X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=resources%2Flang%2FMessages.properties;h=74c42b7214ecba0eceac0ed1206cecc630c0bb21;hb=496e2a7b7be5201d8739523b95fce5899e71aa8a;hp=864e34aa614fa3fa5f4b8691a03b6df9415fdcee;hpb=f269ceeb37293f592c4916dd91cff9c4fdd3f874;p=jalview.git

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index 864e34a..74c42b7 100644
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -3,6 +3,9 @@ action.reset_services = Reset Services
 action.merge_results = Merge Results
 action.load_scheme = Load scheme
 action.save_scheme = Save scheme
+label.scheme_changed = Changes to scheme ''{0}'' have not been saved.<br><br>Save changes, or continue without saving to make a new colour scheme.
+label.save_changes = Save Changes
+label.dont_save_changes = Don't Save
 action.save_image = Save Image
 action.paste = Paste
 action.show_html_source = Show HTML Source
@@ -61,15 +64,14 @@ action.set_as_reference = Set as Reference
 action.remove = Remove
 action.remove_redundancy = Remove Redundancy...
 action.pairwise_alignment = Pairwise Alignment
-action.by_rna_helixes = By RNA Helices
 action.user_defined = User Defined...
 action.by_conservation = By Conservation
 action.wrap = Wrap
 action.show_gaps = Show Gaps
+action.show_occupancy = Show Occupancy
 action.show_hidden_markers = Show Hidden Markers
 action.find = Find
 action.undefine_groups = Undefine Groups
-action.create_groups = Create Groups
 action.make_groups_selection = Make Groups For Selection
 action.copy = Copy
 action.cut = Cut
@@ -125,6 +127,8 @@ action.change_font_tree_panel = Change Font (Tree Panel)
 action.colour = Colour
 action.calculate = Calculate
 action.select_all = Select all
+action.select_highlighted_columns = Select Highlighted Columns
+tooltip.select_highlighted_columns = Press B to mark highlighted columns, Ctrl-(or Cmd)-B to toggle, and Alt-B to mark all but highlighted columns 
 action.deselect_all = Deselect all
 action.invert_selection = Invert selection
 action.using_jmol = Using Jmol
@@ -137,7 +141,8 @@ action.view_flanking_regions = Show flanking regions
 label.view_flanking_regions = Show sequence data either side of the subsequences involved in this alignment
 label.structures_manager = Structures Manager
 label.nickname = Nickname:
-label.url = URL:
+label.url = URL
+label.url\: = URL:
 label.input_file_url = Enter URL or Input File
 label.select_feature = Select feature
 label.name = Name
@@ -177,27 +182,31 @@ label.score_model_conservation = Physicochemical property conservation
 label.score_model_enhconservation = Physicochemical property conservation
 label.status_bar = Status bar
 label.out_to_textbox = Output to Textbox
-label.clustalx = Clustalx
+label.occupancy = Occupancy
+# delete Clustal - use FileFormat name instead
 label.clustal = Clustal
-label.zappo = Zappo
-label.taylor = Taylor
+# label.colourScheme_<schemeName> as in JalviewColourScheme
+label.colourScheme_clustal = Clustalx
+label.colourScheme_blosum62 = BLOSUM62 Score
+label.colourScheme_%_identity = Percentage Identity
+label.colourScheme_zappo = Zappo
+label.colourScheme_taylor = Taylor
+label.colourScheme_hydrophobic = Hydrophobicity
+label.colourScheme_helix_propensity = Helix Propensity
+label.colourScheme_strand_propensity = Strand Propensity
+label.colourScheme_turn_propensity = Turn Propensity
+label.colourScheme_buried_index = Buried Index
+label.colourScheme_purine/pyrimidine = Purine/Pyrimidine
+label.colourScheme_nucleotide = Nucleotide
+label.colourScheme_t-coffee_scores = T-Coffee Scores
+label.colourScheme_rna_helices = By RNA Helices
 label.blc = BLC
 label.fasta = Fasta
 label.msf = MSF
 label.pfam = PFAM
 label.pileup = Pileup
 label.pir = PIR
-label.hydrophobicity = Hydrophobicity
-label.helix_propensity = Helix Propensity
-label.strand_propensity = Strand Propensity
-label.turn_propensity = Turn Propensity
-label.buried_index = Buried Index
-label.purine_pyrimidine = Purine/Pyrimidine
-label.percentage_identity = Percentage Identity
-label.blosum62 = BLOSUM62
-label.blosum62_score = BLOSUM62 Score
-label.tcoffee_scores = T-Coffee Scores
-label.average_distance_bloslum62 = Average Distance Using BLOSUM62
+label.average_distance_blosum62 = Average Distance Using BLOSUM62
 label.neighbour_blosum62 = Neighbour Joining Using BLOSUM62
 label.show_annotations = Show annotations
 label.hide_annotations = Hide annotations
@@ -209,7 +218,7 @@ label.hide_all = Hide all
 label.add_reference_annotations = Add reference annotations
 label.find_tip = Search alignment, selection or sequence ids for a subsequence (ignoring gaps).<br>Accepts regular expressions - search Help for 'regex' for details.
