X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=resources%2Flang%2FMessages.properties;h=c5d566f34a7305672db21b8ca4fbdb41b8d4be2a;hb=4a3def9f59cefe629c9a33d87483283aee085928;hp=13fdc93e507eb2c3278a148b3087a150078a9c39;hpb=726bda0e9aea2d68b90803e142346cc46c8d4772;p=jalview.git

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index 13fdc93..c5d566f 100644
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -118,6 +118,7 @@ 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...
@@ -173,6 +174,9 @@ label.average_distance_identity = Average Distance Using % Identity
 label.neighbour_joining_identity = Neighbour Joining Using % Identity
 label.choose_calculation = Choose Calculation
 label.calc_title = {0} Using {1}
+label.treecalc_title = {0} Using {1}
+label.aptx_title = Archaeopteryx Tree View 
+label.of_x = of {0}
 label.tree_calc_av = Average Distance
 label.tree_calc_nj = Neighbour Joining
 label.score_model_pid = % Identity
@@ -272,7 +276,7 @@ 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.open_viewer_failed = Error opening {0} - is it installed?\nCheck configured path in Structure tab of Jalview''s Preferences 
 label.min_colour = Minimum Colour
 label.max_colour = Maximum Colour
 label.no_colour = No Colour
@@ -301,7 +305,11 @@ label.show_distances = Show distances
 label.mark_unassociated_leaves = Mark Unassociated Leaves
 label.fit_to_window = Fit To Window
 label.newick_format = Newick Format
-label.select_newick_like_tree_file = Select a newick-like tree file
+label.select_tree_file = Select a tree file
+label.treebase_study = TreeBASE Study
+label.treebase = TreeBASE
+label.treefam = TreeFam
+label.tree_of_life = Tree of Life
 label.colours = Colours
 label.view_mapping = View Mapping
 label.wireframe = Wireframe
@@ -328,6 +336,7 @@ 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:
@@ -384,7 +393,12 @@ label.not_enough_sequences = Not enough sequences
 label.selected_region_to_tree_may_only_contain_residues_or_gaps =  The selected region to create a tree may\nonly contain residues or gaps.\nTry using the Pad function in the edit menu,\nor one of the multiple sequence alignment web services.
 label.sequences_selection_not_aligned = Sequences in selection are not aligned
 label.problem_reading_tree_file =  Problem reading tree file
+label.tabs_detected_archaeopteryx = Warning, multiple trees detected in a single tree viewer instance. This will cause problems!
 label.possible_problem_with_tree_file = Possible problem with tree file
+label.aptx_config_not_found = Warning: tree viewer configuration file not found, continue anyway? (this WILL cause the viewer to look different)
+label.tree_url_example = Please enter a complete URL, for example \"http://www.jalview.org/examples/ferredoxin.nw\"
+label.from_database = From Database...
+label.load_tree_url = Tree from URL
 label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation = Please select at least three bases in at least one sequence in order to perform a cDNA translation.
 label.translation_failed = Translation Failed
 label.error_when_translating_sequences_submit_bug_report = Unfortunately, something went wrong when translating your sequences.\nPlease take a look in the Jalview java console\nand submit a bug report including the stacktrace.
@@ -401,7 +415,7 @@ label.pdb_entries_couldnt_be_retrieved = The following pdb entries could not be
 label.couldnt_load_file = Couldn't load file
 label.couldnt_find_pdb_id_in_file = Couldn't find a PDB id in the file supplied. Please enter an Id to identify this structure.
 label.no_pdb_id_in_file = No PDB Id in File
-label.couldnt_read_pasted_text = Couldn't read the pasted text {0}
+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
@@ -511,6 +525,12 @@ 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.threshold_feature_display_by_score = Threshold the feature display by score.
