stash

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index 6736791..d2bd4a6 100644 (file)
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -1,740 +1,740 @@
-action.refresh_services = Refresh Services\r
-action.reset_services = Reset Services\r
-action.merge_results = Merge Results\r
-action.load_scheme = Load scheme\r
-action.save_scheme = Save scheme\r
-action.save_image = Save Image\r
-action.paste = Paste\r
-action.show_html_source = Show HTML Source\r
-action.print = Print\r
-action.web_service = Web Service\r
-action.cancel_job = Cancel Job\r
-action.start_job = Start Job\r
-action.revert = Revert\r
-action.move_down = Move Down\r
-action.move_up = Move Up\r
-action.remove_return_datatype = Remove return datatype\r
-action.add_return_datatype = Add return datatype\r
-action.remove_input_parameter = Remove selected input parameter\r
-action.add_input_parameter = Add input parameter\r
-action.edit = Edit\r
-action.new = New\r
-action.open_file = Open file\r
-action.show_unconserved = Show Unconserved\r
-action.open_new_aligmnent = Open new alignment\r
-action.raise_associated_windows = Raise Associated Windows\r
-action.minimize_associated_windows = Minimize Associated Windows\r
-action.close_all = Close all\r
-action.load_project = Load Project\r
-action.save_project = Save Project\r
-action.quit = Quit\r
-action.expand_views = Expand Views\r
-action.gather_views = Gather Views\r
-action.page_setup = Page Setup\r
-action.reload = Reload\r
-action.load = Load\r
-action.open = Open\r
-action.cancel = Cancel\r
-action.create = Create\r
-action.update = Update\r
-action.delete = Delete\r
-action.snapshot = Snapshot\r
-action.clear = Clear\r
-action.accept = Accept\r
-action.select_ddbb = --- Select Database ---\r
-action.undo = Undo\r
-action.redo = Redo\r
-action.reset = Reset\r
-action.remove_left = Remove left\r
-action.remove_right = Remove right\r
-action.remove_empty_columns = Remove Empty Columns\r
-action.remove_all_gaps = Remove All Gaps\r
-action.left_justify_alignment = Left Justify Alignment\r
-action.right_justify_alignment = Right Justify Alignment\r
-action.boxes = Boxes\r
-action.text = Text\r
-action.by_pairwise_id = by Pairwise Identity\r
-action.by_id = by Id\r
-action.by_length = by Length\r
-action.by_group = by Group\r
-action.remove = Remove\r
-action.remove_redundancy = Remove Redundancy...\r
-action.pairwise_alignment = Pairwise Alignments...\r
-action.by_rna_helixes = by RNA Helices\r
-action.user_defined = User Defined...\r
-action.by_conservation = By Conservation\r
-action.wrap = Wrap\r
-action.show_gaps = Show Gaps\r
-action.show_hidden_markers = Show Hidden Markers\r
-action.find = Find\r
-action.undefine_groups = Undefine Groups\r
-action.create_groups = Create Groups\r
-action.make_groups_selection = Make Groups For Selection\r
-action.copy = Copy\r
-action.cut = Cut\r
-action.font = Font...\r
-action.scale_above = Scale Above\r
-action.scale_left = Scale Left\r
-action.scale_right = Scale Right\r
-action.by_tree_order = By Tree Order\r
-action.sort = Sort\r
-action.calculate_tree = Calculate Tree\r
-action.help = Help\r
-action.by_annotation = by Annotation...\r
-action.invert_sequence_selection = Invert Sequence Selection\r
-action.invert_column_selection = Invert Column Selection\r
-action.show = Show\r
-action.hide = Hide\r
-action.ok = OK\r
-action.set_defaults = Defaults\r
-action.create_group = Create Group\r
-action.remove_group = Remove Group\r
-action.edit_group = Edit Group\r
-action.border_colour = Border colour\r
-action.edit_new_group = Edit New Group\r
-action.hide_sequences = Hide Sequences\r
-action.sequences = Sequences\r
-action.ids = IDS\r
-action.ids_sequences = IDS and sequences\r
-action.reveal_all = Reveal All\r
-action.reveal_sequences = Reveal Sequences\r
-action.find_all = Find all\r
-action.find_next = Find next\r
-action.file = File\r
-action.view = View\r
-action.change_params = Change Parameters\r
-action.apply = Apply\r
-action.apply_threshold_all_groups = Apply threshold to all groups\r
-action.apply_all_groups = Apply to all Groups\r
-action.by_chain = By chain\r
-action.by_sequence = By Sequence\r
-action.paste_annotations = Paste Annotations\r
-action.format = Format\r
-action.select = Select\r
-action.new_view = New View\r
-action.close = Close\r
-action.add = Add\r
-action.save_as_default = Save as default\r
-action.save_as = Save as\r
-action.save = Save\r
-action.cancel_fetch = Cancel Fetch\r
-action.save_omit_hidden_columns = Save / Omit Hidden Columns\r
-action.change_font = Change Font\r
-action.change_font_tree_panel = Change Font (Tree Panel)\r
-action.colour = Colour\r
-action.calculate = Calculate\r
-action.select_all = Select all\r
-action.deselect_all = Deselect all\r
-action.invert_selection = Invert selection\r
-action.using_jmol = Using Jmol\r
-action.link = Link\r
-action.group_link = Group Links\r
-action.show_chain = Show Chain\r
-action.show_group = Show Group\r
-action.fetch_db_references = Fetch DB References\r
-action.edit = Edit\r
-action.view_flanking_regions = Show flanking regions\r
-label.view_flanking_regions = Show sequence data either side of the subsequences involved in this alignment\r
-label.str = Str:\r
-label.seq = Seq:\r
-label.structures_manager = Structures Manager\r
-label.nickname = Nickname:\r
-label.url = URL:\r
-label.input_file_url = Enter URL or Input File\r
-label.select_feature = Select feature:\r
-label.name = Name\r
-label.name_param = Name: {0}\r
-label.group = Group\r
-label.group_name = Group Name\r
-label.group_description = Group Description\r
-label.edit_group_name_description = Edit Group Name/Description\r
-label.colour = Colour:\r
-label.description = Description:\r
-label.start = Start:\r
-label.end = End:\r
-label.current_parameter_set_name = Current parameter set name:\r
-label.service_action = Service Action:\r
-label.post_url = POST URL:\r
-label.url_suffix = URL Suffix\r
-label.sequence_source = Sequence Source\r
-label.per_seq = per Sequence\r
-label.result_vertically_separable = Results are vertically separable\r
-label.amend = Amend\r
-label.undo_command = Undo {0}\r
-label.redo_command = Redo {0}\r
-label.principal_component_analysis = Principal Component Analysis\r
-label.average_distance_identity = Average Distance Using % Identity\r
-label.neighbour_joining_identity = Neighbour Joining Using % Identity\r
-label.treecalc_title = {0} Using {1}\r
-label.tree_calc_av = Average Distance\r
-label.tree_calc_nj = Neighbour Joining\r
-label.select_score_model = Select score model\r
-label.score_model_pid = % Identity\r
-label.score_model_blosum62 = BLOSUM62\r
-label.score_model_pam250 = PAM 250\r
-label.score_model_conservation = Physicochemical property conservation\r
-label.score_model_enhconservation = Physicochemical property conservation\r
-label.status_bar = Status bar\r
-label.out_to_textbox = Output to Textbox\r
-label.clustalx = Clustalx\r
-label.clustal = Clustal\r
-label.zappo = Zappo\r
-label.taylor = Taylor\r
-label.blc = BLC\r
-label.fasta = Fasta\r
-label.msf = MSF\r
-label.pfam = PFAM\r
-label.pileup = Pileup\r
-label.pir = PIR\r
-label.hydrophobicity = Hydrophobicity\r
-label.helix_propensity = Helix Propensity\r
-label.strand_propensity = Strand Propensity\r
-label.turn_propensity = Turn Propensity\r
-label.buried_index = Buried Index\r
-label.purine_pyrimidine = Purine/Pyrimidine\r
-label.percentage_identity = Percentage Identity\r
-label.blosum62 = BLOSUM62\r
-label.blosum62_score = BLOSUM62 Score\r
-label.tcoffee_scores = T-Coffee Scores\r
-label.average_distance_bloslum62 = Average Distance Using BLOSUM62\r
-label.neighbour_blosum62 = Neighbour Joining Using BLOSUM62\r
-label.show_annotations = Show annotations\r
-label.colour_text = Colour Text\r
-label.show_non_conversed = Show nonconserved\r
-label.overview_window = Overview Window\r
-label.none = None\r
-label.above_identity_threshold = Above Identity Threshold\r
-label.show_sequence_features = Show Sequence Features\r
-label.nucleotide = Nucleotide\r
-label.to_new_alignment = To New Alignment\r
-label.to_this_alignment = Add To This Alignment\r
-label.apply_colour_to_all_groups = Apply Colour To All Groups\r
-label.modify_identity_thereshold = Modify Identity Threshold...\r
-label.modify_conservation_thereshold = Modify Conservation Threshold...\r
-label.input_from_textbox = Input from textbox\r
-label.centre_column_labels = Centre column labels\r
-label.automatic_scrolling = Automatic Scrolling\r
-label.documentation = Documentation\r
-label.about = About...\r
-label.show_sequence_limits = Show Sequence Limits\r
-label.feature_settings = Feature Settings...\r
-label.sequence_features = Sequence Features\r
-label.all_columns = All Columns\r
-label.all_sequences = All Sequences\r
-label.selected_columns = Selected Columns \r
-label.selected_sequences = Selected Sequences\r
-label.all_but_selected_region = All but Selected Region (Shift+Ctrl+H)\r
-label.selected_region = Selected Region\r
-label.all_sequences_columns = All Sequences and Columns\r
-label.group_consensus = Group Consensus\r
-label.group_conservation = Group Conservation\r
-label.show_consensus_histogram = Show Consensus Histogram\r
-label.show_consensus_logo = Show Consensus Logo\r
-label.norm_consensus_logo = Normalise Consensus Logo\r
-label.apply_all_groups = Apply to all groups\r
-label.autocalculated_annotation = Autocalculated Annotation\r
-label.min_colour = Minimum Colour\r
-label.max_colour = Maximum Colour\r
-label.use_original_colours = Use Original Colours\r
-label.threshold_minmax = Threshold is min/max\r
-label.represent_group_with = Represent Group with {0}\r
-label.selection = Selection\r
-label.group_colour = Group Colour\r
-label.sequence = Sequence\r
-label.view_pdb_structure = View PDB Structure\r
-label.min = Min:\r
-label.max = Max:\r
-label.colour_by_label = Colour by label\r
-label.new_feature = New Feature\r
-label.match_case = Match Case\r
-label.view_alignment_editor = View in alignment editor\r
-label.labels = Labels\r
-label.output_values = Output Values...\r
-label.output_points = Output points...\r
-label.output_transformed_points = Output transformed points\r
-label.input_data = Input Data...\r
-label.nucleotide_matrix = Nucleotide matrix\r
-label.protein_matrix = Protein matrix\r
-label.show_bootstrap_values = Show Bootstrap Values\r
-label.show_distances = Show distances\r
-label.mark_unassociated_leaves = Mark Unassociated Leaves\r
-label.fit_to_window = Fit To Window\r
-label.newick_format = Newick Format\r
-label.select_newick_like_tree_file = Select a newick-like tree file\r
-label.colours = Colours\r
-label.view_mapping = View Mapping\r
-label.wireframe = Wireframe\r
-label.depthcue = Depthcue\r
-label.z_buffering = Z Buffering\r
-label.charge_cysteine = Charge & Cysteine\r
-label.all_chains_visible = All Chains Visible\r
-label.successfully_added_features_alignment = Successfully added features to alignment\r
-label.keyboard_editing_mode = Keyboard editing mode is {0}\r
-label.paste_features_annotations_Tcoffee_here = Paste your features / annotations / T-coffee score file here.\r
-label.removed_columns = Removed {0} columns.\r
-label.removed_empty_columns = Removed {0} empty columns.\r
-label.paste_newick_tree_file = Paste your Newick tree file here.\r
-label.order_by_params = Order by {0}\r
-label.html_content = <html>{0}</html>\r
-label.paste_pdb_file= Paste your PDB file here.\r
-label.paste_pdb_file_for_sequence = Paste PDB file for sequence {0}\r
-label.could_not_parse_newick_file  = Could not parse Newick file\!\n {0}\r
-label.successfully_pasted_tcoffee_scores_to_alignment= Successfully pasted T-Coffee scores to alignment.\r
-label.failed_add_tcoffee_scores = Failed to add T-Coffee scores: \r
