</tr>
<tr>
<td>
+ <div align="center">-nonews</div>
+ <td>
+ <div align="left">Disable check for <a href="../webServices/newsreader.html">Jalview news</a> on startup (not recommended other than for classroom / demo usage)</div>
+ </td>
+ </tr>
+ <tr>
+ <td>
<div align="center">-nousagestats</div>
<td>
<div align="left">Turn off google analytics usage tracking</div>
</p>
<p>
Jalview includes a client for retrieving sequences and their
- features via the <a href="http://www.biodas.org">Distributed
- Annotation System</a>.
+ features via the Distributed Annotation System.
</p>
<ol>
<li>Open the Feature Settings panel by selecting "View
<p>
<em>DAS support was introduced in Jalview Version 2.1.</em>
</p>
+ <br/>
+ <p>
+ <em>The DAS registry at http://www.dasregistry.org was decommissioned early in 2015. An unmaintained mirror is currently hosted at http://www.ebi.ac.uk/das-srv/registry/.</em>
+ </p>
<p>
</body>
</html>
<strong>The VARNA RNA Viewer</strong>
</p>
<p>
- <a href="http://varna.lri.fr/index.html">VARNA</a> was integrated
+ <a href="http://varna.lri.fr">VARNA</a> was integrated
into Jalview 2.8 to allow interactive viewing of RNA secondary
structure annotation. It is opened by selecting the <strong>"Structure→View
Structure:"</strong> option in the <a href="../menus/popupMenu.html">sequence
NBRF/PIR (including MODELLER variant), Pfam/Stockholm</em>
</p>
<p>
- The EBI has <a href="http://www.ebi.ac.uk/help/formats.html">examples</a>
- of these file formats.
- </p>
- <p>
Additionally, whole sets of coloured and annotated alignments and
trees can be read from a <a href="../features/jalarchive.html">Jalview
(jar) format</a> file using <strong>Desktop→Load
annotation.</li>
<li><em>Clustal files</em> - certain RNA alignment programs,
such as <a
- href="http://rna.informatik.uni-freiburg.de:8080/LocARNA.jsp"
+ href="http://rna.informatik.uni-freiburg.de/LocARNA"
>LocaRNA</a> output consensus RNA secondary structure lines in the
line normally reserved for the Clustal consensus line in a clustal
file.</li>
region export in flat file generation</li>
<li>Export alignment views for display with the <a
- href="http://biojs.io/d/msa">BioJS MSAViewer</a></li>
+ href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
<li>Export scrollable SVG in HTML page</li>
<li>Optional embedding of BioJSON data when exporting
services were maintained by the Barton group at the University of
Dundee, and ran programs on the Life Sciences High-performance
Computing Cluster. With the advent of <a
- href="http://www.compbio.dundee.ac.uk/JABAWS"
+ href="http://www.compbio.dundee.ac.uk/jabaws"
>JABAWS</a>, however, it is possible for anyone to host Jalview web
services.
</p>
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
-<head>Jalview Desktop RSS News Reader
+<head>
</head>
<body>
<p>
<p>The news reader will be launched automatically when you start
the Desktop if new items are available. Should you want to browse
older items, however, you can open it manually from the 'Jalview
- news reader' option in the Desktop's 'Tools' menu.</p>
- <img src="jalviewrssreader.gif" align="center" width="513"
- height="337" alt="Snapshot of the Jalview Desktop's RSS reader"
- />
- <p>
+ news reader' option in the Desktop's <a href="../menus/desktopMenu.html">'Tools' menu</a>.</p><br/>
+ <div style="text-align: center;"><img src="jalviewrssreader.gif" width="513"
+ height="337" alt="Snapshot of the Jalview Desktop's RSS reader"/></div>
+
+ <br/><p>
The <em>Jalview news reader</em> was introduced in <a
href="http://www.jalview.org/releaseHistory.html#Jalview2.7"
>Jalview version 2.7</a>. Its implementation is based on <a
href="http://jswingreader.sourceforge.net/"
>JSwingReader</a>.
</p>
+ <br/><em>From Jalview 2.10.0, check for news on startup can be disabled with <a href="../features/clarguments.html">command-line parameter</a> '-nonews'.
+ This is not recommended for normal use, but may be useful to avoid interruptions when teaching, demonstrating, recording etc.</em>
</body>
</html>
action.create = Create
action.update = Update
action.delete = Delete
-action.snapshot = Snapshot
action.clear = Clear
action.accept = Accept
action.select_ddbb = --- Select Database ---
action.save_as = Save as...
action.save = Save
action.cancel_fetch = Cancel Fetch
-action.save_omit_hidden_columns = Save / Omit Hidden Regions
action.change_font = Change Font
action.change_font_tree_panel = Change Font (Tree Panel)
action.colour = Colour
action.fetch_db_references = Fetch DB References
action.view_flanking_regions = Show flanking regions
label.view_flanking_regions = Show sequence data either side of the subsequences involved in this alignment
-label.str = Str:
-label.seq = Seq:
label.structures_manager = Structures Manager
label.nickname = Nickname:
label.url = URL:
label.input_file_url = Enter URL or Input File
-label.select_feature = Select feature:
+label.select_feature = Select feature
label.name = Name
+label.name\: = Name:
label.name_param = Name: {0}
label.group = Group
+label.group\: = Group:
label.group_name = Group Name
label.group_description = Group Description
label.edit_group_name_description = Edit Group Name/Description
label.colour = Colour:
-label.description = Description:
+label.description = Description
+label.description\: = Description:
label.start = Start:
label.end = End:
label.current_parameter_set_name = Current parameter set name:
label.to_new_alignment = To New Alignment
label.to_this_alignment = Add To This Alignment
label.apply_colour_to_all_groups = Apply Colour To All Groups
-label.modify_identity_thereshold = Modify Identity Threshold...
-label.modify_conservation_thereshold = Modify Conservation Threshold...
+label.modify_identity_threshold = Modify Identity Threshold...
+label.modify_conservation_threshold = Modify Conservation Threshold...
label.input_from_textbox = Input from textbox
label.centre_column_labels = Centre column labels
label.automatic_scrolling = Automatic Scrolling
label.all_but_selected_region = All but Selected Region (Shift+Ctrl+H)
label.selected_region = Selected Region
label.all_sequences_columns = All Sequences and Columns
-label.hide_insertions = Hide columns gapped for selection
label.hide_selected_annotations = Hide selected annotations
label.show_selected_annotations = Show selected annotations
label.group_consensus = Group Consensus
label.font = Font:
label.size = Size:
label.style = Style:
-label.enter_redundancy_threshold = Enter the redundancy threshold
label.calculating = Calculating....
label.modify_conservation_visibility = Modify conservation visibility
label.colour_residues_above_occurence = Colour residues above % occurence
label.example_param = Example: {0}
label.select_file_format_before_saving = You must select a file format before saving!
label.file_format_not_specified = File format not specified
-label.alignment_contains_hidden_columns = The Alignment contains hidden regions (hidden sequences/columns).\nDo you want to save only the visible alignment?
label.couldnt_save_file = Couldn't save file: {0}
label.error_saving_file = Error Saving File
label.remove_from_default_list = Remove from default list?
label.features_can_be_added_from_searches_1 = (Features can be added from searches or
label.features_can_be_added_from_searches_2 = from Jalview / GFF features files)
label.calculating_pca= Calculating PCA
-label.reveal_columns = Reveal Columns
label.jalview_cannot_open_file = Jalview can't open file
label.jalview_applet = Jalview applet
label.loading_data = Loading data
label.calculating_tree = Calculating tree
label.state_queueing = queuing
label.state_running = running
-label.state_complete = complete
label.state_completed = finished
label.state_job_cancelled = job cancelled!!
label.state_job_error = job error!
label.chimera_help = Chimera Help
label.close_viewer = Close Viewer
label.confirm_close_chimera = This will close Jalview''s connection to {0}.<br>Do you want to close the Chimera window as well?
-label.chimera_help = Chimera Help
label.all = All
label.sort_by = Sort alignment by
label.sort_by_score = Sort by Score
label.align_structures_using_linked_alignment_views = Align structures using {0} linked alignment views
label.connect_to_session = Connect to session {0}
label.threshold_feature_display_by_score = Threshold the feature display by score.
-label.threshold_feature_no_thereshold = No Threshold
-label.threshold_feature_above_thereshold = Above Threshold
-label.threshold_feature_below_thereshold = Below Threshold
-label.adjust_thereshold = Adjust threshold
+label.threshold_feature_no_threshold = No Threshold
+label.threshold_feature_above_threshold = Above Threshold
+label.threshold_feature_below_threshold = Below Threshold
+label.adjust_threshold = Adjust threshold
label.toggle_absolute_relative_display_threshold = Toggle between absolute and relative display threshold.
label.display_features_same_type_different_label_using_different_colour = Display features of the same type with a different label using a different colour. (e.g. domain features)
label.select_colour_minimum_value = Select Colour for Minimum Value
label.select_colour_maximum_value = Select Colour for Maximum Value
-label.open_new_jmol_view_with_all_structures_associated_current_selection_superimpose_using_alignment = Open a new structure viewer with all structures associated with the current selection and superimpose them using the alignment.
label.open_url_param = Open URL {0}
label.open_url_seqs_param = Open URL ({0}..) ({1} seqs)
label.load_pdb_file_associate_with_sequence = Load a PDB file and associate it with sequence {0}
label.logo = Logo
label.non_positional_features = List Non-positional Features
label.database_references = List Database References
-label.share_selection_across_views = Share selection across views
-label.scroll_highlighted_regions = Scroll to highlighted regions
+#label.share_selection_across_views = Share selection across views
+#label.scroll_highlighted_regions = Scroll to highlighted regions
label.gap_symbol = Gap Symbol
label.prot_alignment_colour = Protein Alignment Colour
label.nuc_alignment_colour = Nucleotide Alignment Colour
label.adjusting_parameters_for_calculation = Adjusting parameters for existing Calculation
label.2d_rna_structure_line = 2D RNA {0} (alignment)
label.2d_rna_sequence_name = 2D RNA - {0}
-label.edit_name_and_description_current_group = Edit name and description of current group.
-label.view_structure_for = View structure for {0}
-label.view_all_structures = View all {0} structures.
-label.view_all_representative_structures = View all {0} representative structures.
-label.open_new_jmol_view_with_all_representative_structures_associated_current_selection_superimpose_using_alignment = Opens a new structure viewer with all representative structures\nassociated with the current selection\nsuperimposed with the current alignment.
-label.associate_structure_with_sequence = Associate Structure with Sequence
+label.edit_name_and_description_current_group = Edit name and description of current group
label.from_file = From File
label.enter_pdb_id = Enter PDB Id (or pdbid:chaincode)
-label.discover_pdb_ids = Discover PDB IDs
label.text_colour = Text Colour
action.set_text_colour = Text Colour...
label.structure = Structure
-label.view_structure = View Structure
-label.view_protein_structure = View Protein Structure
label.show_pdbstruct_dialog = 3D Structure Data...
label.view_rna_structure = VARNA 2D Structure
label.clustalx_colours = Clustalx colours
label.reverse = Reverse
label.reverse_complement = Reverse Complement
label.linked_view_title = Linked CDS and protein view
-label.align = Align
label.extract_scores = Extract Scores
label.get_cross_refs = Get Cross-References
label.sort_alignment_new_tree = Sort Alignment With New Tree
label.add_local_source = Add Local Source
label.set_as_default = Set as Default
label.show_labels = Show labels
-label.background_colour = Background Colour
action.background_colour = Background Colour...
label.associate_nodes_with = Associate Nodes With
label.jalview_pca_calculation = Jalview PCA Calculation
label.rest_client_submit = {0} using {1}
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 = <html>Click/drag feature types up or down to change render order.<br/>Double click to select columns containing feature in alignment/current selection<br/>Pressing Alt will select columns outside features rather than inside<br/>Pressing Shift to modify current selection (rather than clear current selection)<br/>Press CTRL or Command/Meta to toggle columns in/outside features<br/></html>
label.feature_settings_click_drag = Drag up or down to change render order.<br/>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.service_preset = Service Preset
label.run_with_preset = Run {0} with preset
label.view_service_doc_url = <html>View <a href="{0}">{1}</a></html>
-label.submit_sequence = <html>Submit {0} {1} {2} {3} to<br/>{4}</html>
action.by_title_param = By {0}
-label.alignment = Alignment
-label.secondary_structure_prediction = Secondary Structure Prediction
-label.sequence_database_search = Sequence Database Search
-label.analysis = Analysis
-label.protein_disorder = Protein Disorder
label.source_from_db_source = Sources from {0}
label.from_msname = from {0}
label.superpose_with = Superpose with
-action.do = Do
label.scale_label_to_column = Scale Label to Column
label.add_new_row = Add New Row
label.edit_label_description = Edit Label/Description
label.copied_sequences = Copied sequences
label.cut_sequences = Cut Sequences
label.conservation_colour_increment = Conservation Colour Increment ({0})
-label.percentage_identity_thereshold = Percentage Identity Threshold ({0})
+label.percentage_identity_threshold = Percentage Identity Threshold ({0})
label.error_unsupported_owwner_user_colour_scheme = Unsupported owner for User Colour scheme dialog
label.save_alignment_to_file = Save Alignment to file
label.save_features_to_file = Save Features to File
label.saving_vamsas_doc = Saving VAMSAS Document to {0}
label.load_feature_colours = Load Feature Colours
label.save_feature_colours = Save Feature Colour Scheme
-label.dataset_for = {0} Dataset for {1}
label.select_startup_file = Select startup file
label.select_default_browser = Select default web browser
label.save_tree_as_newick = Save tree as newick file
error.implementation_error_sortbyfeature = Implementation Error - sortByFeature method must be one of FEATURE_SCORE, FEATURE_LABEL or FEATURE_DENSITY.
error.not_yet_implemented = Not yet implemented
error.unknown_type_dna_or_pep = Unknown Type {0} - dna or pep are the only allowed values.
-error.implementation_error_dont_know_thereshold_annotationcolourgradient = Implementation error: don't know about threshold setting for current AnnotationColourGradient.
-error.implementation_error_embeddedpopup_not_null = Implementation error - embeddedPopup must be non-null
-error.invalid_colour_for_mycheckbox = Invalid color for MyCheckBox
-error.implementation_error_unrecognised_render_object_for_features_type = Implementation Error: Unrecognised render object {0} for features of type {1}
-error.implementation_error_unsupported_feature_colour_object = Implementation error: Unsupported feature colour object.
+error.implementation_error_dont_know_threshold_annotationcolourgradient = Implementation error: don't know about threshold setting for current AnnotationColourGradient.
error.invalid_separator_parameter = Invalid separator parameter - must be non-zero length
error.alignment_cigararray_not_implemented = Alignment(CigarArray) not yet implemented
-error.weak_sequencei_equivalence_not_yet_implemented = Weak sequenceI equivalence not yet implemented.
-error.implementation_error_can_only_make_alignmnet_from_cigararray = Implementation Error - can only make an alignment view from a CigarArray of sequences.
error.empty_view_cannot_be_updated = empty view cannot be updated.
error.mismatch_between_number_of_sequences_in_block = Mismatch between number of sequences in block {0} ({1}) and the original view ({2})
error.padding_not_yet_implemented = Padding not yet implemented
error.implementation_bug_cigar_operation = Implementation Bug. Cigar Operation {0} {1} not one of {2}, {3}, or {4}.
error.implementation_error_for_new_cigar = Implementation error for new Cigar(SequenceI)
error.implementation_error_cigar_seq_no_operations = Implementation error: {0}th sequence Cigar has no operations.
-error.implementation_error_jmol_getting_data = Implementation error - Jmol seems to be still working on getting its data - report at http://issues.jalview.org/browse/JAL-1016
error.implementation_error_no_pdbentry_from_index = Implementation error - no corresponding pdbentry (for index {0}) to add sequences mappings to
error.jmol_version_not_compatible_with_jalview_version = Jmol version {0} is not compatible with this version of Jalview. Report this problem at issues.jalview.org
error.not_implemented_remove = Remove: Not implemented
error.not_implemented_clone = Clone: Not implemented
-error.implementation_error_chimera_getting_data = Implementation error - Chimera seems to be still working on getting its data - report at http://issues.jalview.org/browse/JAL-1016
error.call_setprogressbar_before_registering_handler = call setProgressBar before registering the progress bar's handler.
label.cancelled_params = Cancelled {0}
error.implementation_error_cannot_show_view_alignment_frame = Implementation error: cannot show a view from another alignment in an AlignFrame.
-error.implementation_error_dont_know_about_thereshold_setting = Implementation error: don't know about threshold setting for current AnnotationColourGradient.