 label.colour_text = Colour Text
-label.show_non_conversed = Show nonconserved
+label.show_non_conserved = Show nonconserved
 label.overview_window = Overview Window
 label.none = None
 label.above_identity_threshold = Above Identity Threshold
@@ -321,7 +330,7 @@ label.size = Size:
 label.style = Style:
 label.calculating = Calculating....
 label.modify_conservation_visibility = Modify conservation visibility
-label.colour_residues_above_occurence = Colour residues above % occurence
+label.colour_residues_above_occurrence = Colour residues above % occurrence
 label.set_this_label_text = set this label text
 label.sequences_from = Sequences from {0}
 label.successfully_loaded_file  = Successfully loaded file {0}
@@ -409,7 +418,6 @@ label.couldnt_import_as_vamsas_session = Couldn't import {0} as a new vamsas ses
 label.vamsas_document_import_failed = Vamsas Document Import Failed
 label.couldnt_locate = Couldn't locate {0}
 label.url_not_found = URL not found
-label.no_link_selected = No link selected
 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
@@ -511,7 +519,7 @@ label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences =
 label.standard_databases = Standard Databases
 label.fetch_embl_uniprot = Fetch from EMBL/EMBLCDS or Uniprot/PDB and any selected DAS sources
 label.reset_min_max_colours_to_defaults = Reset min and max colours to defaults from user preferences.
-label.align_structures_using_linked_alignment_views = Align structures using {0} linked alignment views
+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
@@ -616,6 +624,8 @@ 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
 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
@@ -663,13 +673,10 @@ label.2d_rna_sequence_name = 2D RNA - {0}
 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.text_colour = Text Colour
-action.set_text_colour = Text Colour...
+label.text_colour = Text Colour...
 label.structure = Structure
 label.show_pdbstruct_dialog = 3D Structure Data...
 label.view_rna_structure = VARNA 2D Structure
-label.clustalx_colours = Clustalx colours
-label.above_identity_percentage = Above % Identity
 label.create_sequence_details_report_annotation_for = Annotation for {0}
 label.sequence_details_for = Sequence Details for {0}
 label.sequence_name = Sequence Name
@@ -711,15 +718,21 @@ 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.align_structures = Align Structures
+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.attributes_set = {0} attribute values set on Chimera
 label.sort_alignment_by_tree = Sort Alignment By Tree
 label.mark_unlinked_leaves = Mark Unlinked Leaves
 label.associate_leaves_with = Associate Leaves With
 label.save_colour_scheme_with_unique_name_added_to_colour_menu = Save your colour scheme with a unique name and it will be added to the Colour menu
 label.case_sensitive = Case Sensitive
-label.lower_case_colour = Lower Case Colour
+label.lower_case_colour = Colour All Lower Case
+label.lower_case_tip = Chosen colour applies to all lower case symbols
 label.index_by_host = Index by Host
 label.index_by_type = Index by Type
 label.enable_jabaws_services = Enable JABAWS Services
@@ -768,7 +781,7 @@ label.original_data_for_params = Original Data for {0}
 label.points_for_params = Points for {0}
 label.transformed_points_for_params = Transformed points for {0}
 label.graduated_color_for_params = Graduated Feature Colour for {0}
-label.select_backgroud_colour = Select Background Colour
+label.select_background_colour = Select Background Colour
 label.invalid_font = Invalid Font
 label.separate_multiple_accession_ids = Enter one or more accession IDs separated by a semi-colon ";"
 label.separate_multiple_query_values = Enter one or more {0}s separated by a semi-colon ";"
@@ -787,9 +800,9 @@ label.hide_columns_containing = Hide columns containing
 label.hide_columns_not_containing = Hide columns that do not contain
 option.trim_retrieved_seqs = Trim retrieved sequences
 label.trim_retrieved_sequences = When the reference sequence is longer than the sequence that you are working with, only keep the relevant subsequences.
