0} sources in {1}<br>First is :{2}<html>
label.feature_settings_click_drag = Drag up or down to change render order.<br/>Double click to select columns containing feature.
+label.feature_settings_select_columns = 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
label.opt_and_params_show_brief_desc_image_link = <html>Click to show brief description<br><img src="{0}"/> Right click for further information.</html>
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}
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
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
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
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
label.SEQUENCE_ID_for_DB_ACCESSION2 = URL links using '$SEQUENCE_ID$' for DB accessions now use '$DB_ACCESSION$'.
label.do_not_display_again = Do not display this message again
exception.url_cannot_have_duplicate_id = {0} cannot be used as a label for more than one line
- label.filter = Filter text:
action.customfilter = Custom only
action.showall = Show All
label.insert = Insert:
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
label.graduated_colour = Graduated Colour
label.by_text_of = By text of
label.by_range_of = By range of
- label.filters_tooltip = Click to set or amend filters
label.or = Or
label.and = And
label.sequence_feature_colours = Sequence Feature Colours
label.most_polymer_residues = Most Polymer Residues
label.cached_structures = Cached Structures
label.free_text_search = Free Text Search
+label.summary_view = Summary View
+label.summary_view_tip = Show only top level ontology terms
+label.apply_to_subtypes = Apply changes also to sub-types of ''{0}''
- label.apply_also_to = Apply also to:
++label.apply_also_to = Apply also to:
+ label.backupfiles_confirm_delete = Confirm delete
+ label.backupfiles_confirm_delete_old_files = Delete the following older backup files? (see the Backups tab in Preferences for more options)
+ label.backupfiles_confirm_save_file = Confirm save file
+ label.backupfiles_confirm_save_file_backupfiles_roll_wrong = Something possibly went wrong with the backups of this file.
+ label.backupfiles_confirm_save_new_saved_file_ok = The new saved file seems okay.
+ label.backupfiles_confirm_save_new_saved_file_not_ok = The new saved file might not be okay.
+ label.backups = Backups
+ label.backup = Backup
+ label.backup_files = Backup Files
+ label.enable_backupfiles = Enable backup files
+ label.backup_filename_strategy = Backup filename strategy
+ 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.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_files = Deleting old backup files
+ label.keep_all_backup_files = Do not delete old backup files
+ label.keep_only_this_number_of_backup_files = Keep only this number of most recent backup files
+ label.autodelete_old_backup_files = Autodelete old backup files:
+ label.always_ask = Always ask
+ label.auto_delete = Automatically delete
+ label.filename = filename
+ label.braced_oldest = (oldest)
+ label.braced_newest = (most recent)
+ label.configuration = Configuration
+ label.configure_feature_tooltip = Click to configure variable colour or filters
+ label.schemes = Schemes
+ label.customise = Customise
+ label.default = Default
+ label.single_file = Single backup
+ label.keep_all_versions = Keep all versions
+ label.rolled_backups = Rolled backup files
+ 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.confirm_deletion = Confirm deletion of ''{0}''?
+ label.delete = Delete
+ label.rename = Rename
+ label.keep = Keep
+ label.file_info = (modified {0}, size {1})
+ label.annotation_name = Annotation Name
+ label.annotation_description = Annotation Description
+ label.edit_annotation_name_description = Edit Annotation Name/Description
+ label.alignment = alignment
+ label.pca = PCA
+ label.create_image_of = Create {0} image of {1}
+ label.click_to_edit = Click to edit, right-click for menu
+ label.by_annotation_tooltip = Annotation Colour is configured from the main Colour menu
action.close_all = Cerrar todo
action.load_project = Cargar proyecto
action.save_project = Guardar proyecto
+ action.save_project_as = Guardar proyecto como...
action.quit = Salir
action.expand_views = Expandir vistas
action.gather_views = Capturar vistas
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
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
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
label.average_distance_identity = Distancia Media Usando % de Identidad
label.neighbour_joining_identity = Unir vecinos utilizando % de Identidad
label.choose_calculation = Elegir el cálculo
- label.treecalc_title = {0} utilizando {1}
+ label.calc_title = {0} utilizando {1}
label.tree_calc_av = Distancia media
label.tree_calc_nj = Unir vecinos
- label.select_score_model = Selecciones modelo de puntuación
label.score_model_pid = % Identidad
label.score_model_blosum62 = BLOSUM62
label.score_model_pam250 = PAM 250
# label.colourScheme_<schemeName> as in JalviewColourScheme
label.colourScheme_clustal = Clustalx
label.colourScheme_blosum62 = Puntuación del BLOSUM62
- label.colourScheme_%_identity = Porcentaje de identidad
+ label.colourScheme_%identity = Porcentaje de identidad
label.colourScheme_zappo = Zappo
label.colourScheme_taylor = Taylor
label.colourScheme_hydrophobic = Hidrofobicidad
- label.colourScheme_helix_propensity = Tendencia de la hélice
- label.colourScheme_strand_propensity = Tendencia de la hebra
- label.colourScheme_turn_propensity = Tendencia de giro
- label.colourScheme_buried_index = Índice de encubrimiento
+ label.colourScheme_helixpropensity = Tendencia de la hélice
+ label.colourScheme_strandpropensity = Tendencia de la hebra
+ label.colourScheme_turnpropensity = Tendencia de giro
+ label.colourScheme_buriedindex = Índice de encubrimiento
label.colourScheme_purine/pyrimidine = Purina/Pirimidina
label.colourScheme_nucleotide = Nucleótido
- label.colourScheme_t-coffee_scores = Puntuación del T-Coffee
- label.colourScheme_rna_helices = Por hélices de RNA
+ label.colourScheme_t-coffeescores = Puntuación del T-Coffee
+ label.colourScheme_rnahelices = Por hélices de RNA
+ label.colourScheme_sequenceid = Color de ID de secuencia
label.blc = BLC
label.fasta = Fasta
label.msf = MSF
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
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
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.
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
label.create_sequence_feature = Crear función de secuencia
label.edit_sequence = Editar secuencia
label.edit_sequences = Editar secuencias
+ label.insert_gap = Insertar 1 hueco
+ label.insert_gaps = Insertar {0} huecos
+ label.delete_gap = Borrar 1 hueco
+ label.delete_gaps = Borrar {0} huecos
label.sequence_details = Detalles de la secuencia
label.jmol_help = Ayuda de Jmol
# Todos/Todas is gender-sensitive, but currently only used for feminine (cadena / anotación)!
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
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
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.view_and_change_parameters_before_running_calculation = Ver y cambiar los parámetros antes de lanzar el cálculo
label.view_documentation = Ver documentación
label.select_return_type = Seleccionar el tipo de retorno
- label.translation_of_params = Traducción de {0}
+ label.translation_of_params = Traducción de {0} (Tabla {1})
label.features_for_params = Características de - {0}
label.annotations_for_params = Anotaciones de - {0}
label.generating_features_for_params = Generando características de - {0}
label.rest_client_submit = {0} utilizando {1}
label.fetch_retrieve_from =Recuperar de {0}
label.fetch_retrieve_from_all_sources = Recuperar de todas las fuentes {0} en {1}<br>La primera es :{2}
-label.feature_settings_click_drag = Haga clic o arrastre los tipos de las características hacia arriba o hacia abajo para cambiar el orden de visualización.<br/>Haga doble clic para seleccionar las columnas que contienen las características del alineamiento/selección actual.<br/>
+label.feature_settings_click_drag = Haga clic o arrastre los tipos de las características hacia arriba o hacia abajo para cambiar el orden de visualización.<br/>Haga doble clic para seleccionar las columnas que contienen las características del alineamiento/selección actual.
+label.feature_settings_select_columns =Haga doble clic para seleccionar las columnas que contienen las características del alineamiento/selección actual
label.opt_and_params_further_details = ver los detalles adicionales haciendo clic en el botón derecho
label.opt_and_params_show_brief_desc_image_link = Haga clic para ver una descripción breve<br><img src="{0}"/>Haga clic en el botón derecho para obtener información adicional.
label.opt_and_params_show_brief_desc = Haga clic para ver una descripción breve<br>
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}
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
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
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
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
label.SEQUENCE_ID_for_DB_ACCESSION2 = URL enlaza usando '$SEQUENCE_ID$' para accesiones DB ahora usar '$DB_ACCESSION$'.
label.do_not_display_again = No mostrar este mensaje de nuevo
exception.url_cannot_have_duplicate_id = {0} no puede ser usada como etiqueta en más de un enlace
- label.filter = Filtrar texto:
action.customfilter = Sólo personalizado
action.showall = Mostrar todo
label.insert = Insertar:
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
label.graduated_colour = Color graduado
label.by_text_of = Por texto de
label.by_range_of = Por rango de
- label.filters_tooltip = Haga clic para configurar o modificar los filtros
label.or = O
label.and = Y
label.sequence_feature_colours = Colores de características de las secuencias
label.most_polymer_residues = Más Residuos de Polímeros
label.cached_structures = Estructuras en Caché
label.free_text_search = Búsqueda de texto libre
+label.summary_view = Vista Resumida
+label.summary_view_tip = Mostrar solo términos de ontología de nivel mayor
+label.apply_to_subtypes = Aplicar cambios también a subtipos de ''{0}''
- label.apply_also_to = Aplicar también a:
++label.apply_also_to = Aplicar también a:
+ label.backupfiles_confirm_delete = Confirmar borrar
+ label.backupfiles_confirm_delete_old_files = ¿Borrar los siguientes archivos? (ver la pestaña 'Copias' de la ventana de Preferencias para más opciones)
+ label.backupfiles_confirm_save_file = Confirmar guardar archivo
+ label.backupfiles_confirm_save_file_backupfiles_roll_wrong = Posiblemente algo está mal con los archivos de respaldos.
+ label.backupfiles_confirm_save_new_saved_file_ok = El nuevo archivo guardado parece estar bien.
+ label.backupfiles_confirm_save_new_saved_file_not_ok = El nuevo archivo guardado podría no estar bien.
+ label.backups = Respaldos
+ label.backup = Respaldo
+ label.backup_files = Archivos de respaldos
+ label.enable_backupfiles = Habilitar archivos de respaldos
+ label.backup_filename_strategy = Estrategia de nombres de archivo de respaldos
+ 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 dígitos a utilizar para el número de respaldo.
+ label.summary_of_backups_scheme = Resumen del esquema de copias de seguridad
+ 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_files = Borrando los respaldos antiguos
+ label.keep_all_backup_files = No borrar respaldos antiguas
+ label.keep_only_this_number_of_backup_files = Mantenga solo este número de respaldos más recientes
+ label.autodelete_old_backup_files = Borrer automáticamente respaldos antiguos:
+ label.always_ask = Pregunta siempre
+ label.auto_delete = Borrer automáticamente
+ label.filename = nombre_de_archivo
+ label.braced_oldest = (mas antiguo)
+ label.braced_newest = (mas nuevo)
+ label.configuration = Configuración
+ label.configure_feature_tooltip = Haga clic para configurar el color o los filtros
+ label.schemes = Esquemas
+ label.customise = Personalizado
+ label.default = Defecto
+ label.single_file = Solo uno respaldo
+ label.keep_all_versions = Mantener todas las versiones
+ label.rolled_backups = Ciclos respaldos
+ 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 dígitos,\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}).
+ label.confirm_deletion = Confirmar eliminar ''{0}''?
+ label.delete = Borrar
+ label.rename = Cambiar
+ label.keep = Mantener
+ label.file_info = (modificado {0}, tamaño {1})
+ label.annotation_name = Nombre de la anotación
+ label.annotation_description = Descripción de la anotación
+ label.edit_annotation_name_description = Editar el nombre/descripción de la anotación
+ label.alignment = alineamiento
+ label.pca = ACP
+ label.create_image_of = Crear imagen {0} de {1}
+ label.click_to_edit = Haga clic para editar, clic en el botón derecho para ver el menú
+ label.by_annotation_tooltip = El color de anotación se configura desde el menú principal de colores
* configure 'full' SO model if preferences say to,
* else use the default (SO Lite)
*/
- if (Cache.getDefault("USE_FULL_SO", false))
+ if (Cache.getDefault("USE_FULL_SO", true))
{
SequenceOntologyFactory.setInstance(new SequenceOntology());
}
FileFormatI format = null;
DataSourceType protocol = null;
FileLoader fileLoader = new FileLoader(!headless);
- Vector<String> getFeatures = null; // vector of das source nicknames to
- // fetch
- // features from
- // loading is done.