+error.implementation_error_dont_know_about_threshold_setting = Implementation error: don't know about threshold setting for current AnnotationColourGradient.
error.eps_generation_not_implemented = EPS Generation not yet implemented
error.png_generation_not_implemented = PNG Generation not yet implemented
error.try_join_vamsas_session_another = Trying to join a vamsas session when another is already connected
error.implementation_error_cannot_find_marshaller_for_param_set =Implementation error: Can't find a marshaller for the parameter set
error.implementation_error_old_jalview_object_not_bound =IMPLEMENTATION ERROR: old jalview object is not bound ! ({0})
error.implementation_error_vamsas_doc_class_should_bind_to_type = Implementation Error: Vamsas Document Class {0} should bind to a {1} (found a {2})
-error.implementation_error_jalview_class_should_bind_to_type = Implementation Error: Jalview Class {0} should bind to a {1} (found a {2})
error.invalid_vamsas_rangetype_cannot_resolve_lists = Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!
error.implementation_error_maplist_is_null = Implementation error. MapList is null for initMapType.
error.implementation_error_cannot_have_null_alignment = Implementation error: Cannot have null alignment property key
error.dbrefsource_implementation_exception =DBRefSource Implementation Exception
error.implementation_error_dbinstance_must_implement_interface = Implmentation Error - getDbInstances must be given a class that implements jalview.ws.seqfetcher.DbSourceProxy (was given{0})
error.implementation_error_must_init_dbsources =Implementation error. Must initialise dbSources
-label.view_controller_toggled_marked = {0} {1} columns containing features of type {2} across {3} sequence(s)
+label.view_controller_toggled_marked = {0} {1} columns {2} features of type {3} across {4} sequence(s)
label.toggled = Toggled
label.marked = Marked
-label.not = not
+label.containing = containing
+label.not_containing = not containing
label.no_feature_of_type_found = No features of type {0} found.
label.submission_params = Submission {0}
label.empty_alignment_job = Empty Alignment Job
label.pca_calculating = Calculating PCA
label.select_foreground_colour = Choose foreground colour
label.select_colour_for_text = Select Colour for Text
-label.adjunst_foreground_text_colour_thereshold = Adjust Foreground Text Colour Threshold
+label.adjunst_foreground_text_colour_threshold = Adjust Foreground Text Colour Threshold
label.select_subtree_colour = Select Sub-Tree Colour
label.create_new_sequence_features = Create New Sequence Feature(s)
label.amend_delete_features = Amend/Delete Features for {0}
exception.mismatched_closing_char = Mismatched closing character {0}
exception.mismatched_opening_char = Mismatched opening character {0} at {1}
exception.invalid_datasource_couldnt_obtain_reader = Invalid datasource. Could not obtain Reader
-exception.index_value_not_in_range = {0}: Index value {1} not in range [0..{2}]
exception.unterminated_cigar_string = Unterminated cigar string
exception.unexpected_operation_cigar_string_pos = Unexpected operation {0} in cigar string (position {1} in {2}
exception.couldnt_parse_responde_from_annotated3d_server = Couldn't parse response from Annotate3d server
exception.pfam_no_sequences_found = No sequences found (PFAM input)
exception.stockholm_invalid_format = This file is not in valid STOCKHOLM format: First line does not contain '# STOCKHOLM'
exception.couldnt_parse_sequence_line = Could not parse sequence line: {0}
-exception.error_parsing_line = Error parsing {0}
exception.unknown_annotation_detected = Unknown annotation detected: {0} {1}
exception.couldnt_store_sequence_mappings = Couldn't store sequence mappings for {0}
exception.matrix_too_many_iteration = Too many iterations in {0} (max is {1})
exception.browser_unable_to_locate = Unable to locate browser: {0}
exception.invocation_target_exception_creating_aedesc = InvocationTargetException while creating AEDesc: {0}
exception.illegal_access_building_apple_evt= IllegalAccessException while building AppleEvent: {0}
-exception.instantiation_creating_aedesc = InstantiationException while creating AEDesc: {0}
exception.unable_to_launch_url = Unable to launch URL: {0}
exception.unable_to_create_internet_config = Unable to create an Internet Config instance: {0}
exception.invocation_target_calling_url = InvocationTargetException while calling openURL: {0}
exception.das_source_doesnt_support_sequence_command = Source {0} does not support the sequence command.
exception.invalid_das_source = Invalid das source: {0}
exception.ebiembl_retrieval_failed_on = EBI EMBL XML retrieval failed on {0}:{1}
-label.no_embl_record_found = # No EMBL record retrieved for {0}:{1}
-label.embl_successfully_parsed = # Successfully parsed the {0} queries into an Alignment
exception.no_pdb_records_for_chain = No PDB Records for {0} chain {1}
exception.unexpected_handling_rnaml_translation_for_pdb = Unexpected exception when handling RNAML translation of PDB data
exception.couldnt_recover_sequence_properties_for_alignment = Couldn't recover sequence properties for alignment
label.add_jabaws_url = Add new JABAWS URL
label.news_from_jalview = News from http://www.jalview.org
label.cut_paste_alignmen_file = Cut & Paste Alignment File
-label.enter_redundancy_thereshold = Enter the redundancy threshold
-label.select_dark_light_set_thereshold = <html><i>Select a dark and light text colour, then set the threshold to<br>switch between colours, based on background colour</i></html>
+label.enter_redundancy_threshold = Enter the redundancy threshold
+label.select_dark_light_set_threshold = <html><i>Select a dark and light text colour, then set the threshold to<br>switch between colours, based on background colour</i></html>
label.select_feature_colour = Select Feature Colour
label.delete_all = Delete all sequences
warn.delete_all = <html>Deleting all sequences will close the alignment window.<br>Confirm deletion or Cancel.
label.no_colour_selection_warn = Error saving colour scheme
label.open_split_window? = Would you like to open as a split window, with cDNA and protein linked?
label.open_split_window = Open split window
-label.no_mappings = No mappings found
action.no = No
action.yes = Yes
label.for = for
label.select_by_annotation = Select/Hide Columns by Annotation
action.select_by_annotation = Select/Hide Columns by Annotation...
label.threshold_filter = Threshold Filter
-action.hide = Hide
-action.select = Select
label.alpha_helix = Alpha Helix
label.beta_strand = Beta Strand
label.turn = Turn
label.select_all = Select All
label.structures_filter = Structures Filter
label.search_filter = Search Filter
-label.description = Description
label.include_description= Include Description
action.back = Back
label.hide_insertions = Hide Insertions
label.mark_as_representative = Mark as representative
label.open_jabaws_web_page = Open JABAWS web page
-label.opens_the_jabaws_server_homepage = Opens the JABAWS server's homepage in web browser
label.pdb_sequence_fetcher = PDB Sequence Fetcher
label.result = result
label.results = results
status.obtaining_mapping_with_sifts = Obtaining mapping with SIFTS
status.obtaining_mapping_with_nw_alignment = Obtaining mapping with NW alignment
status.exporting_alignment_as_x_file = Exporting alignment as {0} file
+label.column = Column
+label.cant_map_cds = Unable to map CDS to protein\nCDS missing or incomplete
+label.operation_failed = Operation failed
action.create = Crear
action.update = Actualizar
action.delete = Borrar
-action.snapshot = Imagen
action.clear = Limpiar
action.accept = Aceptar
action.select_ddbb = --- Seleccionar base de datos ---
action.save_as = Guardar como
action.save = Guardar
action.cancel_fetch = Cancelar búsqueda
-action.save_omit_hidden_columns = Guardar / Omitir las columnas ocultas
action.change_font = Cambiar Fuente
action.change_font_tree_panel = Cambiar fuente (panel del árbol)
action.colour = Color
action.fetch_db_references = Recuperar referencias a base de datos
action.view_flanking_regions = Mostrar flancos
label.view_flanking_regions = Mostrar los datos de la secuencia a ambos lados de las subsecuencias implicadas en este alineamiento
-label.str = Str:
-label.seq = Seq:
label.structures_manager = Administrar estructuras
label.nickname = Sobrenombre:
label.url = URL:
label.input_file_url = Introducir URL en el fichero de entrada
-label.select_feature = Seleccionar función:
-label.name = Nombre:
+label.select_feature = Seleccionar característica
+label.name = Nombre
+label.name\: = Nombre:
label.name_param = Nombre: {0}
-label.group = Grupo:
+label.group = Grupo
+label.group\: = Grupo:
label.group_name = Nombre del grupo
label.group_description = Descripción del grupo
label.edit_group_name_description = Editar nombre/descripción del grupo
label.colour = Color:
-label.description = Descripción:
+label.description = Descripción
+label.description\: = Descripción:
label.start = Comenzar:
label.end = Terminar:
label.current_parameter_set_name = Nombre actual del conjunto de parámetros:
label.to_new_alignment = A nuevo alineamiento
label.to_this_alignment = Añadir a este alineamiento
label.apply_colour_to_all_groups = Aplicar color a todos los grupos
-label.modify_identity_thereshold = Modificar el umbral de identidad...
-label.modify_conservation_thereshold = Modificar el umbral de conservación...
+label.modify_identity_threshold = Modificar el umbral de identidad...
+label.modify_conservation_threshold = Modificar el umbral de conservación...
label.input_from_textbox = Introducir desde el cuadro de texto
label.centre_column_labels = Centrar las etiquetas de las columnas
label.automatic_scrolling = Desplazamiento automático
label.about = Acerca de...
label.show_sequence_limits = Mostrar los límites de la secuencia
label.feature_settings = Ajustar funciones...
-label.sequence_features = Funciones de la secuencia
label.all_columns = Todas las columnas
label.all_sequences = Todas las secuencias
label.selected_columns = Columnas seleccionadas
label.font = Fuente:
label.size = Talla:
label.style = Estilo:
-label.enter_redundancy_threshold = Introducir el umbral de redundancia
label.calculating = Calculando....
label.modify_conservation_visibility = Modificar la visibilidad de conservación
label.colour_residues_above_occurence = Residuos de color por encima del % de aparición
label.select_das_service_from_table = Seleccionar servicio DAS de la tabla para leer una descripción completa aquí.
label.session_update = Actualizar sesión
label.new_vamsas_session = Nueva sesión Vamsas
-label.load_vamsas_session = Cargar sesión Vamsas
-label.save_vamsas_session = Guardar sesión Vamsas
action.save_vamsas_session = Guardar Sesión Vamsas
label.select_vamsas_session_opened_as_new_vamsas_session= Selecciones una sesión vamsas para abrirla como una nueva sesión.
label.open_saved_vamsas_session = Abrir una sesión VAMSAS guardada
label.example_param = Ejemplo: {0}
label.select_file_format_before_saving = Debe seleccionar un formato de fichero antes de guardar!
label.file_format_not_specified = Formato de fichero no especificado
-label.alignment_contains_hidden_columns = El alineamiento contiene columnas ocultas.\nQuieres guardar s\u00F3lo el alineamiento visible?
label.couldnt_save_file = No se pudo guardar el fichero: {0}
label.error_saving_file = Error guardando el fichero
label.remove_from_default_list = eliminar de la lista de defectuosos?
label.features_can_be_added_from_searches_1 = (Las funciones pueden ser añadidas de búsquedas o
label.features_can_be_added_from_searches_2 = de ficheros de funciones Jalview / GFF)
label.calculating_pca= Calculando PCA
-label.reveal_columns = Mostrar Columnas
label.jalview_cannot_open_file = Jalview no puede abrir el fichero
label.jalview_applet = Aplicación Jalview
label.loading_data = Cargando datos
label.calculating_tree = Calculando árbol
label.state_queueing = En cola
label.state_running = Procesando
-label.state_complete = Completar
label.state_completed = Finalizado
label.state_job_cancelled = ¡Trabajo cancelado!
label.state_job_error = Error del trabajo!
label.load_features_annotations = Cargar características/anotaciones ...
label.export_features = Exportar características...
label.export_annotations = Exportar anotaciones ...
-label.jalview_copy = Copiar (sólo Jalview)
-label.jalview_cut = Cortar (sólo Jalview)
label.to_upper_case = Pasar a mayúsculas
label.to_lower_case = Pasar a minúsculas
label.toggle_case = Alternar mayúsculas y minúsculas
label.edit_sequence = Editar secuencia
label.edit_sequences = Editar secuencias
label.sequence_details = Detalles de la secuencia
-label.jmol_help = Ayuda de Jmol
-label.all = Todo
+label.jmol_help = Ayuda de Jmol
+# Todos/Todas is gender-sensitive, but currently only used for feminine (cadena / anotación)!
+label.all = Todas
label.sort_by = Ordenar por
label.sort_by_score = Ordenar por puntuación
label.sort_by_density = Ordenar por densidad
label.align_structures_using_linked_alignment_views = Alinear las estructuras utlizando las {0} vistas de alineamiento enlazadas
label.connect_to_session = Conectar a la sesión {0}
label.threshold_feature_display_by_score = Filtrar la característica mostrada por puntuación.
-label.threshold_feature_no_thereshold = Sin umbral
-label.threshold_feature_above_thereshold = Por encima del umbral
-label.threshold_feature_below_thereshold = Por debajo del umbral
-label.adjust_thereshold = Ajustar umbral
+label.threshold_feature_no_threshold = Sin umbral
+label.threshold_feature_above_threshold = Por encima del umbral
+label.threshold_feature_below_threshold = Por debajo del umbral
+label.adjust_threshold = Ajustar umbral
label.toggle_absolute_relative_display_threshold = Cambiar entre mostrar el umbral absoluto y el relativo.
label.display_features_same_type_different_label_using_different_colour = Mostrar las características del mismo tipo con una etiqueta diferente y empleando un color distinto (p.e. características del dominio)
label.select_colour_minimum_value = Seleccionar el color para el valor mínimo
label.select_colour_maximum_value = Seleccionar el color para el valor máximo
-label.open_new_jmol_view_with_all_structures_associated_current_selection_superimpose_using_alignment = Abrir una nueva vista Jmol con todas las estructuras asociadas con la selección acxtual y superponer las utilizando el alineamiento.
label.open_url_param = Abrir URL {0}
label.open_url_seqs_param = Abrir URL ({0}..) ({1} secuencias)
label.load_pdb_file_associate_with_sequence = Cargar un fichero PDB y asociarlo con la secuencia {0}
label.logo = Logo
label.non_positional_features = Características no posicionales
label.database_references = Referencias a base de datos
-label.share_selection_across_views = Compartir la selección en todas las vistas
-label.scroll_highlighted_regions = Desplazarse hasta las regiones resaltadas
+#label.share_selection_across_views = Compartir la selección en todas las vistas
+#label.scroll_highlighted_regions = Desplazarse hasta las regiones resaltadas
label.gap_symbol = Símbolo del hueco
-label.alignment_colour = Color del alineamiento
label.address = Dirección
label.port = Puerto
label.default_browser_unix = Navegador por defecto (Unix)
label.adjusting_parameters_for_calculation = Ajustar los parámetros para el cálculo existente
label.2d_rna_structure_line = 2D RNA {0}
label.2d_rna_sequence_name = 2D RNA - {0}
-label.edit_name_and_description_current_group = Editar el nombre y la descripción del grupo actual.
-label.view_structure_for = Visualizar la estructura para {0}
-label.view_all_structures = Visualizar todas las {0} estructuras.
-label.view_all_representative_structures = Visualizar todas las {0} estructuras representativas.
-label.open_new_jmol_view_with_all_representative_structures_associated_current_selection_superimpose_using_alignment = Abrir una nueva vista de Jmol con todas las estructuras representativas\nasociadas con la selecci\u00F3n actual\nsuperpuesta con el alineamiento actual.
-label.associate_structure_with_sequence = Asociar estructura con la secuencia
+label.edit_name_and_description_current_group = Editar el nombre y la descripción del grupo actual
label.from_file = desde fichero
label.enter_pdb_id = Introducir PDB Id
-label.discover_pdb_ids = Buscar PDB ids
label.text_colour = Color del texto
label.structure = Estructura
-label.view_structure = Visualizar estructura
label.clustalx_colours = Colores de Clustalx
label.above_identity_percentage = Sobre % identidad
label.create_sequence_details_report_annotation_for = Anotación para {0}
label.add_local_source = Añadir fuente local
label.set_as_default = Establecer por defecto
label.show_labels = Mostrar etiquetas
-label.background_colour = Color de fondo
label.associate_nodes_with = Asociar nodos con
label.jalview_pca_calculation = Cálculo del PCA por Jalview
label.link_name = Nombre del enalce
label.service_preset = Preselección del servicio
label.run_with_preset = Ejecutar {0} con preselección
label.view_service_doc_url = Visualizar <a href="{0}">{1}</a></html>
-label.submit_sequence = Enviar {0} {1} {2} {3} a<br/>{4}</html>
action.by_title_param = por {0}
-label.alignment = Alineamiento
-label.secondary_structure_prediction = Predicción de la estructura secundaria
-label.sequence_database_search = Búsqueda en base de datos de secuencias
-label.analysis = Análisis
-label.protein_disorder = Desorden en la proteína
label.source_from_db_source = Fuentes de {0}
label.from_msname = de {0}
label.superpose_with = Superponer con...
-action.do = Hacer
label.scale_label_to_column = Ajustar la etiqueta a la columna
label.add_new_row = Añadir nuevo fila
label.edit_label_description = Editar etiqueta/descripción
label.copied_sequences = Secuencias copiadas
label.cut_sequences = Cortar secuencias
label.conservation_colour_increment = Incremento de Conservación del Color ({0})
-label.percentage_identity_thereshold = Umbral del Porcentaje de Identidad ({0})
+label.percentage_identity_threshold = Umbral del Porcentaje de Identidad ({0})
label.error_unsupported_owwner_user_colour_scheme = Propietario no soportado para el diálogo del Esquema Cromático del Usuario
label.save_alignment_to_file = Guardar Alineamiento en fichero
label.save_features_to_file = Guardar Características en un fichero
label.saving_vamsas_doc = Guardando el documento VAMSAS en {0}
label.load_feature_colours = Cargar colores de características
label.save_feature_colours = Guardar esquema cromático de características
-label.dataset_for = {0} conjunto de datos para {1}
label.select_startup_file = Seleccionar fichero de arranque
label.select_default_browser = Seleccionar navegador web por defecto
label.save_tree_as_newick = Guardar árbol como fichero newick
error.implementation_error_sortbyfeature = Error de implementación - sortByFeature debe ser uno de FEATURE_SCORE, FEATURE_LABEL o FEATURE_DENSITY.
error.not_yet_implemented = No se ha implementado todavía
error.unknown_type_dna_or_pep = Tipo desconocido {0} - dna o pep son los únicos valores permitidos
-error.implementation_error_dont_know_thereshold_annotationcolourgradient = Error de implementación: no se conoce el valor umbral para el AnnotationColourGradient actual.
-error.implementation_error_embeddedpopup_not_null = Error de implementación - embeddedPopup debe ser no nulo.
-error.invalid_colour_for_mycheckbox = Color no válido para MyCheckBox
-error.implementation_error_unrecognised_render_object_for_features_type = Error de implementación: no se reconoce el objeto de representación {0} para las características de tipo {1}
-error.implementation_error_unsupported_feature_colour_object = Error de implementación: objeto de color de características no soportado.
+error.implementation_error_dont_know_threshold_annotationcolourgradient = Error de implementación: no se conoce el valor umbral para el AnnotationColourGradient actual.
error.invalid_separator_parameter = Separador de parámetros no válido - debe tener longitud mayor que cero
error.alignment_cigararray_not_implemented = Alignment(CigarArray) no se ha implementado todavía
-error.weak_sequencei_equivalence_not_yet_implemented = Equivalencia débil sequenceI no se ha implementado todavía.
-error.implementation_error_can_only_make_alignmnet_from_cigararray = Error de implementación - sólo se puede construir un vista de alineamiento a partir de una CigarArray de secuencias.
error.empty_view_cannot_be_updated = una vista vacía no se puede actualizar.
error.mismatch_between_number_of_sequences_in_block = No hay coincidencia entre el número de secuencias en el bloque {0} ({1}) y la vista original ({2})
error.padding_not_yet_implemented = El relleno no se ha implementado todavía
error.implementation_bug_cigar_operation = Bug de implementación. La operación Cigar {0} {1} no es ni {2}, ni {3} ni {4}.
error.implementation_error_for_new_cigar = Error de implementación en new Cigar(SequenceI)
error.implementation_error_cigar_seq_no_operations = Error de implementación: la {0}a secuencia Cigar no tiene operaciones.
