X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=resources%2Flang%2FMessages.properties;h=bf9cc186b74390b6f06182ad2a82d63270c2fd20;hb=c794c5033adeee182b03a5ea92c0a7495a29661f;hp=33395d2a15f2f6346321d73abcb638dd045fb561;hpb=a82f1e47eef845557e95e61116e6b34bdd3242f3;p=jalview.git

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index 33395d2..bf9cc18 100644
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -60,6 +60,8 @@ action.boxes = Boxes
 action.text = Text
 action.by_pairwise_id = By Pairwise Identity
 action.by_id = By Id
+action.by_evalue = By E-Value
+action.by_bit_score = By Bit Score
 action.by_length = By Length
 action.by_group = By Group
 action.unmark_as_reference = Unmark as Reference 
@@ -133,7 +135,11 @@ action.select_highlighted_columns = Select Highlighted Columns
 tooltip.select_highlighted_columns = Press B to mark highlighted columns, Ctrl-(or Cmd)-B to toggle, and Alt-B to mark all but highlighted columns 
 action.deselect_all = Deselect all
 action.invert_selection = Invert selection
+action.filter_by_evalue = Filter by E-Value
+action.filter_by_score = Filter by Score
 action.using_jmol = Using Jmol
+action.undo_changes_to_feature_settings = Undo all unapplied changes to feature settings
+action.undo_changes_to_feature_settings_and_close_the_dialog = Undo all pending changes and close the feature settings dialog
 action.link = Link
 action.group_link = Group Link
 action.show_chain = Show Chain
@@ -233,6 +239,7 @@ label.nucleotide = Nucleotide
 label.protein = Protein
 label.nucleotides = Nucleotides
 label.proteins = Proteins
+label.CDS = CDS
 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
@@ -365,7 +372,8 @@ 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.select_character_rendering_style = {0} character rendering style
+label.select_character_style_title = {0} Rendering options
 label.invert_selection = Invert Selection
 label.optimise_order = Optimise Order
 label.seq_sort_by_score = Sequence sort by Score
@@ -414,7 +422,7 @@ label.input_alignment_from_url = Input Alignment From URL
 label.input_alignment = Input Alignment
 label.couldnt_import_as_vamsas_session = Couldn't import {0} as a new vamsas session.
 label.vamsas_document_import_failed = Vamsas Document Import Failed
-label.couldnt_locate = Could not locate {0}
+label.couldnt_locate = Couldn''t locate {0}
 label.url_not_found = URL not found
 label.new_sequence_url_link = New sequence URL link
 label.cannot_edit_annotations_in_wrapped_view = Cannot edit annotations in wrapped view
@@ -600,7 +608,7 @@ 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.rendering_style = {0} rendering style
 label.append_start_end = Append /start-end (/15-380)
 label.full_sequence_id = Full Sequence Id
 label.smooth_font = Smooth Font
@@ -681,7 +689,7 @@ label.sequence_details_for = Sequence 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.spaces_converted_to_underscores = 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."
@@ -770,6 +778,9 @@ 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.sequence_feature_settings_for = Sequence Feature Settings for {0}
+label.sequence_feature_settings_for_view = Sequence Feature Settings for view "{0}"
+label.sequence_feature_settings_for_CDS_and_Protein = Sequence Feature Settings for CDS and Protein
 label.pairwise_aligned_sequences = Pairwise Aligned Sequences
 label.original_data_for_params = Original Data for {0}
 label.points_for_params = Points for {0}
@@ -883,8 +894,6 @@ label.save_feature_colours = Save Feature Colour Scheme
 label.select_startup_file = Select startup file
 label.select_default_browser = Select default web browser
 label.save_tree_as_newick = Save tree as newick file
-label.create_eps_from_tree = Create EPS file from tree
-label.create_png_from_tree = Create PNG image from tree
 label.save_colour_scheme = Save colour scheme
 label.edit_params_for = Edit parameters for {0}
 label.choose_filename_for_param_file = Choose a filename for this parameter file
@@ -940,8 +949,6 @@ error.call_setprogressbar_before_registering_handler = call setProgressBar befor
 label.cancelled_params = Cancelled {0}
 error.implementation_error_cannot_show_view_alignment_frame = Implementation error: cannot show a view from another alignment in an AlignFrame.
 error.implementation_error_dont_know_about_threshold_setting = Implementation error: don't know about threshold setting for current AnnotationColourGradient.
