X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=resources%2Flang%2FMessages.properties;h=45f50abdedd3ac5896714beedb74c2ef03138a03;hb=304e64fb34b32659be1bbfd39fb4e15b2f79586e;hp=bf9cc186b74390b6f06182ad2a82d63270c2fd20;hpb=cfb79b69d9fa44595560659bd95d1d1cd27677ad;p=jalview.git

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index bf9cc18..45f50ab 100644
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -122,6 +122,7 @@ action.paste_annotations = Paste Annotations
 action.format = Format
 action.select = Select
 action.new_view = New View
+action.new_structure_view_with = Open new structure view with {0}
 action.close = Close
 action.add = Add
 action.save_as = Save as...
@@ -277,11 +278,11 @@ label.autoadd_secstr = Add secondary structure annotation to alignment
 label.autoadd_temp = Add Temperature Factor annotation to alignment
 label.structure_viewer = Default structure viewer
 label.double_click_to_browse = Double-click to browse for file
-label.chimera_path = Path to Chimera program
-label.chimera_path_tip = Jalview will first try any path entered here, else standard installation locations.<br>Double-click to browse for file.
-label.invalid_chimera_path = Chimera path not found or not executable
-label.chimera_missing = Chimera structure viewer not found.<br/>Please enter the path to Chimera (if installed),<br/>or download and install UCSF Chimera.
-label.chimera_failed = Error opening Chimera - is it installed?\nCheck path in Preferences, Structure
+label.viewer_path = Path to {0} program
+label.viewer_path_tip = Jalview will first try any path entered here, else standard installation locations.<br>Double-click to browse for file.
+label.invalid_viewer_path = Path not found or not executable
+label.viewer_missing = Structure viewer not found.<br/>Please enter the path to the executable (if installed),<br/>or download and install the program.
+label.open_viewer_failed = Error opening {0} - is it installed?\nCheck path in Preferences, Structure
 label.min_colour = Minimum Colour
 label.max_colour = Maximum Colour
 label.no_colour = No Colour
@@ -337,6 +338,7 @@ label.successfully_pasted_alignment_file = Successfully pasted alignment file
 label.paste_your_alignment_file = Paste your alignment file here
 label.paste_your = Paste your
 label.finished_searching = Finished searching
+label.subsequence_matches_found = {0} subsequence matches found
 label.search_results= Search results {0} : {1}
 label.found_match_for = Found match for {0}
 label.font = Font:
@@ -363,12 +365,6 @@ label.status = Status
 label.channels = Channels
 label.channel_title_item_count = {0} ({1})
 label.blog_item_published_on_date = {0} {1} 
-label.session_update = Session Update
-label.new_vamsas_session = New Vamsas Session
-action.load_vamsas_session = Load Vamsas Session...
-action.save_vamsas_session = Save Vamsas Session
-label.select_vamsas_session_opened_as_new_vamsas_session= Select a vamsas session to be opened as a new vamsas session.
-label.open_saved_vamsas_session = Open a saved VAMSAS session
 label.groovy_console = Groovy Console...
 label.lineart = Lineart
 label.dont_ask_me_again = Don't ask me again
@@ -387,7 +383,7 @@ label.example = Example
 label.example_param = Example: {0}
 label.select_file_format_before_saving = You must select a file format before saving!
 label.file_format_not_specified = File format not specified
-label.couldnt_save_file = Couldn't save file: {0}
+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.remove_user_defined_colour = Remove user defined colour
@@ -420,13 +416,10 @@ label.couldnt_read_pasted_text = Couldn't read the pasted text {0}
 label.error_parsing_text = Error parsing text
 label.input_alignment_from_url = Input Alignment From URL
 label.input_alignment = Input Alignment
-label.couldnt_import_as_vamsas_session = Couldn't import {0} as a new vamsas session.
 label.vamsas_document_import_failed = Vamsas Document Import Failed
 label.couldnt_locate = Couldn''t locate {0}
 label.url_not_found = URL not found
 label.new_sequence_url_link = New sequence URL link
-label.cannot_edit_annotations_in_wrapped_view = Cannot edit annotations in wrapped view
-label.wrapped_view_no_edit = Wrapped view - no edit
 label.error_retrieving_data = Error Retrieving Data
 label.user_colour_scheme_must_have_name = User colour scheme must have a name
 label.no_name_colour_scheme = No name for colour scheme
@@ -511,10 +504,9 @@ label.insert_gaps = Insert {0} gaps
 label.delete_gap = Delete 1 gap
 label.delete_gaps = Delete {0} gaps
 label.sequence_details = Sequence Details
-label.jmol_help = Jmol Help
-label.chimera_help = Chimera Help
+label.viewer_help = {0} 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.confirm_close_viewer = This will close Jalview''s connection to {0}.<br>Do you want to close the {1} window as well?