-error.implementation_error_jmol_getting_data = Error de implementación - Jmol parece estar todavía intentando recuperar sus datos - informe de ello en http://issues.jalview.org/browse/JAL-1016
error.implementation_error_no_pdbentry_from_index = Error de implementación - no existe la correspondiente entrada pdb (para el índice {0}) para añadir el mapeo de secuencias a
error.jmol_version_not_compatible_with_jalview_version = La versión {0} de Jmol no es compatible con esta versión de Jalview. Informe de este problema en http://issues.jalview.org
error.not_implemented_remove = Borrar: no implementado
error.not_implemented_clone = Clonar: no implementado
-error.implementation_error_chimera_getting_data = Error de implementación - Chimera parece estar todavía intentando recuperar sus datos - informe de ello en http://issues.jalview.org/browse/JAL-1016
error.call_setprogressbar_before_registering_handler = llamada a setProgressBar antes de registrar el manejador de la barra de estado
label.cancelled_params = {0} cancelado
error.implementation_error_cannot_show_view_alignment_frame = Error de implementación: no es posible mostrar una vista de otro alineamiento en un AlignFrame.
-error.implementation_error_dont_know_about_thereshold_setting = Error de implementación: no se conoce la configuración del umbral para el AnnotationColourGradient actual.
+error.implementation_error_dont_know_about_threshold_setting = Error de implementación: no se conoce la configuración del umbral para el AnnotationColourGradient actual.
error.eps_generation_not_implemented = La generación de EPS no se ha implementado todavía
error.png_generation_not_implemented = La generación de PNG no se ha implementado todavía
error.try_join_vamsas_session_another = Tratando de establecer una sesión VAMSAS cuando ya había otra conectada
error.implementation_error_cannot_find_marshaller_for_param_set =Error de implementación: no puede encontrar un marshaller para el conjunto de parámetros
error.implementation_error_old_jalview_object_not_bound =Error de implementación: ¡el objeto Jalview antiguo no está enlazado! ({0})
error.implementation_error_vamsas_doc_class_should_bind_to_type = Error de implementación: la clase de documento VAMSAS {0} debe enlazar a {1} (pero se ha encontrado que lo está a {2})
-error.implementation_error_jalview_class_should_bind_to_type = Error de implementación: la clase Jalview {0} debe enlazar a {1} (pero se ha encontrado que lo está a {2})
error.invalid_vamsas_rangetype_cannot_resolve_lists = RangeType VAMSAS no válido - ¡no es posible resolver ambas listas de Pos y Seg con los valores elegidos!
error.implementation_error_maplist_is_null = Error de implementación. MapList es nulo en initMapType.
error.implementation_error_cannot_have_null_alignment = Error de implementación: no es posible tener una clave nula en el alineamiento
error.dbrefsource_implementation_exception = Excepción de implementación DBRefSource
error.implementation_error_dbinstance_must_implement_interface = Error de Implementación- getDbInstances debe recibir una clase que implemente jalview.ws.seqfetcher.DbSourceProxy (recibió {0})
error.implementation_error_must_init_dbsources =Error de implementación. Debe inicializar dbSources
-label.view_controller_toggled_marked = {0} {1} columnas conteniendo características del tipo {2} en {3} secuencia(s)
+label.view_controller_toggled_marked = {0} {1} columnas {2} características del tipo {3} en {4} secuencia(s)
label.toggled = Invertida
label.marked = Marcada
-label.not = no
+label.containing = conteniendo
+label.not_containing = no conteniendo
label.no_feature_of_type_found = No se han encontrado características del tipo {0}.
label.submission_params = Envío {0}
label.empty_alignment_job = Trabajo de alineamiento vacío
label.pca_calculating = Calculando PCA
label.select_foreground_colour = Escoger color del primer plano
label.select_colour_for_text = Seleccione el color del texto
-label.adjunst_foreground_text_colour_thereshold = Ajustar el umbral del color del texto en primer plano
+label.adjunst_foreground_text_colour_threshold = Ajustar el umbral del color del texto en primer plano
label.select_subtree_colour = Seleccioanr el color del sub-árbol
label.create_new_sequence_features = Crear nueva(s) característica(s) de secuencia
label.amend_delete_features = Arrelgar/Borrar características de {0}
exception.mismatched_closing_char = Carácter de cierre discordante {0}
exception.mismatched_opening_char = Carácter de apertura discordante {0} en {1}
exception.invalid_datasource_couldnt_obtain_reader = Fuente de datos no válida. No es posible obtener el Reader
-exception.index_value_not_in_range = {0}: el valor del índice {1} en se encuentra en el rango [0..{2}]
exception.unterminated_cigar_string = Cadena cigar sin terminar
exception.unexpected_operation_cigar_string_pos = Operación no esperada {0} en una cadena cigar (posición {1} en {2})
exception.couldnt_parse_responde_from_annotated3d_server = No es posible parsear la respuesta procedente del servidor Annotate3d
exception.pfam_no_sequences_found = No se han encontrado secuencias (entrada PFAM)
exception.stockholm_invalid_format = Este fichero no es tiene un formato STOCKHOLM válido: la primera línea no contiene '# STOCKHOLM'
exception.couldnt_parse_sequence_line = No es posible parse la línea de secuencia: {0}
-exception.error_parsing_line = Error parseando {0}
exception.unknown_annotation_detected = Anotación desconocida detectada: {0} {1}
exception.couldnt_store_sequence_mappings = No es posible almacenar los mapeos de secuencia para {0}
exception.matrix_too_many_iteration = Demasiadas iteraciones en {0} (el máximo es {1})
exception.browser_unable_to_locate = Imposible encontrar el navegador: {0}
exception.invocation_target_exception_creating_aedesc = InvocationTargetException mientras se creaba AEDesc: {0}
exception.illegal_access_building_apple_evt= IllegalAccessException mientras se construía AppleEvent: {0}
-exception.instantiation_creating_aedesc = InstantiationException mientras se creaba AEDesc: {0}
exception.unable_to_launch_url = Imposible lanzar la URL: {0}
exception.unable_to_create_internet_config = Imposible crear una instancia de configuración de Internet: {0}
exception.invocation_target_calling_url = InvocationTargetException mientras se invocaba openURL: {0}
exception.das_source_doesnt_support_sequence_command = La fuente {0} no soporta el comando sequence.
exception.invalid_das_source = Fuente DAS no válida: {0}
exception.ebiembl_retrieval_failed_on = La recuperación de datos EBI EMBL XML ha fallado en {0}:{1}
-label.no_embl_record_found = # No se ha recuperado ningún registro EMBL de {0}:{1}
-label.embl_successfully_parsed = # Se han parseado con éxito las consultas {0} en un alineamiento
exception.no_pdb_records_for_chain = No se han encontrado registros {0} para la cadena {1}
exception.unexpected_handling_rnaml_translation_for_pdb = Excepcion inesperada cuando se traducían a RNAML los datos PDB
exception.couldnt_recover_sequence_properties_for_alignment = No es posible recuperar las propiedades de la secuencia para el alineamiento
label.add_jabaws_url = Añadir nueva JABAWS URL
label.news_from_jalview = Noticias de http://www.jalview.org
label.cut_paste_alignmen_file = Cortar & Pegar fichero de alineamiento
-label.enter_redundancy_thereshold = Introducir el umbral de redundancia
-label.select_dark_light_set_thereshold = <i>Seleccionar un color oscuro y un color claro para el texto y establecer el umbral en que<br>cambiar entre colores, basándose en el color de fondo</i>
+label.enter_redundancy_threshold = Introducir el umbral de redundancia
+label.select_dark_light_set_threshold = <i>Seleccionar un color oscuro y un color claro para el texto y establecer el umbral en que<br>cambiar entre colores, basándose en el color de fondo</i>
label.select_feature_colour = Seleccionar color de las características
label.ignore_gaps_consensus = Ignorar huecos en el consenso
label.show_group_histogram = Mostrar histograma de grupo
info.invalid_msa_notenough=No suficientes datos de sequencia para alinear
label.result=resultado
label.results=resultados
-label.no_mappings=No hay mapeados encontrados
label.struct_from_pdb=Procesar la estructura secundaria PDB
label.hide_selected_annotations=Ocultar anotaciones seleccionados
info.select_annotation_row=Seleccionar Fila de Anotaciones
action.yes=Sí
label.export_settings=Exportar Ajustes
label.linked_view_title=Vista vinculada de cDNA y proteína
-label.view_protein_structure=Ver Estructura Proteica
label.couldnt_read_data=No se pudo leer los datos
status.opening_file=abriendo fichero
label.except_selected_sequences=Todo excepto secuencias seleccionadas
action.export_features=Exportar Características
error.invalid_regex=Expresión regular inválida
label.autoadd_temp=Añadir anotación factor de temperatura al alineamiento
-tooltip.rnalifold_settings=Modificar la configuración de la predicción RNAAlifold. Úselo para ocultar o mostrar resultados del cálculo de RNA, o cambiar parámetros de el plegado de RNA.
label.chimera_path_tip=Jalview intentará primero las rutas introducidas aquí, Y si no las rutas usuales de instalación
label.structure_chooser=Selector de Estructuras
label.structure_chooser_manual_association=Selector de Estructuras - asociación manual
label.show_pdbstruct_dialog=Datos de Estructura 3D...
label.hide_all=Ocultar todos
label.invert=Invertir
-label.pdb_sequence_getcher=Buscador de Secuencias PDB
tooltip.aacon_settings=Cambiar ajustes para cálculos AACon
-label.align=Alinear
label.mark_as_representative=Marcar como representativa
label.include_description=Incluir Descripción
label.for=para
label.protein=Proteína
warn.oneseq_msainput_selection=La selección actual sólo contiene una única secuencia. ¿Quieres enviar todas las secuencias para la alineación en su lugar?
label.use_rnaview=Usar RNAView para estructura secondaria
-label.opens_the_jabaws_server_homepage=Abre la página de inicio del servidor JABAWS en navegador
label.search_all=Introducir uno o más valores de búsqueda separados por punto y coma ";" (Nota: buscará en toda la base de datos PDB)
label.confirm_close_chimera=Cerrará la conexión de Jalview a {0}.<br>¿Quieres cerrar la ventana Chimera también?
tooltip.rnalifold_calculations=Se calcularán predicciones de estructura secondaria de RNA para el alineaminento, y se actualizarán si se efectuan cambios
-Calcular predicciónes de estructura secondaria para el alineamiento
+tooltip.rnalifold_settings=Modificar la configuración de la predicción RNAAlifold. Úselo para ocultar o mostrar resultados del cálculo de RNA, o cambiar parámetros de el plegado de RNA.
label.show_selected_annotations=Mostrar anotaciones seleccionadas
status.colouring_chimera=Coloreando Chimera
label.configure_displayed_columns=Configurar Columnas Mostradas
-exception.pdb_server_error=Error desde el servidor PDB
exception.resource_not_be_found=El recurso solicitado no se ha encontrado
label.aacon_calculations=cálculos AACon
label.pdb_web-service_error=Error de servicio web PDB
warn.delete_all=<html>Borrar todas las secuencias cerrará la ventana del alineamiento.<br>Confirmar o Cancelar.
label.select_all=Seleccionar Todos
label.alpha_helix=Hélice Alfa
-label.sequence_details_for=Detalles de secuencia para {0}
label.chimera_help=Ayuda para Chimera
label.find_tip=Buscar alineamiento, selección o IDs de secuencia para una subsecuencia (sin huecos)
-exception.pdb_server_unreachable=Jalview no puede conectar con el servidor PDBE Solr.\nPor favor, asegúrese de que está conectado a Internet y vuelva a intentarlo.
label.structure_viewer=Visualizador de estructura for defecto
label.embbed_biojson=Incrustar BioJSON al exportar HTML
label.transparency_tip=Ajustar la transparencia a "ver a través" los colores de las características.
info.invalid_msa_input_mininfo=Necesita por lo menos dos secuencias con al menos 3 residuos cada una, sin regiones ocultas entre ellas.
label.chimera_missing=Visualizador de estructura Chimera no encontrado.<br/>Por favor, introduzca la ruta de Chimera,<br/>o descargar e instalar la UCSF Chimera.
label.save_as_biojs_html=Guardar como HTML BioJs
-exception.pdb_rest_service_no_longer_available=Servicios Rest PDB ya no están disponibles!
exception.fts_server_unreachable=Jalview no puede conectar con el servidor {0}. \nPor favor asegúrese de que está conectado a Internet y vuelva a intentarlo.
exception.outofmemory_loading_mmcif_file=Sin memoria al cargar el fichero mmCIF
label.hide_columns_not_containing=Ocultar las columnas que no contengan
status.fetching_dbrefs_for_sequences_without_valid_refs=Buscando referencias para {0} secuencia(s) sin referencia válida necesaria para mapeado SIFTS
status.obtaining_mapping_with_nw_alignment=Obteniendo mapeo por alineamiento Needleman y Wunsch
status.exporting_alignment_as_x_file = Exportando alineamiento como fichero tipo {0}
+label.column = Columna
+label.cant_map_cds = No se pudo mapear CDS a proteína\nDatos CDS faltantes o incompletos
+label.operation_failed = Operación fallada
chain = str.substring(21, 22);
resNumber = Integer.parseInt(str.substring(22, 26).trim());
- resNumIns = str.substring(22, 27);
+ resNumIns = str.substring(22, 27).trim();
insCode = str.substring(26, 27).charAt(0);
this.x = (new Float(str.substring(30, 38).trim()).floatValue());
this.y = (new Float(str.substring(38, 46).trim()).floatValue());
return false; // should only pass alignments with datasets here
}
- // map from dataset sequence to alignment sequence
- Map<SequenceI, SequenceI> alignedDatasets = new HashMap<SequenceI, SequenceI>();
+ // map from dataset sequence to alignment sequence(s)
+ Map<SequenceI, List<SequenceI>> alignedDatasets = new HashMap<SequenceI, List<SequenceI>>();
for (SequenceI seq : aligned.getSequences())
{
- // JAL-2110: fail if two or more alignment sequences have a common dataset
- // sequence.
- alignedDatasets.put(seq.getDatasetSequence(), seq);
+ SequenceI ds = seq.getDatasetSequence();
+ if (alignedDatasets.get(ds) == null)
+ {
+ alignedDatasets.put(ds, new ArrayList<SequenceI>());
+ }
+ alignedDatasets.get(ds).add(seq);
}
/*
}
/*
- * second pass - copy aligned sequences
+ * second pass - copy aligned sequences;
+ * heuristic rule: pair off sequences in order for the case where
+ * more than one shares the same dataset sequence
*/
for (SequenceI seq : unaligned.getSequences())
{
- SequenceI alignedSequence = alignedDatasets.get(seq
+ List<SequenceI> alignedSequences = alignedDatasets.get(seq
.getDatasetSequence());
- // JAL-2110: fail if two or more alignment sequences have common dataset
- // sequence.