-error.eps_generation_not_implemented = EPS Generation not yet implemented
-error.png_generation_not_implemented = PNG Generation not yet implemented
 error.try_join_vamsas_session_another = Trying to join a vamsas session when another is already connected
 error.invalid_vamsas_session_id = Invalid vamsas session id
 label.groovy_support_failed = Jalview Groovy Support Failed
@@ -1012,7 +1019,7 @@ label.pca_recalculating = Recalculating PCA
 label.pca_calculating = Calculating PCA
 label.select_foreground_colour = Choose foreground colour
 label.select_colour_for_text = Select Colour for Text
-label.adjunst_foreground_text_colour_threshold = Adjust Foreground Text Colour Threshold
+label.adjust_foreground_text_colour_threshold = Adjust Foreground Text Colour Threshold
 label.select_subtree_colour = Select Sub-Tree Colour
 label.create_new_sequence_features = Create New Sequence Feature(s)
 label.amend_delete_features = Amend/Delete Features for {0}
@@ -1055,6 +1062,7 @@ exception.ranml_couldnt_process_data = Couldn't process data as RNAML file ({0})
 exception.ranml_invalid_file = Invalid RNAML file ({0})
 exception.ranml_problem_parsing_data = Problem parsing data as RNAML ({0})
 exception.pfam_no_sequences_found = No sequences found (PFAM input)
+exception.hmmer_no_valid_sequences_found = No valid sequences found
 exception.stockholm_invalid_format = This file is not in valid STOCKHOLM format: First line does not contain '# STOCKHOLM'
 exception.couldnt_parse_sequence_line = Could not parse sequence line: {0}
 exception.unknown_annotation_detected = Unknown annotation detected: {0} {1}
@@ -1084,7 +1092,6 @@ error.implementation_error_cannot_find_service_url_in_given_set_param_store = Im
 exception.jobsubmission_invalid_params_set = Invalid parameter set. Check Jalview implementation
 exception.notvaliddata_group_contains_less_than_min_seqs = Group contains less than {0} sequences.
 exception.outofmemory_loading_pdb_file = Out of memory loading PDB File
-exception.eps_coudnt_write_output_file = Could not write to the output file: {0}
 exception.eps_method_not_supported = Method not currently supported by EpsGraphics2D version {0}
 exception.eps_unable_to_get_inverse_matrix = Unable to get inverse of matrix: {0}
 warn.job_cannot_be_cancelled_close_window = This job cannot be cancelled.\nJust close the window.
@@ -1109,8 +1116,7 @@ status.searching_for_sequences_from = Searching for sequences from {0}
 status.finished_searching_for_sequences_from = Finished searching for sequences from {0}
 label.eps_file = EPS file
 label.png_image = PNG image
-status.saving_file = Saving {0}
-status.export_complete = {0} Export completed.
+status.export_complete = {0} Export completed
 status.fetching_pdb = Fetching PDB {0}
 status.refreshing_news = Refreshing news
 status.importing_vamsas_session_from = Importing VAMSAS session from {0}
@@ -1130,7 +1136,7 @@ status.opening_file_for = opening file for
 status.colouring_chimera = Colouring Chimera
 status.running_hmmbuild = Building Hidden Markov Model
 status.running_hmmalign = Creating alignment with Hidden Markov Model
-status.running_hmmsearch = Searching for matching sequences
+status.running_search = Searching for matching sequences
 label.font_doesnt_have_letters_defined = Font doesn't have letters defined\nso cannot be used\nwith alignment data
 label.font_too_small = Font size is too small
 label.error_loading_file_params = Error loading file {0}
@@ -1233,14 +1239,10 @@ label.structure_chooser_filter_time = Structure Chooser - Filter time ({0})
 label.structure_chooser_no_of_structures = Structure Chooser - {0} Found ({1})
 info.no_pdb_entry_found_for = No PDB entry found for {0}
 exception.unable_to_detect_internet_connection = Jalview is unable to detect an internet connection
-exception.fts_rest_service_no_longer_available = {0} rest services no longer available!