@@ -549,7 +569,7 @@ label.select_copy_raw_html = Select this if you want to copy raw html
 label.from_url = from URL
 label.any_trees_calculated_or_loaded_alignment_automatically_sort = When selected, any trees calculated or loaded onto the alignment will automatically sort the alignment
 label.sort_with_new_tree = Sort With New Tree
-label.from_textbox = from Textbox
+label.from_textbox = From Textbox
 label.window = Window
 label.preferences = Preferences
 label.tools = Tools
@@ -579,7 +599,7 @@ label.nuc_alignment_colour = Nucleotide Alignment Colour
 label.address = Address
 label.host = Host
 label.port = Port
-label.default_browser_unix = Default Browser (Unix)
+label.default_browser_unix_windows = Default Browser (Unix, Windows)
 label.send_usage_statistics = Send usage statistics
 label.check_for_questionnaires = Check for questionnaires
 label.check_for_latest_version = Check for latest version
@@ -617,8 +637,8 @@ 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.fetch_chimera_attributes = Fetch Chimera attributes
-label.fetch_chimera_attributes_tip = Copy Chimera attribute to Jalview feature
+label.fetch_viewer_attributes = Fetch {0} attributes
+label.fetch_viewer_attributes_tip = Copy {0} attribute to Jalview feature
 label.marks_leaves_tree_not_associated_with_sequence = Marks leaves of tree not associated with a sequence
 label.index_web_services_menu_by_host_site = Index web services in menu by the host site
 label.option_want_informed_web_service_URL_cannot_be_accessed_jalview_when_starts_up = Check this option if you want to be informed<br>when a web service URL cannot be accessed by Jalview<br>when it starts up
@@ -710,7 +730,7 @@ error.superposition_failed = Superposition failed: {0}
 label.insufficient_residues = Not enough aligned residues ({0}) to perform superposition
 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.attributes_set = {0} attribute values set on {1}
 label.sort_alignment_by_tree = Sort Alignment By Tree
 label.mark_unlinked_leaves = Mark Unlinked Leaves
 label.associate_leaves_with = Associate Leaves With
@@ -847,7 +867,7 @@ label.invalid_name = Invalid name
 label.set_proxy_settings = Please set up your proxy settings in the 'Connections' tab of the Preferences window
 label.proxy_authorization_failed = Proxy Authorization Failed
 label.internal_jalview_error = Internal Jalview Error
-label.secondary_structure_prediction_service_couldnt_be_located = The Secondary Structure Prediction Service named {0} at {1} couldn't be located.
+label.secondary_structure_prediction_service_couldnt_be_located = The Secondary Structure Prediction Service named {0} at {1} couldn''t be located.
 label.service_called_is_not_msa_service = The Service called \n{0}\nis not a \nMultiple Sequence Alignment Service\!
 label.msa_service_is_unknown = The Multiple Sequence Alignment Service named {0} is unknown
 label.service_called_is_not_seq_search_service = The Service called \n{0}\nis not a \nSequence Search Service\!
@@ -890,6 +910,8 @@ label.webservice_job_title_on = {0} using {1} on {2}
 label.loading_file = Loading File: {0}
 label.edit_params = Edit {0}
 label.as_percentage = As Percentage
+error.database_id_has_letters = Database identifier ({0}) should contain only digits
+error.phyloxml_validation = phyloXML XSD-based validation is turned off (enable with line 'validate_against_phyloxml_xsd_schem: true' in configuration file)
 error.not_implemented = Not implemented
 error.no_such_method_as_clone1_for = No such method as clone1 for {0}
 error.null_from_clone1 = Null from clone1!
@@ -931,7 +953,7 @@ 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.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.setstatus_called_non_existent_job_pane = setStatus called for non-existent job pane {0}
@@ -955,14 +977,13 @@ error.implementation_error_minlen_must_be_greater_zero = Implementation error: m
 error.implementation_error_msawbjob_called = Implementation error - StartJob(MsaWSJob) called on a WSJobInstance {0}
 error.implementation_error_cannot_attach_ws_menu_entry = IMPLEMENTATION ERROR: cannot attach WS Menu Entry without service handle reference!
 error.parameter_migration_not_implemented_yet = Parameter migration not implemented yet
-error.implementation_error_cannot_set_jaba_option = Implementation error: cannot set Jaba Option to a value outside its allowed value range!
 error.implementation_error_valuetype_doesnt_support_jabaws_type = IMPLEMENTATION ERROR: jalview.ws.params.ValueConstrainI.ValueType does not support the JABAWS type : {0}
 error.cannot_create_jabaws_param_set = Cannot create a JabaWSParamSet from non-JabaWS parameters
 error.cannot_set_arguments_to_jabaws_param_set = Cannot set arguments to a JabaWSParamSet that are not JabaWS arguments
 error.implementation_error_runner_config_not_available = Implementation Error: Runner Config not available for a JABAWS service of type {0} ({1})
 error.implementation_error_cannot_handle_jaba_param = Implementation Error: Cannot handle Jaba parameter object {0}
 error.implementation_error_attempt_to_delete_service_preset = Implementation error: Attempt to delete a service preset!
-error.implementation_error_cannot_locate_oldname_presetname = Implementation error: Can't locate either oldname ({0}) or presetName ({1}in the datastore!"
+error.implementation_error_cannot_locate_oldname_presetname = Implementation error: Can''t locate either oldname ({0}) or presetName ({1}) in the datastore!"
 error.implementation_error_jabaws_param_set_only_handled_by = Implementation error: JabaWsParamSets can only be handled by JabaParamStore
 error.cannot_set_source_file_for = Cannot set source file for {0}
 error.mismatch_service_instance_preset = Probable mismatch between service instance and preset!