// TODO: getSequenceAsString() will be deprecated in the future
// TODO: need to leave to SequenceI implementor to update gaps
- seq.setSequence(alignedSequence.getSequenceAsString());
+ seq.setSequence(alignedSequences.get(0).getSequenceAsString());
+ if (alignedSequences.size() > 0)
+ {
+ // pop off aligned sequences (except the last one)
+ alignedSequences.remove(0);
+ }
}
return true;
}
}
}
+
+ /*
+ * get selected columns (in the order they were selected);
+ * note this could include right-to-left ranges
+ */
int[] spos = new int[cs.getSelected().size()];
int width = -1;
int i = 0;
{
spos[i++] = pos.intValue();
}
- ;
+
for (i = 0; i < sequences.length; i++)
{
int slen = sequences[i].getLength();
public class APopupMenu extends java.awt.PopupMenu implements
ActionListener, ItemListener
{
- private static final String ALL_ANNOTATIONS = "All";
-
Menu groupMenu = new Menu();
MenuItem editGroupName = new MenuItem();
"label.represent_group_with", new Object[] { "" }));
revealAll.setLabel(MessageManager.getString("action.reveal_all"));
revealSeq.setLabel(MessageManager.getString("action.reveal_sequences"));
- menu1.setLabel(MessageManager.getString("label.group") + ":");
+ menu1.setLabel(MessageManager.getString("label.group:"));
add(groupMenu);
this.add(seqMenu);
this.add(hideSeqs);
showMenu.removeAll();
hideMenu.removeAll();
- final List<String> all = Arrays.asList(ALL_ANNOTATIONS);
+ final List<String> all = Arrays.asList(new String[] { MessageManager
+ .getString("label.all") });
addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true, true);
addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true,
false);
nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
nucleotideColour.addActionListener(this);
modifyPID.setLabel(MessageManager
- .getString("label.modify_identity_thereshold"));
+ .getString("label.modify_identity_threshold"));
modifyPID.addActionListener(this);
modifyConservation.setLabel(MessageManager
- .getString("label.modify_conservation_thereshold"));
+ .getString("label.modify_conservation_threshold"));
modifyConservation.addActionListener(this);
annotationColour.setLabel(MessageManager
.getString("action.by_annotation"));
}
threshold.addItem(MessageManager
- .getString("label.threshold_feature_no_thereshold"));
+ .getString("label.threshold_feature_no_threshold"));
threshold.addItem(MessageManager
- .getString("label.threshold_feature_above_thereshold"));
+ .getString("label.threshold_feature_above_threshold"));
threshold.addItem(MessageManager
- .getString("label.threshold_feature_below_thereshold"));
+ .getString("label.threshold_feature_below_threshold"));
if (oldcs instanceof AnnotationColourGradient)
{
default:
throw new Error(
MessageManager
- .getString("error.implementation_error_dont_know_thereshold_annotationcolourgradient"));
+ .getString("error.implementation_error_dont_know_threshold_annotationcolourgradient"));
}
thresholdIsMin.setState(acg.thresholdIsMinMax);
thresholdValue.setText("" + acg.getAnnotationThreshold());
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceI;
import jalview.renderer.AnnotationRenderer;
import jalview.renderer.AwtRenderPanelI;
+import jalview.schemes.ResidueProperties;
+import jalview.util.Comparison;
import jalview.util.MessageManager;
import java.awt.Color;
if (evt.getActionCommand().equals(REMOVE))
{
- for (int sel : av.getColumnSelection().getSelected())
+ for (int index : av.getColumnSelection().getSelected())
{
- // TODO: JAL-2001 check if applet has faulty 'REMOVE' selected columns
- // of
- // annotation if selection includes hidden columns
- anot[sel] = null;
+ if (av.getColumnSelection().isVisible(index))
+ {
+ anot[index] = null;
+ }
}
}
else if (evt.getActionCommand().equals(LABEL))
}
}
- int res = evt.getX() / av.getCharWidth() + av.getStartRes();
+ int column = evt.getX() / av.getCharWidth() + av.getStartRes();
if (av.hasHiddenColumns())
{
- res = av.getColumnSelection().adjustForHiddenColumns(res);
+ column = av.getColumnSelection().adjustForHiddenColumns(column);
}
- if (row > -1 && res < aa[row].annotations.length
- && aa[row].annotations[res] != null)
+ if (row > -1 && column < aa[row].annotations.length
+ && aa[row].annotations[column] != null)
{
- StringBuffer text = new StringBuffer("Sequence position " + (res + 1));
- if (aa[row].annotations[res].description != null)
+ StringBuilder text = new StringBuilder();
+ text.append(MessageManager.getString("label.column")).append(" ")
+ .append(column + 1);
+ String description = aa[row].annotations[column].description;
+ if (description != null && description.length() > 0)
{
- text.append(" " + aa[row].annotations[res].description);
+ text.append(" ").append(description);
}
+
+ /*
+ * if the annotation is sequence-specific, show the sequence number
+ * in the alignment, and (if not a gap) the residue and position
+ */
+ SequenceI seqref = aa[row].sequenceRef;
+ if (seqref != null)
+ {
+ int seqIndex = av.getAlignment().findIndex(seqref);
+ if (seqIndex != -1)
+ {
+ text.append(", ")
+ .append(MessageManager.getString("label.sequence"))
+ .append(" ").append(seqIndex + 1);
+ char residue = seqref.getCharAt(column);
+ if (!Comparison.isGap(residue))
+ {
+ text.append(" ");
+ String name;
+ if (av.getAlignment().isNucleotide())
+ {
+ name = ResidueProperties.nucleotideName.get(String
+ .valueOf(residue));
+ text.append(" Nucleotide: ").append(
+ name != null ? name : residue);
+ }
+ else
+ {
+ name = 'X' == residue ? "X" : ('*' == residue ? "STOP"
+ : ResidueProperties.aa2Triplet.get(String
+ .valueOf(residue)));
+ text.append(" Residue: ").append(
+ name != null ? name : residue);
+ }
+ int residuePos = seqref.findPosition(column);
+ text.append(" (").append(residuePos).append(")");
+ // int residuePos = seqref.findPosition(column);
+ // text.append(residue).append(" (")
+ // .append(residuePos).append(")");
+ }
+ }
+ }
+
ap.alignFrame.statusBar.setText(text.toString());
}
}
protected void populateThresholdComboBox(Choice threshold)
{
threshold.addItem(MessageManager
- .getString("label.threshold_feature_no_thereshold"));
+ .getString("label.threshold_feature_no_threshold"));
threshold.addItem(MessageManager
- .getString("label.threshold_feature_above_thereshold"));
+ .getString("label.threshold_feature_above_threshold"));
threshold.addItem(MessageManager
- .getString("label.threshold_feature_below_thereshold"));
+ .getString("label.threshold_feature_below_threshold"));
}
public jalview.datamodel.AlignmentAnnotation getCurrentAnnotation()
jPanel4.setBackground(Color.white);
threshold.addItemListener(this);
threshold.addItem(MessageManager
- .getString("label.threshold_feature_no_thereshold"));
+ .getString("label.threshold_feature_no_threshold"));
threshold.addItem(MessageManager
- .getString("label.threshold_feature_above_thereshold"));
+ .getString("label.threshold_feature_above_threshold"));
threshold.addItem(MessageManager
- .getString("label.threshold_feature_below_thereshold"));
+ .getString("label.threshold_feature_below_threshold"));
thresholdValue.addActionListener(this);
slider.setBackground(Color.white);
slider.setEnabled(false);
tmp = new Panel();
panel.add(tmp);
- tmp.add(new Label("Name: ", Label.RIGHT));
+ tmp.add(new Label(MessageManager.getString("label.name:"), Label.RIGHT));
tmp.add(name);
tmp = new Panel();
panel.add(tmp);
- tmp.add(new Label("Group: ", Label.RIGHT));
+ tmp.add(new Label(MessageManager.getString("label.group:"), Label.RIGHT));
tmp.add(source);
tmp = new Panel();
panel.add(tmp);
- tmp.add(new Label("Colour: ", Label.RIGHT));
+ tmp.add(new Label(MessageManager.getString("label.colour"), Label.RIGHT));
tmp.add(colourPanel);
bigPanel.add(panel, BorderLayout.NORTH);
panel = new Panel();
- panel.add(new Label("Description: ", Label.RIGHT));
+ panel.add(new Label(MessageManager.getString("label.description:"),
+ Label.RIGHT));
panel.add(new ScrollPane().add(description));
if (!newFeatures)
bigPanel.add(panel, BorderLayout.SOUTH);
panel = new Panel();
- panel.add(new Label(" Start:", Label.RIGHT));
+ panel.add(new Label(MessageManager.getString("label.start"),
+ Label.RIGHT));
panel.add(start);
- panel.add(new Label(" End:", Label.RIGHT));
+ panel.add(new Label(MessageManager.getString("label.end"),
+ Label.RIGHT));
panel.add(end);
bigPanel.add(panel, BorderLayout.CENTER);
}
// Fill the selected columns
ColumnSelection cs = av.getColumnSelection();
- gg.setColor(new Color(220, 0, 0));
int avCharWidth = av.getCharWidth();
int avcharHeight = av.getCharHeight();
- for (int sel : cs.getSelected())
+ if (cs != null)
{
- // TODO: JAL-2001 - provide a fast method to list visible selected in a
- // given range
- if (av.hasHiddenColumns())
+ gg.setColor(new Color(220, 0, 0));
+ boolean hasHiddenColumns = cs.hasHiddenColumns();
+ for (int sel : cs.getSelected())
{
- sel = av.getColumnSelection().findColumnPosition(sel);
- }
+ // TODO: JAL-2001 - provide a fast method to list visible selected in a
+ // given range
+ if (hasHiddenColumns)
+ {
+ if (cs.isVisible(sel))
+ {
+ sel = cs.findColumnPosition(sel);
+ }
+ else
+ {
+ continue;
+ }
+ }
- if ((sel >= startx) && (sel <= endx))
- {
- gg.fillRect((sel - startx) * avCharWidth, 0, avCharWidth,
- getSize().height);
+ if ((sel >= startx) && (sel <= endx))
+ {
+ gg.fillRect((sel - startx) * avCharWidth, 0, avCharWidth,
+ getSize().height);
+ }
}
}
if (av.getShowHiddenMarkers())
{
int widthx = 1 + endx - startx;
- for (int i = 0; i < av.getColumnSelection().getHiddenColumns()
- .size(); i++)
+ for (int i = 0; i < cs.getHiddenColumns().size(); i++)
{
- res = av.getColumnSelection().findHiddenRegionPosition(i)
- - startx;
+ res = cs.findHiddenRegionPosition(i) - startx;
if (res < 0 || res > widthx)
{
pid.cs = cs;
}
PIDSlider.setTitle(MessageManager
- .formatMessage("label.percentage_identity_thereshold",
+ .formatMessage("label.percentage_identity_threshold",
new String[] { source }));
if (ap.av.getAlignment().getGroups() != null)
* even if the user changes their locale setting
*/
private static final DateFormat date_format = SimpleDateFormat
- .getDateTimeInstance(SimpleDateFormat.LONG,
- SimpleDateFormat.LONG, Locale.UK);
+ .getDateTimeInstance(SimpleDateFormat.MEDIUM,
+ SimpleDateFormat.MEDIUM, Locale.UK);
/**
* Initialises the Jalview Application Log
Cache.log.debug("Starting questionnaire with default url: "
+ defurl);
desktop.checkForQuestionnaire(defurl);
-
}
}
}
{
System.err.println("CMD [-noquestionnaire] executed successfully!");
}
+
if (!aparser.contains("nonews"))
{
desktop.checkForNews();
}
- }
- if (!isHeadlessMode())
- {
BioJsHTMLOutput.updateBioJS();
}
+ "-eps FILE\tCreate EPS file FILE from alignment.\n"
+ "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
+ "-noquestionnaire\tTurn off questionnaire check.\n"
+ + "-nonews\tTurn off check for Jalview news.\n"
+ "-nousagestats\tTurn off google analytics tracking for this session.\n"
+ "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n"
// +
SequenceI rs = sel.getSequenceAt(0);
start = rs.findIndex(start);
end = rs.findIndex(end);
- if (csel != null)
- {
- List<Integer> cs = csel.getSelected();
- // note - the following actually clears cs as well, since
- // csel.getSelected returns a reference. Need to check if we need to
- // have a concurrentModification exception thrown here
- csel.clear();
- for (Integer selectedCol : cs)
- {
- csel.addElement(rs.findIndex(selectedCol));
- }
+ List<Integer> cs = csel.getSelected();
+ csel.clear();
+ for (Integer selectedCol : cs)
+ {
+ csel.addElement(rs.findIndex(selectedCol));
}
}
sel.setStartRes(start);
// JBPNote this routine could also mark rows, not just columns.
// need a decent query structure to allow all types of feature searches
BitSet bs = new BitSet();
- int alw, alStart;
- SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null ? viewport
- .getAlignment() : viewport.getSelectionGroup());
- alStart = sqcol.getStartRes();
- alw = sqcol.getEndRes() + 1;
+ SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null || extendCurrent) ? viewport
+ .getAlignment() : viewport.getSelectionGroup();
+
+ int nseq = findColumnsWithFeature(featureType, sqcol, bs);
+
+ ColumnSelection cs = viewport.getColumnSelection();
+ if (cs == null)
+ {
+ cs = new ColumnSelection();
+ }
+
+ if (bs.cardinality() > 0 || invert)
+ {
+ boolean changed = cs.markColumns(bs, sqcol.getStartRes(),
+ sqcol.getEndRes(), invert, extendCurrent, toggle);
+ if (changed)
+ {
+ viewport.setColumnSelection(cs);
+ alignPanel.paintAlignment(true);
+ int columnCount = invert ? (sqcol.getEndRes() - sqcol.getStartRes() + 1)
+ - bs.cardinality()
+ : bs.cardinality();
+ avcg.setStatus(MessageManager.formatMessage(
+ "label.view_controller_toggled_marked",
+ new String[] {
+ toggle ? MessageManager.getString("label.toggled")
+ : MessageManager.getString("label.marked"),
+ String.valueOf(columnCount),
+ invert ? MessageManager
+ .getString("label.not_containing")
+ : MessageManager.getString("label.containing"),
+ featureType, Integer.valueOf(nseq).toString() }));
+ return true;
+ }
+ }
+ else
+ {
+ avcg.setStatus(MessageManager.formatMessage(
+ "label.no_feature_of_type_found",
+ new String[] { featureType }));
+ if (!extendCurrent)
+ {
+ cs.clear();
+ alignPanel.paintAlignment(true);
+ }
+ }
+ return false;
+ }
+
+ /**
+ * Sets a bit in the BitSet for each column (base 0) in the sequence
+ * collection which includes the specified feature type. Returns the number of
+ * sequences which have the feature in the selected range.
+ *
+ * @param featureType
+ * @param sqcol
+ * @param bs
+ * @return
+ */
+ static int findColumnsWithFeature(String featureType,
+ SequenceCollectionI sqcol, BitSet bs)
+ {
+ final int startPosition = sqcol.getStartRes() + 1; // converted to base 1
+ final int endPosition = sqcol.getEndRes() + 1;
List<SequenceI> seqs = sqcol.getSequences();
int nseq = 0;
for (SequenceI sq : seqs)
{
- int tfeat = 0;
+ boolean sequenceHasFeature = false;
if (sq != null)
{
- SequenceFeature[] sf = sq.getSequenceFeatures();
- if (sf != null)
+ SequenceFeature[] sfs = sq.getSequenceFeatures();
+ if (sfs != null)
{
+ /*
+ * check whether the feature start/end (base 1)
+ * overlaps the selection start/end
+ */
int ist = sq.findIndex(sq.getStart());
int iend = sq.findIndex(sq.getEnd());
- if (iend < alStart || ist > alw)
+ if (iend < startPosition || ist > endPosition)
{
// sequence not in region
continue;
}
- for (SequenceFeature sfpos : sf)
+ for (SequenceFeature sf : sfs)
{
- // future functionalty - featureType == null means mark columns
+ // future functionality - featureType == null means mark columns
// containing all displayed features
- if (sfpos != null && (featureType.equals(sfpos.getType())))
+ if (sf != null && (featureType.equals(sf.getType())))
{
- tfeat++;
// optimisation - could consider 'spos,apos' like cursor argument
// - findIndex wastes time by starting from first character and
// counting
- int i = sq.findIndex(sfpos.getBegin());
- int j = sq.findIndex(sfpos.getEnd());
- if (j < alStart || i > alw)
+ int i = sq.findIndex(sf.getBegin());
+ int j = sq.findIndex(sf.getEnd());
+ if (j < startPosition || i > endPosition)
{
// feature is outside selected region
continue;
}
- if (i < alStart)
+ sequenceHasFeature = true;
+ if (i < startPosition)
{
- i = alStart;
+ i = startPosition;
}
if (i < ist)
{
i = ist;
}
- if (j > alw)
+ if (j > endPosition)
{
- j = alw;
+ j = endPosition;
}
for (; i <= j; i++)
{
- bs.set(i - 1);
+ bs.set(i - 1); // convert to base 0
}
}
}
}
- if (tfeat > 0)
+ if (sequenceHasFeature)
{
nseq++;
}
}
}
- ColumnSelection cs = viewport.getColumnSelection();
- if (bs.cardinality() > 0 || invert)
- {
- boolean changed = false;
- if (cs == null)
- {
- cs = new ColumnSelection();
- }
- else
- {
- if (!extendCurrent)
- {
- changed = !cs.isEmpty();
- cs.clear();
- }
- }
- if (invert)
- {
- // invert only in the currently selected sequence region
- for (int i = bs.nextClearBit(alStart), ibs = bs.nextSetBit(alStart); i >= alStart
- && i < (alw);)
- {
- if (ibs < 0 || i < ibs)
- {
- changed = true;
- if (toggle && cs.contains(i))
- {
- cs.removeElement(i++);
- }
- else
- {
- cs.addElement(i++);
- }
- }
- else
- {
- i = bs.nextClearBit(ibs);
- ibs = bs.nextSetBit(i);
- }
- }
- }
- else
- {
- for (int i = bs.nextSetBit(alStart); i >= alStart; i = bs
- .nextSetBit(i + 1))
- {
- changed = true;
- if (toggle && cs.contains(i))
- {
- cs.removeElement(i);
- }
- else
- {
- cs.addElement(i);
- }
- }
- }
- if (changed)
- {
- viewport.setColumnSelection(cs);
- alignPanel.paintAlignment(true);
- avcg.setStatus(MessageManager.formatMessage(
- "label.view_controller_toggled_marked",
- new String[] {
- (toggle ? MessageManager.getString("label.toggled")
- : MessageManager.getString("label.marked")),
- (invert ? (Integer.valueOf((alw - alStart)
- - bs.cardinality()).toString()) : (Integer
- .valueOf(bs.cardinality()).toString())),
- featureType, Integer.valueOf(nseq).toString() }));
- return true;
- }
- }
- else
- {
- avcg.setStatus(MessageManager.formatMessage(
- "label.no_feature_of_type_found",
- new String[] { featureType }));
- if (!extendCurrent && cs != null)
- {
- cs.clear();
- alignPanel.paintAlignment(true);
- }
- }
- return false;
+ return nseq;
}
@Override
if (!seqcigararray.isSeqCigarArray())
{
throw new Error(
- MessageManager
- .getString("error.implementation_error_can_only_make_alignmnet_from_cigararray"));
+ "Implementation Error - can only make an alignment view from a CigarArray of sequences.");
}
// contigs = seqcigararray.applyDeletions();
contigs = seqcigararray.getDeletedRegions();
/**
* Returns a list of selected columns. The list contains no duplicates but is
* not necessarily ordered. It also may include columns hidden from the
- * current view
+ * current view. This returns a copy of the actual list, and changes to the
+ * copy will not affect the selection.