-exception.resource_not_be_found = The requested resource could not be found
-exception.fts_server_error = There seems to be an error from the {0} server
 exception.fts_server_unreachable = Jalview is unable to reach the {0} server. \nPlease ensure that you are connected to the internet and try again.
 label.nw_mapping = Needleman & Wunsch Alignment
 label.sifts_mapping = SIFTs Mapping
 label.mapping_method = Sequence \u27f7 Structure mapping method
-status.waiting_for_user_to_select_output_file = Waiting for user to select {0} file
 status.cancelled_image_export_operation = Cancelled {0} export operation
 info.error_creating_file = Error creating {0} file
 exception.outofmemory_loading_mmcif_file = Out of memory loading mmCIF File
@@ -1252,8 +1254,6 @@ action.next_page= >>
 action.prev_page= << 
 label.next_page_tooltip=Next Page
 label.prev_page_tooltip=Previous Page
-exception.bad_request=Bad request. There is a problem with your input.
-exception.service_not_available=Service not available. The server is being updated, try again later.
 status.launching_3d_structure_viewer = Launching 3D Structure viewer...
 status.fetching_3d_structures_for_selected_entries = Fetching 3D Structures for selected entries...
 status.fetching_dbrefs_for_sequences_without_valid_refs = Fetching db refs for {0} sequence(s) without valid db ref required for SIFTS mapping
@@ -1325,7 +1325,7 @@ label.delete_condition = Delete this condition
 label.score = Score
 label.colour_by_label = Colour by label
 label.variable_colour = Variable colour...
-label.select_colour = Select colour
+label.select_colour_for = Select colour for {0}
 option.enable_disable_autosearch = When ticked, search is performed automatically
 option.autosearch = Autosearch
 label.retrieve_ids = Retrieve IDs
@@ -1346,10 +1346,19 @@ label.most_bound_molecules = Most Bound Molecules
 label.most_polymer_residues = Most Polymer Residues
 label.cached_structures = Cached Structures
 label.free_text_search = Free Text Search
+label.annotation_name = Annotation Name
+label.annotation_description = Annotation Description 
+label.edit_annotation_name_description = Edit Annotation Name/Description
+label.alignment = alignment
+label.pca = PCA
+label.create_image_of = Create {0} image of {1}
+label.click_to_edit = Click to edit, right-click for menu
 label.hmmalign = hmmalign
 label.use_hmm = HMM profile to use
+label.use_sequence = Sequence to use
 label.hmmbuild = hmmbuild
 label.hmmsearch = hmmsearch
+label.jackhmmer = jackhmmer
 label.installation = Installation
 label.hmmer_location = HMMER Binaries Installation Location
 label.cygwin_location = Cygwin Binaries Installation Location (Windows)
@@ -1363,27 +1372,43 @@ label.trim_termini = Trim Non-Matching Termini
 label.trim_termini_desc = If true, non-matching regions on either end of the resulting alignment are removed.