-label.use_sequence_id_1 = Use $SEQUENCE_ID$ or $SEQUENCE_ID=/<regex>/=$
-label.use_sequence_id_2 = to embed sequence id in URL
-label.use_sequence_id_3 = Use $SEQUENCE_NAME$ similarly to embed sequence name
+label.use_sequence_id_1 = Use $DB_ACCESSION$ or $DB_ACCESSION=/<regex>/=$
+label.use_sequence_id_2 = to embed accession id in URL
+label.use_sequence_id_3 = Use $SEQUENCE_ID$ similarly to embed sequence id
 label.use_sequence_id_4 = 
 label.ws_parameters_for = Parameters for {0}
 label.switch_server = Switch server
@@ -833,7 +846,7 @@ label.colour_by = Colour by...
 label.muscle_multiple_protein_sequence_alignment = Muscle Multiple Protein Sequence Alignment
 label.mafft_multiple_sequence_alignment = MAFFT Multiple Sequence Alignment
 label.clustalw_multiple_sequence_alignment = ClustalW Multiple Sequence Alignment
-label.jnet_secondary_structure_prediction = JNet Secondary Structure Prediction
+label.jnet_secondary_structure_prediction = JPred Secondary Structure Prediction
 label.multiharmony = Multi-Harmony
 label.unable_start_web_service_analysis = Unable to start web service analysis
 label.job_couldnt_be_started_check_input = The Job couldn't be started. Please check your input, and the Jalview console for any warning messages.
@@ -897,6 +910,7 @@ 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
 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!
@@ -958,7 +972,6 @@ error.implementation_error_maplist_is_null = Implementation error. MapList is nu
 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_cannot_duplicate_colour_scheme = Serious implementation error: cannot duplicate colourscheme {0}
 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
@@ -967,7 +980,7 @@ error.cannot_have_zero_length_vector_replacement_strings = Cannot have zero leng
 error.implementation_error_multiple_single_sequence_prediction_jobs_not_supported = Implementation Error! Multiple single sequence prediction jobs are not yet supported
 error.implementation_error_invalid_msa_index_for_job =Implementation Error! Invalid msaIndex for JPredJob on parent MSA input object!
 error.implementation_error_startjob_called = Implementation error - StartJob(JpredJob) called on {0}
-error.multiple_jnet_subjob_merge_not_implemented = Multiple JNet subjob merging not yet implemented
+error.multiple_jnet_subjob_merge_not_implemented = Multiple JPred subjob merging not yet implemented
 label.job_never_ran = Job never ran - input returned to user.
 error.implementation_error_minlen_must_be_greater_zero = Implementation error: minlen must be zero or more
 error.implementation_error_msawbjob_called = Implementation error - StartJob(MsaWSJob) called on a WSJobInstance {0}
@@ -1023,7 +1036,6 @@ exception.replace_null_regex_pointer = Replacer has null Regex pointer
 exception.bad_pattern_to_regex_perl_code = bad pattern to Regex.perlCode: {0}
 exception.no_stub_implementation_for_interface = There is no stub implementation for the interface: {0}
 exception.cannot_set_endpoint_address_unknown_port = Cannot set Endpoint Address for Unknown Port {0}
-exception.querying_matching_opening_parenthesis_for_non_closing_parenthesis = Querying matching opening parenthesis for non-closing parenthesis character {0}
 exception.mismatched_unseen_closing_char = Mismatched (unseen) closing character {0}
 exception.mismatched_closing_char = Mismatched closing character {0}
 exception.mismatched_opening_char = Mismatched opening character {0} at {1}
@@ -1034,7 +1046,6 @@ exception.couldnt_parse_responde_from_annotated3d_server = Couldn't parse respon
 exception.application_test_npe = Application test: throwing an NullPointerException It should arrive at the console
 exception.overwriting_vamsas_id_binding = Overwriting vamsas id binding
 exception.overwriting_jalview_id_binding = Overwriting jalview id binding
-error.implementation_error_unknown_file_format_string = Implementation error: Unknown file format string
 exception.failed_to_resolve_gzip_stream = Failed to resolve GZIP stream
 exception.problem_opening_file_also_tried = Problem opening {0} (also tried {1}) : {2}
 exception.problem_opening_file = Problem opening {0} : {1}
@@ -1075,7 +1086,7 @@ exception.unexpected_handling_rnaml_translation_for_pdb = Unexpected exception w
 exception.couldnt_recover_sequence_properties_for_alignment = Couldn't recover sequence properties for alignment
 exception.unknown_format_for_file = Unknown format {0} for file \: \n{1}
 label.remove_gaps = Remove Gaps
-exception.couldnt_recover_sequence_props_for_jnet_query = Couldn't recover sequence properties for JNet Query sequence!