+
String groovyscript = null; // script to execute after all loading is
// completed one way or another
// extract groovy argument and execute if necessary
data.replaceAll("%20", " ");
ColourSchemeI cs = ColourSchemeProperty
- .getColourScheme(af.getViewport().getAlignment(), data);
+ .getColourScheme(af.getViewport(),
+ af.getViewport().getAlignment(), data);
if (cs != null)
{
// TODO - load PDB structure(s) to alignment JAL-629
// (associate with identical sequence in alignment, or a specified
// sequence)
-
- getFeatures = checkDasArguments(aparser);
- if (af != null && getFeatures != null)
- {
- FeatureFetcher ff = startFeatureFetching(getFeatures);
- if (ff != null)
- {
- while (!ff.allFinished() || af.operationInProgress())
- {
- // wait around until fetching is finished.
- try
- {
- Thread.sleep(100);
- } catch (Exception e)
- {
-
- }
- }
- }
- getFeatures = null; // have retrieved features - forget them now.
- }
if (groovyscript != null)
{
// Execute the groovy script after we've done all the rendering stuff
startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
format);
- getFeatures = checkDasArguments(aparser);
// extract groovy arguments before anything else.
}
- // If the user has specified features to be retrieved,
- // or a groovy script to be executed, do them if they
- // haven't been done already
- // fetch features for the default alignment
- if (getFeatures != null)
- {
- if (startUpAlframe != null)
- {
- startFeatureFetching(getFeatures);
- }
- }
+
// Once all other stuff is done, execute any groovy scripts (in order)
if (groovyscript != null)
{
// (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
}
}
- /**
- * Check commandline for any das server definitions or any fetchfrom switches
- *
- * @return vector of DAS source nicknames to retrieve from
- */
- private static Vector<String> checkDasArguments(ArgsParser aparser)
- {
- Vector<String> source = null;
- String data;
- String locsources = Cache.getProperty(Cache.DAS_LOCAL_SOURCE);
- while ((data = aparser.getValue("dasserver", true)) != null)
- {
- String nickname = null;
- String url = null;
- int pos = data.indexOf('=');
- // determine capabilities
- if (pos > 0)
- {
- nickname = data.substring(0, pos);
- }
- url = data.substring(pos + 1);
- if (url != null && (url.startsWith("http:")
- || url.startsWith("sequence:http:")))
- {
- if (nickname == null)
- {
- nickname = url;
- }
- if (locsources == null)
- {
- locsources = "";
- }
- else
- {
- locsources += "\t";
- }
- locsources = locsources + nickname + "|" + url;
- System.err.println(
- "NOTE! dasserver parameter not yet really supported (got args of "
- + nickname + "|" + url);
- if (source == null)
- {
- source = new Vector<>();
- }
- source.addElement(nickname);
- }
- System.out.println(
- "CMD [-dasserver " + data + "] executed successfully!");
- } // loop until no more server entries are found.
- if (locsources != null && locsources.indexOf('|') > -1)
- {
- Cache.log.debug("Setting local source list in properties file to:\n"
- + locsources);
- Cache.setProperty(Cache.DAS_LOCAL_SOURCE, locsources);
- }
- while ((data = aparser.getValue("fetchfrom", true)) != null)
- {
- System.out.println("adding source '" + data + "'");
- if (source == null)
- {
- source = new Vector<>();
- }
- source.addElement(data);
- }
- return source;
- }
-
- /**
- * start a feature fetcher for every alignment frame
- *
- * @param dasSources
- */
- private FeatureFetcher startFeatureFetching(
- final Vector<String> dasSources)
- {
- FeatureFetcher ff = new FeatureFetcher();
- AlignFrame afs[] = Desktop.getAlignFrames();
- if (afs == null || afs.length == 0)
- {
- return null;
- }
- for (int i = 0; i < afs.length; i++)
- {
- ff.addFetcher(afs[i], dasSources);
- }
- return ff;
- }
-
public static boolean isHeadlessMode()
{
String isheadless = System.getProperty("java.awt.headless");
import jalview.datamodel.SequenceI;
import jalview.io.DataSourceType;
import jalview.io.FeaturesFile;
+ import jalview.schemes.ColourSchemeI;
import jalview.util.MessageManager;
import java.awt.Color;
viewport.getAlignment().deleteAllGroups();
viewport.clearSequenceColours();
viewport.setSelectionGroup(null);
+ ColourSchemeI colours = viewport.getGlobalColourScheme();
// set view properties for each group
for (int g = 0; g < gps.length; g++)
{
// gps[g].setShowunconserved(viewport.getShowUnconserved());
gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
viewport.getAlignment().addGroup(gps[g]);
- Color col = new Color((int) (Math.random() * 255),
- (int) (Math.random() * 255), (int) (Math.random() * 255));
- col = col.brighter();
- for (SequenceI sq : gps[g].getSequences(null))
+ if (colours != null)
{
- viewport.setSequenceColour(sq, col);
+ gps[g].setColourScheme(colours.getInstance(viewport, gps[g]));
}
+ Color col = new Color((int) (Math.random() * 255),
+ (int) (Math.random() * 255), (int) (Math.random() * 255));
+ gps[g].idColour = col;
+ viewport.setUpdateStructures(true);
+ viewport.addSequenceGroup(gps[g]);
}
return true;
}
@Override
public boolean markColumnsContainingFeatures(boolean invert,
- boolean extendCurrent, boolean toggle, String featureType)
+ boolean extendCurrent, boolean toggle, String... featureType)
{
// JBPNote this routine could also mark rows, not just columns.
// need a decent query structure to allow all types of feature searches
|| extendCurrent) ? viewport.getAlignment()
: viewport.getSelectionGroup();
- int nseq = findColumnsWithFeature(featureType, sqcol, bs);
+ int nseq = findColumnsWithFeature(sqcol, bs, featureType);
ColumnSelection cs = viewport.getColumnSelection();
if (cs == null)
cs = new ColumnSelection();
}
+ String featureTypeString = featureType.length == 1 ? featureType[0]
+ : featureType.toString();
+
if (bs.cardinality() > 0 || invert)
{
boolean changed = cs.markColumns(bs, sqcol.getStartRes(),
invert ? MessageManager
.getString("label.not_containing")
: MessageManager.getString("label.containing"),
- featureType, Integer.valueOf(nseq).toString() }));
+ featureTypeString, Integer.valueOf(nseq).toString() }));
return true;
}
}
{
avcg.setStatus(MessageManager
.formatMessage("label.no_feature_of_type_found", new String[]
- { featureType }));
+ { featureTypeString }));
if (!extendCurrent)
{
cs.clear();
/**
* Sets a bit in the BitSet for each column (base 0) in the sequence
- * collection which includes a visible feature of the specified feature type.
- * Returns the number of sequences which have the feature visible in the
- * selected range.
+ * collection which includes a visible feature of the specified feature
+ * type(s). Returns the number of sequences which have the feature(s) visible
+ * in the selected range.
*
- * @param featureType
* @param sqcol
* @param bs
+ * @param featureType
+ *
* @return
*/
- int findColumnsWithFeature(String featureType,
- SequenceCollectionI sqcol, BitSet bs)
+ int findColumnsWithFeature(SequenceCollectionI sqcol,
+ BitSet bs, String... featureType)
{
FeatureRenderer fr = alignPanel == null ? null : alignPanel
.getFeatureRenderer();
import jalview.analysis.AlignmentUtils;
import jalview.analysis.CrossRef;
import jalview.analysis.Dna;
+ import jalview.analysis.GeneticCodeI;
import jalview.analysis.ParseProperties;
import jalview.analysis.SequenceIdMatcher;
import jalview.api.AlignExportSettingI;
import jalview.gui.ViewSelectionMenu.ViewSetProvider;
import jalview.io.AlignmentProperties;
import jalview.io.AnnotationFile;
+ import jalview.io.BackupFiles;
import jalview.io.BioJsHTMLOutput;
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
import java.util.List;
import java.util.Vector;
+ import javax.swing.ButtonGroup;
import javax.swing.JCheckBoxMenuItem;
import javax.swing.JEditorPane;
import javax.swing.JInternalFrame;
int aSize = alignPanels.size();
- tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
+ tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null);
- if (aSize == 1 && ap.av.viewName == null)
+ if (aSize == 1 && ap.av.getViewName() == null)
{
this.getContentPane().add(ap, BorderLayout.CENTER);
}
expandViews.setEnabled(true);
gatherViews.setEnabled(true);
- tabbedPane.addTab(ap.av.viewName, ap);
+ tabbedPane.addTab(ap.av.getViewName(), ap);
ap.setVisible(false);
}
gatherViews.setEnabled(true);
tabbedPane.setVisible(true);
AlignmentPanel first = alignPanels.get(0);
- tabbedPane.addTab(first.av.viewName, first);
+ tabbedPane.addTab(first.av.getViewName(), first);
this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
}
* @param av
* AlignViewport
*/
- void setMenusFromViewport(AlignViewport av)
+ public void setMenusFromViewport(AlignViewport av)
{
padGapsMenuitem.setSelected(av.isPadGaps());
colourTextMenuItem.setSelected(av.isShowColourText());
return progressBar.operationInProgress();
}
+ /**
+ * Sets the text of the status bar. Note that setting a null or empty value
+ * will cause the status bar to be hidden, with possibly undesirable flicker
+ * of the screen layout.
+ */
@Override
public void setStatus(String text)
{
- statusBar.setText(text);
+ statusBar.setText(text == null || text.isEmpty() ? " " : text);
}
/*
shortName.lastIndexOf(java.io.File.separatorChar) + 1);
}
- success = new Jalview2XML().saveAlignment(this, file, shortName);
+ success = new jalview.project.Jalview2XML().saveAlignment(this, file,
+ shortName);
statusBar.setText(MessageManager.formatMessage(
"label.successfully_saved_to_file_in_format", new Object[]
}
else
{
+ // create backupfiles object and get new temp filename destination
+ BackupFiles backupfiles = new BackupFiles(file);
+
try
{
- PrintWriter out = new PrintWriter(new FileWriter(file));
+ PrintWriter out = new PrintWriter(
+ new FileWriter(backupfiles.getTempFilePath()));
out.print(output);
out.close();
success = false;
ex.printStackTrace();
}
+
+ backupfiles.setWriteSuccess(success);
+ // do the backup file roll and rename the temp file to actual file
+ success = backupfiles.rollBackupsAndRenameTempFile();
+
}
}
@Override
public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
{
- SequenceGroup sg = new SequenceGroup();
-
- for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
- {
- sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
- }
+ SequenceGroup sg = new SequenceGroup(
+ viewport.getAlignment().getSequences());
sg.setEndRes(viewport.getAlignment().getWidth() - 1);
viewport.setSelectionGroup(sg);
+ viewport.isSelectionGroupChanged(true);
viewport.sendSelection();
// JAL-2034 - should delegate to
// alignPanel to decide if overview needs
/*
* Create a new AlignmentPanel (with its own, new Viewport)
*/
- AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel);
+ AlignmentPanel newap = new jalview.project.Jalview2XML()
+ .copyAlignPanel(alignPanel);
if (!copyAnnotation)
{
/*
newap.av.setGatherViewsHere(false);
- if (viewport.viewName == null)
+ if (viewport.getViewName() == null)
{
- viewport.viewName = MessageManager
- .getString("label.view_name_original");
+ viewport.setViewName(MessageManager
+ .getString("label.view_name_original"));
}
/*
newap.av.setRedoList(viewport.getRedoList());
/*
+ * copy any visualisation settings that are not saved in the project
+ */
+ newap.av.setColourAppliesToAllGroups(
+ viewport.getColourAppliesToAllGroups());
+
+ /*
* Views share the same mappings; need to deregister any new mappings
* created by copyAlignPanel, and register the new reference to the shared
* mappings
newap.refresh(true); // adjust layout of annotations
}
- newap.av.viewName = getNewViewName(viewTitle);
+ newap.av.setViewName(getNewViewName(viewTitle));
addAlignmentPanel(newap, true);
newap.alignmentChanged();
if (comp instanceof AlignmentPanel)
{
AlignmentPanel ap = (AlignmentPanel) comp;
- if (!existingNames.contains(ap.av.viewName))
+ if (!existingNames.contains(ap.av.getViewName()))
{
- existingNames.add(ap.av.viewName);
+ existingNames.add(ap.av.getViewName());
}
}
}
viewport.setFollowHighlight(state);
if (state)
{
- alignPanel.scrollToPosition(viewport.getSearchResults(), false);
+ alignPanel.scrollToPosition(viewport.getSearchResults());
}
}
viewport.expandColSelection(sg, false);
viewport.hideAllSelectedSeqs();
viewport.hideSelectedColumns();
+ alignPanel.updateLayout();
alignPanel.paintAlignment(true, true);
viewport.sendSelection();
}
public void hideSelColumns_actionPerformed(ActionEvent e)
{
viewport.hideSelectedColumns();
+ alignPanel.updateLayout();
alignPanel.paintAlignment(true, true);
viewport.sendSelection();
}
protected void scaleAbove_actionPerformed(ActionEvent e)
{
viewport.setScaleAboveWrapped(scaleAbove.isSelected());
- // TODO: do we actually need to update overview for scale above change ?