-label.successfully_pasted_annotation_to_alignment= Successfully pasted annotation to alignment.\r
-label.couldnt_parse_pasted_text_as_valid_annotation_feature_GFF_tcoffee_file = Couldn't parse pasted text as a valid annotation, feature, GFF, or T-Coffee score file\r
-label.successfully_pasted_alignment_file = Successfully pasted alignment file\r
-label.paste_your_alignment_file = Paste your alignment file here\r
-label.paste_your = Paste your\r
-label.finished_searching = Finished searching\r
-label.search_results= Search results {0} : {1}\r
-label.found_match_for = Found match for {0}\r
-label.font = Font:\r
-label.size = Size:\r
-label.style = Style:\r
-label.enter_redundancy_threshold = Enter the redundancy threshold\r
-label.calculating = Calculating....\r
-label.modify_conservation_visibility = Modify conservation visibility\r
-label.colour_residues_above_occurence = Colour residues above % occurence\r
-label.set_this_label_text = set this label text\r
-label.sequences_from = Sequences from {0}\r
-label.successfully_loaded_file  = Successfully loaded file {0}\r
-label.successfully_saved_to_file_in_format = Successfully saved to file: {0} in {1} format.\r
-label.copied_sequences_to_clipboard = Copied {0} sequences to clipboard.\r
-label.check_file_matches_sequence_ids_alignment = Check that the file matches sequence IDs in the alignment.\r
-label.problem_reading_tcoffee_score_file = Problem reading T-COFFEE score file\r
-label.source_to_target = {0} ... {1}\r
-label.per_sequence_only= Per-sequence only\r
-label.to_file = to File\r
-label.to_textbox = to Textbox\r
-label.jalview = Jalview\r
-label.csv_spreadsheet = CSV (Spreadsheet)\r
-label.status =  [Status]\r
-label.channels = Channels\r
-label.channel_title_item_count = {0} ({1})\r
-label.blog_item_published_on_date = {0} {1} \r
-label.select_das_service_from_table = Select a DAS service from the table to read a full description here.</font></html>\r
-label.session_update = Session Update\r
-label.new_vamsas_session = New Vamsas Session\r
-label.load_vamsas_session = Load Vamsas Session\r
-label.save_vamsas_session = Save Vamsas Session\r
-label.select_vamsas_session_opened_as_new_vamsas_session= Select a vamsas session to be opened as a new vamsas session.\r
-label.open_saved_vamsas_session = Open a saved VAMSAS session\r
-label.groovy_console = Groovy Console...\r
-label.lineart = Lineart\r
-label.dont_ask_me_again = Don't ask me again\r
-label.select_eps_character_rendering_style = Select EPS character rendering style\r
-label.invert_selection = Invert Selection\r
-label.optimise_order = Optimise Order\r
-label.seq_sort_by_score = Seq sort by Score\r
-label.load_colours = Load Colours\r
-label.save_colours = Save Colours\r
-label.fetch_das_features = Fetch DAS Features\r
-label.selected_database_to_fetch_from = Selected {0} database {1} to fetch from {2} \r
-label.database_param = Database: {0}\r
-label.example = Example\r
-label.example_param = Example: {0}\r
-label.select_file_format_before_saving = You must select a file format before saving!\r
-label.file_format_not_specified = File format not specified\r
-label.alignment_contains_hidden_columns = The Alignment contains hidden columns.\nDo you want to save only the visible alignment?\r
-label.couldnt_save_file = Couldn't save file: {0}\r
-label.error_saving_file = Error Saving File\r
-label.remove_from_default_list = Remove from default list?\r
-label.remove_user_defined_colour = Remove user defined colour\r
-label.you_must_select_least_two_sequences = You must select at least 2 sequences.\r
-label.invalid_selection = Invalid Selection\r
-label.principal_component_analysis_must_take_least_four_input_sequences = Principal component analysis must take\nat least 4 input sequences.\r
-label.sequence_selection_insufficient = Sequence selection insufficient\r
-label.you_need_more_two_sequences_selected_build_tree = You need to have more than two sequences selected to build a tree!\r
-label.not_enough_sequences = Not enough sequences\r
-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.\r
-label.sequences_selection_not_aligned = Sequences in selection are not aligned\r
-label.sequences_must_be_aligned_before_creating_tree = The sequences must be aligned before creating a tree.\nTry using the Pad function in the edit menu,\n or one of the multiple sequence alignment web services.\r
-label.sequences_not_aligned = Sequences not aligned\r
-label.problem_reading_tree_file =  Problem reading tree file\r
-label.possible_problem_with_tree_file = Possible problem with tree file\r
-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.\r
-label.translation_failed = Translation Failed\r
-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.\r
-label.implementation_error  = Implementation error:\r
-label.automatically_associate_pdb_files_with_sequences_same_name = Do you want to automatically associate the {0} PDB files with sequences in the alignment that have the same name?\r
-label.automatically_associate_pdb_files_by_name = Automatically Associate PDB files by name\r
-label.ignore_unmatched_dropped_files_info = <html>Do you want to <em>ignore</em> the {0} files whose names did not match any sequence IDs ?</html>\r
-label.ignore_unmatched_dropped_files = Ignore unmatched dropped files?\r
-label.enter_view_name = Enter View Name\r
-label.enter_label = Enter label\r
-label.enter_label_for_the_structure = Enter a label for the structure?\r
-label.pdb_entry_is_already_displayed = {0} is already displayed.\nDo you want to re-use this viewer ?\r
-label.map_sequences_to_visible_window = Map Sequences to Visible Window: {0}\r
-label.add_pdbentry_to_view = Do you want to add {0} to the view called\n'{1}'\n\r
-label.align_to_existing_structure_view = Align to existing structure view\r
-label.pdb_entries_couldnt_be_retrieved = The following pdb entries could not be retrieved from the PDB\:\n{0}\nPlease try downloading them manually.\r
-label.couldnt_load_file = Couldn't load file\r
-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.\r
-label.no_pdb_id_in_file = No PDB Id in File\r
-label.couldnt_read_pasted_text = Couldn't read the pasted text {0}\r
-label.error_parsing_text = Error parsing text\r
-label.enter_local_das_source = Enter Nickname & URL of Local DAS Source\r
-label.you_can_only_edit_or_remove_local_das_sources = You can only edit or remove local DAS Sources!\r
-label.public_das_source = Public DAS source - not editable\r
-label.input_alignment_from_url = Input Alignment From URL\r
-label.input_alignment = Input Alignment\r
-label.couldnt_import_as_vamsas_session = Couldn't import '{0}' as a new vamsas session.\r
-label.vamsas_document_import_failed = Vamsas Document Import Failed\r
-label.couldnt_locate = Couldn't locate {0}\r
-label.url_not_found = URL not found\r
-label.no_link_selected = No link selected\r
-label.new_sequence_url_link = New sequence URL link\r
-label.cannot_edit_annotations_in_wrapped_view = Cannot edit annotations in wrapped view\r
-label.wrapped_view_no_edit = Wrapped view - no edit\r
-label.error_retrieving_data = Error Retrieving Data\r
-label.user_colour_scheme_must_have_name = User colour scheme must have a name\r
-label.no_name_colour_scheme = No name for colour scheme\r
-label.invalid_url = Invalid URL !\r
-label.error_loading_file = Error loading file\r
-label.problems_opening_file = Encountered problems opening {0}!!\r
-label.file_open_error = File open error\r
-label.no_das_sources_selected_warn = No das sources were selected.\nPlease select some sources and\ntry again.\r
-label.no_das_sources_selected_title = No DAS Sources Selected\r
-label.colour_scheme_exists_overwrite = Colour scheme {0} exists.\nContinue saving colour scheme as {1}?"\r
-label.duplicate_scheme_name = Duplicate scheme name\r
-label.jalview_new_questionnaire = There is a new Questionnaire available. Would you like to complete it now ?\n\r
-label.jalview_user_survey = Jalview User Survey\r
-label.alignment_properties = Alignment Properties: {0}\r
-label.alignment_props = Alignment Properties\r
-label.input_cut_paste = Cut & Paste Input\r
-label.input_cut_paste_params = Cut & Paste Input - {0}\r
-label.alignment_output_command = Alignment output - {0}\r
-label.annotations = Annotations\r
-label.features = Features\r
-label.overview_params = Overview {0}\r
-label.paste_newick_file = Paste Newick file\r
-label.load_tree_from_file = From File - \r
-label.colour_by_annotation = Colour by Annotation\r
-label.selection_output_command = Selection output - {0}\r
-label.annotation_for_displayid = <p><h2>Annotation for {0} </h2></p><p>\r
-label.pdb_sequence_mapping = PDB - Sequence Mapping\r
-label.pca_details = PCA details\r
-label.redundancy_threshold_selection = Redundancy threshold selection\r
-label.user_defined_colours = User defined colours\r
-label.jalviewLite_release = JalviewLite - Release {0}\r
-label.jaview_build_date = Build date: {0}\r
-label.jalview_authors_1 = Authors: :  Jim Procter, Andrew Waterhouse, Lauren Lui, Jan Engelhardt, Natasha Sherstnev,\r
-label.jalview_authors_2 = Daniel Barton, Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton.\r
-label.jalview_dev_managers = Development managed by The Barton Group, University of Dundee, Scotland, UK.\r
-label.jalview_distribution_lists = For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list\r
-label.jalview_please_cite = If  you use Jalview, please cite:\r
-label.jalview_cite_1_authors = Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)\r
-label.jalview_cite_1_title = Jalview Version 2 - a multiple sequence alignment editor and analysis workbench\r
-label.jalview_cite_1_ref = Bioinformatics doi: 10.1093/bioinformatics/btp033\r
-label.right_click = Right click\r
-label.to_add_annotation = to add annotation\r
-label.alignment_has_no_annotations = Alignment has no annotations\r
-label.retrieving_pdb_data = Retrieving PDB data...\r
-label.label = Label\r
-label.no_features_added_to_this_alignment = No Features added to this alignment!!\r
-label.features_can_be_added_from_searches_1 = (Features can be added from searches or\r
-label.features_can_be_added_from_searches_2 = from Jalview / GFF features files)\r
-label.calculating_pca= Calculating PCA\r
-label.reveal_columns = Reveal Columns\r
-label.jalview_cannot_open_file = Jalview can't open file\r
-label.jalview_applet = Jalview applet\r
-label.loading_data = Loading data\r
-label.memory_stats = Total Free Memory: {0} MB; Max Memory: {1} MB; {2} %\r
-label.calculating_tree = Calculating tree\r
-label.state_queueing = queuing\r
-label.state_running = running\r
-label.state_complete = complete\r
-label.state_completed = finished\r
-label.state_job_cancelled = job cancelled!!\r
-label.state_job_error = job error!\r
-label.server_error_try_later = Server Error! (try later)\r
-label.error_loading_pdb_data = Error loading PDB data!!\r
-label.fetching_pdb_data = Fetching PDB data...\r
-label.structure_type = Structure type\r
-label.settings_for_type = Settings for {0}\r
-label.view_full_application = View in Full Application\r
-label.load_associated_tree = Load Associated Tree ...\r
-label.load_features_annotations = Load Features/Annotations ...\r
-label.export_features = Export Features ...\r
-label.export_annotations = Export Annotations ...\r
-label.jalview_copy = Copy (Jalview Only)\r
-label.jalview_cut = Cut (Jalview Only)\r
-label.to_upper_case = To Upper Case\r
-label.to_lower_case = To Lower Case\r
-label.toggle_case = Toggle Case\r
-label.edit_name_description = Edit Name/Description ...\r
-label.create_sequence_feature = Create Sequence Feature ...\r
-label.edit_sequence = Edit Sequence\r
-label.edit_sequences = Edit Sequences\r
-label.sequence_details = Sequence Details\r
-label.jmol_help = Jmol Help\r