+exception.couldnt_recover_sequence_props_for_jnet_query = Couldn't recover sequence properties for JPred Query sequence!
 exception.server_timeout_try_later = Server timed out - try again later\n
 exception.web_service_returned_null_try_later= Server at {0} returned null object, it probably cannot be contacted. Try again later.
 exception.cannot_contact_service_endpoint_at = Cannot contact service endpoint at {0}
@@ -1097,7 +1108,7 @@ info.job_couldnt_be_run_exceeded_hard_limit = Job could not be run because it ex
 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
 info.failed_to_submit_prediction = Failed to submit the prediction\:\n{0} {1}
-info.invalid_jnet_job_result_data ={0}\n{1}\nInvalid JNet job result data\!\n{2}
+info.invalid_jnet_job_result_data ={0}\n{1}\nInvalid JPred job result data\!\n{2}
 info.failed_to_submit_sequences_for_alignment = Failed to submit sequences for alignment.\nIt is most likely that there is a problem with the server.\nJust close the window\n
 info.alignment_object_method_notes = \nAlignment Object Method Notes\n
 info.server_exception = \n{0} Server exception\!\n{1}
@@ -1144,7 +1155,7 @@ warn.user_defined_width_requirements = The user defined width for the\nannotatio
 label.couldnt_create_sequence_fetcher = Couldn't create SequenceFetcher
 warn.couldnt_create_sequence_fetcher_client = Could not create the sequence fetcher client. Check error logs for details.
 warn.server_didnt_pass_validation = Service did not pass validation.\nCheck the Jalview Console for more details.
-warn.url_must_contain = Sequence URL must contain $SEQUENCE_ID$ or a regex $SEQUENCE_ID=/<regex>/=$
+warn.url_must_contain = Sequence URL must contain $SEQUENCE_ID$, $DB_ACCESSION$, or a regex
 warn.urls_not_contacted = URLs that could not be contacted
 warn.urls_no_jaba = URLs without any JABA Services
 info.validate_jabaws_server = Validate JabaWS Server ?\n(Look in console output for results)
@@ -1230,7 +1241,6 @@ action.export_hidden_columns = Export Hidden Columns
 action.export_hidden_sequences = Export Hidden Sequences
 action.export_features = Export Features
 label.export_settings = Export Settings
-label.save_as_biojs_html = Save as BioJs HTML
 label.pdb_web-service_error = PDB Web-service Error
 label.structure_chooser_manual_association = Structure Chooser - Manual association
 label.structure_chooser_filter_time = Structure Chooser - Filter time ({0})
@@ -1268,3 +1278,31 @@ 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
+label.SEQUENCE_ID_no_longer_used = $SEQUENCE_ID$ is no longer used for DB accessions
+label.SEQUENCE_ID_for_DB_ACCESSION1 = Please review your URL links in the 'Connections' tab of the Preferences window:
+label.SEQUENCE_ID_for_DB_ACCESSION2 = URL links using '$SEQUENCE_ID$' for DB accessions now use '$DB_ACCESSION$'.
+label.do_not_display_again = Do not display this message again
+exception.url_cannot_have_miriam_id = {0} is a MIRIAM id and cannot be used as a custom url name
+exception.url_cannot_have_duplicate_id = {0} cannot be used as a label for more than one line
+label.filter = Filter text:
+action.customfilter = Custom only
+action.showall = Show All
+label.insert = Insert:
+action.seq_id = $SEQUENCE_ID$
+action.db_acc = $DB_ACCESSION$
+label.primary = Double Click
+label.inmenu = In Menu
+label.id = ID
+label.database = Database
+label.urltooltip = Only one url, which must use a sequence id, can be selected for the 'On Click' option
+label.edit_sequence_url_link = Edit sequence URL link
+warn.name_cannot_be_duplicate = User-defined URL names must be unique and cannot be MIRIAM ids
+label.invalid_name = Invalid Name !
+label.output_seq_details = Output Sequence Details to list all database references
+<<<<<<< HEAD
+label.phyre2_model_prediction = 3D Protein Model prediction with Phyre2
+label.run_phyre2_prediction = Run Phyre2 Prediction
+status.obtaining_mapping_with_phyre2_template_alignment = Obtaining mapping with Phyre2 Template alignment 
+=======
+label.urllinks = Links
+>>>>>>> develop