 label.all = All
 label.sort_by = Sort alignment by
 label.sort_by_score = Sort by Score
@@ -530,9 +522,14 @@ label.load_tree_file = Load a tree file
 label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences = Retrieve and parse sequence database records for the alignment or the currently selected sequences
 label.standard_databases = Standard Databases
 label.fetch_embl_uniprot = Fetch from EMBL/EMBLCDS or Uniprot/PDB and any selected DAS sources
+label.fetch_uniprot_references = Fetch Uniprot references
+label.search_3dbeacons = 3D-Beacons Search
+label.find_models_from_3dbeacons = Search 3D-Beacons for 3D structures and models
+label.3dbeacons = 3D-Beacons
+label.fetch_references_for = Fetch database references for {0} sequences ?
+label.fetch_references_for_3dbeacons = 3D Beacons needs Uniprot References. Fetch database references for {0} sequences ?
 label.reset_min_max_colours_to_defaults = Reset min and max colours to defaults from user preferences.
 label.align_structures_using_linked_alignment_views = Superpose structures using {0} selected alignment view(s)
-label.connect_to_session = Connect to session {0}
 label.threshold_feature_display_by_score = Threshold the feature display by score.
 label.threshold_feature_no_threshold = No Threshold
 label.threshold_feature_above_threshold = Above Threshold
@@ -566,9 +563,6 @@ label.right_align_sequence_id = Right Align Sequence Id
 label.sequence_id_tooltip = Sequence ID Tooltip
 label.no_services = <No Services>
 label.select_copy_raw_html = Select this if you want to copy raw html
-label.share_data_vamsas_applications = Share data with other vamsas applications
-label.connect_to = Connect to
-label.join_existing_vamsas_session = Join an existing vamsas session
 label.from_url = from URL
 label.any_trees_calculated_or_loaded_alignment_automatically_sort = When selected, any trees calculated or loaded onto the alignment will automatically sort the alignment
 label.sort_with_new_tree = Sort With New Tree
@@ -578,7 +572,6 @@ label.preferences = Preferences
 label.tools = Tools
 label.fetch_sequences = Fetch Sequences
 action.fetch_sequences = Fetch Sequences...
-label.stop_vamsas_session = Stop Vamsas Session
 label.collect_garbage = Collect Garbage
 label.show_memory_usage = Show Memory Usage
 label.show_java_console = Show Java Console
@@ -601,13 +594,21 @@ label.gap_symbol = Gap Symbol
 label.prot_alignment_colour = Protein Alignment Colour
 label.nuc_alignment_colour = Nucleotide Alignment Colour
 label.address = Address
+label.host = Host
 label.port = Port
 label.default_browser_unix = Default Browser (Unix)
 label.send_usage_statistics = Send usage statistics
 label.check_for_questionnaires = Check for questionnaires
 label.check_for_latest_version = Check for latest version
 label.url_linkfrom_sequence_id = URL link from Sequence ID
-label.use_proxy_server = Use a proxy server
+label.no_proxy = No proxy servers
+label.system_proxy = System proxy servers (http={0}; https={1})
+label.use_proxy_server = Use these proxy servers
+label.auth_required = Authentication required
+label.username = Username
+label.password = Password
+label.proxy_password_required = Proxy password required
+label.not_stored = not stored in Preferences file
 label.rendering_style = {0} rendering style
 label.append_start_end = Append /start-end (/15-380)
 label.full_sequence_id = Full Sequence Id
@@ -633,7 +634,6 @@ label.editing = Editing
 label.web_services = Web Services
 label.right_click_to_edit_currently_selected_parameter = Right click to edit currently selected parameter.