-label.all = All\r
-label.sort_by = Sort by\r
-label.sort_by_score = Sort by Score\r
-label.sort_by_density = Sort by Density\r
-label.sequence_sort_by_density = Sequence sort by Density\r
-label.reveal = Reveal\r
-label.hide_columns = Hide Columns\r
-label.load_jalview_annotations = Load Jalview Annotations or Features File\r
-label.load_tree_file = Load a tree file\r
-label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences = Retrieve and parse sequence database records for the alignment or the currently selected sequences\r
-label.standard_databases = Standard Databases\r
-label.fetch_embl_uniprot = Fetch from EMBL/EMBLCDS or Uniprot/PDB and any selected DAS sources\r
-label.reset_min_max_colours_to_defaults = Reset min and max colours to defaults from user preferences.\r
-label.align_structures_using_linked_alignment_views = Align structures using {0} linked alignment views\r
-label.connect_to_session = Connect to session {0}\r
-label.threshold_feature_display_by_score = Threshold the feature display by score.\r
-label.threshold_feature_no_thereshold = No Threshold\r
-label.threshold_feature_above_thereshold = Above Threshold\r
-label.threshold_feature_below_thereshold = Below Threshold\r
-label.adjust_thereshold = Adjust threshold\r
-label.toggle_absolute_relative_display_threshold = Toggle between absolute and relative display threshold.\r
-label.display_features_same_type_different_label_using_different_colour = Display features of the same type with a different label using a different colour. (e.g. domain features)\r
-label.select_colour_minimum_value = Select Colour for Minimum Value\r
-label.select_colour_maximum_value = Select Colour for Maximum Value\r
-label.open_new_jmol_view_with_all_structures_associated_current_selection_superimpose_using_alignment = Open a new Jmol view with all structures associated with the current selection and superimpose them using the alignment.\r
-label.open_url_param = Open URL {0}\r
-label.open_url_seqs_param = Open URL ({0}..) ({1} seqs)\r
-label.load_pdb_file_associate_with_sequence = Load a PDB file and associate it with sequence '{0}'\r
-label.reveal_hidden_columns = Reveal Hidden Columns with Right Mouse Button\r
-label.dark_colour = Dark Colour\r
-label.light_colour = Light Colour\r
-label.highlightnode = Left click to select leaves.<br>Double-click to invert leaves.<br>Right click to change colour.\r
-label.load_colour_scheme = Load colour scheme\r
-label.toggle_enabled_views = When enabled, allows many views to be selected.\r
-label.edit_notes_parameter_set = Click to edit the notes for this parameter set.\r
-label.open_local_file = Open local file\r
-label.enable_automatically_sort_alignment_when_open_new_tree = Enable this to automatically sort<br>the alignment when you open<br> a new tree.\r
-label.listen_for_selections = Listen for selections\r
-label.selections_mirror_selections_made_same_sequences_other_views = When selected, selections in this view will mirror<br>selections made on the same sequences in other views.\r
-label.toggle_sequence_visibility = Shift+H toggles sequence visiblity\r
-label.toggle_columns_visibility = Ctrl+H toggles column visiblity.\r
-label.toggles_visibility_hidden_selected_regions = H toggles visibility of hidden or selected regions\r
-label.rename_tab_eXpand_reGroup=  Right-click to rename tab <br> Press X to eXpand tabs, G to reGroup.\r
-label.right_align_sequence_id = Right Align Sequence Id\r
-label.sequence_id_tooltip = Sequence ID Tooltip\r
-label.no_services = <No Services>\r
-label.select_copy_raw_html = Select this if you want to copy raw html\r
-label.share_data_vamsas_applications = Share data with other vamsas applications\r
-label.connect_to = Connect to\r
-label.join_existing_vamsas_session = Join an existing vamsas session\r
-label.from_url = from URL\r
-label.any_trees_calculated_or_loaded_alignment_automatically_sort = When selected, any trees calculated or loaded onto the alignment will automatically sort the alignment\r
-label.sort_with_new_tree = Sort With New Tree\r
-label.from_textbox = from Textbox\r
-label.window = Window\r
-label.preferences = Preferences\r
-label.tools = Tools\r
-label.fetch_sequences = Fetch Sequence(s)\r
-label.stop_vamsas_session = Stop Vamsas Session\r
-label.collect_garbage = Collect Garbage\r
-label.show_memory_usage = Show Memory Usage\r
-label.show_java_console = Show Java Console\r
-label.show_jalview_news = Show Jalview News\r
-label.monospaced_fonts_faster_to_render = Monospaced fonts are faster to render\r
-label.anti_alias_fonts = Anti-alias Fonts (Slower to render)\r
-label.monospaced_font= Monospaced\r
-label.quality = Quality\r
-label.maximize_window = Maximize Window\r
-label.conservation = Conservation\r
-label.consensus = Consensus\r
-label.histogram = Histogram\r
-label.logo = Logo\r
-label.non_positional_features = Non-positional Features\r
-label.database_references = Database References\r
-label.share_selection_across_views = Share selection across views\r
-label.scroll_highlighted_regions = Scroll to highlighted regions\r
-label.gap_symbol = Gap Symbol\r
-label.alignment_colour = Alignment Colour\r
-label.address = Address\r
-label.port = Port\r
-label.default_browser_unix = Default Browser (Unix)\r
-label.send_usage_statistics = Send usage statistics\r
-label.check_for_questionnaires = Check for questionnaires\r
-label.check_for_latest_version = Check for latest version\r
-label.url_linkfrom_sequence_id = URL link from Sequence ID\r
-label.use_proxy_server = Use a proxy server\r
-label.eps_rendering_style = EPS rendering style\r
-label.append_start_end = Append /start-end (/15-380)\r
-label.full_sequence_id = Full Sequence Id\r
-label.smooth_font = Smooth Font\r
-label.autocalculate_consensus = AutoCalculate Consensus\r
-label.pad_gaps = Pad Gaps\r
-label.pad_gaps_when_editing = Pad Gaps When Editing\r
-label.automatically_set_id_width = Automatically set ID width\r
-label.figure_id_column_width = Figure ID column width\r
-label.use_modeller_output = Use Modeller Output\r
-label.wrap_alignment = Wrap Alignment\r
-label.right_align_ids = Right Align Ids\r
-label.sequence_name_italics = Sequence Name Italics\r
-label.open_overview = Open Overview\r
-label.default_colour_scheme_for_alignment = Default Colour Scheme for alignment\r
-label.annotation_shading_default = Annotation Shading Default\r
-label.default_minimum_colour_annotation_shading = Default Minimum Colour for annotation shading\r
-label.default_maximum_colour_annotation_shading = Default Maximum Colour for annotation shading\r
-label.visual = Visual\r
-label.connections = Connections\r
-label.output = Output\r
-label.editing = Editing\r
-label.das_settings = DAS Settings\r
-label.web_services = Web Services\r
-label.right_click_to_edit_currently_selected_parameter = Right click to edit currently selected parameter.\r
-label.let_jmol_manage_structure_colours = Let Jmol manage structure colours\r
-label.marks_leaves_tree_not_associated_with_sequence = Marks leaves of tree not associated with a sequence\r
-label.index_web_services_menu_by_host_site = Index web services in menu by the host site\r
-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\r
-label.new_service_url = New Service URL\r
-label.edit_service_url = Edit Service URL\r
-label.delete_service_url = Delete Service URL\r
-label.details = Details\r
-label.options = Options\r
-label.parameters = Parameters\r
-label.available_das_sources = Available DAS Sources\r
-label.full_details = Full Details\r
-label.authority = Authority\r
-label.type = Type\r
-label.proxy_server = Proxy Server\r
-label.file_output = File Output\r
-label.select_input_type = Select input type\r
-label.set_options_for_type = Set options for type\r
-label.data_input_parameters = Data input parameters\r
-label.data_returned_by_service = Data returned by service\r
-label.rsbs_encoded_service = RSBS Encoded Service\r
-label.parsing_errors = Parsing errors\r
-label.simple_bioinformatics_rest_services = Simple Bioinformatics Rest Services\r
-label.web_service_discovery_urls = Web Service Discovery URLS\r
-label.input_parameter_name = Input Parameter name\r
-label.short_descriptive_name_for_service = Short descriptive name for service\r
-label.function_service_performs = What kind of function the service performs (e.g. alignment, analysis, search, etc).\r
-label.brief_description_service = Brief description of service\r
-label.url_post_data_service = URL to post data to service. Include any special parameters needed here\r
-label.optional_suffix = Optional suffix added to URL when retrieving results from service\r
-label.preferred_gap_character = Which gap character does this service prefer?\r
-label.gap_character = Gap character\r
-label.move_return_type_up_order= Move return type up order\r
-label.move_return_type_down_order= Move return type down order\r
-label.update_user_parameter_set = Update this existing user parameter set\r
-label.delete_user_parameter_set = Delete the currently selected user parameter set\r
-label.create_user_parameter_set = Create a new parameter set with the current settings.\r
-label.revert_changes_user_parameter_set = Undo all changes to the current parameter set\r
-label.start_job_current_settings = Start Job with current settings\r
-label.cancel_job_close_dialog = Close this dialog and cancel job\r
-label.input_output = Input/Output\r
-label.cut_paste = Cut'n'Paste\r
-label.adjusting_parameters_for_calculation = Adjusting parameters for existing Calculation\r
-label.2d_rna_structure_line = 2D RNA {0}\r
-label.2d_rna_sequence_name = 2D RNA - {0}\r
-label.edit_name_and_description_current_group = Edit name and description of current group.\r
-label.view_structure_for = View structure for {0}\r
-label.view_all_structures = View all {0} structures.\r
-label.view_all_representative_structures = View all {0} representative structures.\r
-label.open_new_jmol_view_with_all_representative_structures_associated_current_selection_superimpose_using_alignment = Opens a new Jmol view with all representative structures\nassociated with the current selection\nsuperimposed with the current alignment.\r
-label.associate_structure_with_sequence = Associate Structure with Sequence\r
-label.from_file = from file\r
-label.enter_pdb_id = Enter PDB Id\r
-label.discover_pdb_ids = Discover PDB ids\r
-label.text_colour = Text Colour\r
-label.structure = Structure\r
-label.view_structure = View Structure\r
-label.clustalx_colours = Clustalx colours\r
-label.above_identity_percentage = Above % Identity\r
-label.create_sequence_details_report_annotation_for = Annotation for {0}\r
-label.sequece_details_for = Sequece Details for {0}\r
-label.sequence_name = Sequence Name\r
-label.sequence_description = Sequence Description\r
-label.edit_sequence_name_description = Edit Sequence Name/Description\r
-label.spaces_converted_to_backslashes = Spaces have been converted to _\r
-label.no_spaces_allowed_sequence_name = No spaces allowed in Sequence Name\r
-label.select_outline_colour = Select Outline Colour\r
-label.web_browser_not_found_unix = Unixers\: Couldn't find default web browser.\nAdd the full path to your browser in Preferences."\r
-label.web_browser_not_found = Web browser not found\r
-label.select_pdb_file_for = Select a PDB file for {0}\r
-label.html = HTML\r
-label.wrap = Wrap\r
-label.show_database_refs = Show Database Refs\r
-label.show_non_positional_features = Show Non-Positional Features\r
-label.save_png_image = Save As PNG Image\r
-label.load_tree_for_sequence_set = Load a tree for this sequence set\r
-label.export_image = Export Image\r
-label.vamsas_store = VAMSAS store\r
-label.translate_cDNA = Translate cDNA\r
-label.extract_scores = Extract Scores\r
-label.get_cross_refs = Get Cross References\r