+ alignPanel.updateLayout();
alignPanel.paintAlignment(true, false);
}
protected void scaleLeft_actionPerformed(ActionEvent e)
{
viewport.setScaleLeftWrapped(scaleLeft.isSelected());
+ alignPanel.updateLayout();
alignPanel.paintAlignment(true, false);
}
protected void scaleRight_actionPerformed(ActionEvent e)
{
viewport.setScaleRightWrapped(scaleRight.isSelected());
+ alignPanel.updateLayout();
alignPanel.paintAlignment(true, false);
}
* otherwise set the chosen colour scheme (or null for 'None')
*/
ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
+ viewport,
viewport.getAlignment(), viewport.getHiddenRepSequences());
changeColour(cs);
}
frameTitle += " from ";
- if (viewport.viewName != null)
+ if (viewport.getViewName() != null)
{
- frameTitle += viewport.viewName + " of ";
+ frameTitle += viewport.getViewName() + " of ";
}
frameTitle += this.title;
* frame's DNA sequences to their aligned protein (amino acid) equivalents.
*/
@Override
- public void showTranslation_actionPerformed(ActionEvent e)
+ public void showTranslation_actionPerformed(GeneticCodeI codeTable)
{
AlignmentI al = null;
try
{
Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
- al = dna.translateCdna();
+ al = dna.translateCdna(codeTable);
} catch (Exception ex)
{
jalview.bin.Cache.log.error(
af.setFileFormat(this.currentFileFormat);
final String newTitle = MessageManager
.formatMessage("label.translation_of_params", new Object[]
- { this.getTitle() });
+ { this.getTitle(), codeTable.getId() });
af.setTitle(newTitle);
if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
{
if (reply != null)
{
- viewport.viewName = reply;
+ viewport.setViewName(reply);
// TODO warn if reply is in getExistingViewNames()?
tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
}
{
PaintRefresher.Refresh(this, viewport.getSequenceSetId());
alignPanel.updateAnnotation();
- alignPanel.paintAlignment(true, true);
+ alignPanel.paintAlignment(true,
+ viewport.needToUpdateStructureViews());
}
}
*/
public List<? extends AlignmentViewPanel> getAlignPanels()
{
- return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
+ // alignPanels is never null
+ // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
+ return alignPanels;
}
/**
}
/**
- * Hides columns containing (or not containing) a specified feature, provided
- * that would not leave all columns hidden
+ * Hides columns containing (or not containing) the specified feature(s),
+ * provided that would not leave all columns hidden
*
- * @param featureType
* @param columnsContaining
+ * @param featureTypes
+ *
* @return
*/
- public boolean hideFeatureColumns(String featureType,
- boolean columnsContaining)
+ public boolean hideFeatureColumns(boolean columnsContaining,
+ String... featureTypes)
{
boolean notForHiding = avc.markColumnsContainingFeatures(
- columnsContaining, false, false, featureType);
+ columnsContaining, false, false, featureTypes);
if (notForHiding)
{
if (avc.markColumnsContainingFeatures(!columnsContaining, false,
- false, featureType))
+ false, featureTypes))
{
getViewport().hideSelectedColumns();
return true;
colourMenu.add(textColour);
colourMenu.addSeparator();
- ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(),
- false);
+ ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this,
+ viewport.getAlignment(), false);
+ colourMenu.add(annotationColour);
+ bg.add(annotationColour);
colourMenu.addSeparator();
colourMenu.add(conservationMenuItem);
colourMenu.add(modifyConservation);
colourMenu.add(abovePIDThreshold);
colourMenu.add(modifyPID);
- colourMenu.add(annotationColour);
ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
import jalview.api.FeatureSettingsControllerI;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
+ import jalview.datamodel.features.FeatureMatcher;
import jalview.datamodel.features.FeatureMatcherI;
import jalview.datamodel.features.FeatureMatcherSet;
import jalview.datamodel.features.FeatureMatcherSetI;
+import jalview.datamodel.ontology.OntologyI;
import jalview.gui.Help.HelpId;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
+import jalview.io.gff.SequenceOntologyFactory;
- import jalview.schemabinding.version2.Filter;
- import jalview.schemabinding.version2.JalviewUserColours;
- import jalview.schemabinding.version2.MatcherSet;
import jalview.schemes.FeatureColour;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean;
+ import jalview.xml.binding.jalview.JalviewUserColours;
+ import jalview.xml.binding.jalview.JalviewUserColours.Colour;
+ import jalview.xml.binding.jalview.JalviewUserColours.Filter;
+ import jalview.xml.binding.jalview.ObjectFactory;
import java.awt.BorderLayout;
import java.awt.Color;
import java.io.InputStreamReader;
import java.io.OutputStreamWriter;
import java.io.PrintWriter;
+import java.util.ArrayList;
import java.util.Arrays;
import java.util.Comparator;
import java.util.HashMap;
import javax.swing.Icon;
import javax.swing.JButton;
import javax.swing.JCheckBox;
- import javax.swing.JCheckBoxMenuItem;
import javax.swing.JColorChooser;
import javax.swing.JDialog;
import javax.swing.JInternalFrame;
import javax.swing.JSlider;
import javax.swing.JTable;
import javax.swing.ListSelectionModel;
+import javax.swing.RowFilter;
import javax.swing.SwingConstants;
+ import javax.swing.border.Border;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
import javax.swing.table.AbstractTableModel;
+ import javax.swing.table.JTableHeader;
import javax.swing.table.TableCellEditor;
import javax.swing.table.TableCellRenderer;
import javax.swing.table.TableColumn;
+import javax.swing.table.TableRowSorter;
+ import javax.xml.bind.JAXBContext;
+ import javax.xml.bind.JAXBElement;
+ import javax.xml.bind.Marshaller;
+ import javax.xml.stream.XMLInputFactory;
+ import javax.xml.stream.XMLStreamReader;
public class FeatureSettings extends JPanel
implements FeatureSettingsControllerI
{
+ private static final Font VERDANA_12 = new Font("Verdana", Font.PLAIN, 12);
+
private static final String SEQUENCE_FEATURE_COLOURS = MessageManager
.getString("label.sequence_feature_colours");
private static final int MIN_HEIGHT = 400;
+ private final static String BASE_TOOLTIP = MessageManager.getString("label.click_to_edit");
+
final FeatureRenderer fr;
public final AlignFrame af;
*/
Map<String, float[]> typeWidth = null;
+ /*
+ * if true, 'child' feature types are not displayed
+ */
+ JCheckBox summaryView;
+
+ /*
+ * those feature types that do not have a parent feature type present
+ * (as determined by an Ontology relationship)
+ */
+ List<String> topLevelTypes;
+
/**
* Constructor
*
originalFilters = new HashMap<>(fr.getFeatureFilters()); // shallow copy
+ topLevelTypes = new ArrayList<>();
+
try
{
jbInit();
ex.printStackTrace();
}
+ initTable();
+
+ scrollPane.setViewportView(table);
+
+ if (af.getViewport().isShowSequenceFeatures() || !fr.hasRenderOrder())
+ {
+ fr.findAllFeatures(true); // display everything!
+ }
+
+ discoverAllFeatureData();
+ final PropertyChangeListener change;
+ final FeatureSettings fs = this;
+ fr.addPropertyChangeListener(change = new PropertyChangeListener()
+ {
+ @Override
+ public void propertyChange(PropertyChangeEvent evt)
+ {
+ if (!fs.resettingTable && !fs.handlingUpdate)
+ {
+ fs.handlingUpdate = true;
+ fs.resetTable(null);
+ // new groups may be added with new sequence feature types only
+ fs.handlingUpdate = false;
+ }
+ }
+ });
+
+ frame = new JInternalFrame();
+ frame.setContentPane(this);
+ if (Platform.isAMac())
+ {
+ Desktop.addInternalFrame(frame,
+ MessageManager.getString("label.sequence_feature_settings"),
+ 600, 480);
+ }
+ else
+ {
+ Desktop.addInternalFrame(frame,
+ MessageManager.getString("label.sequence_feature_settings"),
+ 600, 450);
+ }
+ frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
+
+ frame.addInternalFrameListener(
+ new javax.swing.event.InternalFrameAdapter()
+ {
+ @Override
+ public void internalFrameClosed(
+ javax.swing.event.InternalFrameEvent evt)
+ {
+ fr.removePropertyChangeListener(change);
+ };
+ });
+ frame.setLayer(JLayeredPane.PALETTE_LAYER);
+ inConstruction = false;
+ }
+
+ /**
+ * Constructs and configures the JTable which displays columns of data for
+ * each feature type
+ */
+ protected void initTable()
+ {
table = new JTable()
{
@Override
{
String tip = null;
int column = table.columnAtPoint(e.getPoint());
+ int row = table.rowAtPoint(e.getPoint());
switch (column)
{
case TYPE_COLUMN:
- tip = JvSwingUtils.wrapTooltip(true, MessageManager
+ /*
+ * drag to reorder not enabled in Summary View
+ */
+ tip = summaryView.isSelected()
+ ? MessageManager.getString(
+ "label.feature_settings_select_columns")
+ : JvSwingUtils.wrapTooltip(true, MessageManager
.getString("label.feature_settings_click_drag"));
break;
+ case COLOUR_COLUMN:
+ FeatureColourI colour = (FeatureColourI) table.getValueAt(row,
+ column);
+ tip = getColorTooltip(colour, true);
+ break;
case FILTER_COLUMN:
FeatureMatcherSet o = (FeatureMatcherSet) table.getValueAt(row,
column);
tip = o.isEmpty()
- ? MessageManager.getString("label.filters_tooltip")
+ ? MessageManager
+ .getString("label.configure_feature_tooltip")
: o.toString();
break;
default:
break;
}
-
return tip;
}
+
+ /**
+ * Position the tooltip near the bottom edge of, and half way across, the
+ * current cell
+ */
+ @Override
+ public Point getToolTipLocation(MouseEvent e)
+ {
+ Point point = e.getPoint();
+ int column = table.columnAtPoint(point);
+ int row = table.rowAtPoint(point);
+ Rectangle r = getCellRect(row, column, false);
+ Point loc = new Point(r.x + r.width / 2, r.y + r.height - 3);
+ return loc;
+ }
};
- table.getTableHeader().setFont(VERDANA_12);
++
+ JTableHeader tableHeader = table.getTableHeader();
- tableHeader.setFont(new Font("Verdana", Font.PLAIN, 12));
++ tableHeader.setFont(VERDANA_12);
+ tableHeader.setReorderingAllowed(false);
- table.setFont(new Font("Verdana", Font.PLAIN, 12));
+ table.setFont(VERDANA_12);
table.setDefaultEditor(FeatureColour.class, new ColorEditor(this));
table.setDefaultRenderer(FeatureColour.class, new ColorRenderer());
String type = (String) table.getValueAt(selectedRow, TYPE_COLUMN);
if (evt.isPopupTrigger())
{
-- Object colour = table.getValueAt(selectedRow, COLOUR_COLUMN);
- popupMenu(selectedRow, type, colour, evt.getX(), evt.getY());
- popupSort(selectedRow, type, colour, fr.getMinMax(), evt.getX(),
- evt.getY());
++ popupMenu(selectedRow, type, evt.getX(), evt.getY());
}
else if (evt.getClickCount() == 2)
{
boolean invertSelection = evt.isAltDown();
boolean toggleSelection = Platform.isControlDown(evt);
boolean extendSelection = evt.isShiftDown();
+ String[] terms = getTermsInScope(type);
fr.ap.alignFrame.avc.markColumnsContainingFeatures(
- invertSelection, extendSelection, toggleSelection, type);
+ invertSelection, extendSelection, toggleSelection, terms);
}
}
if (evt.isPopupTrigger())
{
String type = (String) table.getValueAt(selectedRow, TYPE_COLUMN);
-- Object colour = table.getValueAt(selectedRow, COLOUR_COLUMN);
- popupMenu(selectedRow, type, colour, evt.getX(), evt.getY());
- popupSort(selectedRow, type, colour, fr.getMinMax(), evt.getX(),
- evt.getY());
++ popupMenu(selectedRow, type, evt.getX(), evt.getY());
}
}
});
public void mouseDragged(MouseEvent evt)
{
int newRow = table.rowAtPoint(evt.getPoint());
- if (newRow != selectedRow && selectedRow != -1 && newRow != -1)
- {
- /*
- * reposition 'selectedRow' to 'newRow' (the dragged to location)
- * this could be more than one row away for a very fast drag action
- * so just swap it with adjacent rows until we get it there
- */
- Object[][] data = ((FeatureTableModel) table.getModel())
- .getData();
- int direction = newRow < selectedRow ? -1 : 1;
- for (int i = selectedRow; i != newRow; i += direction)
- {
- Object[] temp = data[i];
- data[i] = data[i + direction];
- data[i + direction] = temp;
- }
- updateFeatureRenderer(data);
- table.repaint();
- selectedRow = newRow;
- }
+ dragRow(newRow);
}
});
- // table.setToolTipText(JvSwingUtils.wrapTooltip(true,
- // MessageManager.getString("label.feature_settings_click_drag")));
- scrollPane.setViewportView(table);
+ }
- if (af.getViewport().isShowSequenceFeatures() || !fr.hasRenderOrder())
+ /**
+ * Answers an array consisting of the given type, and also (if 'Summary View'
+ * is selected), any child terms in the sequence ontology
+ *
+ * @param type
+ * @return
+ */
+ protected String[] getTermsInScope(String type)
+ {
+ if (!summaryView.isSelected())
{
- fr.findAllFeatures(true); // display everything!
