X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=resources%2Flang%2FMessages.properties;h=f720f39439a81e69a4a0a06ee8ac572f85bb7e0c;hb=refs%2Fheads%2Ffeatures%2FJAL-2316;hp=9ffa292588872e2532aa4ce965174e6c78de0bf3;hpb=2d18ff6c5ccbd11297b80f70591dc0cb2f6aace6;p=jalview.git

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index 9ffa292..f720f39 100644
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -61,7 +61,6 @@ 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
@@ -125,6 +124,8 @@ 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
@@ -178,27 +179,30 @@ 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
+# 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
@@ -210,7 +214,7 @@ 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
@@ -322,7 +326,7 @@ 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}
@@ -668,8 +672,6 @@ action.set_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
@@ -719,7 +721,8 @@ 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 +771,7 @@ 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 ";"
@@ -833,7 +836,7 @@ 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.
@@ -958,7 +961,6 @@ 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 +969,7 @@ 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 +1025,6 @@ 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 +1035,6 @@ 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 +1075,7 @@ 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 +1097,7 @@ 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}
@@ -1230,7 +1230,6 @@ 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})
@@ -1280,8 +1279,13 @@ action.showall = Show All
 label.insert = Insert:
 action.seq_id = $SEQUENCE_ID$
 action.db_acc = $DB_ACCESSION$
-label.default = On Click
+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
\ No newline at end of file
+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
+label.urllinks = Links
\ No newline at end of file