@@ -970,7 +991,7 @@ error.cannot_set_params_for_ws_preset = Cannot set Parameters for a Jaba Web ser
 error.implementation_error_can_only_instantiate_jaba_param_sets = Implementation error: Can only instantiate Jaba parameter sets
 error.no_aacon_service_found = No AACon service found
 error.implementation_error_couldnt_copy_value_constraint = Implementation error: could not copy ValueConstrain!
-error.couldnt_encode_as_utf8 = Couldn't encode {0} as UTF-8.
+error.couldnt_encode_as_utf8 = Couldn''t encode {0} as UTF-8.
 error.tree_inputtype_not_yet_implemented = Tree InputType not yet implemented
 error.implementation_error_need_to_have_httpresponse = Implementation Error: need to have an HttpResponse to process
 error.dbrefsource_implementation_exception =DBRefSource Implementation Exception
@@ -1027,21 +1048,24 @@ error.implementation_error_reset_called_for_invalid_source = Implementation Erro
 exception.number_of_residues_in_query_sequence_differ_from_prediction = Number of residues in {0} supposed query sequence ({1}\n{2})\ndiffer from number of prediction sites in prediction ({3})
 label.mapped = mapped
 exception.jpredconcide_entry_has_unexpected_number_of_columns = JPredConcise: Entry ({0}) has an unexpected number of columns
-exception.couldnt_parse_concise_annotation_for_prediction = Couldn't parse concise annotation for prediction profile.\n{0}
+exception.couldnt_parse_concise_annotation_for_prediction = Couldn''t parse concise annotation for prediction profile.\n{0}
 exception.newfile = NewickFile\: {0}\n
 label.no_tree_read_in = No Tree read in
-exception.rnaml_couldnt_access_datasource = Couldn't access datasource ({0})
-exception.ranml_couldnt_process_data = Couldn't process data as RNAML file ({0})
+exception.rnaml_couldnt_access_datasource = Couldn''t access datasource ({0})
+exception.ranml_couldnt_process_data = Couldn''t process data as RNAML file ({0})
 exception.ranml_invalid_file = Invalid RNAML file ({0})
 exception.ranml_problem_parsing_data = Problem parsing data as RNAML ({0})
 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.unknown_annotation_detected = Unknown annotation detected: {0} {1}
-exception.couldnt_store_sequence_mappings = Couldn't store sequence mappings for {0}
+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.invalid_matrix_identifier = Sequence identifier {0} not found in distance matrix.
 exception.browser_not_found = Exception in finding browser: {0}
+exception.browser_unable_to_launch = Unable to launch browser: {0}
 exception.browser_unable_to_locate = Unable to locate browser: {0}
+exception.browser_os_not_supported = Launching browser on this operating system not supported.  Use URL\n{0}
 exception.invocation_target_exception_creating_aedesc = InvocationTargetException while creating AEDesc: {0}
 exception.illegal_access_building_apple_evt= IllegalAccessException while building AppleEvent: {0}
 exception.unable_to_launch_url = Unable to launch URL: {0}
@@ -1049,7 +1073,6 @@ exception.unable_to_create_internet_config = Unable to create an Internet Config
 exception.invocation_target_calling_url = InvocationTargetException while calling openURL: {0}
 exception.illegal_access_calling_url = IllegalAccessException while calling openURL: {0}
 exception.interrupted_launching_browser = InterruptedException while launching browser: {0}
-exception.ebiembl_retrieval_failed_on = EBI EMBL XML retrieval failed on {0}:{1}
 exception.no_pdb_records_for_chain = No PDB Records for {0} chain {1}
 exception.unexpected_handling_rnaml_translation_for_pdb = Unexpected exception when handling RNAML translation of PDB data
 exception.couldnt_recover_sequence_properties_for_alignment = Couldn't recover sequence properties for alignment
@@ -1071,7 +1094,7 @@ warn.service_not_supported = Service not supported!
 warn.input_is_too_big = Input is too big!
 warn.invalid_job_param_set = Invalid job parameter set!
 warn.oneseq_msainput_selection = The current selection only contains a single sequence. Do you want to submit all sequences for alignment instead ?   
-info.job_couldnt_be_run_server_doesnt_support_program = Job could not be run because the server doesn't support this program.\n{0}
+info.job_couldnt_be_run_server_doesnt_support_program = Job could not be run because the server doesn''t support this program.\n{0}
 info.job_couldnt_be_run_exceeded_hard_limit = Job could not be run because it exceeded a hard limit on the server.\n{0}
 info.job_couldnt_be_run_incorrect_param_setting = Job could not be run because some of the parameter settings are not supported by the server.\n{0}\nPlease check to make sure you have used the correct parameter set for this service\!\n
 info.no_jobs_ran = No jobs ran
@@ -1101,6 +1124,8 @@ 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_structures = Colouring structures
 label.font_doesnt_have_letters_defined = Font doesn't have letters defined\nso cannot be used\nwith alignment data
@@ -1134,6 +1159,7 @@ 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