+ return new String[] { type };
}
- discoverAllFeatureData();
- final PropertyChangeListener change;
- final FeatureSettings fs = this;
- fr.addPropertyChangeListener(change = new PropertyChangeListener()
- {
- @Override
- public void propertyChange(PropertyChangeEvent evt)
- {
- if (!fs.resettingTable && !fs.handlingUpdate)
- {
- fs.handlingUpdate = true;
- fs.resetTable(null);
- // new groups may be added with new sequence feature types only
- fs.handlingUpdate = false;
- }
- }
+ List<String> terms = new ArrayList<>();
+ terms.add(type);
- });
+ OntologyI so = SequenceOntologyFactory.getInstance();
- frame = new JInternalFrame();
- frame.setContentPane(this);
- if (Platform.isAMac())
- {
- Desktop.addInternalFrame(frame,
- MessageManager.getString("label.sequence_feature_settings"),
- 600, 480);
- }
- else
+ Object[][] data = ((FeatureTableModel) table.getModel()).getData();
+ for (Object[] row : data)
{
- Desktop.addInternalFrame(frame,
- MessageManager.getString("label.sequence_feature_settings"),
- 600, 450);
+ String type2 = (String) row[TYPE_COLUMN];
+ if (!type2.equals(type) && so.isA(type2, type))
+ {
+ terms.add(type2);
+ }
}
- frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
-
- frame.addInternalFrameListener(
- new javax.swing.event.InternalFrameAdapter()
- {
- @Override
- public void internalFrameClosed(
- javax.swing.event.InternalFrameEvent evt)
- {
- fr.removePropertyChangeListener(change);
- };
- });
- frame.setLayer(JLayeredPane.PALETTE_LAYER);
- inConstruction = false;
+ return terms.toArray(new String[terms.size()]);
}
- protected void popupMenu(final int rowSelected, final String type,
- final Object typeCol, int x, int y)
- protected void popupSort(final int rowSelected, final String type,
- final Object typeCol, final Map<String, float[][]> minmax, int x,
++ protected void popupMenu(final int rowSelected, final String type, int x,
+ int y)
{
-- final FeatureColourI featureColour = (FeatureColourI) typeCol;
--
JPopupMenu men = new JPopupMenu(MessageManager
.formatMessage("label.settings_for_param", new String[]
{ type }));
final FeatureSettings me = this;
scr.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- me.af.avc
- .sortAlignmentByFeatureScore(Arrays.asList(new String[]
- { type }));
+ String[] types = getTermsInScope(type);
+ me.af.avc.sortAlignmentByFeatureScore(Arrays.asList(types));
}
-
});
JMenuItem dens = new JMenuItem(
MessageManager.getString("label.sort_by_density"));
dens.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- me.af.avc
- .sortAlignmentByFeatureDensity(Arrays.asList(new String[]
- { type }));
+ String[] types = getTermsInScope(type);
+ me.af.avc.sortAlignmentByFeatureDensity(Arrays.asList(types));
}
});
men.add(dens);
- /*
- * variable colour options include colour by label, by score,
- * by selected attribute text, or attribute value
- */
- final JCheckBoxMenuItem mxcol = new JCheckBoxMenuItem(
- MessageManager.getString("label.variable_colour"));
- mxcol.setSelected(!featureColour.isSimpleColour());
- men.add(mxcol);
- mxcol.addActionListener(new ActionListener()
- {
- JColorChooser colorChooser;
-
- @Override
- public void actionPerformed(ActionEvent e)
- {
- if (e.getSource() == mxcol)
- {
- if (featureColour.isSimpleColour())
- {
- FeatureTypeSettings fc = new FeatureTypeSettings(me.fr, type);
- fc.addActionListener(this);
- }
- else
- {
- // bring up simple color chooser
- colorChooser = new JColorChooser();
- String title = MessageManager
- .getString("label.select_colour");
- JDialog dialog = JColorChooser.createDialog(me,
- title, true, // modal
- colorChooser, this, // OK button handler
- null); // no CANCEL button handler
- colorChooser.setColor(featureColour.getMaxColour());
- dialog.setVisible(true);
- }
- }
- else
- {
- if (e.getSource() instanceof FeatureTypeSettings)
- {
- /*
- * update after OK in feature colour dialog; the updated
- * colour will have already been set in the FeatureRenderer
- */
- FeatureColourI fci = fr.getFeatureColours().get(type);
- table.setValueAt(fci, rowSelected, 1);
- table.validate();
- }
- else
- {
- // probably the color chooser!
- table.setValueAt(new FeatureColour(colorChooser.getColor()),
- rowSelected, 1);
- table.validate();
- me.updateFeatureRenderer(
- ((FeatureTableModel) table.getModel()).getData(),
- false);
- }
- }
- }
- });
-
JMenuItem selCols = new JMenuItem(
MessageManager.getString("label.select_columns_containing"));
selCols.addActionListener(new ActionListener()
@Override
public void actionPerformed(ActionEvent arg0)
{
+ String[] types = getTermsInScope(type);
fr.ap.alignFrame.avc.markColumnsContainingFeatures(false, false,
- false, type);
+ false, types);
}
});
JMenuItem clearCols = new JMenuItem(MessageManager
@Override
public void actionPerformed(ActionEvent arg0)
{
+ String[] types = getTermsInScope(type);
fr.ap.alignFrame.avc.markColumnsContainingFeatures(true, false,
- false, type);
+ false, types);
}
});
JMenuItem hideCols = new JMenuItem(
@Override
public void actionPerformed(ActionEvent arg0)
{
- fr.ap.alignFrame.hideFeatureColumns(type, true);
+ String[] types = getTermsInScope(type);
+ fr.ap.alignFrame.hideFeatureColumns(true, types);
}
});
JMenuItem hideOtherCols = new JMenuItem(
@Override
public void actionPerformed(ActionEvent arg0)
{
- fr.ap.alignFrame.hideFeatureColumns(type, false);
+ String[] types = getTermsInScope(type);
+ fr.ap.alignFrame.hideFeatureColumns(false, types);
}
});
men.add(selCols);
*/
Set<String> types = seq.getFeatures().getFeatureTypesForGroups(true,
visibleGroups.toArray(new String[visibleGroups.size()]));
+
for (String type : types)
{
displayableTypes.add(type);
}
}
+ /*
+ * enable 'Summary View' if some types are sub-types of others
+ */
+ Set<String> parents = SequenceOntologyFactory.getInstance()
+ .getParentTerms(displayableTypes);
+ summaryView.setEnabled(parents.size() < displayableTypes.size());
+
Object[][] data = new Object[displayableTypes.size()][COLUMN_COUNT];
int dataIndex = 0;
{
continue;
}
-
data[dataIndex][TYPE_COLUMN] = type;
data[dataIndex][COLOUR_COLUMN] = fr.getFeatureStyle(type);
FeatureMatcherSetI featureFilter = fr.getFeatureFilter(type);
updateOriginalData(data);
}
- table.setModel(new FeatureTableModel(data));
+ /*
+ * recreate the table model
+ */
+ FeatureTableModel dataModel = new FeatureTableModel(data);
+ table.setModel(dataModel);
+
+ /*
+ * we want to be able to filter out rows for sub-types, but not to sort
+ * rows, so have to add a RowFilter to a disabled TableRowSorter (!)