 label.let_jmol_manage_structure_colours = Let Jmol manage structure colours
-label.let_chimera_manage_structure_colours = Let Chimera manage structure colours
 label.fetch_chimera_attributes = Fetch Chimera attributes
 label.fetch_chimera_attributes_tip = Copy Chimera attribute to Jalview feature
 label.marks_leaves_tree_not_associated_with_sequence = Marks leaves of tree not associated with a sequence
@@ -645,7 +645,7 @@ label.delete_service_url = Delete Service URL
 label.details = Details
 label.options = Options
 label.parameters = Parameters
-label.proxy_server = Proxy Server
+label.proxy_servers = Proxy Servers
 label.file_output = File Output
 label.select_input_type = Select input type
 label.set_options_for_type = Set options for type
@@ -720,14 +720,13 @@ label.associate_nodes_with = Associate Nodes With
 label.link_name = Link Name
 label.pdb_file = PDB file
 label.colour_with_jmol = Colour with Jmol
-label.colour_with_chimera = Colour with Chimera
+label.let_viewer_manage_structure_colours = Let viewer manage structure colours
+label.colour_with_viewer = Colour in structure viewer
 label.superpose_structures = Superpose Structures
 error.superposition_failed = Superposition failed: {0}
 label.insufficient_residues = Not enough aligned residues ({0}) to perform superposition
-label.jmol = Jmol
-label.chimera = Chimera
-label.create_chimera_attributes = Write Jalview features
-label.create_chimera_attributes_tip = Set Chimera residue attributes for visible features
+label.create_viewer_attributes = Write Jalview features
+label.create_viewer_attributes_tip = Set structure residue attributes for Jalview features
 label.attributes_set = {0} attribute values set on Chimera
 label.sort_alignment_by_tree = Sort Alignment By Tree
 label.mark_unlinked_leaves = Mark Unlinked Leaves
@@ -819,8 +818,8 @@ label.fetch_retrieve_from_all_sources = Retrieve from all {0} sources in {1}<br>
 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.opt_and_params_show_brief_desc_image_link = Click to show brief description<br><img src="{0}"/> Right click for further information. 
-label.opt_and_params_show_brief_desc = Click to show brief description<br>
+label.opt_and_params_show_brief_desc_image_link = <html>Click to show brief description<br><img src="{0}"/> Right click for further information.</html> 
+label.opt_and_params_show_brief_desc = <html>Click to show brief description<br></html>
 label.adjusts_width_generated_eps_png = <html>Adjusts the width of the generated EPS or PNG file to ensure even the longest sequence ID or annotation label is displayed</html>
 label.manually_specify_width_left_column = <html>Manually specify the width of the left hand column where sequence IDs and annotation labels will be rendered in exported alignment figures. This setting will be ignored if 'Automatically set ID width' is set</html>
 label.job_created_when_checked = <html>When checked, a job is created for every sequence in the current selection.</html>
@@ -887,8 +886,6 @@ label.save_state = Save State
 label.restore_state = Restore State
 label.saving_jalview_project = Saving jalview project {0}
 label.loading_jalview_project = Loading jalview project {0}
-label.save_vamsas_document_archive = Save Vamsas Document Archive
-label.saving_vamsas_doc = Saving VAMSAS Document to {0}
 label.load_feature_colours = Load Feature Colours
 label.save_feature_colours = Save Feature Colour Scheme
 label.select_startup_file = Select startup file
@@ -908,7 +905,6 @@ label.visible = Visible
 label.select_unselect_visible_regions_from = select and unselected {0} regions from {1}
 label.visible_region_of = visible region of
 label.webservice_job_title_on = {0} using {1} on {2}
-label.updating_vamsas_session = Updating vamsas session
 label.loading_file = Loading File: {0}
 label.edit_params = Edit {0}
 label.as_percentage = As Percentage
@@ -949,26 +945,20 @@ error.call_setprogressbar_before_registering_handler = call setProgressBar befor
 label.cancelled_params = Cancelled {0}
 error.implementation_error_cannot_show_view_alignment_frame = Implementation error: cannot show a view from another alignment in an AlignFrame.
 error.implementation_error_dont_know_about_threshold_setting = Implementation error: don't know about threshold setting for current AnnotationColourGradient.
-error.try_join_vamsas_session_another = Trying to join a vamsas session when another is already connected
-error.invalid_vamsas_session_id = Invalid vamsas session id
 label.groovy_support_failed = Jalview Groovy Support Failed
 label.couldnt_create_groovy_shell = Couldn't create the groovy Shell. Check the error log for the details of what went wrong.
 error.unsupported_version_calcIdparam = Unsupported Version for calcIdparam {0}
 error.implementation_error_cant_reorder_tree = Implementation Error: Can't reorder this tree. Not DefaultMutableTreeNode.
+error.invalid_value_for_option = Invalid value ''{0}'' for option ''{1}''
 error.implementation_error_cannot_import_vamsas_doc = Implementation Error - cannot import existing vamsas document into an existing session, Yet!
 label.vamsas_doc_couldnt_be_opened_as_new_session = VAMSAS Document could not be opened as a new session - please choose another
-error.implementation_error_vamsas_operation_not_init = Impementation error! Vamsas Operations when client not initialised and connected
-error.jalview_no_connected_vamsas_session = Jalview not connected to Vamsas session
-error.implementation_error_cannot_recover_vamsas_object_mappings = IMPLEMENTATION ERROR: Cannot recover vamsas object mappings - no backup was made
 error.setstatus_called_non_existent_job_pane = setStatus called for non-existent job pane {0}
 error.implementation_error_cannot_find_marshaller_for_param_set =Implementation error: Can't find a marshaller for the parameter set
 error.implementation_error_old_jalview_object_not_bound =IMPLEMENTATION ERROR: old jalview object is not bound ! ({0})
 error.implementation_error_vamsas_doc_class_should_bind_to_type = Implementation Error: Vamsas Document Class {0} should bind to a {1} (found a {2})
 error.invalid_vamsas_rangetype_cannot_resolve_lists = Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!