 label.no_of_sequences = Number of sequences returned
 label.reporting_cutoff = Reporting Cut-off
+label.inclusion_threshold = Inlcusion Threshold
 label.freq_alignment = Use alignment background frequencies
 label.freq_uniprot = Use Uniprot background frequencies
 label.hmmalign_options = hmmalign options
 label.hmmsearch_options = hmmsearch options
+label.jackhmmer_options = jackhmmer options
 label.executable_not_found = The ''{0}'' executable file was not found
 warn.command_failed = {0} failed
 label.invalid_folder = Invalid Folder
 label.number_of_results = Number of Results to Return
+label.number_of_iterations = Number of jackhmmer Iterations
 label.auto_align_seqs = Automatically Align Fetched Sequences
+label.new_returned = new sequences returned
 label.use_accessions = Return Accessions
-label.seq_evalue = Sequence E-value Cut-off
-label.seq_score = Sequence Score Threshold
-label.dom_evalue = Domain E-value Cut-off
-label.dom_score = Domain Score Threshold
+label.check_for_new_sequences = Return Number of New Sequences
+label.evalue = E-Value
+label.reporting_seq_evalue = Reporting Sequence E-value Cut-off
+label.reporting_seq_score = Reporting Sequence Score Threshold
+label.reporting_dom_evalue = Reporting Domain E-value Cut-off
+label.reporting_dom_score = Reporting Domain Score Threshold
+label.inclusion_seq_evalue = Inclusion Sequence E-value Cut-off
+label.inclusion_seq_score = Inclusion Sequence Score Threshold
+label.inclusion_dom_evalue = Inclusion Domain E-value Cut-off
+label.inclusion_dom_score = Inclusion Domain Score Threshold
 label.number_of_results_desc = The maximum number of hmmsearch results to display
+label.number_of_iterations_desc = The number of iterations jackhmmer will complete when searching for new sequences
 label.auto_align_seqs_desc = If true, all fetched sequences will be aligned to the hidden Markov model with which the search was performed
+label.check_for_new_sequences_desc = Display number of new sequences returned from hmmsearch compared to the previous alignment 
 label.use_accessions_desc = If true, the accession number of each sequence is returned, rather than that sequence's name
-label.seq_e_value_desc = The E-value cutoff for returned sequences (hmmsearch -E)
-label.seq_score_desc = The score threshold for returned sequences (hmmsearch -T)
-label.dom_e_value_desc = The E-value cutoff for returned domains (hmmsearch --domE)
-label.dom_score_desc = The score threshold for returned domains (hmmsearch --domT)
+label.reporting_seq_e_value_desc = The E-value cutoff for returned sequences 
+label.reporting_seq_score_desc = The score threshold for returned sequences 
+label.reporting_dom_e_value_desc = The E-value cutoff for returned domains 
+label.reporting_dom_score_desc = The score threshold for returned domains 
+label.inclusion_seq_e_value_desc = Sequences with an E-value less than this cut-off are classed as significant
+label.inclusion_seq_score_desc = Sequences with a bit score greater than this threshold are classed as significant
+label.inclusion_dom_e_value_desc = Domains with an E-value less than this cut-off are classed as significant
+label.inclusion_dom_score_desc = Domains with a bit score greater than this threshold are classed as significant
 label.add_database = Add Database
 label.this_alignment = This alignment
 warn.invalid_format = This is not a valid database file format. The current supported formats are Fasta, Stockholm and Pfam.
@@ -1401,8 +1426,6 @@ label.groups = All groups
 label.selected_group = Selected group
 label.use_info_for_height = Use Information Content as Letter Height
 action.search = Search
-||||||| merged common ancestors
-=======
 label.backupfiles_confirm_delete = Confirm delete
 label.backupfiles_confirm_delete_old_files = Delete the following older backup files? (see the Backups tab in Preferences for more options)
 label.backupfiles_confirm_save_file = Confirm save file
@@ -1469,4 +1492,10 @@ label.pca = PCA
 label.create_image_of = Create {0} image of {1}
 label.click_to_edit = Click to edit, right-click for menu
 label.by_annotation_tooltip = Annotation Colour is configured from the main Colour menu
->>>>>>> develop
+label.show_linked_features = Show {0} features
+label.on_top = on top
+label.include_linked_features = Include {0} features
+label.include_linked_tooltip = Include visible {0} features<br>converted to local sequence coordinates
+label.features_not_shown = {0} feature(s) not shown
+label.no_features_to_sort_by = No features to sort by
+