*/
public List<Integer> getSelected()
{
- return selection.getList();
+ return new ArrayList<Integer>(selection.getList());
}
/**
SequenceI[] seqs)
{
int i, iSize = seqs.length;
- String selection[] = new String[iSize];
+ String selections[] = new String[iSize];
if (hiddenColumns != null && hiddenColumns.size() > 0)
{
for (i = 0; i < iSize; i++)
visibleSeq.append(seqs[i].getSequence(blockStart, end));
}
- selection[i] = visibleSeq.toString();
+ selections[i] = visibleSeq.toString();
}
}
else
{
for (i = 0; i < iSize; i++)
{
- selection[i] = seqs[i].getSequenceAsString(start, end);
+ selections[i] = seqs[i].getSequenceAsString(start, end);
}
}
- return selection;
+ return selections;
}
/**
return true;
}
+ /**
+ * Updates the column selection depending on the parameters, and returns true
+ * if any change was made to the selection
+ *
+ * @param markedColumns
+ * a set identifying marked columns (base 0)
+ * @param startCol
+ * the first column of the range to operate over (base 0)
+ * @param endCol
+ * the last column of the range to operate over (base 0)
+ * @param invert
+ * if true, deselect marked columns and select unmarked
+ * @param extendCurrent
+ * if true, extend rather than replacing the current column selection
+ * @param toggle
+ * if true, toggle the selection state of marked columns
+ *
+ * @return
+ */
+ public boolean markColumns(BitSet markedColumns, int startCol,
+ int endCol, boolean invert, boolean extendCurrent, boolean toggle)
+ {
+ boolean changed = false;
+ if (!extendCurrent && !toggle)
+ {
+ changed = !this.isEmpty();
+ clear();
+ }
+ if (invert)
+ {
+ // invert only in the currently selected sequence region
+ int i = markedColumns.nextClearBit(startCol);
+ int ibs = markedColumns.nextSetBit(startCol);
+ while (i >= startCol && i <= endCol)
+ {
+ if (ibs < 0 || i < ibs)
+ {
+ changed = true;
+ if (toggle && contains(i))
+ {
+ removeElement(i++);
+ }
+ else
+ {
+ addElement(i++);
+ }
+ }
+ else
+ {
+ i = markedColumns.nextClearBit(ibs);
+ ibs = markedColumns.nextSetBit(i);
+ }
+ }
+ }
+ else
+ {
+ int i = markedColumns.nextSetBit(startCol);
+ while (i >= startCol && i <= endCol)
+ {
+ changed = true;
+ if (toggle && contains(i))
+ {
+ removeElement(i);
+ }
+ else
+ {
+ addElement(i);
+ }
+ i = markedColumns.nextSetBit(i + 1);
+ }
+ }
+ return changed;
+ }
+
}
* Castor binding file
*
* For example:
- * http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=ena_sequence&id=J03321
- * &format=emblxml
+ * http://www.ebi.ac.uk/ena/data/view/J03321&display=xml
*
* @see embl_mapping.xml
*/
public SequenceI getSequence(String sourceDb, List<SequenceI> peptides)
{
SequenceI dna = makeSequence(sourceDb);
+ if (dna == null)
+ {
+ return null;
+ }
dna.setDescription(description);
DBRefEntry retrievedref = new DBRefEntry(sourceDb,
getSequenceVersion(), accession);
*/
SequenceI makeSequence(String sourceDb)
{
+ if (sequence == null)
+ {
+ System.err.println("No sequence was returned for ENA accession "
+ + accession);
+ return null;
+ }
SequenceI dna = new Sequence(sourceDb + "|" + accession,
sequence.getSequence());
return dna;
* changes to Ensembl REST API
* @see https://github.com/Ensembl/ensembl-rest/wiki/Change-log
*/
- private static final String LATEST_ENSEMBLGENOMES_REST_VERSION = "4.4";
+ private static final String LATEST_ENSEMBLGENOMES_REST_VERSION = "4.6";
- private static final String LATEST_ENSEMBL_REST_VERSION = "4.5";
+ private static final String LATEST_ENSEMBL_REST_VERSION = "4.6";
+
+ private static final String REST_CHANGE_LOG = "https://github.com/Ensembl/ensembl-rest/wiki/Change-log";
private static Map<String, EnsemblInfo> domainData;
if (laterVersion)
{
System.err.println(String.format(
- "Expected %s REST version %s but found %s", getDbSource(),
- expected,
- version));
+ "Expected %s REST version %s but found %s, see %s",
+ getDbSource(), expected, version, REST_CHANGE_LOG));
}
info.restVersion = version;
} catch (Throwable t)
curAtom.resNumber = atom.getResno();
curAtom.occupancy = ms.occupancies != null ? ms.occupancies[atom
.getIndex()] : Float.valueOf(atom.getOccupancy100());
- curAtom.resNumIns = "" + curAtom.resNumber + curAtom.insCode;
+ curAtom.resNumIns = ("" + curAtom.resNumber + curAtom.insCode)
+ .trim();
curAtom.tfactor = atom.getBfactor100() / 100f;
curAtom.type = 0;
// significantAtoms.add(curAtom);
showGroupConservation.setEnabled(!nucleotide);
rnahelicesColour.setEnabled(nucleotide);
purinePyrimidineColour.setEnabled(nucleotide);
- showComplementMenuItem.setText(MessageManager
- .getString(nucleotide ? "label.protein" : "label.nucleotide"));
+ showComplementMenuItem.setText(nucleotide ? MessageManager
+ .getString("label.protein") : MessageManager
+ .getString("label.nucleotide"));
setColourSelected(jalview.bin.Cache.getDefault(
nucleotide ? Preferences.DEFAULT_COLOUR_NUC
: Preferences.DEFAULT_COLOUR_PROT, "None"));
}
/**
- * Set or clear 'Show Sequence Features'
- *
- * @param evt
- * DOCUMENT ME!
- */
- @Override
- public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
- {
- viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
- .isSelected());
- if (viewport.isShowSequenceFeaturesHeight())
- {
- // ensure we're actually displaying features
- viewport.setShowSequenceFeatures(true);
- showSeqFeatures.setSelected(true);
- }
- alignPanel.paintAlignment(true);
- if (alignPanel.getOverviewPanel() != null)
- {
- alignPanel.getOverviewPanel().updateOverviewImage();
- }
- }
-
- /**
* Action on toggle of the 'Show annotations' menu item. This shows or hides
* the annotations panel as a whole.
*
// object broker mechanism.
final Vector<JMenu> wsmenu = new Vector<JMenu>();
final IProgressIndicator af = me;
+
+ /*
+ * do not i18n these strings - they are hard-coded in class
+ * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
+ * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
+ */
final JMenu msawsmenu = new JMenu("Alignment");
final JMenu secstrmenu = new JMenu(
"Secondary Structure Prediction");
final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
final JMenu analymenu = new JMenu("Analysis");
final JMenu dismenu = new JMenu("Protein Disorder");
- // final JMenu msawsmenu = new
- // JMenu(MessageManager.getString("label.alignment"));
- // final JMenu secstrmenu = new
- // JMenu(MessageManager.getString("label.secondary_structure_prediction"));
- // final JMenu seqsrchmenu = new
- // JMenu(MessageManager.getString("label.sequence_database_search"));
- // final JMenu analymenu = new
- // JMenu(MessageManager.getString("label.analysis"));
- // final JMenu dismenu = new
- // JMenu(MessageManager.getString("label.protein_disorder"));
// JAL-940 - only show secondary structure prediction services from
// the legacy server
if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
xrefsAlignment.getSequencesArray());
if (copyAlignment.getHeight() == 0)
{
+ JOptionPane.showMessageDialog(AlignFrame.this,
+ MessageManager.getString("label.cant_map_cds"),
+ MessageManager.getString("label.operation_failed"),
+ JOptionPane.OK_OPTION);
System.err.println("Failed to make CDS alignment");
}
{
newFrame.hideFeatureColumns(SequenceOntologyI.EXON, false);
}
- String newtitle = String.format("%s %s %s", MessageManager
- .getString(dna ? "label.proteins" : "label.nucleotides"),
+ String newtitle = String.format("%s %s %s",
+ dna ? MessageManager.getString("label.proteins")
+ : MessageManager.getString("label.nucleotides"),
MessageManager.getString("label.for"), getTitle());
newFrame.setTitle(newtitle);
/**
* DOCUMENT ME!
*
- * @return DOCUMENT ME!
- */
- @Override
- public ColumnSelection getColumnSelection()
- {
- return colSel;
- }
-
- /**
- * DOCUMENT ME!
- *
* @param tree
* DOCUMENT ME!
*/
void makeAlignmentImage(jalview.util.ImageMaker.TYPE type, File file)
{
+ int boarderBottomOffset = 5;
long pSessionId = System.currentTimeMillis();
headless = (System.getProperty("java.awt.headless") != null && System
.getProperty("java.awt.headless").equals("true"));
}
im = new jalview.util.ImageMaker(this, type, imageAction,
- aDimension.getWidth(), aDimension.getHeight(), file,
+ aDimension.getWidth(), aDimension.getHeight()
+ + boarderBottomOffset, file,
imageTitle, alignFrame, pSessionId, headless);
if (av.getWrapAlignment())
{
if (im.getGraphics() != null)
{
printWrappedAlignment(im.getGraphics(), aDimension.getWidth(),
- aDimension.getHeight(), 0);
+ aDimension.getHeight() + boarderBottomOffset, 0);
im.writeImage();
}
}
default:
throw new Error(
MessageManager
- .getString("error.implementation_error_dont_know_about_thereshold_setting"));
+ .getString("error.implementation_error_dont_know_about_threshold_setting"));
}
thresholdIsMin.setSelected(acg.thresholdIsMinMax);
thresholdValue.setText("" + acg.getAnnotationThreshold());
import jalview.datamodel.SequenceI;
import jalview.renderer.AnnotationRenderer;
import jalview.renderer.AwtRenderPanelI;
+import jalview.schemes.ResidueProperties;
+import jalview.util.Comparison;
import jalview.util.MessageManager;
import java.awt.AlphaComposite;
import java.awt.event.MouseWheelEvent;
import java.awt.event.MouseWheelListener;
import java.awt.image.BufferedImage;
+import java.util.Collections;
+import java.util.List;
import javax.swing.JColorChooser;
import javax.swing.JMenuItem;
if (evt.getActionCommand().equals(REMOVE))
{
- for (int sel : av.getColumnSelection().getSelected())
+ for (int index : av.getColumnSelection().getSelected())
{
- anot[sel] = null;
+ if (av.getColumnSelection().isVisible(index))
+ {
+ anot[index] = null;
+ }
}
}
else if (evt.getActionCommand().equals(LABEL))
}
}
else
- // HELIX OR SHEET
+ // HELIX, SHEET or STEM
{
char type = 0;
String symbol = "\u03B1";
}
}
+
av.getAlignment().validateAnnotation(aa[activeRow]);
ap.alignmentChanged();
-
+ ap.alignFrame.setMenusForViewport();
adjustPanelHeight();
repaint();
return;
}
- private String collectAnnotVals(Annotation[] anot, String label2)
+ /**
+ * Returns any existing annotation concatenated as a string. For each
+ * annotation, takes the description, if any, else the secondary structure
+ * character (if type is HELIX, SHEET or STEM), else the display character (if
+ * type is LABEL).
+ *
+ * @param anots
+ * @param type
+ * @return
+ */
+ private String collectAnnotVals(Annotation[] anots, String type)
{
- String collatedInput = "";
+ // TODO is this method wanted? why? 'last' is not used
+
+ StringBuilder collatedInput = new StringBuilder(64);
String last = "";
ColumnSelection viscols = av.getColumnSelection();
// TODO: refactor and save av.getColumnSelection for efficiency
- for (int index : viscols.getSelected())
+ List<Integer> selected = viscols.getSelected();
+ Collections.sort(selected);
+ for (int index : selected)
{
// always check for current display state - just in case
if (!viscols.isVisible(index))
continue;
}
String tlabel = null;
- if (anot[index] != null)
+ if (anots[index] != null)
{ // LML added stem code
- if (label2.equals(HELIX) || label2.equals(SHEET)
- || label2.equals(STEM) || label2.equals(LABEL))
+ if (type.equals(HELIX) || type.equals(SHEET)
+ || type.equals(STEM) || type.equals(LABEL))
{
- tlabel = anot[index].description;
+ tlabel = anots[index].description;
if (tlabel == null || tlabel.length() < 1)
{
- if (label2.equals(HELIX) || label2.equals(SHEET)
- || label2.equals(STEM))
+ if (type.equals(HELIX) || type.equals(SHEET)
+ || type.equals(STEM))
{
- tlabel = "" + anot[index].secondaryStructure;
+ tlabel = "" + anots[index].secondaryStructure;
}
else
{
- tlabel = "" + anot[index].displayCharacter;
+ tlabel = "" + anots[index].displayCharacter;
}
}
}
{
if (last.length() > 0)
{
- collatedInput += " ";
+ collatedInput.append(" ");
}
- collatedInput += tlabel;
+ collatedInput.append(tlabel);
}
}
}
- return collatedInput;
+ return collatedInput.toString();
}
/**
}
/**
- * DOCUMENT ME!
+ * Constructs the tooltip, and constructs and displays a status message, for
+ * the current mouse position
*
* @param evt
- * DOCUMENT ME!
*/
@Override
public void mouseMoved(MouseEvent evt)
if (evt.getY() < height)
{
row = i;
-
break;
}
}
return;
}
- int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+ int column = (evt.getX() / av.getCharWidth()) + av.getStartRes();
if (av.hasHiddenColumns())
{
- res = av.getColumnSelection().adjustForHiddenColumns(res);
+ column = av.getColumnSelection().adjustForHiddenColumns(column);
}
- if (row > -1 && aa[row].annotations != null
- && res < aa[row].annotations.length)
+ AlignmentAnnotation ann = aa[row];
+ if (row > -1 && ann.annotations != null
+ && column < ann.annotations.length)
{
- if (aa[row].graphGroup > -1)
+ buildToolTip(ann, column, aa);
+ setStatusMessage(column, ann);
+ }
+ else
+ {
+ this.setToolTipText(null);
+ ap.alignFrame.statusBar.setText(" ");
+ }
+ }
+
+ /**
+ * Builds a tooltip for the annotation at the current mouse position.
+ *
+ * @param ann
+ * @param column
+ * @param anns
+ */
+ void buildToolTip(AlignmentAnnotation ann, int column,
+ AlignmentAnnotation[] anns)
+ {
+ if (ann.graphGroup > -1)
+ {
+ StringBuilder tip = new StringBuilder(32);
+ tip.append("<html>");
+ for (int i = 0; i < anns.length; i++)
{
- StringBuffer tip = new StringBuffer("<html>");
- for (int gg = 0; gg < aa.length; gg++)
+ if (anns[i].graphGroup == ann.graphGroup
+ && anns[i].annotations[column] != null)
{
- if (aa[gg].graphGroup == aa[row].graphGroup
- && aa[gg].annotations[res] != null)
+ tip.append(anns[i].label);
+ String description = anns[i].annotations[column].description;
+ if (description != null && description.length() > 0)
{
- tip.append(aa[gg].label + " "
- + aa[gg].annotations[res].description + "<br>");
+ tip.append(" ").append(description);
}
- }
- if (tip.length() != 6)
- {
- tip.setLength(tip.length() - 4);
- this.setToolTipText(tip.toString() + "</html>");
+ tip.append("<br>");
}
}
- else if (aa[row].annotations[res] != null
- && aa[row].annotations[res].description != null
- && aa[row].annotations[res].description.length() > 0)
+ if (tip.length() != 6)
{
- this.setToolTipText(JvSwingUtils.wrapTooltip(true,
- aa[row].annotations[res].description));
+ tip.setLength(tip.length() - 4);
+ this.setToolTipText(tip.toString() + "</html>");
}
- else
+ }
+ else if (ann.annotations[column] != null)
+ {
+ String description = ann.annotations[column].description;
+ if (description != null && description.length() > 0)
{
- // clear the tooltip.
- this.setToolTipText(null);
+ this.setToolTipText(JvSwingUtils.wrapTooltip(true, description));
}
+ }
+ else
+ {
+ // clear the tooltip.