+ */
+ final TableRowSorter<FeatureTableModel> sorter = new TableRowSorter<>(
+ dataModel);
+ for (int i = 0; i < table.getColumnCount(); i++)
+ {
+ sorter.setSortable(i, false);
+ }
+
+ /*
+ * filter rows to only top-level Ontology types if requested
+ */
+ sorter.setRowFilter(new RowFilter<FeatureTableModel, Integer>()
+ {
+ @Override
+ public boolean include(
+ Entry<? extends FeatureTableModel, ? extends Integer> entry)
+ {
+ if (!summaryView.isSelected())
+ {
+ return true;
+ }
+ int row = entry.getIdentifier(); // this is model, not view, row number
+ String featureType = (String) entry.getModel().getData()[row][TYPE_COLUMN];
+ return parents.contains(featureType);
+ }
+ });
+ table.setRowSorter(sorter);
+
table.getColumnModel().getColumn(0).setPreferredWidth(200);
groupPanel.setLayout(
InputStreamReader in = new InputStreamReader(
new FileInputStream(file), "UTF-8");
- JalviewUserColours jucs = JalviewUserColours.unmarshal(in);
+ JAXBContext jc = JAXBContext
+ .newInstance("jalview.xml.binding.jalview");
+ javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
+ XMLStreamReader streamReader = XMLInputFactory.newInstance()
+ .createXMLStreamReader(in);
+ JAXBElement<JalviewUserColours> jbe = um.unmarshal(streamReader,
+ JalviewUserColours.class);
+ JalviewUserColours jucs = jbe.getValue();
+
+ // JalviewUserColours jucs = JalviewUserColours.unmarshal(in);
/*
* load feature colours
*/
- for (int i = jucs.getColourCount() - 1; i >= 0; i--)
+ for (int i = jucs.getColour().size() - 1; i >= 0; i--)
{
- jalview.schemabinding.version2.Colour newcol = jucs.getColour(i);
- FeatureColourI colour = Jalview2XML.unmarshalColour(newcol);
+ Colour newcol = jucs.getColour().get(i);
+ FeatureColourI colour = jalview.project.Jalview2XML
+ .parseColour(newcol);
fr.setColour(newcol.getName(), colour);
- fr.setOrder(newcol.getName(), i / (float) jucs.getColourCount());
+ fr.setOrder(newcol.getName(), i / (float) jucs.getColour().size());
}
/*
* load feature filters; loaded filters will replace any that are
* currently defined, other defined filters are left unchanged
*/
- for (int i = 0; i < jucs.getFilterCount(); i++)
+ for (int i = 0; i < jucs.getFilter().size(); i++)
{
- jalview.schemabinding.version2.Filter filterModel = jucs
- .getFilter(i);
+ Filter filterModel = jucs.getFilter().get(i);
String featureType = filterModel.getFeatureType();
- FeatureMatcherSetI filter = Jalview2XML.unmarshalFilter(featureType,
- filterModel.getMatcherSet());
+ FeatureMatcherSetI filter = jalview.project.Jalview2XML
+ .parseFilter(featureType, filterModel.getMatcherSet());
if (!filter.isEmpty())
{
fr.setFeatureFilter(featureType, filter);
for (String featureType : sortedTypes)
{
FeatureColourI fcol = fr.getFeatureStyle(featureType);
- jalview.schemabinding.version2.Colour col = Jalview2XML.marshalColour(
- featureType, fcol);
- ucs.addColour(col);
+ Colour col = jalview.project.Jalview2XML.marshalColour(featureType,
+ fcol);
+ ucs.getColour().add(col);
}
/*
{
Iterator<FeatureMatcherI> iterator = filter.getMatchers().iterator();
FeatureMatcherI firstMatcher = iterator.next();
- MatcherSet ms = Jalview2XML.marshalFilter(firstMatcher, iterator,
+ jalview.xml.binding.jalview.FeatureMatcherSet ms = jalview.project.Jalview2XML
+ .marshalFilter(firstMatcher, iterator,
filter.isAnded());
Filter filterModel = new Filter();
filterModel.setFeatureType(featureType);
filterModel.setMatcherSet(ms);
- ucs.addFilter(filterModel);
+ ucs.getFilter().add(filterModel);
}
}
+ JAXBContext jaxbContext = JAXBContext
+ .newInstance(JalviewUserColours.class);
+ Marshaller jaxbMarshaller = jaxbContext.createMarshaller();
+ jaxbMarshaller.marshal(
+ new ObjectFactory().createJalviewUserColours(ucs), out);
+
+ // jaxbMarshaller.marshal(object, pout);
+ // marshaller.marshal(object);
+ out.flush();
- ucs.marshal(out);
+ // ucs.marshal(out);
out.close();
} catch (Exception ex)
{
}
}
});
- help.setFont(JvSwingUtils.getLabelFont());
- help.setText(MessageManager.getString("action.help"));
- help.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- try
- {
- Help.showHelpWindow(HelpId.SequenceFeatureSettings);
- } catch (HelpSetException e1)
- {
- e1.printStackTrace();
- }
- }
- });
JButton cancel = new JButton(MessageManager.getString("action.cancel"));
cancel.setFont(JvSwingUtils.getLabelFont());
}
});
+ summaryView = new JCheckBox(
+ MessageManager.getString("label.summary_view"));
+ summaryView
+ .setToolTipText(
+ MessageManager.getString("label.summary_view_tip"));
+ summaryView.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ resetTable(null);
+ }
+ });
+
transparency.setMaximum(70);
transparency.setToolTipText(
MessageManager.getString("label.transparency_tip"));
- JPanel transPanel = new JPanel(new GridLayout(1, 2));
- bigPanel.add(transPanel, BorderLayout.SOUTH);
+ JPanel lowerPanel = new JPanel(new GridLayout(1, 2));
+ bigPanel.add(lowerPanel, BorderLayout.SOUTH);
JPanel transbuttons = new JPanel(new GridLayout(5, 1));
transbuttons.add(optimizeOrder);
transbuttons.add(sortByScore);
transbuttons.add(sortByDens);
transbuttons.add(help);
+ JPanel transPanel = new JPanel(new GridLayout(3, 1));
+ transPanel.add(summaryView);
+ transPanel.add(new JLabel(" Colour transparency" + ":"));
transPanel.add(transparency);
- transPanel.add(transbuttons);
+ lowerPanel.add(transPanel);
+ lowerPanel.add(transbuttons);
JPanel buttonPanel = new JPanel();
buttonPanel.add(ok);
}
/**
+ * Reorders features by 'dragging' selectedRow to 'newRow'
+ *
+ * @param newRow
+ */
+ protected void dragRow(int newRow)
+ {
+ if (summaryView.isSelected())
+ {
+ // no drag while in summary view
+ return;
+ }
+
+ if (newRow != selectedRow && selectedRow != -1 && newRow != -1)
+ {
+ /*
+ * reposition 'selectedRow' to 'newRow' (the dragged to location)
+ * this could be more than one row away for a very fast drag action
+ * so just swap it with adjacent rows until we get it there
+ */
+ Object[][] data = ((FeatureTableModel) table.getModel())
+ .getData();
+ int direction = newRow < selectedRow ? -1 : 1;
+ for (int i = selectedRow; i != newRow; i += direction)
+ {
+ Object[] temp = data[i];
+ data[i] = data[i + direction];
+ data[i + direction] = temp;
+ }
+ updateFeatureRenderer(data);
+ table.repaint();
+ selectedRow = newRow;
+ }
+ }
+
+ protected void refreshTable()
+ {
+ Object[][] data = ((FeatureTableModel) table.getModel()).getData();
+ for (Object[] row : data)
+ {
+ String type = (String) row[TYPE_COLUMN];
+ FeatureColourI colour = fr.getFeatureColours().get(type);
+ FeatureMatcherSetI filter = fr.getFeatureFilter(type);
+ if (filter == null)
+ {
+ filter = new FeatureMatcherSet();
+ }
+ row[COLOUR_COLUMN] = colour;
+ row[FILTER_COLUMN] = filter;
+ }
+ repaint();
+ }
+
++ /*
+ * Answers a suitable tooltip to show on the colour cell of the table
+ *
+ * @param fcol
+ * @param withHint
+ * if true include 'click to edit' and similar text
+ * @return
+ */
+ public static String getColorTooltip(FeatureColourI fcol,
+ boolean withHint)
+ {
+ if (fcol == null)
+ {
+ return null;
+ }
+ if (fcol.isSimpleColour())
+ {
+ return withHint ? BASE_TOOLTIP : null;
+ }
+ String description = fcol.getDescription();
+ description = description.replaceAll("<", "<");
+ description = description.replaceAll(">", ">");
+ StringBuilder tt = new StringBuilder(description);
+ if (withHint)
+ {
+ tt.append("<br>").append(BASE_TOOLTIP).append("</br>");
+ }
+ return JvSwingUtils.wrapTooltip(true, tt.toString());
+ }
+
+ public static void renderGraduatedColor(JLabel comp, FeatureColourI gcol,
+ int w, int h)
+ {
+ boolean thr = false;
+ StringBuilder tx = new StringBuilder();
+
+ if (gcol.isColourByAttribute())
+ {
+ tx.append(FeatureMatcher
+ .toAttributeDisplayName(gcol.getAttributeName()));
+ }
+ else if (!gcol.isColourByLabel())
+ {
+ tx.append(MessageManager.getString("label.score"));
+ }
+ tx.append(" ");
+ if (gcol.isAboveThreshold())
+ {
+ thr = true;
+ tx.append(">");
+ }
+ if (gcol.isBelowThreshold())
+ {
+ thr = true;
+ tx.append("<");
+ }
+ if (gcol.isColourByLabel())
+ {
+ if (thr)
+ {
+ tx.append(" ");
+ }
+ if (!gcol.isColourByAttribute())
+ {
+ tx.append("Label");
+ }
+ comp.setIcon(null);
+ }
+ else
+ {
+ Color newColor = gcol.getMaxColour();
+ comp.setBackground(newColor);
+ // System.err.println("Width is " + w / 2);
+ Icon ficon = new FeatureIcon(gcol, comp.getBackground(), w, h, thr);
+ comp.setIcon(ficon);
+ // tt+="RGB value: Max (" + newColor.getRed() + ", "
+ // + newColor.getGreen() + ", " + newColor.getBlue()
+ // + ")\nMin (" + minCol.getRed() + ", " + minCol.getGreen()
+ // + ", " + minCol.getBlue() + ")");
+ }
+ comp.setHorizontalAlignment(SwingConstants.CENTER);
+ comp.setText(tx.toString());
+ }
+
// ///////////////////////////////////////////////////////////////////////
// http://java.sun.com/docs/books/tutorial/uiswing/components/table.html
// ///////////////////////////////////////////////////////////////////////
private String[] columnNames = {
MessageManager.getString("label.feature_type"),
MessageManager.getString("action.colour"),
- MessageManager.getString("label.filter"),
+ MessageManager.getString("label.configuration"),
MessageManager.getString("label.show") };
private Object[][] data;
}
/**
- * Answers the class of the object in column c of the first row of the table
+ * Answers the class of column c of the table
*/
@Override
public Class<?> getColumnClass(int c)
{
- Object v = getValueAt(0, c);
- return v == null ? null : v.getClass();
+ switch (c)
+ {
+ case TYPE_COLUMN:
+ return String.class;
+ case COLOUR_COLUMN:
+ return FeatureColour.class;
+ case FILTER_COLUMN:
+ return FeatureMatcherSet.class;
+ default:
+ return Boolean.class;
+ }
}
+ /**
+ * Answers true for all columns except Feature Type
+ */
@Override
public boolean isCellEditable(int row, int col)
{
- return col == 0 ? false : true;
+ return col != TYPE_COLUMN;
}
+ /**
+ * Sets the value in the model for a given row and column. If Visibility
+ * (Show/Hide) is being set, and the table is in Summary View, then it is
+ * set also on any sub-types of the row's feature type.
+ */
@Override
public void setValueAt(Object value, int row, int col)
{
data[row][col] = value;
fireTableCellUpdated(row, col);
+ if (summaryView.isSelected() && col == SHOW_COLUMN)
+ {
+ setSubtypesVisibility(row, (Boolean) value);
+ }
updateFeatureRenderer(data);
}
+ /**
+ * Sets the visibility of any feature types which are sub-types of the type
+ * in the given row of the table
+ *
+ * @param row
+ * @param value
+ */
+ protected void setSubtypesVisibility(int row, Boolean value)
+ {
+ String type = (String) data[row][TYPE_COLUMN];
+ OntologyI so = SequenceOntologyFactory.getInstance();
+
+ for (int r = 0; r < data.length; r++)
+ {
+ if (r != row)
+ {
+ String type2 = (String) data[r][TYPE_COLUMN];
+ if (so.isA(type2, type))
+ {
+ data[r][SHOW_COLUMN] = value;
+ fireTableCellUpdated(r, SHOW_COLUMN);
+ }
+ }
+ }
+ }
}
class ColorRenderer extends JLabel implements TableCellRenderer
{
- javax.swing.border.Border unselectedBorder = null;
+ Border unselectedBorder = null;
- javax.swing.border.Border selectedBorder = null;
-
- final String baseTT = "Click to edit, right/apple click for menu.";
+ Border selectedBorder = null;
public ColorRenderer()
{
{
FeatureColourI cellColour = (FeatureColourI) color;
setOpaque(true);
- setToolTipText(baseTT);
setBackground(tbl.getBackground());
if (!cellColour.isSimpleColour())
{
renderGraduatedColor(comp, gcol, w, h);
}
- public static void renderGraduatedColor(JLabel comp, FeatureColourI gcol,
- int w, int h)
- {
- boolean thr = false;
- StringBuilder tt = new StringBuilder();
- StringBuilder tx = new StringBuilder();
-
- if (gcol.isColourByAttribute())
- {
- tx.append(String.join(":", gcol.getAttributeName()));
- }
- else if (!gcol.isColourByLabel())
- {
- tx.append(MessageManager.getString("label.score"));
- }
- tx.append(" ");
- if (gcol.isAboveThreshold())
- {
- thr = true;
- tx.append(">");
- tt.append("Thresholded (Above ").append(gcol.getThreshold())
- .append(") ");
- }
- if (gcol.isBelowThreshold())
- {
- thr = true;
- tx.append("<");
- tt.append("Thresholded (Below ").append(gcol.getThreshold())
- .append(") ");
- }
- if (gcol.isColourByLabel())
- {
- tt.append("Coloured by label text. ").append(tt);
- if (thr)
- {
- tx.append(" ");
- }
- if (!gcol.isColourByAttribute())
- {
- tx.append("Label");
- }
- comp.setIcon(null);
- }
- else
- {
- Color newColor = gcol.getMaxColour();
- comp.setBackground(newColor);
- // System.err.println("Width is " + w / 2);
- Icon ficon = new FeatureIcon(gcol, comp.getBackground(), w, h, thr);
- comp.setIcon(ficon);
- // tt+="RGB value: Max (" + newColor.getRed() + ", "
- // + newColor.getGreen() + ", " + newColor.getBlue()
- // + ")\nMin (" + minCol.getRed() + ", " + minCol.getGreen()
- // + ", " + minCol.getBlue() + ")");
- }
- comp.setHorizontalAlignment(SwingConstants.CENTER);
- comp.setText(tx.toString());
- if (tt.length() > 0)
- {
- if (comp.getToolTipText() == null)
- {
- comp.setToolTipText(tt.toString());
- }
- else
- {
- comp.setToolTipText(
- tt.append(" ").append(comp.getToolTipText()).toString());
- }
- }
- }
-
class ColorEditor extends AbstractCellEditor
implements TableCellEditor, ActionListener
{
String type;
- JButton button;
+ JButton colourButton;
JColorChooser colorChooser;
// which is a button.