-error.implementation_error_maplist_is_null = Implementation error. MapList is null for initMapType.
 error.implementation_error_cannot_have_null_alignment = Implementation error: Cannot have null alignment property key
 error.implementation_error_null_fileparse = Implementation error. Null FileParse in copy constructor
-error.implementation_error_cannot_map_alignment_sequences = IMPLEMENTATION ERROR: Cannot map an alignment of sequences from different datasets into a single alignment in the vamsas document.
 error.implementation_error_structure_selection_manager_null = Implementation error. Structure selection manager's context is 'null'
 exception.ssm_context_is_null = SSM context is null
 error.idstring_seqstrings_only_one_per_sequence = idstrings and seqstrings contain one string each per sequence
@@ -1005,6 +995,7 @@ 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 {2} features of type {3}  across {4} sequence(s)
+label.no_highlighted_regions_marked = No highlighted regions marked
 label.toggled = Toggled
 label.marked = Marked
 label.containing = containing
@@ -1119,7 +1110,6 @@ label.png_image = PNG image
 status.export_complete = {0} Export completed
 status.fetching_pdb = Fetching PDB {0}
 status.refreshing_news = Refreshing news
-status.importing_vamsas_session_from = Importing VAMSAS session from {0}
 status.opening_params = Opening {0}
 status.waiting_sequence_database_fetchers_init = Waiting for Sequence Database Fetchers to initialise
 status.init_sequence_database_fetchers = Initialising Sequence Database Fetchers
@@ -1132,11 +1122,13 @@ status.collecting_job_results = Collecting job results.
 status.fetching_db_refs = Fetching db refs
 status.loading_cached_pdb_entries = Loading Cached PDB Entries
 status.searching_for_pdb_structures = Searching for PDB Structures
+status.searching_3d_beacons = Searching 3D Beacons
+status.no_structures_discovered_from_3d_beacons = No models discovered from 3D Beacons
 status.opening_file_for = opening file for
-status.colouring_chimera = Colouring Chimera
 status.running_hmmbuild = Building Hidden Markov Model
 status.running_hmmalign = Creating alignment with Hidden Markov Model
 status.running_search = Searching for matching sequences
+status.colouring_structures = Colouring structures
 label.font_doesnt_have_letters_defined = Font doesn't have letters defined\nso cannot be used\nwith alignment data
 label.font_too_small = Font size is too small
 label.error_loading_file_params = Error loading file {0}
@@ -1172,6 +1164,7 @@ label.add_annotations_for = Add annotations for
 action.choose_annotations = Choose Annotations...
 label.choose_annotations = Choose Annotations
 label.find = Find
+label.in = in
 label.invalid_search = Search string invalid
 error.invalid_regex = Invalid regular expression
 label.ignore_gaps_consensus = Ignore Gaps In Consensus
@@ -1432,6 +1425,7 @@ label.backupfiles_confirm_save_file = Confirm save file
 label.backupfiles_confirm_save_file_backupfiles_roll_wrong = Something possibly went wrong with the backups of this file.
 label.backupfiles_confirm_save_new_saved_file_ok = The new saved file seems okay.
 label.backupfiles_confirm_save_new_saved_file_not_ok = The new saved file might not be okay.
+label.continue_operation = Continue operation?
 label.backups = Backups
 label.backup = Backup
 label.backup_files = Backup Files
@@ -1498,4 +1492,9 @@ label.include_linked_features = Include {0} features
 label.include_linked_tooltip = Include visible {0} features<br>converted to local sequence coordinates
 label.features_not_shown = {0} feature(s) not shown
 label.no_features_to_sort_by = No features to sort by
-
+label.ignore_hidden = Ignore hidden columns
+label.ignore_hidden_tooltip = Ignore any characters in hidden columns when matching
+label.log_level = Log level
+label.log_level_tooltip = Temporarily set the log level for this console. The log level will revert to {0} when this Java console is closed.
+label.copy_to_clipboard = Copy to clipboard
+label.copy_to_clipboard_tooltip = Copy all of the log text in this console to the system clipboard