-label.sort_alignment_new_tree = Sort Alignment With New Tree\r
-label.add_sequences = Add Sequences\r
-label.new_window = New Window\r
-label.refresh_available_sources = Refresh Available Sources\r
-label.use_registry = Use Registry\r
-label.add_local_source = Add Local Source\r
-label.set_as_default = Set as Default\r
-label.show_labels = Show labels\r
-label.background_colour = Background Colour\r
-label.associate_nodes_with = Associate Nodes With\r
-label.jalview_pca_calculation = Jalview PCA Calculation\r
-label.link_name = Link Name\r
-label.pdb_file = PDB file\r
-label.colour_with_jmol = Colour with Jmol\r
-label.align_structures = Align structures\r
-label.jmol = Jmol\r
-label.sort_alignment_by_tree = Sort Alignment By Tree\r
-label.mark_unlinked_leaves = Mark Unlinked Leaves\r
-label.associate_leaves_with = Associate Leaves With\r
-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\r
-label.case_sensitive = Case Sensitive\r
-label.lower_case_colour = Lower Case Colour\r
-label.index_by_host = Index by host\r
-label.index_by_type = Index by type\r
-label.enable_jabaws_services = Enable JABAWS Services\r
-label.display_warnings = Display warnings\r
-label.move_url_up = Move URL up\r
-label.move_url_down = Move URL down\r
-label.add_sbrs_definition = Add a SBRS definition\r
-label.edit_sbrs_definition = Edit SBRS definition\r
-label.delete_sbrs_definition = Delete SBRS definition\r
-label.your_sequences_have_been_verified = Your sequences have been verified against known sequence databases. Some of the ids have been\n altered, most likely the start/end residue will have been updated.\n Save your alignment to maintain the updated id.\n\n\r
-label.sequence_names_updated = Sequence names updated\r
-label.dbref_search_completed = DBRef search completed\r
-label.show_all_chains = Show all chains\r
-label.fetch_all_param = Fetch all {0}\r
-label.paste_new_window = Paste To New Window\r
-label.settings_for_param = Settings for {0}\r
-label.view_params = View {0}\r
-label.select_all_views = Select all views\r
-label.align_sequences_to_existing_alignment = Align sequences to an existing alignment\r
-label.realign_with_params = Realign with {0}\r
-label.calcname_with_default_settings = {0} with Defaults\r
-label.action_with_default_settings = {0} with default settings\r
-label.edit_settings_and_run = Edit settings and run...\r
-label.view_and_change_parameters_before_alignment = View and change the parameters before alignment\r
-label.run_with_preset_params = Run {0} with preset\r
-label.view_and_change_parameters_before_running_calculation = View and change parameters before running calculation\r
-label.view_documentation = View documentation\r
-label.select_return_type = Select return type\r
-label.translation_of_params = Translation of {0}\r
-label.features_for_params = Features for - {0}\r
-label.annotations_for_params = Annotations for - {0}\r
-label.generating_features_for_params = Generating features for - {0}\r
-label.generating_annotations_for_params = Generating annotations for - {0}\r
-label.varna_params = VARNA - {0}\r
-label.sequence_feature_settings = Sequence Feature Settings\r
-label.pairwise_aligned_sequences = Pairwise Aligned Sequences\r
-label.original_data_for_params = Original Data for {0}\r
-label.points_for_params = Points for {0}\r
-label.transformed_points_for_params = Transformed points for {0}\r
-label.graduated_color_for_params = Graduated Feature Colour for {0}\r
-label.select_backgroud_colour = Select Background Colour\r
-label.invalid_font = Invalid Font\r
-label.separate_multiple_accession_ids = Separate multiple accession ids with semi colon ";"\r
-label.replace_commas_semicolons = Replace commas with semi-colons\r
-label.parsing_failed_syntax_errors_shown_below_param = Parsing failed. Syntax errors shown below {0}\r
-label.parsing_failed_unrecoverable_exception_thrown_param = \nParsing failed. An unrecoverable exception was thrown:\n {0}\r
-label.example_query_param = Example query: {0}\r
-label.enter_value_increase_conservation_visibility = Enter value to increase conservation visibility\r
-label.enter_percentage_identity_above_which_colour_residues = Enter % identity above which to colour residues\r
-label.wswublast_client_credits = To display sequence features an exact Uniprot id with 100% sequence identity match must be entered.\nIn order to display these features, try changing the names of your sequences to the ids suggested below.\n\nRunning WSWUBlast at EBI.\nPlease quote Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate J., Velankar S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez R.\nSOAP-based services provided by the European Bioinformatics Institute.\nNucleic Acids Res. 33(1):W25-W28 (2005));\r
+action.refresh_services = Refresh Services
+action.reset_services = Reset Services
+action.merge_results = Merge Results
+action.load_scheme = Load scheme
+action.save_scheme = Save scheme
+action.save_image = Save Image
+action.paste = Paste
+action.show_html_source = Show HTML Source
+action.print = Print
+action.web_service = Web Service
+action.cancel_job = Cancel Job
+action.start_job = Start Job
+action.revert = Revert
+action.move_down = Move Down
+action.move_up = Move Up
+action.remove_return_datatype = Remove return datatype
+action.add_return_datatype = Add return datatype
+action.remove_input_parameter = Remove selected input parameter
+action.add_input_parameter = Add input parameter
+action.edit = Edit
+action.new = New
+action.open_file = Open file
+action.show_unconserved = Show Unconserved
+action.open_new_aligmnent = Open new alignment
+action.raise_associated_windows = Raise Associated Windows
+action.minimize_associated_windows = Minimize Associated Windows
+action.close_all = Close all
+action.load_project = Load Project
+action.save_project = Save Project
+action.quit = Quit
+action.expand_views = Expand Views
+action.gather_views = Gather Views
+action.page_setup = Page Setup
+action.reload = Reload
+action.load = Load
+action.open = Open
+action.cancel = Cancel
+action.create = Create
+action.update = Update
+action.delete = Delete
+action.snapshot = Snapshot
+action.clear = Clear
+action.accept = Accept
+action.select_ddbb = --- Select Database ---
+action.undo = Undo
+action.redo = Redo
+action.reset = Reset
+action.remove_left = Remove left
+action.remove_right = Remove right
+action.remove_empty_columns = Remove Empty Columns
+action.remove_all_gaps = Remove All Gaps
+action.left_justify_alignment = Left Justify Alignment
+action.right_justify_alignment = Right Justify Alignment
+action.boxes = Boxes
+action.text = Text
+action.by_pairwise_id = by Pairwise Identity
+action.by_id = by Id
+action.by_length = by Length
+action.by_group = by Group
+action.remove = Remove
+action.remove_redundancy = Remove Redundancy...
+action.pairwise_alignment = Pairwise Alignments...
+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_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
+action.font = Font...
+action.scale_above = Scale Above
+action.scale_left = Scale Left
+action.scale_right = Scale Right
+action.by_tree_order = By Tree Order
+action.sort = Sort
+action.calculate_tree = Calculate Tree
+action.help = Help
+action.by_annotation = by Annotation...
+action.invert_sequence_selection = Invert Sequence Selection
+action.invert_column_selection = Invert Column Selection
+action.show = Show
+action.hide = Hide
+action.ok = OK
+action.set_defaults = Defaults
+action.create_group = Create Group
+action.remove_group = Remove Group
+action.edit_group = Edit Group
+action.border_colour = Border colour
+action.edit_new_group = Edit New Group
+action.hide_sequences = Hide Sequences
+action.sequences = Sequences
+action.ids = IDS
+action.ids_sequences = IDS and sequences
+action.reveal_all = Reveal All
+action.reveal_sequences = Reveal Sequences
+action.find_all = Find all
+action.find_next = Find next
+action.file = File
+action.view = View
+action.change_params = Change Parameters
+action.apply = Apply
+action.apply_threshold_all_groups = Apply threshold to all groups
+action.apply_all_groups = Apply to all Groups
+action.by_chain = By chain
+action.by_sequence = By Sequence
+action.paste_annotations = Paste Annotations
+action.format = Format
+action.select = Select
+action.new_view = New View
+action.close = Close
+action.add = Add
+action.save_as_default = Save as default
+action.save_as = Save as
+action.save = Save
+action.cancel_fetch = Cancel Fetch
+action.save_omit_hidden_columns = Save / Omit Hidden Columns
+action.change_font = Change Font
+action.change_font_tree_panel = Change Font (Tree Panel)
+action.colour = Colour
+action.calculate = Calculate
+action.select_all = Select all
+action.deselect_all = Deselect all
+action.invert_selection = Invert selection
+action.using_jmol = Using Jmol
+action.link = Link
+action.group_link = Group Links
+action.show_chain = Show Chain
+action.show_group = Show Group
+action.fetch_db_references = Fetch DB References
+action.edit = Edit
+action.view_flanking_regions = Show flanking regions
+label.view_flanking_regions = Show sequence data either side of the subsequences involved in this alignment
+label.str = Str:
+label.seq = Seq:
+label.structures_manager = Structures Manager
+label.nickname = Nickname:
+label.url = URL:
+label.input_file_url = Enter URL or Input File
+label.select_feature = Select feature:
+label.name = Name
+label.name_param = Name: {0}
+label.group = Group
+label.group_name = Group Name
+label.group_description = Group Description
+label.edit_group_name_description = Edit Group Name/Description
+label.colour = Colour:
+label.description = Description:
+label.start = Start:
+label.end = End:
+label.current_parameter_set_name = Current parameter set name:
+label.service_action = Service Action:
+label.post_url = POST URL:
+label.url_suffix = URL Suffix
+label.sequence_source = Sequence Source
+label.per_seq = per Sequence
+label.result_vertically_separable = Results are vertically separable
+label.amend = Amend
+label.undo_command = Undo {0}
+label.redo_command = Redo {0}
+label.principal_component_analysis = Principal Component Analysis
+label.average_distance_identity = Average Distance Using % Identity
+label.neighbour_joining_identity = Neighbour Joining Using % Identity
+label.treecalc_title = {0} Using {1}
+label.tree_calc_av = Average Distance
+label.tree_calc_nj = Neighbour Joining
+label.select_score_model = Select score model
+label.score_model_pid = % Identity
+label.score_model_blosum62 = BLOSUM62
+label.score_model_pam250 = PAM 250
+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.clustal = Clustal
+label.zappo = Zappo
+label.taylor = Taylor
+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.neighbour_blosum62 = Neighbour Joining Using BLOSUM62
+label.show_annotations = Show annotations
+label.colour_text = Colour Text
+label.show_non_conversed = Show nonconserved
+label.overview_window = Overview Window
+label.none = None
+label.above_identity_threshold = Above Identity Threshold
+label.show_sequence_features = Show Sequence Features
+label.nucleotide = Nucleotide
+label.to_new_alignment = To New Alignment
+label.to_this_alignment = Add To This Alignment
+label.apply_colour_to_all_groups = Apply Colour To All Groups
+label.modify_identity_thereshold = Modify Identity Threshold...
+label.modify_conservation_thereshold = Modify Conservation Threshold...
+label.input_from_textbox = Input from textbox
+label.centre_column_labels = Centre column labels
+label.automatic_scrolling = Automatic Scrolling
+label.documentation = Documentation
+label.about = About...
+label.show_sequence_limits = Show Sequence Limits
+label.feature_settings = Feature Settings...