// This button brings up the color chooser dialog,
// which is the editor from the user's point of view.
- button = new JButton();
- button.setActionCommand(EDIT);
- button.addActionListener(this);
- button.setBorderPainted(false);
+ colourButton = new JButton();
+ colourButton.setActionCommand(EDIT);
+ colourButton.addActionListener(this);
+ colourButton.setBorderPainted(false);
// Set up the dialog that the button brings up.
colorChooser = new JColorChooser();
- dialog = JColorChooser.createDialog(button,
+ dialog = JColorChooser.createDialog(colourButton,
MessageManager.getString("label.select_colour"), true, // modal
colorChooser, this, // OK button handler
null); // no CANCEL button handler
if (currentColor.isSimpleColour())
{
// bring up simple color chooser
- button.setBackground(currentColor.getColour());
+ colourButton.setBackground(currentColor.getColour());
colorChooser.setColor(currentColor.getColour());
dialog.setVisible(true);
}
{
// bring up graduated chooser.
chooser = new FeatureTypeSettings(me.fr, type);
- /**
- * @j2sNative
- */
- {
- chooser.setRequestFocusEnabled(true);
- chooser.requestFocus();
- }
+ chooser.setRequestFocusEnabled(true);
+ chooser.requestFocus();
chooser.addActionListener(this);
// Make the renderer reappear.
fireEditingStopped();
* (or filters!) are already set in FeatureRenderer, so just
* update table data without triggering updateFeatureRenderer
*/
- currentColor = fr.getFeatureColours().get(type);
- FeatureMatcherSetI currentFilter = me.fr.getFeatureFilter(type);
- if (currentFilter == null)
- {
- currentFilter = new FeatureMatcherSet();
- }
- Object[] data = ((FeatureTableModel) table.getModel())
- .getData()[rowSelected];
- data[COLOUR_COLUMN] = currentColor;
- data[FILTER_COLUMN] = currentFilter;
+ refreshTable();
}
fireEditingStopped();
me.table.validate();
currentColor = (FeatureColourI) value;
this.rowSelected = row;
type = me.table.getValueAt(row, TYPE_COLUMN).toString();
- button.setOpaque(true);
- button.setBackground(me.getBackground());
+ colourButton.setOpaque(true);
+ colourButton.setBackground(me.getBackground());
if (!currentColor.isSimpleColour())
{
JLabel btn = new JLabel();
- btn.setSize(button.getSize());
+ btn.setSize(colourButton.getSize());
FeatureSettings.renderGraduatedColor(btn, currentColor);
- button.setBackground(btn.getBackground());
- button.setIcon(btn.getIcon());
- button.setText(btn.getText());
+ colourButton.setBackground(btn.getBackground());
+ colourButton.setIcon(btn.getIcon());
+ colourButton.setText(btn.getText());
}
else
{
- button.setText("");
- button.setIcon(null);
- button.setBackground(currentColor.getColour());
+ colourButton.setText("");
+ colourButton.setIcon(null);
+ colourButton.setBackground(currentColor.getColour());
}
- return button;
+ return colourButton;
}
}
String type;
- JButton button;
+ JButton filterButton;
protected static final String EDIT = "edit";
public FilterEditor(FeatureSettings me)
{
this.me = me;
- button = new JButton();
- button.setActionCommand(EDIT);
- button.addActionListener(this);
- button.setBorderPainted(false);
+ filterButton = new JButton();
+ filterButton.setActionCommand(EDIT);
+ filterButton.addActionListener(this);
+ filterButton.setBorderPainted(false);
}
/**
@Override
public void actionPerformed(ActionEvent e)
{
- if (button == e.getSource())
+ if (filterButton == e.getSource())
{
FeatureTypeSettings chooser = new FeatureTypeSettings(me.fr, type);
chooser.addActionListener(this);
}
else if (e.getSource() instanceof Component)
{
-
/*
* after OK in variable colour dialog, any changes to filter
* (or colours!) are already set in FeatureRenderer, so just
* update table data without triggering updateFeatureRenderer
*/
- FeatureColourI currentColor = fr.getFeatureColours().get(type);
- currentFilter = me.fr.getFeatureFilter(type);
- if (currentFilter == null)
- {
- currentFilter = new FeatureMatcherSet();
- }
- Object[] data = ((FeatureTableModel) table.getModel())
- .getData()[rowSelected];
- data[COLOUR_COLUMN] = currentColor;
- data[FILTER_COLUMN] = currentFilter;
+ refreshTable();
fireEditingStopped();
me.table.validate();
}
currentFilter = (FeatureMatcherSetI) value;
this.rowSelected = row;
type = me.table.getValueAt(row, TYPE_COLUMN).toString();
- button.setOpaque(true);
- button.setBackground(me.getBackground());
- button.setText(currentFilter.toString());
- button.setIcon(null);
- return button;
+ filterButton.setOpaque(true);
+ filterButton.setBackground(me.getBackground());
+ filterButton.setText(currentFilter.toString());
+ filterButton.setToolTipText(currentFilter.toString());
+ filterButton.setIcon(null);
+ return filterButton;
}
}
}
class FeatureIcon implements Icon
{
+ private static final Font VERDANA_9 = new Font("Verdana", Font.PLAIN, 9);
+
FeatureColourI gcol;
Color backg;
// need an icon here.
g.setColor(gcol.getMaxColour());
- g.setFont(new Font("Verdana", Font.PLAIN, 9));
+ g.setFont(VERDANA_9);
// g.setFont(g.getFont().deriveFont(
// AffineTransform.getScaleInstance(
import jalview.datamodel.features.FeatureMatcherI;
import jalview.datamodel.features.FeatureMatcherSet;
import jalview.datamodel.features.FeatureMatcherSetI;
+import jalview.io.gff.SequenceOntologyFactory;
import jalview.schemes.FeatureColour;
import jalview.util.ColorUtils;
import jalview.util.MessageManager;
import java.awt.event.MouseEvent;
import java.text.DecimalFormat;
import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashMap;
import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
import javax.swing.BorderFactory;
import javax.swing.BoxLayout;
/*
* the colour and filters to reset to on Cancel
+ * (including feature sub-types if modified)
*/
- private final FeatureColourI originalColour;
+ private Map<String, FeatureColourI> originalColours;
- private final FeatureMatcherSetI originalFilter;
+ private Map<String, FeatureMatcherSetI> originalFilters;
/*
* set flag to true when setting values programmatically,
private JPanel chooseFiltersPanel;
+ /*
+ * feature types present in Feature Renderer which are
+ * sub-types of the one this editor is acting on
+ */
+ private final List<String> subTypes;
+
+ /*
+ * if true, filter or colour settings are also applied to
+ * any feature sub-types in the Sequence Ontology
+ */
+ private boolean applyFiltersToSubtypes;
+
+ private boolean applyColourToSubtypes;
+
/**
* Constructor
*
this.fr = frender;
this.featureType = theType;
ap = fr.ap;
- originalFilter = fr.getFeatureFilter(theType);
- originalColour = fr.getFeatureColours().get(theType);
-
+
+ /*
+ * determine sub-types (if any) of this feature type
+ */
+ List<String> types = fr.getRenderOrder();
+ subTypes = SequenceOntologyFactory.getInstance()
+ .getChildTerms(this.featureType, types);
+ Collections.sort(subTypes); // sort for ease of reading in tooltip
+
+ /*
+ * save original colours and filters for this feature type
+ * and any sub-types, to restore on Cancel
+ */
+ originalFilters = new HashMap<>();
+ originalFilters.put(theType, fr.getFeatureFilter(theType));
+ originalColours = new HashMap<>();
+ originalColours.put(theType, fr.getFeatureColours().get(theType));
+ for (String child : subTypes)
+ {
+ originalFilters.put(child, fr.getFeatureFilter(child));
+ originalColours.put(child, fr.getFeatureColours().get(child));
+ }
+
adjusting = true;
try
String title = MessageManager
.formatMessage("label.display_settings_for", new String[]
{ theType });
- initDialogFrame(this, true, false, title, 500, 500);
-
+ initDialogFrame(this, true, false, title, 580, 500);
waitForInput();
}
: BELOW_THRESHOLD_OPTION);
slider.setEnabled(true);
slider.setValue((int) (fc.getThreshold() * scaleFactor));
- thresholdValue.setText(String.valueOf(getRoundedSliderValue()));
+ thresholdValue.setText(String.valueOf(fc.getThreshold()));
thresholdValue.setEnabled(true);
thresholdIsMin.setEnabled(true);
}
maxColour.setBorder(new LineBorder(Color.black));
/*
- * default max colour to last plain colour;
- * make min colour a pale version of max colour
+ * if not set, default max colour to last plain colour,
+ * and make min colour a pale version of max colour
*/
- FeatureColourI fc = fr.getFeatureColours().get(featureType);
- Color bg = fc.getColour() == null ? Color.BLACK : fc.getColour();
- maxColour.setBackground(bg);
- minColour.setBackground(ColorUtils.bleachColour(bg, 0.9f));
++ FeatureColourI originalColour = originalColours.get(featureType);
+ Color max = originalColour.getMaxColour();
+ if (max == null)
+ {
+ max = originalColour.getColour();
+ minColour.setBackground(ColorUtils.bleachColour(max, 0.9f));
+ }
+ else
+ {
+ maxColour.setBackground(max);
+ minColour.setBackground(originalColour.getMinColour());
+ }
noValueCombo = new JComboBox<>();
noValueCombo.addItem(MessageManager.getString("label.no_colour"));
{
thresholdValue
.setText(String.valueOf(slider.getValue() / scaleFactor));
+ thresholdValue.setBackground(Color.white); // to reset red for invalid
sliderValueChanged();
}
}
MessageManager.getString("action.colour"), true);
/*
+ * option to apply colour to sub-types as well (if there are any)
+ */
+ if (!subTypes.isEmpty())
+ {
+ applyColourToSubtypes = false;
+ colourByPanel.add(initSubtypesPanel(false));
+ }
+
+ /*
* simple colour radio button and colour picker
*/
JPanel simpleColourPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
singleColour.setFont(JvSwingUtils.getLabelFont());
singleColour.setBorder(BorderFactory.createLineBorder(Color.black));
singleColour.setPreferredSize(new Dimension(40, 20));
- // if (originalColour.isGraduatedColour())
- // {
- // singleColour.setBackground(originalColour.getMaxColour());
- // singleColour.setForeground(originalColour.getMaxColour());
- // }
- // else
- // {
- singleColour.setBackground(originalColour.getColour());
- singleColour.setForeground(originalColour.getColour());
- // }
++ FeatureColourI originalColour = originalColours.get(featureType);
++ singleColour.setBackground(originalColour.getColour());
++ singleColour.setForeground(originalColour.getColour());
++
singleColour.addMouseListener(new MouseAdapter()
{
@Override
return colourByPanel;
}
+ /**
+ * Constructs and returns a panel with a checkbox for the option to apply any
+ * changes also to sub-types of the feature type
+ *
+ * @return
+ */
+ protected JPanel initSubtypesPanel(final boolean forFilters)
+ {
+ JPanel toSubtypes = new JPanel(new FlowLayout(FlowLayout.LEFT));
+ toSubtypes.setBackground(Color.WHITE);
+ JCheckBox applyToSubtypesCB = new JCheckBox(MessageManager
+ .formatMessage("label.apply_to_subtypes", featureType));
+ applyToSubtypesCB.setToolTipText(getSubtypesTooltip());