+ this.setToolTipText(null);
+ }
+ }
- if (aa[row].annotations[res] != null)
+ /**
+ * Constructs and displays the status bar message
+ *
+ * @param column
+ * @param ann
+ */
+ void setStatusMessage(int column, AlignmentAnnotation ann)
+ {
+ /*
+ * show alignment column and annotation description if any
+ */
+ StringBuilder text = new StringBuilder(32);
+ text.append(MessageManager.getString("label.column")).append(" ")
+ .append(column + 1);
+
+ if (ann.annotations[column] != null)
+ {
+ String description = ann.annotations[column].description;
+ if (description != null && description.trim().length() > 0)
{
- StringBuffer text = new StringBuffer("Sequence position "
- + (res + 1));
+ text.append(" ").append(description);
+ }
+ }
- if (aa[row].annotations[res].description != null)
+ /*
+ * if the annotation is sequence-specific, show the sequence number
+ * in the alignment, and (if not a gap) the residue and position
+ */
+ SequenceI seqref = ann.sequenceRef;
+ if (seqref != null)
+ {
+ int seqIndex = av.getAlignment().findIndex(seqref);
+ if (seqIndex != -1)
+ {
+ text.append(", ")
+ .append(MessageManager.getString("label.sequence"))
+ .append(" ")
+ .append(seqIndex + 1);
+ char residue = seqref.getCharAt(column);
+ if (!Comparison.isGap(residue))
{
- text.append(" " + aa[row].annotations[res].description);
+ text.append(" ");
+ String name;
+ if (av.getAlignment().isNucleotide())
+ {
+ name = ResidueProperties.nucleotideName.get(String
+ .valueOf(residue));
+ text.append(" Nucleotide: ").append(
+ name != null ? name : residue);
+ }
+ else
+ {
+ name = 'X' == residue ? "X" : ('*' == residue ? "STOP"
+ : ResidueProperties.aa2Triplet.get(String
+ .valueOf(residue)));
+ text.append(" Residue: ").append(name != null ? name : residue);
+ }
+ int residuePos = seqref.findPosition(column);
+ text.append(" (").append(residuePos).append(")");
}
-
- ap.alignFrame.statusBar.setText(text.toString());
}
}
- else
- {
- this.setToolTipText(null);
- }
+
+ ap.alignFrame.statusBar.setText(text.toString());
}
/**
protected void populateThresholdComboBox(JComboBox<String> threshold)
{
threshold.addItem(MessageManager
- .getString("label.threshold_feature_no_thereshold"));
+ .getString("label.threshold_feature_no_threshold"));
threshold.addItem(MessageManager
- .getString("label.threshold_feature_above_thereshold"));
+ .getString("label.threshold_feature_above_threshold"));
threshold.addItem(MessageManager
- .getString("label.threshold_feature_below_thereshold"));
+ .getString("label.threshold_feature_below_threshold"));
}
protected void seqAssociated_actionPerformed(ActionEvent arg0,
seqs.setSelected(seqsrc);
JPanel panel = new JPanel(new BorderLayout());
JPanel pane12 = new JPanel(new BorderLayout());
- pane12.add(new JLabel(MessageManager.getString("label.name")),
+ pane12.add(new JLabel(MessageManager.getString("label.name:")),
BorderLayout.CENTER);
pane12.add(nametf, BorderLayout.EAST);
panel.add(pane12, BorderLayout.NORTH);
threshold.setToolTipText(MessageManager
.getString("label.threshold_feature_display_by_score"));
threshold.addItem(MessageManager
- .getString("label.threshold_feature_no_thereshold")); // index 0
+ .getString("label.threshold_feature_no_threshold")); // index 0
threshold.addItem(MessageManager
- .getString("label.threshold_feature_above_thereshold")); // index 1
+ .getString("label.threshold_feature_above_threshold")); // index 1
threshold.addItem(MessageManager
- .getString("label.threshold_feature_below_thereshold")); // index 2
+ .getString("label.threshold_feature_below_threshold")); // index 2
jPanel3.setLayout(flowLayout2);
thresholdValue.addActionListener(new ActionListener()
{
slider.setOpaque(false);
slider.setPreferredSize(new Dimension(100, 32));
slider.setToolTipText(MessageManager
- .getString("label.adjust_thereshold"));
+ .getString("label.adjust_threshold"));
thresholdValue.setEnabled(false);
thresholdValue.setColumns(7);
jPanel3.setBackground(Color.white);
{
panel = new JPanel(new GridLayout(4, 1));
tmp = new JPanel();
- tmp.add(new JLabel(MessageManager.getString("label.select_feature")));
+ tmp.add(new JLabel(MessageManager.getString("label.select_feature")
+ + ":"));
overlaps = new JComboBox();
for (int i = 0; i < features.length; i++)
{
tmp = new JPanel();
panel.add(tmp);
- tmp.add(new JLabel(MessageManager.getString("label.name"), JLabel.RIGHT));
+ tmp.add(new JLabel(MessageManager.getString("label.name:"),
+ JLabel.RIGHT));
tmp.add(name);
tmp = new JPanel();
panel.add(tmp);
- tmp.add(new JLabel(MessageManager.getString("label.group") + ":",
+ tmp.add(new JLabel(MessageManager.getString("label.group:"),
JLabel.RIGHT));
tmp.add(source);
bigPanel.add(panel, BorderLayout.NORTH);
panel = new JPanel();
- panel.add(new JLabel(MessageManager.getString("label.description"),
+ panel.add(new JLabel(MessageManager.getString("label.description:"),
JLabel.RIGHT));
description.setFont(JvSwingUtils.getTextAreaFont());
description.setLineWrap(true);
public void mousePressed(MouseEvent evt)
{
selectedRow = table.rowAtPoint(evt.getPoint());
- if (SwingUtilities.isRightMouseButton(evt))
+ boolean ctrlDown = Platform.isControlDown(evt);
+ if (SwingUtilities.isRightMouseButton(evt) && !ctrlDown)
{
popupSort(selectedRow, (String) table.getValueAt(selectedRow, 0),
table.getValueAt(selectedRow, 1), fr.getMinMax(),
}
else if (evt.getClickCount() == 2)
{
+ boolean invertSelection = evt.isAltDown();
+ boolean toggleSelection = ctrlDown;
+ boolean extendSelection = evt.isShiftDown();
fr.ap.alignFrame.avc.markColumnsContainingFeatures(
- evt.isAltDown(), evt.isShiftDown() || evt.isMetaDown(),
- evt.isMetaDown(),
+ invertSelection, extendSelection, toggleSelection,
(String) table.getValueAt(selectedRow, 0));
}
}
init = false;
}
+ @Override
public void smoothFont_actionPerformed(ActionEvent e)
{
ap.av.antiAlias = smoothFont.isSelected();
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void ok_actionPerformed(ActionEvent e)
{
try
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void cancel_actionPerformed(ActionEvent e)
{
if (ap != null)
double iw = iBounds.getWidth();
if (mw < 1 || iw < 1)
{
- final String messageKey = iBounds.getHeight() < 1 ? "label.font_doesnt_have_letters_defined"
- : "label.font_too_small";
- JOptionPane.showInternalMessageDialog(this,
- MessageManager.getString(messageKey),
+ String message = iBounds.getHeight() < 1 ? MessageManager
+ .getString("label.font_doesnt_have_letters_defined")
+ : MessageManager.getString("label.font_too_small");
+ JOptionPane.showInternalMessageDialog(this, message,
MessageManager.getString("label.invalid_font"),
JOptionPane.WARNING_MESSAGE);
/*
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void fontName_actionPerformed(ActionEvent e)
{
if (init)
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void fontSize_actionPerformed(ActionEvent e)
{
if (init)
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void fontStyle_actionPerformed(ActionEvent e)
{
if (init)
*
* @param e
*/
+ @Override
public void defaultButton_actionPerformed(ActionEvent e)
{
Cache.setProperty("FONT_NAME", fontName.getSelectedItem().toString());
{
// create an entry for this score matrix for use in PCA
JCheckBoxMenuItem jm = new JCheckBoxMenuItem();
- jm.setText(MessageManager
- .getStringOrReturn("label.score_model", sm));
+ jm.setText(MessageManager.getStringOrReturn("label.score_model_",
+ sm));
jm.setSelected(pcaModel.getScore_matrix().equals(sm));
if ((ResidueProperties.scoreMatrices.get(sm).isDNA() && ResidueProperties.scoreMatrices
.get(sm).isProtein())
*/
public class PopupMenu extends JPopupMenu
{
- private static final String ALL_ANNOTATIONS = "All";
-
JMenu groupMenu = new JMenu();
JMenuItem groupName = new JMenuItem();
if (sg != null && sg.getSize() > 0)
{
- groupName.setText(MessageManager.formatMessage("label.name_param",
- new Object[] { sg.getName() }));
groupName.setText(MessageManager
.getString("label.edit_name_and_description_current_group"));
showMenu.removeAll();
hideMenu.removeAll();
- final List<String> all = Arrays.asList(ALL_ANNOTATIONS);
+ final List<String> all = Arrays.asList(new String[] { MessageManager
+ .getString("label.all") });
addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true, true);
addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true,
false);
*/
private void jbInit() throws Exception
{
- groupMenu.setText(MessageManager.getString("label.group"));
groupMenu.setText(MessageManager.getString("label.selection"));
groupName.setText(MessageManager.getString("label.name"));
groupName.addActionListener(new java.awt.event.ActionListener()
progress = null;
label.setText(MessageManager
- .getString("label.enter_redundancy_thereshold"));
+ .getString("label.enter_redundancy_threshold"));
slider.setVisible(true);
applyButton.setEnabled(true);
valueField.setVisible(true);
import jalview.renderer.ScaleRenderer;
import jalview.renderer.ScaleRenderer.ScaleMark;
import jalview.util.MessageManager;
+import jalview.util.Platform;
import java.awt.Color;
import java.awt.FontMetrics;
*/
protected void leftMouseButtonPressed(MouseEvent evt, final int res)
{
- if (!evt.isControlDown() && !evt.isShiftDown())
+ if (!Platform.isControlDown(evt) && !evt.isShiftDown())
{
av.getColumnSelection().clear();
}
* Sequence number (if known), and sequence name.
*/
String seqno = seq == -1 ? "" : " " + (seq + 1);
- text.append("Sequence" + seqno + " ID: " + sequence.getName());
+ text.append("Sequence").append(seqno).append(" ID: ")
+ .append(sequence.getName());
String residue = null;
/*
}
PIDSlider.setTitle(MessageManager
- .formatMessage("label.percentage_identity_thereshold",
+ .formatMessage("label.percentage_identity_threshold",
new String[] { source }));
if (ap.av.getAlignment().getGroups() != null)
new JLabel(
"<html>"
+ MessageManager
- .getString("label.select_dark_light_set_thereshold")
+ .getString("label.select_dark_light_set_threshold")
+ "</html>"), BorderLayout.NORTH);
panel.add(col1);
panel.add(slider);
ap,
bigpanel,
MessageManager
- .getString("label.adjunst_foreground_text_colour_thereshold"),
+ .getString("label.adjunst_foreground_text_colour_threshold"),
JOptionPane.OK_CANCEL_OPTION,
JOptionPane.QUESTION_MESSAGE, null, null, null);
return this.formatSequences(format, alignment, suffix);
}
- public AlignmentI readFile(String inFile, String type, String format)
- throws java.io.IOException
- {
- AlignmentI al = super.readFile(inFile, type, format);
- return al;
- }
-
- public AlignmentI readFromFile(FileParse source, String format)
- throws java.io.IOException
- {
- AlignmentI al = super.readFromFile(source, format);
- return al;
- }
-
/**
* validate format is valid for IO in Application. This is basically the
* AppletFormatAdapter.isValidFormat call with additional checks for
@Override
public void configureForView(AlignmentViewPanel avpanel)
{
+ if (avpanel == null)
+ {
+ return;
+ }
super.configureForView(avpanel);
AlignViewportI viewport = avpanel.getAlignViewport();
AlignmentI alignment = viewport.getAlignment();
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
import jalview.util.Format;
import java.io.IOException;
+import java.util.ArrayList;
import java.util.Hashtable;
+import java.util.List;
import java.util.StringTokenizer;
-import java.util.Vector;
/**
* DOCUMENT ME!
}
/**
- * DOCUMENT ME!
+ * Read and parse MSF sequence data
*/
@Override
public void parse() throws IOException
{
- int i = 0;
boolean seqFlag = false;
- String key = new String();
- Vector headers = new Vector();
- Hashtable seqhash = new Hashtable();
- String line;
+ List<String> headers = new ArrayList<String>();
+ Hashtable<String, StringBuilder> seqhash = new Hashtable<String, StringBuilder>();
try
{
+ String line;
while ((line = nextLine()) != null)
{
StringTokenizer str = new StringTokenizer(line);
+ String key = null;
while (str.hasMoreTokens())
{
String inStr = str.nextToken();
if (inStr.indexOf("Name:") != -1)
{
key = str.nextToken();
- headers.addElement(key);
+ headers.add(key);
}
- // if line has // set SeqFlag to 1 so we know sequences are coming
+ // if line has // set SeqFlag so we know sequences are coming
if (inStr.indexOf("//") != -1)
{
seqFlag = true;
}
// Process lines as sequence lines if seqFlag is set
- if ((inStr.indexOf("//") == -1) && (seqFlag == true))
+ if ((inStr.indexOf("//") == -1) && seqFlag)
{
- // seqeunce id is the first field
+ // sequence id is the first field
key = inStr;
- StringBuffer tempseq;
+ StringBuilder tempseq;
// Get sequence from hash if it exists
if (seqhash.containsKey(key))
{
- tempseq = (StringBuffer) seqhash.get(key);
+ tempseq = seqhash.get(key);
}
else
{
- tempseq = new StringBuffer();
+ tempseq = new StringBuilder(64);
seqhash.put(key, tempseq);
}
while (str.hasMoreTokens())
{
// append the word to the sequence
- tempseq.append(str.nextToken());
+ String sequenceBlock = str.nextToken();
+ tempseq.append(sequenceBlock);
}
}
}
this.noSeqs = headers.size();
// Add sequences to the hash
- for (i = 0; i < headers.size(); i++)
+ for (int i = 0; i < headers.size(); i++)
{
- if (seqhash.get(headers.elementAt(i)) != null)
+ if (seqhash.get(headers.get(i)) != null)
{
- String head = headers.elementAt(i).toString();
+ String head = headers.get(i);
String seq = seqhash.get(head).toString();
if (maxLength < head.length())
maxLength = head.length();
}
- // Replace ~ with a sensible gap character
- seq = seq.replace('~', '-');
+ /*
+ * replace ~ (leading/trailing positions) with the gap character;
+ * use '.' as this is the internal gap character required by MSF
+ */
+ seq = seq.replace('~', '.');
Sequence newSeq = parseId(head);
else
{
System.err.println("MSFFile Parser: Can't find sequence for "
- + headers.elementAt(i));
+ + headers.get(i));
}
}
}
*
* @return DOCUMENT ME!
*/
- public String print(SequenceI[] seqs)
+ public String print(SequenceI[] sqs)
{
- boolean is_NA = jalview.util.Comparison.isNucleotide(seqs);
+ boolean is_NA = Comparison.isNucleotide(sqs);
- SequenceI[] s = new SequenceI[seqs.length];
+ SequenceI[] s = new SequenceI[sqs.length];
- StringBuffer out = new StringBuffer("!!" + (is_NA ? "NA" : "AA")
- + "_MULTIPLE_ALIGNMENT 1.0");
+ StringBuilder out = new StringBuilder(256);
+ out.append("!!").append(is_NA ? "NA" : "AA")
+ .append("_MULTIPLE_ALIGNMENT 1.0");
// TODO: JBPNote : Jalview doesn't remember NA or AA yet.
out.append(newline);
out.append(newline);
int maxid = 0;
int i = 0;
- while ((i < seqs.length) && (seqs[i] != null))
+ while ((i < sqs.length) && (sqs[i] != null))
{
- // Replace all internal gaps with . and external spaces with ~
- s[i] = new Sequence(seqs[i].getName(), seqs[i].getSequenceAsString()
- .replace('-', '.'), seqs[i].getStart(), seqs[i].getEnd());
+ /*
+ * modify to MSF format: uses '.' for internal gaps,
+ * and '~' for leading or trailing gaps
+ */
+ String seqString = sqs[i].getSequenceAsString()
+ .replace('-', '.');
- StringBuffer sb = new StringBuffer();
- sb.append(s[i].getSequence());
+ StringBuilder sb = new StringBuilder(seqString);
for (int ii = 0; ii < sb.length(); ii++)
{
break;
}
}
+ s[i] = new Sequence(sqs[i].getName(), sb.toString(),
+ sqs[i].getStart(), sqs[i].getEnd());
- s[i].setSequence(sb.toString());
-
- if (s[i].getSequence().length > max)
+ if (sb.length() > max)
{
- max = s[i].getSequence().length;
+ max = sb.length();
}
i++;
}
if (spces + 1 < line.length())
{
- tempseq.append(line.substring(spces + 1));
+ tempseq.append(line.substring(spces + 1).trim());
}
}
super(source);
}
+ @Override
public void initData()
{
super.initData();
* @throws IOException
* If there is an error with the input file
*/
+ @Override
public void parse() throws IOException
{
StringBuffer treeString = new StringBuffer();
}
else
{
- // throw new IOException(MessageManager.formatMessage(
- // "exception.error_parsing_line", new String[] { line }));
+ // throw new IOException("Error parsing " + line);
System.err.println(">> missing annotation: " + line);
}
}
return seq;
}
+ @Override
public String print()
{
out = new StringBuffer();
public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
- public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
-
JMenuItem copy = new JMenuItem();
JMenuItem cut = new JMenuItem();
});
JMenuItem modifyPID = new JMenuItem(
- MessageManager.getString("label.modify_identity_thereshold"));
+ MessageManager.getString("label.modify_identity_threshold"));
modifyPID.addActionListener(new ActionListener()
{
@Override
}
});
modifyConservation.setText(MessageManager
- .getString("label.modify_conservation_thereshold"));
+ .getString("label.modify_conservation_threshold"));
modifyConservation.addActionListener(new ActionListener()
{
@Override
}
- protected void showSeqFeaturesHeight_actionPerformed(
- ActionEvent actionEvent)
- {
- // TODO Auto-generated method stub
-
- }
-
protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
{
// TODO Auto-generated method stub
*/
public class ScaleRenderer
{
- public class ScaleMark
+ public final class ScaleMark
{
public final boolean major;
return f.toString();
}
+ /**
+ * Answers true if the mouse event has Meta-down (on Mac) or Ctrl-down (on
+ * other o/s)
+ *
+ * @param e
+ * @return
+ */
public static boolean isControlDown(MouseEvent e)
{
- return (jalview.util.Platform.isAMac() ? (Toolkit.getDefaultToolkit()
- .getMenuShortcutKeyMask() & e.getModifiers()) != 0 : e
- .isControlDown());
+ if (isAMac())
+ {
+ return (Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() & e
+ .getModifiers()) != 0;
+ // could we use e.isMetaDown() here?
+ }
+ return e.isControlDown();
}
}
import jalview.ws.dbsources.Pdb;
import jalview.ws.dbsources.PfamFull;
import jalview.ws.dbsources.PfamSeed;
-import jalview.ws.dbsources.RfamFull;
import jalview.ws.dbsources.RfamSeed;
import jalview.ws.dbsources.Uniprot;
-import jalview.ws.dbsources.UniprotName;
import jalview.ws.dbsources.das.api.jalviewSourceI;
import jalview.ws.seqfetcher.ASequenceFetcher;
import jalview.ws.seqfetcher.DbSourceProxy;
addDBRefSourceImpl(EmblSource.class);
addDBRefSourceImpl(EmblCdsSource.class);
addDBRefSourceImpl(Uniprot.class);
- addDBRefSourceImpl(UniprotName.class);
addDBRefSourceImpl(Pdb.class);
addDBRefSourceImpl(PfamFull.class);
addDBRefSourceImpl(PfamSeed.class);
addDBRefSourceImpl(RfamSeed.class);
+
if (addDas)
{
registerDasSequenceSources();
assertEquals("GLN", a.resName);
assertEquals("A", a.chain);
assertEquals(48, a.resNumber);
- assertEquals(" 48 ", a.resNumIns);
+ assertEquals("48", a.resNumIns);
assertEquals(' ', a.insCode);
assertEquals(22.290, a.x, 0.00001);
assertEquals(8.595, a.y, 0.00001);
{
SequenceI dna1 = new Sequence("dna1", "cccGGGTTTaaa");
SequenceI dna2 = new Sequence("dna2", "CCCgggtttAAA");
- SequenceI as1 = dna1.deriveSequence(), as2 = dna1.deriveSequence()
- .getSubSequence(3, 7), as3 = dna2.deriveSequence();
+ SequenceI as1 = dna1.deriveSequence();
+ SequenceI as2 = dna1.deriveSequence().getSubSequence(3, 7);
+ SequenceI as3 = dna2.deriveSequence();
as1.insertCharAt(6, 5, '-');
String s_as1 = as1.getSequenceAsString();
as2.insertCharAt(6, 5, '-');
// why do we need to cast this still ?