+label.sequence_features = Sequence Features
+label.all_columns = All Columns
+label.all_sequences = All Sequences
+label.selected_columns = Selected Columns 
+label.selected_sequences = Selected Sequences
+label.all_but_selected_region = All but Selected Region (Shift+Ctrl+H)
+label.selected_region = Selected Region
+label.all_sequences_columns = All Sequences and Columns
+label.group_consensus = Group Consensus
+label.group_conservation = Group Conservation
+label.show_consensus_histogram = Show Consensus Histogram
+label.show_consensus_logo = Show Consensus Logo
+label.norm_consensus_logo = Normalise Consensus Logo
+label.apply_all_groups = Apply to all groups
+label.autocalculated_annotation = Autocalculated Annotation
+label.min_colour = Minimum Colour
+label.max_colour = Maximum Colour
+label.use_original_colours = Use Original Colours
+label.threshold_minmax = Threshold is min/max
+label.represent_group_with = Represent Group with {0}
+label.selection = Selection
+label.group_colour = Group Colour
+label.sequence = Sequence
+label.view_pdb_structure = View PDB Structure
+label.min = Min:
+label.max = Max:
+label.colour_by_label = Colour by label
+label.new_feature = New Feature
+label.match_case = Match Case
+label.view_alignment_editor = View in alignment editor
+label.labels = Labels
+label.output_values = Output Values...
+label.output_points = Output points...
+label.output_transformed_points = Output transformed points
+label.input_data = Input Data...
+label.nucleotide_matrix = Nucleotide matrix
+label.protein_matrix = Protein matrix
+label.show_bootstrap_values = Show Bootstrap Values
+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.colours = Colours
+label.view_mapping = View Mapping
+label.wireframe = Wireframe
+label.depthcue = Depthcue
+label.z_buffering = Z Buffering
+label.charge_cysteine = Charge & Cysteine
+label.all_chains_visible = All Chains Visible
+label.successfully_added_features_alignment = Successfully added features to alignment
+label.keyboard_editing_mode = Keyboard editing mode is {0}
+label.paste_features_annotations_Tcoffee_here = Paste your features / annotations / T-coffee score file here.
+label.removed_columns = Removed {0} columns.
+label.removed_empty_columns = Removed {0} empty columns.
+label.paste_newick_tree_file = Paste your Newick tree file here.
+label.order_by_params = Order by {0}
+label.html_content = <html>{0}</html>
+label.paste_pdb_file= Paste your PDB file here.
+label.paste_pdb_file_for_sequence = Paste PDB file for sequence {0}
+label.could_not_parse_newick_file  = Could not parse Newick file\!\n {0}
+label.successfully_pasted_tcoffee_scores_to_alignment= Successfully pasted T-Coffee scores to alignment.
+label.failed_add_tcoffee_scores = Failed to add T-Coffee scores: 
+label.successfully_pasted_annotation_to_alignment= Successfully pasted annotation to alignment.
+label.couldnt_parse_pasted_text_as_valid_annotation_feature_GFF_tcoffee_file = Couldn't parse pasted text as a valid annotation, feature, GFF, or T-Coffee score file
+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.search_results= Search results {0} : {1}
+label.found_match_for = Found match for {0}
+label.font = Font:
+label.size = Size:
+label.style = Style:
+label.enter_redundancy_threshold = Enter the redundancy threshold
+label.calculating = Calculating....
+label.modify_conservation_visibility = Modify conservation visibility
+label.colour_residues_above_occurence = Colour residues above % occurence
+label.set_this_label_text = set this label text
+label.sequences_from = Sequences from {0}
+label.successfully_loaded_file  = Successfully loaded file {0}
+label.successfully_saved_to_file_in_format = Successfully saved to file: {0} in {1} format.
+label.copied_sequences_to_clipboard = Copied {0} sequences to clipboard.
+label.check_file_matches_sequence_ids_alignment = Check that the file matches sequence IDs in the alignment.
+label.problem_reading_tcoffee_score_file = Problem reading T-COFFEE score file
+label.source_to_target = {0} ... {1}
+label.per_sequence_only= Per-sequence only
+label.to_file = to File
+label.to_textbox = to Textbox
+label.jalview = Jalview
+label.csv_spreadsheet = CSV (Spreadsheet)
+label.status =  [Status]
+label.channels = Channels
+label.channel_title_item_count = {0} ({1})
+label.blog_item_published_on_date = {0} {1} 
+label.select_das_service_from_table = Select a DAS service from the table to read a full description here.</font></html>
+label.session_update = Session Update
+label.new_vamsas_session = New Vamsas Session
+label.load_vamsas_session = Load Vamsas Session
+label.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
+label.select_eps_character_rendering_style = Select EPS character rendering style
+label.invert_selection = Invert Selection
+label.optimise_order = Optimise Order
+label.seq_sort_by_score = Seq sort by Score
+label.load_colours = Load Colours
+label.save_colours = Save Colours
+label.fetch_das_features = Fetch DAS Features
+label.selected_database_to_fetch_from = Selected {0} database {1} to fetch from {2} 
+label.database_param = Database: {0}
+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.alignment_contains_hidden_columns = The Alignment contains hidden columns.\nDo you want to save only the visible alignment?
+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
+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.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.sequences_must_be_aligned_before_creating_tree = The sequences must be aligned before creating a tree.\nTry using the Pad function in the edit menu,\n or one of the multiple sequence alignment web services.
+label.sequences_not_aligned = Sequences not aligned
+label.problem_reading_tree_file =  Problem reading tree file
+label.possible_problem_with_tree_file = Possible problem with tree file
+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.
+label.implementation_error  = Implementation error:
+label.automatically_associate_pdb_files_with_sequences_same_name = Do you want to automatically associate the {0} PDB files with sequences in the alignment that have the same name?
+label.automatically_associate_pdb_files_by_name = Automatically Associate PDB files by name
+label.ignore_unmatched_dropped_files_info = <html>Do you want to <em>ignore</em> the {0} files whose names did not match any sequence IDs ?</html>
+label.ignore_unmatched_dropped_files = Ignore unmatched dropped files?
+label.enter_view_name = Enter View Name
+label.enter_label = Enter label
+label.enter_label_for_the_structure = Enter a label for the structure?
+label.pdb_entry_is_already_displayed = {0} is already displayed.\nDo you want to re-use this viewer ?
+label.map_sequences_to_visible_window = Map Sequences to Visible Window: {0}
+label.add_pdbentry_to_view = Do you want to add {0} to the view called\n'{1}'\n
+label.align_to_existing_structure_view = Align to existing structure view
+label.pdb_entries_couldnt_be_retrieved = The following pdb entries could not be retrieved from the PDB\:\n{0}\nPlease try downloading them manually.
+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.error_parsing_text = Error parsing text
+label.enter_local_das_source = Enter Nickname & URL of Local DAS Source
+label.you_can_only_edit_or_remove_local_das_sources = You can only edit or remove local DAS Sources!
+label.public_das_source = Public DAS source - not editable
+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.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
+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
+label.invalid_url = Invalid URL !
+label.error_loading_file = Error loading file
+label.problems_opening_file = Encountered problems opening {0}!!
+label.file_open_error = File open error
+label.no_das_sources_selected_warn = No das sources were selected.\nPlease select some sources and\ntry again.
+label.no_das_sources_selected_title = No DAS Sources Selected
+label.colour_scheme_exists_overwrite = Colour scheme {0} exists.\nContinue saving colour scheme as {1}?"
+label.duplicate_scheme_name = Duplicate scheme name
+label.jalview_new_questionnaire = There is a new Questionnaire available. Would you like to complete it now ?\n
+label.jalview_user_survey = Jalview User Survey
+label.alignment_properties = Alignment Properties: {0}
+label.alignment_props = Alignment Properties
+label.input_cut_paste = Cut & Paste Input
+label.input_cut_paste_params = Cut & Paste Input - {0}
+label.alignment_output_command = Alignment output - {0}
+label.annotations = Annotations
+label.features = Features
+label.overview_params = Overview {0}
+label.paste_newick_file = Paste Newick file
+label.load_tree_from_file = From File - 
+label.colour_by_annotation = Colour by Annotation
+label.selection_output_command = Selection output - {0}
+label.annotation_for_displayid = <p><h2>Annotation for {0} </h2></p><p>
+label.pdb_sequence_mapping = PDB - Sequence Mapping
+label.pca_details = PCA details
+label.redundancy_threshold_selection = Redundancy threshold selection
+label.user_defined_colours = User defined colours
+label.jalviewLite_release = JalviewLite - Release {0}
+label.jaview_build_date = Build date: {0}
+label.jalview_authors_1 = Authors: :  Jim Procter, Andrew Waterhouse, Lauren Lui, Jan Engelhardt, Natasha Sherstnev,
+label.jalview_authors_2 = Daniel Barton, Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton.
+label.jalview_dev_managers = Development managed by The Barton Group, University of Dundee, Scotland, UK.
+label.jalview_distribution_lists = For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list
+label.jalview_please_cite = If  you use Jalview, please cite:
+label.jalview_cite_1_authors = Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)
+label.jalview_cite_1_title = Jalview Version 2 - a multiple sequence alignment editor and analysis workbench
+label.jalview_cite_1_ref = Bioinformatics doi: 10.1093/bioinformatics/btp033
+label.right_click = Right click
+label.to_add_annotation = to add annotation
+label.alignment_has_no_annotations = Alignment has no annotations
+label.retrieving_pdb_data = Retrieving PDB data...
+label.label = Label
+label.no_features_added_to_this_alignment = No Features added to this alignment!!
+label.features_can_be_added_from_searches_1 = (Features can be added from searches or
+label.features_can_be_added_from_searches_2 = from Jalview / GFF features files)
+label.calculating_pca= Calculating PCA
+label.reveal_columns = Reveal Columns
+label.jalview_cannot_open_file = Jalview can't open file
+label.jalview_applet = Jalview applet
+label.loading_data = Loading data
+label.memory_stats = Total Free Memory: {0} MB; Max Memory: {1} MB; {2} %
+label.calculating_tree = Calculating tree
+label.state_queueing = queuing
+label.state_running = running
+label.state_complete = complete
+label.state_completed = finished
+label.state_job_cancelled = job cancelled!!
+label.state_job_error = job error!
+label.server_error_try_later = Server Error! (try later)
+label.error_loading_pdb_data = Error loading PDB data!!
+label.fetching_pdb_data = Fetching PDB data...
+label.structure_type = Structure type
+label.settings_for_type = Settings for {0}
+label.view_full_application = View in Full Application
+label.load_associated_tree = Load Associated Tree ...
+label.load_features_annotations = Load Features/Annotations ...
+label.export_features = Export Features ...
+label.export_annotations = Export Annotations ...
+label.jalview_copy = Copy (Jalview Only)
+label.jalview_cut = Cut (Jalview Only)
+label.to_upper_case = To Upper Case
+label.to_lower_case = To Lower Case
+label.toggle_case = Toggle Case
+label.edit_name_description = Edit Name/Description ...
+label.create_sequence_feature = Create Sequence Feature ...
+label.edit_sequence = Edit Sequence
+label.edit_sequences = Edit Sequences
+label.sequence_details = Sequence Details
+label.jmol_help = Jmol Help
+label.all = All
+label.sort_by = Sort by
+label.sort_by_score = Sort by Score
+label.sort_by_density = Sort by Density
+label.sequence_sort_by_density = Sequence sort by Density
+label.reveal = Reveal
+label.hide_columns = Hide Columns
+label.load_jalview_annotations = Load Jalview Annotations or Features File
+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.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.connect_to_session = Connect to session {0}
+label.threshold_feature_display_by_score = Threshold the feature display by score.
+label.threshold_feature_no_thereshold = No Threshold
+label.threshold_feature_above_thereshold = Above Threshold
+label.threshold_feature_below_thereshold = Below Threshold
+label.adjust_thereshold = Adjust threshold
+label.toggle_absolute_relative_display_threshold = Toggle between absolute and relative display threshold.
+label.display_features_same_type_different_label_using_different_colour = Display features of the same type with a different label using a different colour. (e.g. domain features)
+label.select_colour_minimum_value = Select Colour for Minimum Value
+label.select_colour_maximum_value = Select Colour for Maximum Value
+label.open_new_jmol_view_with_all_structures_associated_current_selection_superimpose_using_alignment = Open a new Jmol view with all structures associated with the current selection and superimpose them using the alignment.