+ applyToSubtypesCB.addActionListener(new ActionListener()
+ {
+ /*
+ * reset and reapply settings on toggle of checkbox
+ */
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ if (forFilters)
+ {
+ applyFiltersToSubtypes = applyToSubtypesCB.isSelected();
+ restoreOriginalFilters();
+ filtersChanged();
+ }
+ else
+ {
+ applyColourToSubtypes = applyToSubtypesCB.isSelected();
+ restoreOriginalColours();
+ colourChanged(true);
+ }
+ }
+ });
+ toSubtypes.add(applyToSubtypesCB);
+
+ return toSubtypes;
+ }
+
private void showColourChooser(JPanel colourPanel, String key)
{
Color col = JColorChooser.showDialog(this,
FeatureColourI acg = makeColourFromInputs();
/*
- * save the colour, and repaint stuff
+ * save the colour, and set on subtypes if selected
*/
fr.setColour(featureType, acg);
+ if (applyColourToSubtypes)
+ {
+ for (String child : subTypes)
+ {
+ fr.setColour(child, acg);
+ }
+ }
+ refreshFeatureSettings();
ap.paintAlignment(updateStructsAndOverview, updateStructsAndOverview);
updateColoursTab();
private FeatureColourI makeColourFromInputs()
{
/*
- * easiest case - a single colour
- */
- if (simpleColour.isSelected())
- {
- return new FeatureColour(singleColour.getBackground());
- }
-
- /*
- * next easiest case - colour by Label, or attribute text
- */
- if (byCategory.isSelected())
- {
- Color c = singleColour.getBackground();
- FeatureColourI fc = new FeatureColour(c);
- fc.setColourByLabel(true);
- String byWhat = (String) colourByTextCombo.getSelectedItem();
- if (!LABEL_18N.equals(byWhat))
- {
- fc.setAttributeName(
- FeatureMatcher.fromAttributeDisplayName(byWhat));
- }
- return fc;
- }
-
- /*
- * remaining case - graduated colour by score, or attribute value
+ * min-max range is to (or from) threshold value if
+ * 'threshold is min/max' is selected
*/
- Color noColour = null;
- if (noValueCombo.getSelectedIndex() == MIN_COLOUR_OPTION)
- {
- noColour = minColour.getBackground();
- }
- else if (noValueCombo.getSelectedIndex() == MAX_COLOUR_OPTION)
- {
- noColour = maxColour.getBackground();
- }
float thresh = 0f;
try
{
// invalid inputs are already handled on entry
}
-
- /*
- * min-max range is to (or from) threshold value if
- * 'threshold is min/max' is selected
- */
float minValue = min;
float maxValue = max;
final int thresholdOption = threshold.getSelectedIndex();
{
maxValue = thresh;
}
+ Color noColour = null;
+ if (noValueCombo.getSelectedIndex() == MIN_COLOUR_OPTION)
+ {
+ noColour = minColour.getBackground();
+ }
+ else if (noValueCombo.getSelectedIndex() == MAX_COLOUR_OPTION)
+ {
+ noColour = maxColour.getBackground();
+ }
/*
- * make the graduated colour
+ * construct a colour that 'remembers' all the options, including
+ * those not currently selected
*/
- FeatureColourI fc = new FeatureColour(minColour.getBackground(),
- maxColour.getBackground(), noColour, minValue, maxValue);
+ FeatureColourI fc = new FeatureColour(singleColour.getBackground(),
+ minColour.getBackground(), maxColour.getBackground(), noColour,
+ minValue, maxValue);
/*
+ * easiest case - a single colour
+ */
+ if (simpleColour.isSelected())
+ {
+ ((FeatureColour) fc).setGraduatedColour(false);
+ return fc;
+ }
+
+ /*
+ * next easiest case - colour by Label, or attribute text
+ */
+ if (byCategory.isSelected())
+ {
+ fc.setColourByLabel(true);
+ String byWhat = (String) colourByTextCombo.getSelectedItem();
+ if (!LABEL_18N.equals(byWhat))
+ {
+ fc.setAttributeName(
+ FeatureMatcher.fromAttributeDisplayName(byWhat));
+ }
+ return fc;
+ }
+
+ /*
+ * remaining case - graduated colour by score, or attribute value;
* set attribute to colour by if selected
*/
String byWhat = (String) colourByRangeCombo.getSelectedItem();
@Override
protected void raiseClosed()
{
+ refreshFeatureSettings();
+ }
+
+ protected void refreshFeatureSettings()
+ {
if (this.featureSettings != null)
{
- featureSettings.actionPerformed(new ActionEvent(this, 0, "CLOSED"));
+ featureSettings.actionPerformed(new ActionEvent(this, 0, "REFRESH"));
}
}
/**
* Action on Cancel is to restore colour scheme and filters as they were when
- * the dialog was opened
+ * the dialog was opened (including any feature sub-types that may have been
+ * changed)
*/
@Override
public void cancelPressed()
{
- fr.setColour(featureType, originalColour);
- fr.setFeatureFilter(featureType, originalFilter);
+ restoreOriginalColours();
+ restoreOriginalFilters();
ap.paintAlignment(true, true);
}
+ protected void restoreOriginalFilters()
+ {
+ for (Entry<String, FeatureMatcherSetI> entry : originalFilters
+ .entrySet())
+ {
+ fr.setFeatureFilter(entry.getKey(), entry.getValue());
+ }
+ }
+
+ protected void restoreOriginalColours()
+ {
+ for (Entry<String, FeatureColourI> entry : originalColours.entrySet())
+ {
+ fr.setColour(entry.getKey(), entry.getValue());
+ }
+ }
+
/**
* Action on text entry of a threshold value
*/
{
try
{
+ /*
+ * set 'adjusting' flag while moving the slider, so it
+ * doesn't then in turn change the value (with rounding)
+ */
adjusting = true;
float f = Float.parseFloat(thresholdValue.getText());
+ f = Float.max(f, this.min);
+ f = Float.min(f, this.max);
+ thresholdValue.setText(String.valueOf(f));
slider.setValue((int) (f * scaleFactor));
threshline.value = f;
thresholdValue.setBackground(Color.white); // ok
-
- /*
- * force repaint of any Overview window or structure
- */
- ap.paintAlignment(true, true);
+ adjusting = false;
+ colourChanged(true);
} catch (NumberFormatException ex)
{
thresholdValue.setBackground(Color.red); // not ok
- } finally
- {
adjusting = false;
}
}
{
filters = new ArrayList<>();
+ JPanel outerPanel = new JPanel();
+ outerPanel.setLayout(new BoxLayout(outerPanel, BoxLayout.Y_AXIS));
+ outerPanel.setBackground(Color.white);
+
+ /*
+ * option to apply colour to sub-types as well (if there are any)
+ */
+ if (!subTypes.isEmpty())
+ {
+ applyFiltersToSubtypes = false;
+ outerPanel.add(initSubtypesPanel(true));
+ }
+
JPanel filtersPanel = new JPanel();
filtersPanel.setLayout(new BoxLayout(filtersPanel, BoxLayout.Y_AXIS));
filtersPanel.setBackground(Color.white);
JvSwingUtils.createTitledBorder(filtersPanel,
MessageManager.getString("label.filters"), true);
+ outerPanel.add(filtersPanel);
JPanel andOrPanel = initialiseAndOrPanel();
filtersPanel.add(andOrPanel);
chooseFiltersPanel.setBackground(Color.white);
filtersPanel.add(chooseFiltersPanel);
- return filtersPanel;
+ return outerPanel;
}
/**
*/
private JPanel initialiseAndOrPanel()
{
- JPanel andOrPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
+ JPanel andOrPanel = new JPanel(new BorderLayout());
andOrPanel.setBackground(Color.white);
+
+// JPanel panel1 = new JPanel(new FlowLayout(FlowLayout.LEFT));
+// andOrPanel.add(panel1, BorderLayout.WEST);
+// panel1.setBackground(Color.white);
+// panel1.setBorder(BorderFactory.createLineBorder(debugBorderColour));
andFilters = new JRadioButton(MessageManager.getString("label.and"));
orFilters = new JRadioButton(MessageManager.getString("label.or"));
ActionListener actionListener = new ActionListener()
new JLabel(MessageManager.getString("label.join_conditions")));
andOrPanel.add(andFilters);
andOrPanel.add(orFilters);
+
return andOrPanel;
}
/**
+ * Builds a tooltip for the 'Apply to subtypes' checkbox with a list of
+ * subtypes of this feature type
+ *
+ * @return
+ */
+ protected String getSubtypesTooltip()
+ {
+ StringBuilder sb = new StringBuilder(20 * subTypes.size());
+ sb.append(MessageManager.getString("label.apply_also_to"));
+ for (String child : subTypes)
+ {
+ sb.append("<br>").append(child);
+ }
+ String tooltip = JvSwingUtils.wrapTooltip(true, sb.toString());
+ return tooltip;
+ }
+
+ /**
* Refreshes the display to show any filters currently configured for the
* selected feature type (editable, with 'remove' option), plus one extra row
* for adding a condition. This should be called after a filter has been
* (note this might now be an empty filter with no conditions)
*/
fr.setFeatureFilter(featureType, combined.isEmpty() ? null : combined);
+ if (applyFiltersToSubtypes)
+ {
+ for (String child : subTypes)
+ {
+ fr.setFeatureFilter(child, combined.isEmpty() ? null : combined);
+ }
+ }
+
+ refreshFeatureSettings();
ap.paintAlignment(true, true);
updateFiltersTab();
}
if (Cache.getDefault("HIDE_INTRONS", true))
{
- af.hideFeatureColumns(SequenceOntologyI.EXON, false);
+ af.hideFeatureColumns(false, SequenceOntologyI.EXON);
}
if (newAlframes != null)
{
Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
- af.statusBar.setText(MessageManager
+ af.setStatus(MessageManager
.getString("label.successfully_pasted_alignment_file"));
try
import jalview.analysis.Finder;
import jalview.api.AlignViewControllerI;
import jalview.api.FeatureColourI;
+ import jalview.api.FinderI;
import jalview.datamodel.Alignment;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SearchResultsI;
public void testFindColumnsWithFeature()
{
SequenceI seq1 = new Sequence("seq1", "-a-MMMaaaaaaaaaaaaaaaa");
- SequenceI seq2 = new Sequence("seq2", "aa--aMM-MMMMMaaaaaaaaaa");
+ SequenceI seq2 = new Sequence("seq2/11-30", "aa--aMM-MMMMMaaaaaaaaaa");
SequenceI seq3 = new Sequence("seq3", "abcab-caD-aaMMMMMaaaaa");
SequenceI seq4 = new Sequence("seq4", "abc--abcaaaaaaaaaaaaaa");
/*
- * features start/end are base 1
+ * features
*/
- seq1.addSequenceFeature(new SequenceFeature("Metal", "desc", 2, 4, 0f,
- null));
- seq1.addSequenceFeature(new SequenceFeature("Helix", "desc", 1, 15, 0f,
- null));
- seq2.addSequenceFeature(new SequenceFeature("Metal", "desc", 4, 10,
- 10f,
- null));
- seq3.addSequenceFeature(new SequenceFeature("Metal", "desc", 11, 15,
- 10f, null));
+ seq1.addSequenceFeature(
+ new SequenceFeature("Metal", "desc", 2, 4, 0f, null));
+ seq1.addSequenceFeature(
+ new SequenceFeature("Helix", "desc", 1, 15, 0f, null));
+ seq2.addSequenceFeature(
+ new SequenceFeature("Metal", "desc", 14, 20, 10f, null));
+ seq3.addSequenceFeature(
+ new SequenceFeature("Metal", "desc", 11, 15, 10f, null));
// disulfide bond is a 'contact feature' - only select its 'start' and 'end'
- seq3.addSequenceFeature(new SequenceFeature("disulfide bond", "desc",
- 8, 12, 0f, null));
+ seq3.addSequenceFeature(
+ new SequenceFeature("disulfide bond", "desc", 8, 12, 0f, null));
/*
* select the first five columns --> Metal in seq1 cols 4-5
/*
* set features visible on a viewport as only visible features are selected
*/
- AlignFrame af = new AlignFrame(new Alignment(new SequenceI[] { seq1,
- seq2, seq3, seq4 }), 100, 100);
+ Alignment al = new Alignment(
+ new SequenceI[]
+ { seq1, seq2, seq3, seq4 });
+ AlignFrame af = new AlignFrame(al, 100, 100);
af.getFeatureRenderer().findAllFeatures(true);