((Alignment) aligned).createDatasetAlignment();
- SequenceI uas1 = dna1.deriveSequence(), uas2 = dna1.deriveSequence()
- .getSubSequence(3, 7), uas3 = dna2.deriveSequence();
+ SequenceI uas1 = dna1.deriveSequence();
+ SequenceI uas2 = dna1.deriveSequence().getSubSequence(3, 7);
+ SequenceI uas3 = dna2.deriveSequence();
AlignmentI tobealigned = new Alignment(new SequenceI[] { uas1, uas2,
uas3 });
((Alignment) tobealigned).createDatasetAlignment();
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
-import java.util.ArrayList;
import java.util.Arrays;
import org.testng.AssertJUnit;
Sequence s5 = new Sequence("s5", "AAAADDEDTTEE");
- SequenceGroup sg1 = new SequenceGroup(Arrays.asList(new SequenceI[] { s1,
+ SequenceGroup sg_12 = new SequenceGroup(Arrays.asList(new SequenceI[] { s1,
s2 }), "Group1", null, false, false, false, 0, 5);
- SequenceGroup sg2 = new SequenceGroup(Arrays.asList(new SequenceI[] { s3,
+ SequenceGroup sg_345 = new SequenceGroup(Arrays.asList(new SequenceI[] { s3,
s4, s5 }), "Group2", null, false, false, false, 0, 5);
AlignmentI alignment = new Alignment(
new SequenceI[] { s1, s2, s3, s4, s5 });
- int[] positions = new int[] { 1, 7, 9 };
+ /*
+ * test for the case where column selections are not added in
+ * left to right order
+ */
+ int[] positions = new int[] { 7, 9, 1 };
@Test(groups = { "Functional" })
public void testMakeGroupsWithBoth()
{
- ArrayList<String> str = new ArrayList<String>();
+ String[] str = new String[alignment.getHeight()];
+ int seq = 0;
for (SequenceI s : alignment.getSequences())
{
StringBuilder sb = new StringBuilder();
{
sb.append(s.getCharAt(p));
}
- str.add(sb.toString());
+ str[seq++] = sb.toString();
}
SequenceGroup[] seqgroupsString = Grouping.makeGroupsFrom(
- alignment.getSequencesArray(),
- str.toArray(new String[str.size()]),
- Arrays.asList(new SequenceGroup[] { sg1, sg2 }));
+ alignment.getSequencesArray(), str,
+ Arrays.asList(new SequenceGroup[] { sg_12, sg_345 }));
+
ColumnSelection cs = new ColumnSelection();
for (int p : positions)
{
}
SequenceGroup[] seqgroupsColSel = Grouping.makeGroupsFromCols(
alignment.getSequencesArray(), cs,
- Arrays.asList(new SequenceGroup[] { sg1, sg2 }));
+ Arrays.asList(new SequenceGroup[] { sg_12, sg_345 }));
AssertJUnit
.assertEquals(seqgroupsString.length, seqgroupsColSel.length);
for (int p = 0; p < seqgroupsString.length; p++)
--- /dev/null
+package jalview.controller;
+
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertTrue;
+
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+
+import java.util.BitSet;
+
+import org.testng.annotations.Test;
+
+public class AlignViewControllerTest
+{
+ @Test(groups = "Functional")
+ public void testFindColumnsWithFeature()
+ {
+ SequenceI seq1 = new Sequence("seq1", "aMMMaaaaaaaaaaaaaaaa");
+ SequenceI seq2 = new Sequence("seq2", "aaaMMMMMMMaaaaaaaaaa");
+ SequenceI seq3 = new Sequence("seq3", "aaaaaaaaaaMMMMMaaaaa");
+ SequenceI seq4 = new Sequence("seq3", "aaaaaaaaaaaaaaaaaaaa");
+
+ /*
+ * features start/end are base 1
+ */
+ 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, 0f,
+ null));
+ seq3.addSequenceFeature(new SequenceFeature("Metal", "desc", 11, 15,
+ 0f, null));
+
+ /*
+ * select the first three columns --> Metal in seq1 2-3
+ */
+ SequenceGroup sg = new SequenceGroup();
+ sg.setStartRes(0); // base 0
+ sg.setEndRes(2);
+ sg.addSequence(seq1, false);
+ sg.addSequence(seq2, false);
+ sg.addSequence(seq3, false);
+ sg.addSequence(seq4, false);
+
+ BitSet bs = new BitSet();
+ int seqCount = AlignViewController.findColumnsWithFeature("Metal", sg,
+ bs);
+ assertEquals(1, seqCount);
+ assertEquals(2, bs.cardinality());
+ assertTrue(bs.get(1));
+ assertTrue(bs.get(2));
+
+ /*
+ * select the first four columns: Metal in seq1 2:4, seq2 4:4
+ */
+ sg.setEndRes(3);
+ bs.clear();
+ seqCount = AlignViewController.findColumnsWithFeature("Metal", sg,
+ bs);
+ assertEquals(2, seqCount);
+ assertEquals(3, bs.cardinality());
+ assertTrue(bs.get(1));
+ assertTrue(bs.get(2));
+ assertTrue(bs.get(3));
+
+ /*
+ * select column 11: Metal in seq3 only
+ */
+ sg.setStartRes(10);
+ sg.setEndRes(10);
+ bs.clear();
+ seqCount = AlignViewController.findColumnsWithFeature("Metal", sg, bs);
+ assertEquals(1, seqCount);
+ assertEquals(1, bs.cardinality());
+ assertTrue(bs.get(10));
+
+ /*
+ * select columns 16-20: no Metal feature
+ */
+ sg.setStartRes(15);
+ sg.setEndRes(19);
+ bs.clear();
+ seqCount = AlignViewController.findColumnsWithFeature("Metal", sg, bs);
+ assertEquals(0, seqCount);
+ assertEquals(0, bs.cardinality());
+
+ /*
+ * look for a feature that isn't there
+ */
+ sg.setStartRes(0);
+ sg.setEndRes(19);
+ bs.clear();
+ seqCount = AlignViewController.findColumnsWithFeature("Pfam", sg, bs);
+ assertEquals(0, seqCount);
+ assertEquals(0, bs.cardinality());
+ }
+}
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertNotSame;
import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
import java.util.Arrays;
+import java.util.BitSet;
import java.util.List;
import org.testng.annotations.Test;
// removing an element in the list removes it
cs.removeElement(2);
+ // ...but not from the copy list!
+ assertEquals(2, sel.size());
+ sel = cs.getSelected();
assertEquals(1, sel.size());
assertEquals(new Integer(5), sel.get(0));
}
* this fails, HideSelectedColumns may also fail
*/
@Test(groups = { "Functional" })
- public void testgetSelectedRanges()
+ public void testGetSelectedRanges()
{
+ /*
+ * getSelectedRanges returns ordered columns regardless
+ * of the order in which they are added
+ */
ColumnSelection cs = new ColumnSelection();
- int[] sel = { 2, 3, 4, 7, 8, 9, 20, 21, 22 };
+ int[] sel = { 4, 3, 7, 21, 9, 20, 8, 22, 2 };
for (int col : sel)
{
cs.addElement(col);
cs.addElement(88);
assertTrue(cs.equals(cs2));
}
+
+ /**
+ * Test the method that returns selected columns, in the order in which they
+ * were added
+ */
+ @Test(groups = { "Functional" })
+ public void testGetSelection()
+ {
+ ColumnSelection cs = new ColumnSelection();
+ int[] sel = { 4, 3, 7, 21 };
+ for (int col : sel)
+ {
+ cs.addElement(col);
+ }
+
+ List<Integer> selected1 = cs.getSelected();
+ assertEquals(4, selected1.size());
+
+ /*
+ * getSelected returns a copy, verify the list
+ * is externally immutable
+ */
+ selected1.clear();
+ List<Integer> selected2 = cs.getSelected();
+ assertNotSame(selected1, selected2);
+ assertEquals(4, selected2.size());
+ int i = 0;
+ for (int col : sel)
+ {
+ assertEquals(col, selected2.get(i++).intValue());
+ }
+
+ cs.removeElement(7);
+ cs.addElement(1);
+ cs.removeElement(4);
+
+ List<Integer> selected3 = cs.getSelected();
+ assertEquals(3, selected3.size());
+ assertEquals(3, selected3.get(0).intValue());
+ assertEquals(21, selected3.get(1).intValue());
+ assertEquals(1, selected3.get(2).intValue());
+ }
+
+ @Test(groups = "Functional")
+ public void testMarkColumns()
+ {
+ ColumnSelection cs = new ColumnSelection();
+ cs.addElement(5); // this will be cleared
+ BitSet toMark = new BitSet();
+ toMark.set(1);
+ toMark.set(3);
+ toMark.set(6);
+ toMark.set(9);
+
+ assertTrue(cs.markColumns(toMark, 3, 8, false, false, false));
+ List<Integer> selected = cs.getSelected();
+ assertEquals(2, selected.size());
+ assertTrue(selected.contains(3));
+ assertTrue(selected.contains(6));
+ }
+
+ @Test(groups = "Functional")
+ public void testMarkColumns_extend()
+ {
+ ColumnSelection cs = new ColumnSelection();
+ cs.addElement(1);
+ cs.addElement(5);
+ BitSet toMark = new BitSet();
+ toMark.set(1);
+ toMark.set(3);
+ toMark.set(6);
+ toMark.set(9);
+
+ /*
+ * extending selection of {3, 6} should leave {1, 3, 5, 6} selected
+ */
+ assertTrue(cs.markColumns(toMark, 3, 8, false, true, false));
+ List<Integer> selected = cs.getSelected();
+ assertEquals(4, selected.size());
+ assertTrue(selected.contains(1));
+ assertTrue(selected.contains(3));
+ assertTrue(selected.contains(5));
+ assertTrue(selected.contains(6));
+ }
+
+ @Test(groups = "Functional")
+ public void testMarkColumns_invert()
+ {
+ ColumnSelection cs = new ColumnSelection();
+ cs.addElement(5); // this will be cleared
+ BitSet toMark = new BitSet();
+ toMark.set(1);
+ toMark.set(3);
+ toMark.set(6);
+ toMark.set(9);
+
+ /*
+ * inverted selection of {3, 6} should select {4, 5, 7, 8}
+ */
+ assertTrue(cs.markColumns(toMark, 3, 8, true, false, false));
+ List<Integer> selected = cs.getSelected();
+ assertEquals(4, selected.size());
+ assertTrue(selected.contains(4));
+ assertTrue(selected.contains(5));
+ assertTrue(selected.contains(7));
+ assertTrue(selected.contains(8));
+ }
+
+ @Test(groups = "Functional")
+ public void testMarkColumns_toggle()
+ {
+ ColumnSelection cs = new ColumnSelection();
+ cs.addElement(1); // outside change range
+ cs.addElement(3);
+ cs.addElement(4);
+ cs.addElement(10); // outside change range
+ BitSet toMark = new BitSet();
+ toMark.set(1);
+ toMark.set(3);
+ toMark.set(6);
+ toMark.set(9);
+
+ /*
+ * toggling state of {3, 6} should leave {1, 4, 6, 10} selected
+ */
+ assertTrue(cs.markColumns(toMark, 3, 8, false, false, true));
+ List<Integer> selected = cs.getSelected();
+ assertEquals(4, selected.size());
+ assertTrue(selected.contains(1));
+ assertTrue(selected.contains(4));
+ assertTrue(selected.contains(6));
+ assertTrue(selected.contains(10));
+ }
}
{
AlignmentAnnotation ann1 = addAnnotation("label1", "desc1", "calcId1",
1f);
- AlignmentAnnotation ann2 = addAnnotation("label2", "desc2", "calcId2",
- 1f);
+ addAnnotation("label2", "desc2", "calcId2", 1f);
AlignmentAnnotation ann3 = addAnnotation("label1", "desc3", "calcId3",
1f);
AlignmentAnnotation[] anns = seq.getAnnotation("label1");
@Test(groups = { "Functional" })
public void testGetAlignmentAnnotations_forCalcIdAndLabel()
{
- AlignmentAnnotation ann1 = addAnnotation("label1", "desc1", "calcId1",
- 1f);
+ addAnnotation("label1", "desc1", "calcId1", 1f);
AlignmentAnnotation ann2 = addAnnotation("label2", "desc2", "calcId2",
1f);
- AlignmentAnnotation ann3 = addAnnotation("label2", "desc3", "calcId3",
- 1f);
+ addAnnotation("label2", "desc3", "calcId3", 1f);
AlignmentAnnotation ann4 = addAnnotation("label2", "desc3", "calcId2",
1f);
- AlignmentAnnotation ann5 = addAnnotation("label5", "desc3", null, 1f);
- AlignmentAnnotation ann6 = addAnnotation(null, "desc3", "calcId3", 1f);
+ addAnnotation("label5", "desc3", null, 1f);
+ addAnnotation(null, "desc3", "calcId3", 1f);
+
List<AlignmentAnnotation> anns = seq.getAlignmentAnnotations("calcId2",
"label2");
assertEquals(2, anns.size());
pdbId = al.getSequenceAt(0).getDatasetSequence().getAllPDBEntries()
.get(0).getId();
StructureImportSettings.setDefaultStructureFileFormat("PDB");
- StructureImportSettings
- .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER);
+ // StructureImportSettings
+ // .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER);
}
@Test(groups = { "Functional" })
{
System.out.println("CalcId: " + aa.getCalcId());
+ if (StructureImportSettings.getDefaultPDBFileParser().equals(
+ StructureParser.JALVIEW_PARSER))
+ {
assertTrue(MCview.PDBfile.isCalcIdForFile(aa, pdbId));
+ }
}
}
}
SequenceFeature[] sf = al.getSequenceAt(0).getSequenceFeatures();
assertEquals(296, sf.length);
assertEquals("RESNUM", sf[0].getType());
- assertEquals("GLU: 19 1gaqA", sf[0].getDescription());
+ assertEquals("GLU:19 1gaqA", sf[0].getDescription());
assertEquals("RESNUM", sf[295].getType());
- assertEquals("TYR: 314 1gaqA", sf[295].getDescription());
+ assertEquals("TYR:314 1gaqA", sf[295].getDescription());
/*
* 1GAQ/B
sf = al.getSequenceAt(1).getSequenceFeatures();
assertEquals(98, sf.length);
assertEquals("RESNUM", sf[0].getType());
- assertEquals("ALA: 1 1gaqB", sf[0].getDescription());
+ assertEquals("ALA:1 1gaqB", sf[0].getDescription());
assertEquals("RESNUM", sf[97].getType());
- assertEquals("ALA: 98 1gaqB", sf[97].getDescription());
+ assertEquals("ALA:98 1gaqB", sf[97].getDescription());
/*
* 1GAQ/C
sf = al.getSequenceAt(2).getSequenceFeatures();
assertEquals(296, sf.length);
assertEquals("RESNUM", sf[0].getType());
- assertEquals("GLU: 19 1gaqC", sf[0].getDescription());
+ assertEquals("GLU:19 1gaqC", sf[0].getDescription());
assertEquals("RESNUM", sf[295].getType());
- assertEquals("TYR: 314 1gaqC", sf[295].getDescription());
+ assertEquals("TYR:314 1gaqC", sf[295].getDescription());
}
@Test(groups = { "Functional" })
--- /dev/null
+package jalview.io;
+
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.fail;
+
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+public class FormatAdapterTest
+{
+
+ /**
+ * Test saving and re-reading in a specified format
+ *
+ * @throws IOException
+ */
+ @Test(groups = { "Functional" }, dataProvider = "formats")
+ public void testRoundTrip(String format) throws IOException
+ {
+ try
+ {
+ AlignmentI al = new FormatAdapter().readFile("examples/uniref50.fa",
+ FormatAdapter.FILE, "FASTA");
+
+ /*
+ * 'gap' is the gap character used in the alignment data file here,
+ * not the user preferred gap character
+ */
+ char gap = al.getGapCharacter();
+ assertNotNull(al);
+
+ SequenceI[] seqs = al.getSequencesArray();
+ String formatted = new FormatAdapter().formatSequences(format, al,
+ false);
+
+ AlignmentI reloaded = new FormatAdapter().readFile(formatted,
+ FormatAdapter.PASTE, format);
+ List<SequenceI> reread = reloaded.getSequences();
+ assertEquals("Wrong number of reloaded sequences", seqs.length,
+ reread.size());
+
+ int i = 0;
+ for (SequenceI seq : reread)
+ {
+ String sequenceString = seq.getSequenceAsString();
+
+ /*
+ * special case: MSF always uses '.' as gap character
+ */
+ sequenceString = adjustForGapTreatment(sequenceString, gap, format);
+ assertEquals(
+ String.format("Sequence %d: %s", i,
+ seqs[i].getName()), seqs[i].getSequenceAsString(),
+ sequenceString);
+ i++;
+ }
+ } catch (IOException e)
+ {
+ fail(String
+ .format("Format %s failed with %s", format, e.getMessage()));
+ }
+ }
+
+ /**
+ * Optionally change the gap character in the string to the given character,
+ * depending on the sequence file format
+ *
+ * @param sequenceString
+ * a sequence (as written in 'format' format)
+ * @param gap
+ * the sequence's original gap character
+ * @param format
+ * @return
+ */
+ String adjustForGapTreatment(String sequenceString, char gap,
+ String format)
+ {
+ if ("MSF".equals(format))
+ {
+ /*
+ * MSF forces gap character to '.', so change it back
+ * for comparison purposes
+ */
+ sequenceString = sequenceString.replace('.', gap);
+ }
+ return sequenceString;
+ }
+
+ /**
+ * Data provider that serves alignment formats that are both readable and
+ * writable
+ *
+ * @return
+ */
+ @DataProvider(name = "formats")
+ static Object[][] getFormats()
+ {
+ List<String> both = new ArrayList<String>();
+ String[] readable = FormatAdapter.READABLE_FORMATS;
+ List<String> writeable = Arrays.asList(FormatAdapter.WRITEABLE_FORMATS);
+ for (String r : readable)
+ {
+ if (writeable.contains(r))
+ {
+ both.add(r);
+ }
+ }
+
+ Object[][] formats = new Object[both.size()][];
+ int i = 0;
+ for (String format : both)
+ {
+ formats[i] = new Object[] { format };
+ i++;
+ }
+ return formats;
+ }
+
+ /**
+ * Enable this to isolate testing to a single file format
+ *
+ * @throws IOException
+ */
+ @Test(groups = { "Functional" }, enabled = false)
+ public void testOneFormatRoundTrip() throws IOException
+ {
+ testRoundTrip("JSON");
+ }
+}
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.HiddenSequences;
+import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
+import jalview.gui.AlignmentPanel;
import jalview.gui.Desktop;
import jalview.gui.Jalview2XML;
import jalview.schemes.AnnotationColourGradient;
hidden.size(), hs.getSize());
}
}
+
+ /**
+ * Test save and reload of PDBEntry in Jalview project
+ *
+ * @throws Exception
+ */
+ @Test(groups = { "Functional" })
+ public void testStoreAndRecoverPDBEntry() throws Exception
+ {
+ Desktop.instance.closeAll_actionPerformed(null);
+ String exampleFile = "examples/3W5V.pdb";
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(exampleFile,
+ FormatAdapter.FILE);
+ assertTrue("Didn't read in the example file correctly.", af != null);
+ String afid = af.getViewport().getSequenceSetId();
+
+ AlignmentPanel[] alignPanels = Desktop.getAlignmentPanels(afid);
+ System.out.println();
+ AlignmentViewPanel ap = alignPanels[0];
+ String tfileBase = new File(".").getAbsolutePath().replace(".", "");
+ String testFile = tfileBase + exampleFile;
+ AlignmentI alignment = ap.getAlignment();
+ System.out.println("blah");
+ SequenceI[] seqs = alignment.getSequencesArray();
+ Assert.assertNotNull(seqs[0]);
+ Assert.assertNotNull(seqs[1]);
+ Assert.assertNotNull(seqs[2]);
+ Assert.assertNotNull(seqs[3]);
+ Assert.assertNotNull(seqs[0].getDatasetSequence());
+ Assert.assertNotNull(seqs[1].getDatasetSequence());
+ Assert.assertNotNull(seqs[2].getDatasetSequence());
+ Assert.assertNotNull(seqs[3].getDatasetSequence());
+ PDBEntry[] pdbEntries = new PDBEntry[4];
+ pdbEntries[0] = new PDBEntry("3W5V", "A", null, testFile);
+ pdbEntries[1] = new PDBEntry("3W5V", "B", null, testFile);
+ pdbEntries[2] = new PDBEntry("3W5V", "C", null, testFile);
+ pdbEntries[3] = new PDBEntry("3W5V", "D", null, testFile);
+ Assert.assertTrue(seqs[0].getDatasetSequence().getAllPDBEntries()
+ .get(0).equals(pdbEntries[0]));
+ Assert.assertTrue(seqs[1].getDatasetSequence().getAllPDBEntries()
+ .get(0).equals(pdbEntries[1]));
+ Assert.assertTrue(seqs[2].getDatasetSequence().getAllPDBEntries()
+ .get(0).equals(pdbEntries[2]));
+ Assert.assertTrue(seqs[3].getDatasetSequence().getAllPDBEntries()
+ .get(0).equals(pdbEntries[3]));
+
+ File tfile = File.createTempFile("testStoreAndRecoverPDBEntry", ".jvp");
+ try
+ {
+ new Jalview2XML(false).saveState(tfile);
+ } catch (Throwable e)
+ {
+ Assert.fail("Didn't save the state", e);
+ }
+ Desktop.instance.closeAll_actionPerformed(null);
+ if (Desktop.getAlignFrames() != null)
+ {
+ Assert.assertEquals(Desktop.getAlignFrames().length, 0);
+ }
+
+ AlignFrame restoredFrame = new FileLoader().LoadFileWaitTillLoaded(
+ tfile.getAbsolutePath(), FormatAdapter.FILE);
+ String rfid = restoredFrame.getViewport().getSequenceSetId();
+ AlignmentPanel[] rAlignPanels = Desktop.getAlignmentPanels(rfid);
+ AlignmentViewPanel rap = rAlignPanels[0];
+ AlignmentI rAlignment = rap.getAlignment();
+ System.out.println("blah");
+ SequenceI[] rseqs = rAlignment.getSequencesArray();
+ Assert.assertNotNull(rseqs[0]);
+ Assert.assertNotNull(rseqs[1]);
+ Assert.assertNotNull(rseqs[2]);
+ Assert.assertNotNull(rseqs[3]);
+ Assert.assertNotNull(rseqs[0].getDatasetSequence());
+ Assert.assertNotNull(rseqs[1].getDatasetSequence());
+ Assert.assertNotNull(rseqs[2].getDatasetSequence());
+ Assert.assertNotNull(rseqs[3].getDatasetSequence());
+
+ // The Asserts below are expected to fail until the PDB chainCode is
+ // recoverable from a Jalview projects
+ Assert.assertTrue(rseqs[0].getDatasetSequence().getAllPDBEntries()
+ .get(0).equals(pdbEntries[0]));
+ Assert.assertTrue(rseqs[1].getDatasetSequence().getAllPDBEntries()
+ .get(0).equals(pdbEntries[1]));
+ Assert.assertTrue(rseqs[2].getDatasetSequence().getAllPDBEntries()
+ .get(0).equals(pdbEntries[2]));
+ Assert.assertTrue(rseqs[3].getDatasetSequence().getAllPDBEntries()
+ .get(0).equals(pdbEntries[3]));
+ }
}
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertTrue;
+import static org.testng.AssertJUnit.fail;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
* 'secondary' or generated alignment from some datapreserving
* transformation
* @param ignoreFeatures
- * when true, differences in seuqence feature annotation are ignored.