+label.open_url_param = Open URL {0}
+label.open_url_seqs_param = Open URL ({0}..) ({1} seqs)
+label.load_pdb_file_associate_with_sequence = Load a PDB file and associate it with sequence '{0}'
+label.reveal_hidden_columns = Reveal Hidden Columns with Right Mouse Button
+label.dark_colour = Dark Colour
+label.light_colour = Light Colour
+label.highlightnode = Left click to select leaves.<br>Double-click to invert leaves.<br>Right click to change colour.
+label.load_colour_scheme = Load colour scheme
+label.toggle_enabled_views = When enabled, allows many views to be selected.
+label.edit_notes_parameter_set = Click to edit the notes for this parameter set.
+label.open_local_file = Open local file
+label.enable_automatically_sort_alignment_when_open_new_tree = Enable this to automatically sort<br>the alignment when you open<br> a new tree.
+label.listen_for_selections = Listen for selections
+label.selections_mirror_selections_made_same_sequences_other_views = When selected, selections in this view will mirror<br>selections made on the same sequences in other views.
+label.toggle_sequence_visibility = Shift+H toggles sequence visiblity
+label.toggle_columns_visibility = Ctrl+H toggles column visiblity.
+label.toggles_visibility_hidden_selected_regions = H toggles visibility of hidden or selected regions
+label.rename_tab_eXpand_reGroup=  Right-click to rename tab <br> Press X to eXpand tabs, G to reGroup.
+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
+label.from_textbox = from Textbox
+label.window = Window
+label.preferences = Preferences
+label.tools = Tools
+label.fetch_sequences = Fetch Sequence(s)
+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
+label.show_jalview_news = Show Jalview News
+label.monospaced_fonts_faster_to_render = Monospaced fonts are faster to render
+label.anti_alias_fonts = Anti-alias Fonts (Slower to render)
+label.monospaced_font= Monospaced
+label.quality = Quality
+label.maximize_window = Maximize Window
+label.conservation = Conservation
+label.consensus = Consensus
+label.histogram = Histogram
+label.logo = Logo
+label.non_positional_features = Non-positional Features
+label.database_references = Database References
+label.share_selection_across_views = Share selection across views
+label.scroll_highlighted_regions = Scroll to highlighted regions
+label.gap_symbol = Gap Symbol
+label.alignment_colour = Alignment Colour
+label.address = Address
+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.eps_rendering_style = EPS rendering style
+label.append_start_end = Append /start-end (/15-380)
+label.full_sequence_id = Full Sequence Id
+label.smooth_font = Smooth Font
+label.autocalculate_consensus = AutoCalculate Consensus
+label.pad_gaps = Pad Gaps
+label.pad_gaps_when_editing = Pad Gaps When Editing
+label.automatically_set_id_width = Automatically set ID width
+label.figure_id_column_width = Figure ID column width
+label.use_modeller_output = Use Modeller Output
+label.wrap_alignment = Wrap Alignment
+label.right_align_ids = Right Align Ids
+label.sequence_name_italics = Sequence Name Italics
+label.open_overview = Open Overview
+label.default_colour_scheme_for_alignment = Default Colour Scheme for alignment
+label.annotation_shading_default = Annotation Shading Default
+label.default_minimum_colour_annotation_shading = Default Minimum Colour for annotation shading
+label.default_maximum_colour_annotation_shading = Default Maximum Colour for annotation shading
+label.visual = Visual
+label.connections = Connections
+label.output = Output
+label.editing = Editing
+label.das_settings = DAS Settings
+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.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
+label.new_service_url = New Service URL
+label.edit_service_url = Edit Service URL
+label.delete_service_url = Delete Service URL
+label.details = Details
+label.options = Options
+label.parameters = Parameters
+label.available_das_sources = Available DAS Sources
+label.full_details = Full Details
+label.authority = Authority
+label.type = Type
+label.proxy_server = Proxy Server
+label.file_output = File Output
+label.select_input_type = Select input type
+label.set_options_for_type = Set options for type
+label.data_input_parameters = Data input parameters
+label.data_returned_by_service = Data returned by service
+label.rsbs_encoded_service = RSBS Encoded Service
+label.parsing_errors = Parsing errors
+label.simple_bioinformatics_rest_services = Simple Bioinformatics Rest Services
+label.web_service_discovery_urls = Web Service Discovery URLS
+label.input_parameter_name = Input Parameter name
+label.short_descriptive_name_for_service = Short descriptive name for service
+label.function_service_performs = What kind of function the service performs (e.g. alignment, analysis, search, etc).
+label.brief_description_service = Brief description of service
+label.url_post_data_service = URL to post data to service. Include any special parameters needed here
+label.optional_suffix = Optional suffix added to URL when retrieving results from service
+label.preferred_gap_character = Which gap character does this service prefer?
+label.gap_character = Gap character
+label.move_return_type_up_order= Move return type up order
+label.move_return_type_down_order= Move return type down order
+label.update_user_parameter_set = Update this existing user parameter set
+label.delete_user_parameter_set = Delete the currently selected user parameter set
+label.create_user_parameter_set = Create a new parameter set with the current settings.
+label.revert_changes_user_parameter_set = Undo all changes to the current parameter set
+label.start_job_current_settings = Start Job with current settings
+label.cancel_job_close_dialog = Close this dialog and cancel job
+label.input_output = Input/Output
+label.cut_paste = Cut'n'Paste
+label.adjusting_parameters_for_calculation = Adjusting parameters for existing Calculation
+label.2d_rna_structure_line = 2D RNA {0}
+label.2d_rna_sequence_name = 2D RNA - {0}
+label.edit_name_and_description_current_group = Edit name and description of current group.
+label.view_structure_for = View structure for {0}
+label.view_all_structures = View all {0} structures.
+label.view_all_representative_structures = View all {0} representative structures.
+label.open_new_jmol_view_with_all_representative_structures_associated_current_selection_superimpose_using_alignment = Opens a new Jmol view with all representative structures\nassociated with the current selection\nsuperimposed with the current alignment.
+label.associate_structure_with_sequence = Associate Structure with Sequence
+label.from_file = from file
+label.enter_pdb_id = Enter PDB Id
+label.discover_pdb_ids = Discover PDB ids
+label.text_colour = Text Colour
+label.structure = Structure
+label.view_structure = View Structure
+label.clustalx_colours = Clustalx colours
+label.above_identity_percentage = Above % Identity
+label.create_sequence_details_report_annotation_for = Annotation for {0}
+label.sequece_details_for = Sequece Details for {0}
+label.sequence_name = Sequence Name
+label.sequence_description = Sequence Description
+label.edit_sequence_name_description = Edit Sequence Name/Description
+label.spaces_converted_to_backslashes = Spaces have been converted to _
+label.no_spaces_allowed_sequence_name = No spaces allowed in Sequence Name
+label.select_outline_colour = Select Outline Colour
+label.web_browser_not_found_unix = Unixers\: Couldn't find default web browser.\nAdd the full path to your browser in Preferences."
+label.web_browser_not_found = Web browser not found
+label.select_pdb_file_for = Select a PDB file for {0}
+label.html = HTML
+label.wrap = Wrap
+label.show_database_refs = Show Database Refs
+label.show_non_positional_features = Show Non-Positional Features
+label.save_png_image = Save As PNG Image
+label.load_tree_for_sequence_set = Load a tree for this sequence set
+label.export_image = Export Image
+label.vamsas_store = VAMSAS store
+label.translate_cDNA = Translate cDNA
+label.extract_scores = Extract Scores
+label.get_cross_refs = Get Cross References
+label.sort_alignment_new_tree = Sort Alignment With New Tree
+label.add_sequences = Add Sequences
+label.new_window = New Window
+label.refresh_available_sources = Refresh Available Sources
+label.use_registry = Use Registry
+label.add_local_source = Add Local Source
+label.set_as_default = Set as Default
+label.show_labels = Show labels
+label.background_colour = Background Colour
+label.associate_nodes_with = Associate Nodes With
+label.jalview_pca_calculation = Jalview PCA Calculation
+label.link_name = Link Name
+label.pdb_file = PDB file
+label.colour_with_jmol = Colour with Jmol
+label.align_structures = Align structures
+label.jmol = Jmol
+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.index_by_host = Index by host
+label.index_by_type = Index by type
+label.enable_jabaws_services = Enable JABAWS Services
+label.display_warnings = Display warnings
+label.move_url_up = Move URL up
+label.move_url_down = Move URL down
+label.add_sbrs_definition = Add a SBRS definition
+label.edit_sbrs_definition = Edit SBRS definition
+label.delete_sbrs_definition = Delete SBRS definition
+label.your_sequences_have_been_verified = Your sequences have been verified against known sequence databases. Some of the ids have been\n altered, most likely the start/end residue will have been updated.\n Save your alignment to maintain the updated id.\n\n
+label.sequence_names_updated = Sequence names 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}
+label.view_params = View {0}
+label.select_all_views = Select all views
+label.align_sequences_to_existing_alignment = Align sequences to an existing alignment
+label.realign_with_params = Realign with {0}
+label.calcname_with_default_settings = {0} with Defaults
+label.action_with_default_settings = {0} with default settings
+label.edit_settings_and_run = Edit settings and run...
+label.view_and_change_parameters_before_alignment = View and change the parameters before alignment
+label.run_with_preset_params = Run {0} with preset
+label.view_and_change_parameters_before_running_calculation = View and change parameters before running calculation
+label.view_documentation = View documentation
+label.select_return_type = Select return type
+label.translation_of_params = Translation of {0}
+label.features_for_params = Features for - {0}
+label.annotations_for_params = Annotations for - {0}
+label.generating_features_for_params = Generating features for - {0}
+label.generating_annotations_for_params = Generating annotations for - {0}
+label.varna_params = VARNA - {0}
+label.sequence_feature_settings = Sequence Feature Settings
+label.pairwise_aligned_sequences = Pairwise Aligned Sequences
+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.invalid_font = Invalid Font
+label.separate_multiple_accession_ids = Separate multiple accession ids with semi colon ";"
+label.replace_commas_semicolons = Replace commas with semi-colons
+label.parsing_failed_syntax_errors_shown_below_param = Parsing failed. Syntax errors shown below {0}
+label.parsing_failed_unrecoverable_exception_thrown_param = \nParsing failed. An unrecoverable exception was thrown:\n {0}
+label.example_query_param = Example query: {0}
+label.enter_value_increase_conservation_visibility = Enter value to increase conservation visibility
+label.enter_percentage_identity_above_which_colour_residues = Enter % identity above which to colour residues
+label.wswublast_client_credits = To display sequence features an exact Uniprot id with 100% sequence identity match must be entered.\nIn order to display these features, try changing the names of your sequences to the ids suggested below.\n\nRunning WSWUBlast at EBI.\nPlease quote Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate J., Velankar S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez R.\nSOAP-based services provided by the European Bioinformatics Institute.\nNucleic Acids Res. 33(1):W25-W28 (2005));
 label.blasting_for_unidentified_sequence = BLASTing for unidentified sequences
-label.select_columns_containing = Select columns containing\r
-label.select_columns_not_containing = Select columns that do not contain\r
-option.trim_retrieved_seqs = Trim retrieved sequences\r
-label.trim_retrieved_sequences = When the reference sequence is longer than the sequence that you are working with, only keep the relevant subsequences.\r
+label.select_columns_containing = Select columns containing
+label.select_columns_not_containing = Select 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.

