X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=resources%2Flang%2FMessages.properties;h=90379d22df404769225bf93787c0e97aef543031;hb=906147c935f2a9d079f02f2ffc14a4f4ea7c0f5d;hp=198430ed0ae9c1cf38007af9caf98969eef9aa9c;hpb=19e044a2ce25aa395f9cf22f15c7378221636d21;p=jalview.git

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index 198430e..90379d2 100644
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -173,6 +173,8 @@ label.average_distance_identity = Average Distance Using % Identity
 label.neighbour_joining_identity = Neighbour Joining Using % Identity
 label.choose_calculation = Choose Calculation
 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.select_score_model = Select score model
@@ -299,7 +301,11 @@ 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
@@ -381,15 +387,18 @@ label.remove_from_default_list = Remove from default list?
 label.remove_user_defined_colour = Remove user defined colour
 label.you_must_select_least_two_sequences = You must select at least 2 sequences.
 label.invalid_selection = Invalid Selection
-label.principal_component_analysis_must_take_least_four_input_sequences = Principal component analysis must take\nat least 4 input sequences.
 label.sequence_selection_insufficient = Sequence selection insufficient
-label.you_need_more_two_sequences_selected_build_tree = You need to have more than two sequences selected to build a tree!
-label.you_need_more_than_n_sequences = You need to have more than {0} sequences
+label.you_need_at_least_n_sequences = You need to select at least {0} sequences
 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.
@@ -419,7 +428,7 @@ 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.couldnt_locate = Could not 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
@@ -561,10 +570,10 @@ 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.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
@@ -675,7 +684,8 @@ 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.from_file = From File
-label.enter_pdb_id = Enter PDB Id (or pdbid:chaincode)
+label.enter_pdb_id = Enter PDB Id
+label.enter_pdb_id_tip = Enter PDB Id (or pdbid:chaincode)
 label.text_colour = Text Colour...
 label.structure = Structure
 label.show_pdbstruct_dialog = 3D Structure Data...
@@ -747,7 +757,6 @@ label.delete_sbrs_definition = Delete SBRS Definition
 label.your_sequences_have_been_verified = Your sequences have been verified against known sequence databases.\n(Use Calculate | Show flanking regions to show enclosing sequence.)\nTo preserve data changes, save your alignment.\n\n
 label.sequences_updated = Sequences updated
 label.dbref_search_completed = DBRef search completed
-label.show_all_chains = Show all chains
 label.fetch_all_param = Fetch all {0}
 label.paste_new_window = Paste To New Window
 label.settings_for_param = Settings for {0}
@@ -913,10 +922,11 @@ label.updating_vamsas_session = Updating vamsas session
 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!
-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_threshold_annotationcolourgradient = Implementation error: don't know about threshold setting for current AnnotationColourGradient.
@@ -1071,6 +1081,7 @@ 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.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_locate = Unable to locate browser: {0}
 exception.invocation_target_exception_creating_aedesc = InvocationTargetException while creating AEDesc: {0}
@@ -1227,6 +1238,7 @@ label.configure_displayed_columns = Customise Displayed Options
 label.start_jalview = Start Jalview
 label.biojs_html_export = BioJS
 label.scale_as_cdna = Scale protein residues to codons
+label.font_as_cdna = Use same font for cDNA and peptide
 label.scale_protein_to_cdna = Scale Protein to cDNA
 label.scale_protein_to_cdna_tip = Make protein residues same width as codons in split frame views
 info.select_annotation_row = Select Annotation Row
@@ -1284,7 +1296,6 @@ label.SEQUENCE_ID_no_longer_used = $SEQUENCE_ID$ is no longer used for DB access
 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
@@ -1299,13 +1310,37 @@ 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
 label.urllinks = Links
+label.default_cache_size = Default Cache Size
+action.clear_cached_items = Clear Cached Items
+label.togglehidden = Show hidden regions
 label.quality_descr = Alignment Quality based on Blosum62 scores
 label.conservation_descr = Conservation of total alignment less than {0}% gaps
 label.consensus_descr = PID
 label.complement_consensus_descr = PID for cDNA
 label.strucconsensus_descr = PID for base pairs
-label.occupancy_descr = Number of aligned positions
-label.warning_hidden = Warning: {0} {1} is currently hidden
\ No newline at end of file
+label.occupancy_descr = Number of aligned positions 
+label.show_experimental = Enable experimental features
+label.show_experimental_tip = Enable any new and currently 'experimental' features (see Latest Release Notes for details)
+label.warning_hidden = Warning: {0} {1} is currently hidden
+label.overview_settings = Overview settings
+label.ov_legacy_gap = Use legacy gap colouring (gaps are white)
+label.gap_colour = Gap colour:
+label.ov_show_hide_default = Show hidden regions when opening overview
+label.hidden_colour = Hidden colour:
+label.select_gap_colour = Select gap colour
+label.select_hidden_colour = Select hidden colour
+label.overview = Overview
+label.reset_to_defaults = Reset to defaults
+label.oview_calc = Recalculating overview...
+option.enable_disable_autosearch = When ticked, search is performed automatically
+option.autosearch = Autosearch
+label.retrieve_ids = Retrieve IDs
+label.best_quality = Best Quality
+label.best_resolution = Best Resolution
+label.most_protein_chain = Most Protein Chain
+label.most_bound_molecules = Most Bound Molecules
+label.most_polymer_residues = Most Polymer Residues
+label.cached_structures = Cached Structures
+label.free_text_search = Free Text Search