AlignViewController avc = new AlignViewController(af, af.getViewport(),
af.alignPanel);
BitSet bs = new BitSet();
- int seqCount = avc.findColumnsWithFeature("Metal", sg, bs);
+ int seqCount = avc.findColumnsWithFeature(sg, bs, "Metal");
assertEquals(1, seqCount);
assertEquals(2, bs.cardinality());
assertTrue(bs.get(3)); // base 0
*/
sg.setEndRes(6);
bs.clear();
- seqCount = avc.findColumnsWithFeature("Metal", sg, bs);
+ seqCount = avc.findColumnsWithFeature(sg, bs, "Metal");
assertEquals(2, seqCount);
assertEquals(4, bs.cardinality());
assertTrue(bs.get(3));
sg.setStartRes(13);
sg.setEndRes(13);
bs.clear();
- seqCount = avc.findColumnsWithFeature("Metal", sg, bs);
+ seqCount = avc.findColumnsWithFeature(sg, bs, "Metal");
assertEquals(1, seqCount);
assertEquals(1, bs.cardinality());
assertTrue(bs.get(13));
sg.setStartRes(17);
sg.setEndRes(19);
bs.clear();
- seqCount = avc.findColumnsWithFeature("Metal", sg, bs);
+ seqCount = avc.findColumnsWithFeature(sg, bs, "Metal");
assertEquals(0, seqCount);
assertEquals(0, bs.cardinality());
* seq1 feature in columns 4-6 is hidden
* seq2 feature in columns 6-7 is shown
*/
- FeatureColourI fc = new FeatureColour(Color.red, Color.blue, 0f, 10f);
+ FeatureColourI fc = new FeatureColour(null, Color.red, Color.blue, null,
+ 0f, 10f);
fc.setAboveThreshold(true);
fc.setThreshold(5f);
af.getFeatureRenderer().setColour("Metal", fc);
sg.setStartRes(0);
sg.setEndRes(6);
bs.clear();
- seqCount = avc.findColumnsWithFeature("Metal", sg, bs);
+ seqCount = avc.findColumnsWithFeature(sg, bs, "Metal");
assertEquals(1, seqCount);
assertEquals(2, bs.cardinality());
assertTrue(bs.get(5));
sg.setStartRes(10);
sg.setEndRes(12);
bs.clear();
- seqCount = avc.findColumnsWithFeature("disulfide bond", sg, bs);
+ seqCount = avc.findColumnsWithFeature(sg, bs, "disulfide bond");
assertEquals(0, seqCount);
assertEquals(0, bs.cardinality());
sg.setStartRes(5);
sg.setEndRes(17);
bs.clear();
- seqCount = avc.findColumnsWithFeature("disulfide bond", sg, bs);
+ seqCount = avc.findColumnsWithFeature(sg, bs, "disulfide bond");
assertEquals(1, seqCount);
assertEquals(2, bs.cardinality());
assertTrue(bs.get(8));
assertTrue(bs.get(13));
/*
+ * look for multiple features; should match
+ * transcript_variant in seq3 positions 3-6, columns 3-7
+ * sequence_variant in seq2 positions 15-18, columns 7-11
+ * transcript_variant in seq3 positions 8 and 12, columns 9 and 14
+ */
+ seq3.addSequenceFeature(new SequenceFeature("transcript_variant",
+ "desc", 3, 6, 0f, null));
+ seq2.addSequenceFeature(new SequenceFeature("sequence_variant", "desc",
+ 15, 18, 0f, null));
+ sg.setStartRes(0);
+ sg.setEndRes(20);
+ bs.clear();
+ seqCount = avc.findColumnsWithFeature(sg, bs, "transcript_variant",
+ "sequence_variant", "disulfide bond", "junk");
+ assertEquals(2, seqCount);
+ assertEquals(10, bs.cardinality()); // 2-10 and 13, base 0
+ for (int i = 2; i <= 10; i++)
+ {
+ assertTrue(bs.get(i));
+ }
+ assertTrue(bs.get(13));
+
+ /*
* look for a feature that isn't there
*/
sg.setStartRes(0);
sg.setEndRes(19);
bs.clear();
- seqCount = avc.findColumnsWithFeature("Pfam", sg, bs);
+ seqCount = avc.findColumnsWithFeature(sg, bs, "Pfam");
assertEquals(0, seqCount);
assertEquals(0, bs.cardinality());
}
/*
* test Match/Find works first
*/
- Finder f = new Finder(af.getViewport().getAlignment(), null);
- f.setFindAll(true);
- f.setCaseSensitive(true);
- f.find("M+");
+ FinderI f = new Finder(af.getViewport());
+ f.findAll("M+", true, false);
assertEquals(
"Finder found different set of results to manually created SearchResults",
sr, f.getSearchResults());
*/
package jalview.gui;
+ import static org.junit.Assert.assertNotEquals;
import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertFalse;
import static org.testng.Assert.assertNotSame;
import jalview.datamodel.SequenceI;
import jalview.io.DataSourceType;
import jalview.io.FileLoader;
- import jalview.io.Jalview2xmlTests;
+ import jalview.project.Jalview2xmlTests;
import jalview.renderer.ResidueShaderI;
import jalview.schemes.BuriedColourScheme;
import jalview.schemes.FeatureColour;
@Test(groups = "Functional")
public void testHideFeatureColumns()
{
- SequenceI seq1 = new Sequence("Seq1", "ABCDEFGHIJ");
- SequenceI seq2 = new Sequence("Seq2", "ABCDEFGHIJ");
- seq1.addSequenceFeature(new SequenceFeature("Metal", "", 1, 5, 0f, null));
- seq2.addSequenceFeature(new SequenceFeature("Metal", "", 6, 10, 10f,
- null));
- seq1.addSequenceFeature(new SequenceFeature("Turn", "", 2, 4,
- Float.NaN, null));
- seq2.addSequenceFeature(new SequenceFeature("Turn", "", 7, 9,
- Float.NaN, null));
+ SequenceI seq1 = new Sequence("Seq1/01-10", "A---BCDEFG-HIJ");
+ SequenceI seq2 = new Sequence("Seq2/11-20", "-AB-CDEF--GHIJ");
+ String METAL = "Metal";
+ String TURN = "Turn";
+ seq1.addSequenceFeature(
+ new SequenceFeature(METAL, "", 1, 5, 0f, null));
+ seq2.addSequenceFeature(
+ new SequenceFeature(METAL, "", 16, 20, 10f, null));
+ seq1.addSequenceFeature(
+ new SequenceFeature(TURN, "", 2, 4, Float.NaN, null));
+ seq2.addSequenceFeature(
+ new SequenceFeature(TURN, "", 17, 19, Float.NaN, null));
AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
AlignFrame alignFrame = new AlignFrame(al, al.getWidth(),
al.getHeight());
/*
* hiding a feature not present does nothing
*/
- assertFalse(alignFrame.hideFeatureColumns("exon", true));
+ assertFalse(alignFrame.hideFeatureColumns(true, "exon"));
assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
.getNumberOfRegions(), 0);
- assertFalse(alignFrame.hideFeatureColumns("exon", false));
+ assertFalse(alignFrame.hideFeatureColumns(false, "exon"));
assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
-
assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
.getNumberOfRegions(), 0);
/*
* hiding a feature in all columns does nothing
*/
- assertFalse(alignFrame.hideFeatureColumns("Metal", true));
+ assertFalse(alignFrame.hideFeatureColumns(true, METAL));
assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
-
assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
.getNumberOfRegions(), 0);
/*
* threshold Metal to hide features where score < 5
- * seq1 feature in columns 1-5 is hidden
- * seq2 feature in columns 6-10 is shown
+ * seq1 feature in columns 1-8 is hidden
+ * seq2 feature in columns 8-14 is shown
+ * result: columns 8-14 are hidden
+ * note this includes gapped columns spanned by the feature
*/
- FeatureColourI fc = new FeatureColour(Color.red, Color.blue, 0f, 10f);
+ FeatureColourI fc = new FeatureColour(null, Color.red, Color.blue, null,
+ 0f, 10f);
fc.setAboveThreshold(true);
fc.setThreshold(5f);
- alignFrame.getFeatureRenderer().setColour("Metal", fc);
- assertTrue(alignFrame.hideFeatureColumns("Metal", true));
+ alignFrame.getFeatureRenderer().setColour(METAL, fc);
+ assertTrue(alignFrame.hideFeatureColumns(true, METAL));
HiddenColumns hidden = alignFrame.getViewport().getAlignment().getHiddenColumns();
assertEquals(hidden.getNumberOfRegions(), 1);
Iterator<int[]> regions = hidden.iterator();
- int[] next = regions.next();
- assertEquals(next[0], 5);
- assertEquals(next[1], 9);
+ assertEquals(regions.next(), new int[] { 7, 13 }); // base 0
+ assertFalse(regions.hasNext());
/*
* hide a feature present in some columns
- * sequence positions [2-4], [7-9] are column positions
- * [1-3], [6-8] base zero
+ * seq1 positions [2-4] are column positions [4-6] base zero
+ * seq2 positions [17-19] are column positions [10-12] base zero
*/
alignFrame.getViewport().showAllHiddenColumns();
- assertTrue(alignFrame.hideFeatureColumns("Turn", true));
+ assertTrue(alignFrame.hideFeatureColumns(true, TURN));
regions = alignFrame.getViewport().getAlignment()
.getHiddenColumns().iterator();
assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
.getNumberOfRegions(), 2);
- next = regions.next();
- assertEquals(next[0], 1);
- assertEquals(next[1], 3);
- next = regions.next();
- assertEquals(next[0], 6);
- assertEquals(next[1], 8);
+ assertEquals(regions.next(), new int[] { 4, 6 });
+ assertEquals(regions.next(), new int[] { 10, 12 });
+ assertFalse(regions.hasNext());
+
+ /*
+ * hiding a contact feature should only hide start and end positions,
+ * not the intermediate columns
+ */
+ String DISULFIDE = "Disulfide Bond";
+ seq1.addSequenceFeature(
+ new SequenceFeature(DISULFIDE, "", 1, 5, 0f, null));
+ alignFrame.getViewport().showAllHiddenColumns();
+ assertTrue(alignFrame.hideFeatureColumns(true, DISULFIDE));
+ regions = alignFrame.getViewport().getAlignment().getHiddenColumns()
+ .iterator();
+ assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
+ .getNumberOfRegions(), 2);
+ assertEquals(regions.next(), new int[] { 0, 0 });
+ assertEquals(regions.next(), new int[] { 7, 7 });
+ assertFalse(regions.hasNext());
+
+ /*
+ * hide multiple feature types:
+ * TURN columns hides 4-6, 10-12
+ * DISULFIDE columns hides 0, 7
+ * combined is { 0-0, 4-7, 10-12 }
+ */
+ alignFrame.getViewport().showAllHiddenColumns();
+ assertTrue(alignFrame.hideFeatureColumns(true, TURN, DISULFIDE));
+ regions = alignFrame.getViewport().getAlignment().getHiddenColumns()
+ .iterator();
+ assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
+ .getNumberOfRegions(), 3);
+ assertEquals(regions.next(), new int[] { 0, 0 });
+ assertEquals(regions.next(), new int[] { 4, 7 });
+ assertEquals(regions.next(), new int[] { 10, 12 });
+ assertFalse(regions.hasNext());
}
@BeforeClass(alwaysRun = true)
/*
* use read-only test properties file
*/
- Cache.loadProperties("test/jalview/io/testProps.jvprops");
- Jalview.main(new String[] { "-nonews" });
+ Jalview.main(
+ new String[]
+ { "-nonews", "-props", "test/jalview/io/testProps.jvprops" });
}
@AfterMethod(alwaysRun = true)
sp.valueChanged(22);
assertEquals(av2.getResidueShading().getConservationInc(), 22);
}
+
+ /**
+ * Verify that making a New View preserves the dataset reference for the
+ * alignment. Otherwise, see a 'duplicate jar entry' reference when trying to
+ * save alignments with multiple views, and codon mappings will not be shared
+ * across all panels in a split frame.
+ *
+ * @see Jalview2xmlTests#testStoreAndRecoverColourThresholds()
+ */
+ @Test(groups = "Functional")
+ public void testNewView_dsRefPreserved()
+ {
+ AlignViewport av = af.getViewport();
+ AlignmentI al = av.getAlignment();
+ AlignmentI original_ds = al.getDataset();
+ af.newView_actionPerformed(null);
+ assertNotEquals("New view didn't select the a new panel", av,
+ af.getViewport());
+ org.testng.Assert.assertEquals(original_ds,
+ af.getViewport().getAlignment().getDataset(),
+ "Dataset was not preserved in new view");
+ }
}
git://source.jalview.org / jalview.git / commitdiff