diff --git a/resources/lang/Messages_es.properties b/resources/lang/Messages_es.properties
index c1fb406..4b533ad 100644 (file)
--- a/resources/lang/Messages_es.properties
+++ b/resources/lang/Messages_es.properties
@@ -1,7 +1,7 @@
-action.cancel = Cancelar\r
-action.create = Crear\r
-action.update = Actualizar\r
-action.delete = Borrar\r
-action.snapshot = Captura\r
-action.clear = Limpiar\r
-action.accept = Aceptar\r
+action.cancel = Cancelar
+action.create = Crear
+action.update = Actualizar
+action.delete = Borrar
+action.snapshot = Captura
+action.clear = Limpiar
+action.accept = Aceptar

diff --git a/src/castor.properties b/src/castor.properties
index 593fd58..c691302 100644 (file)
--- a/src/castor.properties
+++ b/src/castor.properties
@@ -16,239 +16,239 @@
 # You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
 # The Jalview Authors are detailed in the 'AUTHORS' file.
 ###############################################################################
-# THE CASTOR PROPERTIES FILE\r
-# This file specifies values for Castor run-time which may be configured\r
-# by the user.\r
-# $Id$\r
-\r
-# This section defines Backwards compatibility switches.\r
-#\r
-# Hashtable/Map default mapping.\r
-# For backward compatibility with 0.9.5.2 and earlier.\r
-#\r
-#org.exolab.castor.xml.saveMapKeys=false\r
-\r
-# Defines the default XML parser to be used by Castor.\r
-# The parser must implement org.xml.sax.Parser.\r
-#\r
-org.exolab.castor.parser=org.apache.xerces.parsers.SAXParser\r
-\r
-# Defines the (default) XML serializer factory to use by Castor, which must\r
-# implement org.exolab.castor.xml.SerializerFactory; default is \r
-# org.exolab.castor.xml.XercesXMLSerializerFactory\r
-# \r
-# When using Castor XML with JDK 5.0, you may switch to the XercesJDK5XMLSerializerFactory\r
-# which will use the Xerces instance as shipped with the JDK itself; this avoids\r
-# having to download another Xerces instance and installing it. \r
-org.exolab.castor.xml.serializer.factory=org.exolab.castor.xml.XercesXMLSerializerFactory\r
-#org.exolab.castor.xml.serializer.factory=org.exolab.castor.xml.XercesJDK5XMLSerializerFactory\r
-\r
-# Defines the NodeType for use with Java primitive types (int, long, boolean,\r
-# etc). This value is only used by the Introspector.  Valid values are either\r
-# "attribute" or "element". By default, all primitives are marshaled as\r
-# attributes. Uncomment the following line to change the NodeType to element.\r
-#\r
-#org.exolab.castor.xml.introspector.primitive.nodetype=element\r
-\r
-# Defines the Naming "style" or conventions to use when creating XML names\r
-# from Java class or field names.\r
-# Valid values are as follows:\r
-# -----------------------------------------------------------------\r
-# lower (default)  |  All names are lowercase with hyphens\r
-#                  |  separating words.\r
-#                  |\r
-#                  |  Example: personInfo = person-info\r
-# -----------------------------------------------------------------\r
-# mixed            |  All names are mixed case, with Uppercase\r
-#                  |  character as the first letter of a new word.\r
-#                  |\r
-#                  |  Example: personInfo = personInfo\r
-#                  |  Example: FooBar     = fooBar\r
-# -----------------------------------------------------------------\r
-# {Any ClassName}  |  Any Class which implements\r
-#                  |  org.exolab.castor.xml.XMLNaming\r
-# -----------------------------------------------------------------\r
-#\r
-# By default, all names are treated as the "lower" option.  To preserve the\r
-# Java mixed-case conventions, uncomment the following line.\r
-#\r
-#org.exolab.castor.xml.naming=mixed\r
-\r
-###############################\r
-# REGULAR EXPRESSION EVALUATORS\r
-#\r
-# Defines the Regular Expression Evaluator to be used by Castor.\r
-# The evaluator must implement org.exolab.castor.util.RegExpEvaluator.\r
-#\r
-# Uncomment the following to basically suppress Regular expressions evaluation:\r
-#org.exolab.castor.regexp=org.exolab.castor.xml.util.AlwaysTrueRegExpEvaluator\r
-#\r
-# An implementation which uses the Jakarta RegExp library:\r
-#org.exolab.castor.regexp=org.exolab.castor.util.JakartaRegExpEvaluator\r
-#\r
-# An implementation which uses the Jakarta ORO library:\r
-org.exolab.castor.regexp=org.exolab.castor.util.JakartaOroEvaluator\r
-\r
-# True if all documents should be indented on output by default.\r
-# Defaults to false.\r
-#\r
-#org.exolab.castor.indent=true\r
-\r
-# True if xml documents should be validated by the SAX Parser\r
-# Defaults to false.\r
-#\r
-org.exolab.castor.parser.validation=false\r
-\r
-# True for parser to support Namespaces.\r
-# Defaults to false.\r
-#\r
-org.exolab.castor.parser.namespaces=false\r
-\r
-# True if all documents should be validated by the marshaling framework\r
-# Defaults to true.\r
-#\r
-org.exolab.castor.marshalling.validation=true\r
-\r
-# Comma separated list of SAX 2 features that should be enabled for the\r
-# default parser.\r
-#\r
-#org.exolab.castor.sax.features=\r
-\r
-# Comma separated list of SAX 2 features that should be disabled for the\r
-# default parser.\r
-#\r
-#org.exolab.castor.sax.features-to-disable\r
-\r
-# True if debugging output should be generated.\r
-# Defaults to false.\r
-#\r
-org.exolab.castor.debug=false\r
-\r
-# List of collection handlers for Java 1.1 and Java 1.2 run-times:\r
-#\r
-org.exolab.castor.mapping.collections=\\r
-  org.exolab.castor.mapping.loader.J1CollectionHandlers,\\r
-  org.exolab.castor.mapping.loader.J2CollectionHandlers\r
-\r
-# List of persistence factories for the supported database servers:\r
-#\r
-org.exolab.castor.jdo.engines=\\r
-  org.exolab.castor.jdo.drivers.OracleFactory,\\r
-  org.exolab.castor.jdo.drivers.PostgreSQLFactory,\\r
-  org.exolab.castor.jdo.drivers.SybaseFactory,\\r
-  org.exolab.castor.jdo.drivers.SQLServerFactory,\\r
-  org.exolab.castor.jdo.drivers.DB2Factory,\\r
-  org.exolab.castor.jdo.drivers.InformixFactory,\\r
-  org.exolab.castor.jdo.drivers.HsqlFactory,\\r
-  org.exolab.castor.jdo.drivers.InstantDBFactory,\\r
-  org.exolab.castor.jdo.drivers.InterbaseFactory,\\r
-  org.exolab.castor.jdo.drivers.MySQLFactory,\\r
-  org.exolab.castor.jdo.drivers.SapDbFactory,\\r
-  org.exolab.castor.jdo.drivers.GenericFactory,\\r
-  org.exolab.castor.jdo.drivers.DerbyFactory,\\r
-  org.castor.jdo.drivers.PointbaseFactory,\\r
-  org.castor.jdo.drivers.ProgressFactory\r
-\r
-# List of key generator factories:\r
-#\r
-org.exolab.castor.jdo.keyGeneratorFactories=\\r
-  org.exolab.castor.jdo.keygen.MaxKeyGeneratorFactory,\\r
-  org.exolab.castor.jdo.keygen.HighLowKeyGeneratorFactory,\\r
-  org.exolab.castor.jdo.keygen.IdentityKeyGeneratorFactory,\\r
-  org.exolab.castor.jdo.keygen.SequenceKeyGeneratorFactory,\\r
-  org.exolab.castor.jdo.keygen.UUIDKeyGeneratorFactory\r
-\r
-# Collection handlers for the source code generator:\r
-#\r
-org.exolab.castor.builder.type.j2=\\r
-  org.exolab.castor.builder.FieldInfoFactoryJ2\r
-org.exolab.castor.builder.type.j1=\\r
-  org.exolab.castor.builder.FieldInfoFactory\r
-org.exolab.castor.builder.type.odmg=\\r
-  org.exolab.castor.builder.FieldInfoFactoryODMG30\r
-\r
-# Configures the default time zone to apply to dates/times fetched from\r
-# database fields (if not already part of the data).  Specify same format as\r
-# in java.util.TimeZone.getTimeZone, or the empty string to use the computer's\r
-# local time zone. Please see http://de.wikipedia.org/wiki/Zeitzone for\r
-# detailed information about time zones.\r
-#\r
-org.exolab.castor.jdo.defaultTimeZone=\r
-#org.exolab.castor.jdo.defaultTimeZone=GMT-8:00\r
-\r
-# List of TxSynchronizeable implementations:\r
-#\r
-#org.exolab.castor.persist.TxSynchronizable=\r
-\r
-# Sets the buffer size in bytes for fetching LOBs (this is dependent upon\r
-# the JDBC driver implementation).  The value below == 5k.\r
-#\r
-org.exolab.castor.jdo.lobBufferSize=5120\r
-\r
-# True if database configuration should be initalization\r
-# when loading it (default: true).\r
-#\r
-#org.exolab.castor.jdo.DatabaseInitializeAtLoad=true\r
-\r
-# True if proxy classes should be used for JDBC connections and\r
-# prepared statements.\r
-# Defaults to true.\r
-#\r
-org.exolab.castor.persist.useProxies=false\r
-\r
-# MappingLoader implementations:\r
-#\r
-org.castor.mapping.loaderFactories=\\r
-  org.castor.mapping.JDOMappingLoaderFactory,\\r
-  org.castor.mapping.XMLMappingLoaderFactory\r
-\r
-# Cache implementations:\r
-#\r
-org.castor.cache.Factories=\\r
-  org.castor.cache.simple.NoCacheFactory,\\r
-  org.castor.cache.simple.TimeLimitedFactory,\\r
-  org.castor.cache.simple.CountLimitedFactory,\\r
-  org.castor.cache.simple.UnlimitedFactory,\\r
-  org.castor.cache.distributed.FKCacheFactory,\\r
-  org.castor.cache.distributed.JcsCacheFactory,\\r
-  org.castor.cache.distributed.JCacheFactory,\\r
-  org.castor.cache.distributed.CoherenceCacheFactory,\\r
-  org.castor.cache.distributed.OsCacheFactory,\\r
-  org.castor.cache.hashbelt.FIFOHashbeltFactory,\\r
-  org.castor.cache.hashbelt.LRUHashbeltFactory,\\r
-  org.castor.cache.distributed.EHCacheFactory,\\r
-  org.castor.cache.distributed.GigaspacesCacheFactory\r
-\r
-# TransactionManagerFactory implementations:\r
-#\r
-org.castor.transactionmanager.Factories=\\r
-  org.castor.transactionmanager.WebSphereTransactionManagerFactory,\\r
-  org.castor.transactionmanager.WebSphere5TransactionManagerFactory,\\r
-  org.castor.transactionmanager.WebSphere51TransactionManagerFactory,\\r
-  org.castor.transactionmanager.LocalTransactionManagerFactory,\\r
-  org.castor.transactionmanager.JNDIENCTransactionManagerFactory,\\r
-  org.castor.transactionmanager.JOTMTransactionManagerFactory\r
-\r
-# Selects whether the TransactionManager should be initialized at registration,\r
-# or lazily when requested for the first time.\r
-# Defaults to false.\r
-#\r
-org.castor.transactionmanager.InitializeAtRegistration=false\r
-\r
-# Instructs Castor JDO to use the JDBC 3.0-specific features to obtain\r
-# the generated value of an identity column.\r
-# Defaults to false.\r
-#\r
-org.castor.jdo.use.jdbc30=false\r
-\r
-# Specifies whether to use ANSI-compliant SQL for MS SQL Server.\r
-# Defaults to false.\r
-#\r
-org.exolab.castor.jdo.sqlserver.ansi-compliant=false\r
-\r
-# Specifyies whether the ClassDescriptorResolver should (automatically) search\r
-# for and consult with package mapping files (.castor.xml) to retrieve class\r
-# descriptor information; on by default.\r
-# Defaults to true.\r
-#\r
-#org.exolab.castor.xml.loadPackageMappings=false\r
+# THE CASTOR PROPERTIES FILE
+# This file specifies values for Castor run-time which may be configured
+# by the user.
+# $Id$
+
+# This section defines Backwards compatibility switches.
+#
+# Hashtable/Map default mapping.
+# For backward compatibility with 0.9.5.2 and earlier.
+#
+#org.exolab.castor.xml.saveMapKeys=false
+
+# Defines the default XML parser to be used by Castor.
+# The parser must implement org.xml.sax.Parser.