+ * when true, differences in sequence feature annotation are ignored
*/
public static void testAlignmentEquivalence(AlignmentI al,
AlignmentI al_input, boolean ignoreFeatures)
assertNotNull("Original alignment was null", al);
assertNotNull("Generated alignment was null", al_input);
- assertTrue(
- "Alignment dimension mismatch: originl contains "
- + al.getHeight() + " and generated has "
- + al_input.getHeight() + " sequences; original has "
- + al.getWidth() + " and generated has "
- + al_input.getWidth() + " columns.",
+ assertTrue("Alignment dimension mismatch: original: " + al.getHeight()
+ + "x" + al.getWidth() + ", generated: " + al_input.getHeight()
+ + "x" + al_input.getWidth(),
al.getHeight() == al_input.getHeight()
&& al.getWidth() == al_input.getWidth());
// note - at moment we do not distinguish between alignment without any
// annotation rows and alignment with no annotation row vector
// we might want to revise this in future
- int aa_new_size = (aa_new == null ? 0 : aa_new.length), aa_original_size = (aa_original == null ? 0
- : aa_original.length);
- Map<Integer, java.util.BitSet> orig_groups = new HashMap<Integer, java.util.BitSet>(), new_groups = new HashMap<Integer, java.util.BitSet>();
+ int aa_new_size = (aa_new == null ? 0 : aa_new.length);
+ int aa_original_size = (aa_original == null ? 0 : aa_original.length);
+ Map<Integer, BitSet> orig_groups = new HashMap<Integer, BitSet>();
+ Map<Integer, BitSet> new_groups = new HashMap<Integer, BitSet>();
if (aa_new != null && aa_original != null)
{
assertTrue("Different alignment annotation at position " + i,
equalss(aa_original[i], aa_new[i]));
// compare graphGroup or graph properties - needed to verify JAL-1299
- assertTrue("Graph type not identical.",
- aa_original[i].graph == aa_new[i].graph);
- assertTrue("Visibility not identical.",
- aa_original[i].visible == aa_new[i].visible);
- assertTrue(
- "Threshold line not identical.",
- aa_original[i].threshold == null ? aa_new[i].threshold == null
- : aa_original[i].threshold
- .equals(aa_new[i].threshold));
+ assertEquals("Graph type not identical.", aa_original[i].graph,
+ aa_new[i].graph);
+ assertEquals("Visibility not identical.", aa_original[i].visible,
+ aa_new[i].visible);
+ assertEquals("Threshold line not identical.",
+ aa_original[i].threshold, aa_new[i].threshold);
// graphGroup may differ, but pattern should be the same
- Integer o_ggrp = new Integer(aa_original[i].graphGroup + 2), n_ggrp = new Integer(
- aa_new[i].graphGroup + 2);
- BitSet orig_g = orig_groups.get(o_ggrp), new_g = new_groups
- .get(n_ggrp);
+ Integer o_ggrp = new Integer(aa_original[i].graphGroup + 2);
+ Integer n_ggrp = new Integer(aa_new[i].graphGroup + 2);
+ BitSet orig_g = orig_groups.get(o_ggrp);
+ BitSet new_g = new_groups.get(n_ggrp);
if (orig_g == null)
{
orig_groups.put(o_ggrp, orig_g = new BitSet());
{
new_groups.put(n_ggrp, new_g = new BitSet());
}
- assertTrue("Graph Group pattern differs at annotation " + i,
- orig_g.equals(new_g));
+ assertEquals("Graph Group pattern differs at annotation " + i,
+ orig_g, new_g);
orig_g.set(i);
new_g.set(i);
}
}
}
}
- assertTrue(
- "Generated and imported alignment have different annotation sets ("
- + aa_new_size + " != " + aa_original_size + ")",
- aa_new_size == aa_original_size);
+ assertEquals(
+ "Generated and imported alignment have different annotation sets",
+ aa_new_size, aa_original_size);
// check sequences, annotation and features
SequenceI[] seq_original = new SequenceI[al.getSequencesArray().length];
{
String ss_original = seq_original[i].getSequenceAsString();
String ss_new = seq_new[in].getSequenceAsString();
- assertTrue("The sequences " + name + "/" + start + "-" + end
- + " are not equal", ss_original.equals(ss_new));
+ assertEquals("The sequences " + name + "/" + start + "-" + end
+ + " are not equal", ss_original, ss_new);
assertTrue(
"Sequence Features were not equivalent"
.getSequenceFeatures().length];
sequenceFeatures_new = seq_new[in].getSequenceFeatures();
- assertTrue("different number of features", seq_original[i]
- .getSequenceFeatures().length == seq_new[in]
+ assertEquals("different number of features",
+ seq_original[i].getSequenceFeatures().length,
+ seq_new[in]
.getSequenceFeatures().length);
for (int feat = 0; feat < seq_original[i].getSequenceFeatures().length; feat++)
{
- assertTrue("Different features",
- sequenceFeatures_original[feat]
- .equals(sequenceFeatures_new[feat]));
+ assertEquals("Different features",
+ sequenceFeatures_original[feat],
+ sequenceFeatures_new[feat]);
}
}
// compare alignment annotation
else if (al.getSequenceAt(i).getAnnotation() != null
&& al_input.getSequenceAt(in).getAnnotation() == null)
{
- assertTrue("Annotations differed between sequences ("
+ fail("Annotations differed between sequences ("
+ al.getSequenceAt(i).getName() + ") and ("
- + al_input.getSequenceAt(i).getName() + ")", false);
+ + al_input.getSequenceAt(i).getName() + ")");
}
break;
}
SequenceFeature sf = pmap.getSeqs().get(0).getSequenceFeatures()[0];
assertEquals("RESNUM", sf.getType());
assertEquals("1gaq", sf.getFeatureGroup());
- assertEquals("GLU: 19 1gaqA", sf.getDescription());
+ assertEquals("GLU:19 1gaqA", sf.getDescription());
/*
* Verify a RESNUM sequence feature in the StructureSelectionManager mapped
sf = map.sequence.getSequenceFeatures()[0];
assertEquals("RESNUM", sf.getType());
assertEquals("1gaq", sf.getFeatureGroup());
- assertEquals("ALA: 1 1gaqB", sf.getDescription());
+ assertEquals("ALA:1 1gaqB", sf.getDescription());
}
}
import jalview.datamodel.AlignmentI;
import jalview.gui.Jalview2XML;
import jalview.io.AnnotationFile;
+import jalview.io.FileLoader;
import jalview.io.FormatAdapter;
import jalview.io.StockholmFileTest;
import jalview.ws.jws2.Jws2Discoverer;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
+import compbio.metadata.Argument;
import compbio.metadata.WrongParameterException;
public class RNAStructExportImport
Assert.fail("no web service");
}
- jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
+ FileLoader fl = new FileLoader(false);
- af = fl.LoadFileWaitTillLoaded(testseqs, jalview.io.FormatAdapter.FILE);
+ af = fl.LoadFileWaitTillLoaded(testseqs, FormatAdapter.FILE);
assertNotNull("Couldn't load test data ('" + testseqs + "')", af);
} catch (InterruptedException x)
{
}
- ;
} while (af.getViewport().getCalcManager().isWorking());
AlignmentI orig_alig = af.getViewport().getAlignment();
} catch (InterruptedException x)
{
}
- ;
} while (af.getViewport().getCalcManager().isWorking());
AlignmentI orig_alig = af.getViewport().getAlignment();
String anfileout = new AnnotationFile()
.printAnnotationsForAlignment(al);
- assertTrue(
+ assertNotNull(
"Test "
+ testname
+ "\nAlignment annotation file was not regenerated. Null string",
- anfileout != null);
+ anfileout);
assertTrue(
"Test "
+ testname
@Test(groups = { "Functional" })
public void testRnaalifoldSettingsRecovery()
{
- List<compbio.metadata.Argument> opts = new ArrayList<compbio.metadata.Argument>();
- for (compbio.metadata.Argument rg : (List<compbio.metadata.Argument>) rnaalifoldws
+ List<Argument> opts = new ArrayList<Argument>();
+ for (Argument rg : (List<Argument>) rnaalifoldws
.getRunnerConfig().getArguments())
{
if (rg.getDescription().contains("emperature"))
return;
}
- internetAvailable &= connectToUrl("http://www.example.com");
+ internetAvailable &= connectToUrl("http://www.example.org");
Map<String, String> tocTargets = checkHelpMappings(helpFolder);
import java.util.HashSet;
import java.util.Properties;
import java.util.TreeSet;
+import java.util.regex.Pattern;
/**
* This class scans Java source files for calls to MessageManager and reports
public class MessageBundleChecker
{
/*
+ * regex ^"[^"]*"$
+ * opening quote, closing quote, no quotes in between
+ */
+ static Pattern STRING_PATTERN = Pattern.compile("^\"[^\"]*\"$");
+
+ /*
* number of text lines to read at a time in order to parse
* code that is split over several lines
*/
static int bufferSize = 3;
+ /*
+ * resource bundle key is arg0 for these methods
+ */
static final String METHOD1 = "MessageManager.getString(";
- static final String METHOD2 = "MessageManager.getStringOrReturn(";
+ static final String METHOD2 = "MessageManager.formatMessage(";
- static final String METHOD3 = "MessageManager.formatMessage(";
+ static final String METHOD3 = "MessageManager.getStringOrReturn(";
- static final String[] METHODS = { METHOD1, METHOD2, METHOD3 };
+ /*
+ * resource bundle key is arg1 for this method
+ */
+ static final String JVINIT = "JvSwingUtils.jvInitComponent(";
+
+ static final String[] METHODS = { METHOD1, METHOD2, METHOD3, JVINIT };
/*
* root of the Java source folders we want to scan
+ " possibly invalid parameter calls");
System.out.println(messageKeys.size()
- + " keys not found, possibly unused");
+ + " keys not found, either unused or constructed dynamically");
for (String key : messageKeys)
{
System.out.println(" " + key);
}
javaCount++;
+ /*
+ * skip class with designed dynamic lookup call
+ */
+ if (path.endsWith("gui/JvSwingUtils.java"))
+ {
+ return;
+ }
+
String[] lines = new String[bufferSize];
BufferedReader br = new BufferedReader(new FileReader(f));
for (int i = 0; i < bufferSize; i++)
{
continue;
}
- String methodArgs = combined.substring(pos + method.length());
+
+ /*
+ * extract what follows the opening bracket of the method call
+ */
+ String methodArgs = combined.substring(pos + method.length()).trim();
if ("".equals(methodArgs))
{
/*
- * continues on next line - catch in the next read loop iteration
+ * arguments are on next line - catch in the next read loop iteration
*/
continue;
}
- if (!methodArgs.startsWith("\""))
+ if (methodArgs.indexOf(",") == -1 && methodArgs.indexOf(")") == -1)
{
- System.out.println(String.format(
- "Possible dynamic key at %s line %s %s",
+ /*
+ * arguments continue on next line - catch in the next read loop iteration
+ */
+ continue;
+ }
+
+ if (JVINIT == method && methodArgs.indexOf(",") == -1)
+ {
+ /*
+ * not interested in 1-arg calls to jvInitComponent
+ */
+ continue;
+ }
+
+ if (METHOD3 == method)
+ {
+ System.out.println(String.format("Dynamic key at %s line %s %s",
path.substring(sourcePath.length()), lineNos, combined));
continue;
}
- methodArgs = methodArgs.substring(1);
- int quotePos = methodArgs.indexOf("\"");
- if (quotePos == -1)
+
+ String messageKey = getMessageKey(method, methodArgs);
+ if (messageKey == null)
{
System.out.println(String.format("Trouble parsing %s line %s %s",
path.substring(sourcePath.length()), lineNos, combined));
continue;
}
- String messageKey = methodArgs.substring(0, quotePos);
+
+ if (!(STRING_PATTERN.matcher(messageKey).matches()))
+ {
+ System.out.println(String.format("Dynamic key at %s line %s %s",
+ path.substring(sourcePath.length()), lineNos, combined));
+ continue;
+ }
+
+ /*
+ * strip leading and trailing quote
+ */
+ messageKey = messageKey.substring(1, messageKey.length() - 1);
+
if (!this.messages.containsKey(messageKey))
{
System.out.println(String.format(
}
}
+ /**
+ * Helper method to parse out the resource bundle key parameter of a method
+ * call
+ *
+ * @param method
+ * @param methodArgs
+ * the rest of the source line starting with arguments to method
+ * @return
+ */
+ private String getMessageKey(String method, String methodArgs)
+ {
+ String key = methodArgs;
+
+ /*
+ * locate second argument if calling jvInitComponent()
+ */
+ if (method == JVINIT)
+ {
+ int commaLoc = methodArgs.indexOf(",");
+ if (commaLoc == -1)
+ {
+ return null;
+ }
+ key = key.substring(commaLoc + 1).trim();
+ }
+
+ /*
+ * take up to next comma or ) or end of line
+ */
+ int commaPos = key.indexOf(",");
+ int bracePos = key.indexOf(")");
+ int endPos = commaPos == -1 ? bracePos : (bracePos == -1 ? commaPos
+ : Math.min(commaPos, bracePos));
+ if (endPos == -1 && key.length() > 1 && key.endsWith("\""))
+ {
+ endPos = key.length();
+ }
+
+ return endPos == -1 ? null : key.substring(0, endPos);
+ }
+
private String combineLines(String[] lines)
{
String combined = "";
var logger = project.getBuildListeners( ).firstElement( );
logger.setMessageOutputLevel( 1 );
</script>
- <echo message="Missing message labels compared to Messages.properties"/>
- <foreach target="compareProperties" param="file2">
+ <foreach target="compareBundles" param="file2">
<path>
<fileset dir="${basedir}/resources/lang">
<exclude name="Messages.properties" />
</foreach>
</target>
+<target name="compareBundles" description="compare a properties file with Messages.properties and vice versa">
+ <echo message=" "/>
+ <echo message="Missing message labels in ${file2} compared to Messages.properties"/>
+ <antcall target="compareProperties">
+ <param name="file1" value="resources/lang/Messages.properties"/>
+ <param name="file2" value="${file2}" />
+ </antcall>
+ <echo message=" "/>
+ <echo message="Missing message labels in Messages.properties compare to ${file2}"/>
+ <antcall target="compareProperties">
+ <param name="file2" value="resources/lang/Messages.properties"/>
+ <param name="file1" value="${file2}" />
+ </antcall>
+</target>
+
<target name="compareProperties" description="reports missing entries in one message bundle">
- <loadproperties srcFile="resources/lang/Messages.properties" prefix="prefixfile1"/>
+ <loadproperties srcFile="${file1}" prefix="prefixfile1"/>
<loadproperties srcFile="${file2}" prefix="prefixfile2"/>
<propertyselector property="file1.list" delimiter="," match="prefixfile1\.(.+)" select="\1"/>
<propertyselector property="file2.list" delimiter="," match="prefixfile2\.(.+)" select="\1"/>
- <echo message=" "/>
- <echo message="*** ${file2}:" />
<for list="${file1.list}" param="file1.property">
<sequential>
<if>
git://source.jalview.org / jalview.git / commitdiff