+#
+org.exolab.castor.parser=org.apache.xerces.parsers.SAXParser
+
+# Defines the (default) XML serializer factory to use by Castor, which must
+# implement org.exolab.castor.xml.SerializerFactory; default is 
+# org.exolab.castor.xml.XercesXMLSerializerFactory
+# 
+# When using Castor XML with JDK 5.0, you may switch to the XercesJDK5XMLSerializerFactory
+# which will use the Xerces instance as shipped with the JDK itself; this avoids
+# having to download another Xerces instance and installing it. 
+org.exolab.castor.xml.serializer.factory=org.exolab.castor.xml.XercesXMLSerializerFactory
+#org.exolab.castor.xml.serializer.factory=org.exolab.castor.xml.XercesJDK5XMLSerializerFactory
+
+# Defines the NodeType for use with Java primitive types (int, long, boolean,
+# etc). This value is only used by the Introspector.  Valid values are either
+# "attribute" or "element". By default, all primitives are marshaled as
+# attributes. Uncomment the following line to change the NodeType to element.
+#
+#org.exolab.castor.xml.introspector.primitive.nodetype=element
+
+# Defines the Naming "style" or conventions to use when creating XML names
+# from Java class or field names.
+# Valid values are as follows:
+# -----------------------------------------------------------------
+# lower (default)  |  All names are lowercase with hyphens
+#                  |  separating words.
+#                  |
+#                  |  Example: personInfo = person-info
+# -----------------------------------------------------------------
+# mixed            |  All names are mixed case, with Uppercase
+#                  |  character as the first letter of a new word.
+#                  |
+#                  |  Example: personInfo = personInfo
+#                  |  Example: FooBar     = fooBar
+# -----------------------------------------------------------------
+# {Any ClassName}  |  Any Class which implements
+#                  |  org.exolab.castor.xml.XMLNaming
+# -----------------------------------------------------------------
+#
+# By default, all names are treated as the "lower" option.  To preserve the
+# Java mixed-case conventions, uncomment the following line.
+#
+#org.exolab.castor.xml.naming=mixed
+
+###############################
+# REGULAR EXPRESSION EVALUATORS
+#
+# Defines the Regular Expression Evaluator to be used by Castor.
+# The evaluator must implement org.exolab.castor.util.RegExpEvaluator.
+#
+# Uncomment the following to basically suppress Regular expressions evaluation:
+#org.exolab.castor.regexp=org.exolab.castor.xml.util.AlwaysTrueRegExpEvaluator
+#
+# An implementation which uses the Jakarta RegExp library:
+#org.exolab.castor.regexp=org.exolab.castor.util.JakartaRegExpEvaluator
+#
+# An implementation which uses the Jakarta ORO library:
+org.exolab.castor.regexp=org.exolab.castor.util.JakartaOroEvaluator
+
+# True if all documents should be indented on output by default.
+# Defaults to false.
+#
+#org.exolab.castor.indent=true
+
+# True if xml documents should be validated by the SAX Parser
+# Defaults to false.
+#
+org.exolab.castor.parser.validation=false
+
+# True for parser to support Namespaces.
+# Defaults to false.
+#
+org.exolab.castor.parser.namespaces=false
+
+# True if all documents should be validated by the marshaling framework
+# Defaults to true.
+#
+org.exolab.castor.marshalling.validation=true
+
+# Comma separated list of SAX 2 features that should be enabled for the
+# default parser.
+#
+#org.exolab.castor.sax.features=
+
+# Comma separated list of SAX 2 features that should be disabled for the
+# default parser.
+#
+#org.exolab.castor.sax.features-to-disable
+
+# True if debugging output should be generated.
+# Defaults to false.
+#
+org.exolab.castor.debug=false
+
+# List of collection handlers for Java 1.1 and Java 1.2 run-times:
+#
+org.exolab.castor.mapping.collections=\
+  org.exolab.castor.mapping.loader.J1CollectionHandlers,\
+  org.exolab.castor.mapping.loader.J2CollectionHandlers
+
+# List of persistence factories for the supported database servers:
+#
+org.exolab.castor.jdo.engines=\
+  org.exolab.castor.jdo.drivers.OracleFactory,\
+  org.exolab.castor.jdo.drivers.PostgreSQLFactory,\
+  org.exolab.castor.jdo.drivers.SybaseFactory,\
+  org.exolab.castor.jdo.drivers.SQLServerFactory,\
+  org.exolab.castor.jdo.drivers.DB2Factory,\
+  org.exolab.castor.jdo.drivers.InformixFactory,\
+  org.exolab.castor.jdo.drivers.HsqlFactory,\
+  org.exolab.castor.jdo.drivers.InstantDBFactory,\
+  org.exolab.castor.jdo.drivers.InterbaseFactory,\
+  org.exolab.castor.jdo.drivers.MySQLFactory,\
+  org.exolab.castor.jdo.drivers.SapDbFactory,\
+  org.exolab.castor.jdo.drivers.GenericFactory,\
+  org.exolab.castor.jdo.drivers.DerbyFactory,\
+  org.castor.jdo.drivers.PointbaseFactory,\
+  org.castor.jdo.drivers.ProgressFactory
+
+# List of key generator factories:
+#
+org.exolab.castor.jdo.keyGeneratorFactories=\
+  org.exolab.castor.jdo.keygen.MaxKeyGeneratorFactory,\
+  org.exolab.castor.jdo.keygen.HighLowKeyGeneratorFactory,\
+  org.exolab.castor.jdo.keygen.IdentityKeyGeneratorFactory,\
+  org.exolab.castor.jdo.keygen.SequenceKeyGeneratorFactory,\
+  org.exolab.castor.jdo.keygen.UUIDKeyGeneratorFactory
+
+# Collection handlers for the source code generator:
+#
+org.exolab.castor.builder.type.j2=\
+  org.exolab.castor.builder.FieldInfoFactoryJ2
+org.exolab.castor.builder.type.j1=\
+  org.exolab.castor.builder.FieldInfoFactory
+org.exolab.castor.builder.type.odmg=\
+  org.exolab.castor.builder.FieldInfoFactoryODMG30
+
+# Configures the default time zone to apply to dates/times fetched from
+# database fields (if not already part of the data).  Specify same format as
+# in java.util.TimeZone.getTimeZone, or the empty string to use the computer's
+# local time zone. Please see http://de.wikipedia.org/wiki/Zeitzone for
+# detailed information about time zones.
+#
+org.exolab.castor.jdo.defaultTimeZone=
+#org.exolab.castor.jdo.defaultTimeZone=GMT-8:00
+
+# List of TxSynchronizeable implementations:
+#
+#org.exolab.castor.persist.TxSynchronizable=
+
+# Sets the buffer size in bytes for fetching LOBs (this is dependent upon
+# the JDBC driver implementation).  The value below == 5k.
+#
+org.exolab.castor.jdo.lobBufferSize=5120
+
+# True if database configuration should be initalization
+# when loading it (default: true).
+#
+#org.exolab.castor.jdo.DatabaseInitializeAtLoad=true
+
+# True if proxy classes should be used for JDBC connections and
+# prepared statements.
+# Defaults to true.
+#
+org.exolab.castor.persist.useProxies=false
+
+# MappingLoader implementations:
+#
+org.castor.mapping.loaderFactories=\
+  org.castor.mapping.JDOMappingLoaderFactory,\
+  org.castor.mapping.XMLMappingLoaderFactory
+
+# Cache implementations:
+#
+org.castor.cache.Factories=\
+  org.castor.cache.simple.NoCacheFactory,\
+  org.castor.cache.simple.TimeLimitedFactory,\
+  org.castor.cache.simple.CountLimitedFactory,\
+  org.castor.cache.simple.UnlimitedFactory,\
+  org.castor.cache.distributed.FKCacheFactory,\
+  org.castor.cache.distributed.JcsCacheFactory,\
+  org.castor.cache.distributed.JCacheFactory,\
+  org.castor.cache.distributed.CoherenceCacheFactory,\
+  org.castor.cache.distributed.OsCacheFactory,\
+  org.castor.cache.hashbelt.FIFOHashbeltFactory,\
+  org.castor.cache.hashbelt.LRUHashbeltFactory,\
+  org.castor.cache.distributed.EHCacheFactory,\
+  org.castor.cache.distributed.GigaspacesCacheFactory
+
+# TransactionManagerFactory implementations:
+#
+org.castor.transactionmanager.Factories=\
+  org.castor.transactionmanager.WebSphereTransactionManagerFactory,\
+  org.castor.transactionmanager.WebSphere5TransactionManagerFactory,\
+  org.castor.transactionmanager.WebSphere51TransactionManagerFactory,\
+  org.castor.transactionmanager.LocalTransactionManagerFactory,\
+  org.castor.transactionmanager.JNDIENCTransactionManagerFactory,\
+  org.castor.transactionmanager.JOTMTransactionManagerFactory
+
+# Selects whether the TransactionManager should be initialized at registration,
+# or lazily when requested for the first time.
+# Defaults to false.
+#
+org.castor.transactionmanager.InitializeAtRegistration=false
+
+# Instructs Castor JDO to use the JDBC 3.0-specific features to obtain
+# the generated value of an identity column.
+# Defaults to false.
+#
+org.castor.jdo.use.jdbc30=false
+
+# Specifies whether to use ANSI-compliant SQL for MS SQL Server.
+# Defaults to false.
+#
+org.exolab.castor.jdo.sqlserver.ansi-compliant=false
+
+# Specifyies whether the ClassDescriptorResolver should (automatically) search
+# for and consult with package mapping files (.castor.xml) to retrieve class
+# descriptor information; on by default.
+# Defaults to true.
+#
+#org.exolab.castor.xml.loadPackageMappings=false

diff --git a/utils/splitstockholm.pl b/utils/splitstockholm.pl
index 65e6644..76ff05b 100644 (file)
--- a/utils/splitstockholm.pl
+++ b/utils/splitstockholm.pl
@@ -17,33 +17,33 @@
 # You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
 # The Jalview Authors are detailed in the 'AUTHORS' file.
 ##
- \r
-# Splits a concatenated set of Stockholm Files into several individual files.\r
-\r
-use strict;\r
-use FileHandle;\r
-my $ac;\r
-my $lns="";\r
-my $fh;\r
-while (<>) {\r
-    if ($_=~m!^//!) {\r
-       $fh->print("//\n");\r
-       $fh->close();\r
-       $ac = undef;\r
-       $lns = "";\r
-    } else {\r
-       if ($_=~/GF\s+AC\s+([0-9.RPF]+)/) { \r
-           $ac=$1; \r
-           ($fh=new FileHandle)->open(">$ac.stk") or die("Couldn't open file '$ac.stk'"); \r
-           $lns=~/^. STOCKHOLM 1.0/ or $fh->print("# STOCKHOLM 1.0\n");\r
-       };\r
-       if (defined($fh)) {\r
-           if (defined $lns) { \r
-               $fh->print($lns); $lns=undef; }\r
-           \r
-           $fh->print($_);\r
-       } else {\r
-           $lns .= $_;\r
-       }\r
-    }\r
-}\r
+ 
+# Splits a concatenated set of Stockholm Files into several individual files.
+
+use strict;
+use FileHandle;
+my $ac;
+my $lns="";
+my $fh;
+while (<>) {
+    if ($_=~m!^//!) {
+       $fh->print("//\n");
+       $fh->close();
+       $ac = undef;
+       $lns = "";
+    } else {
+       if ($_=~/GF\s+AC\s+([0-9.RPF]+)/) { 
+           $ac=$1; 
+           ($fh=new FileHandle)->open(">$ac.stk") or die("Couldn't open file '$ac.stk'"); 
+           $lns=~/^. STOCKHOLM 1.0/ or $fh->print("# STOCKHOLM 1.0\n");
+       };
+       if (defined($fh)) {
+           if (defined $lns) { 
+               $fh->print($lns); $lns=undef; }
+           
+           $fh->print($_);
+       } else {
+           $lns .= $_;
+       }
+    }
+}