X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=resources%2Flang%2FMessages.properties;h=bf9cc186b74390b6f06182ad2a82d63270c2fd20;hb=c794c5033adeee182b03a5ea92c0a7495a29661f;hp=05f05eacad7a46a2c4b8b64e0e556732748b229b;hpb=5fefa2921f96368c895ff07e8340653a477cd68b;p=jalview.git

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index 05f05ea..bf9cc18 100644
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -11,6 +11,7 @@ action.paste = Paste
 action.show_html_source = Show HTML Source
 action.print = Print...
 action.web_service = Web Service
+action.hmmer = HMMER
 action.cancel_job = Cancel Job
 action.start_job = Start Job
 action.revert = Revert
@@ -59,6 +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 
@@ -98,6 +101,7 @@ action.edit_group = Edit Group
 action.border_colour = Border colour
 action.edit_new_group = Edit New Group
 action.hide_sequences = Hide Sequences
+action.add_background_frequencies = Add Background Frequencies
 action.sequences = Sequences
 action.ids = IDS
 action.ids_sequences = IDS and sequences
@@ -131,7 +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
@@ -198,6 +206,9 @@ label.colourScheme_turnpropensity = Turn Propensity
 label.colourScheme_buriedindex = Buried Index
 label.colourScheme_purine/pyrimidine = Purine/Pyrimidine
 label.colourScheme_nucleotide = Nucleotide
+label.colourScheme_hmmer-uniprot = HMMER profile v global background
+label.colourScheme_hmmer-alignment = HMMER profile v alignment background
+label.colourScheme_hmm_match_score = HMM Match Score
 label.colourScheme_t-coffeescores = T-Coffee Scores
 label.colourScheme_rnahelices = By RNA Helices
 label.colourScheme_sequenceid = Sequence ID Colour
@@ -228,6 +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
@@ -360,7 +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
@@ -409,7 +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
@@ -595,7 +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
@@ -676,7 +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."
@@ -765,6 +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}
@@ -803,8 +819,8 @@ label.fetch_retrieve_from_all_sources = Retrieve from all {0} sources in {1}<br>
 label.feature_settings_click_drag = Drag up or down to change render order.<br/>Double click to select columns containing feature.
 label.transparency_tip = Adjust transparency to 'see through' feature colours.
 label.opt_and_params_further_details = see further details by right-clicking
-label.opt_and_params_show_brief_desc_image_link = <html>Click to show brief description<br><img src="{0}"/> Right click for further information.</html> 
-label.opt_and_params_show_brief_desc = <html>Click to show brief description<br></html>
+label.opt_and_params_show_brief_desc_image_link = Click to show brief description<br><img src="{0}"/> Right click for further information. 
+label.opt_and_params_show_brief_desc = Click to show brief description<br>
 label.adjusts_width_generated_eps_png = <html>Adjusts the width of the generated EPS or PNG file to ensure even the longest sequence ID or annotation label is displayed</html>
 label.manually_specify_width_left_column = <html>Manually specify the width of the left hand column where sequence IDs and annotation labels will be rendered in exported alignment figures. This setting will be ignored if 'Automatically set ID width' is set</html>
 label.job_created_when_checked = <html>When checked, a job is created for every sequence in the current selection.</html>
@@ -878,8 +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
@@ -935,15 +949,12 @@ 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
 label.couldnt_create_groovy_shell = Couldn't create the groovy Shell. Check the error log for the details of what went wrong.
 error.unsupported_version_calcIdparam = Unsupported Version for calcIdparam {0}
 error.implementation_error_cant_reorder_tree = Implementation Error: Can't reorder this tree. Not DefaultMutableTreeNode.
-error.invalid_value_for_option = Invalid value {0} for option {1}
 error.implementation_error_cannot_import_vamsas_doc = Implementation Error - cannot import existing vamsas document into an existing session, Yet!
 label.vamsas_doc_couldnt_be_opened_as_new_session = VAMSAS Document could not be opened as a new session - please choose another
 error.implementation_error_vamsas_operation_not_init = Impementation error! Vamsas Operations when client not initialised and connected
@@ -1008,7 +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}
@@ -1051,6 +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}
@@ -1080,7 +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.
@@ -1105,8 +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}
@@ -1124,6 +1134,9 @@ status.loading_cached_pdb_entries = Loading Cached PDB Entries
 status.searching_for_pdb_structures = Searching for PDB Structures
 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_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}
@@ -1230,7 +1243,6 @@ exception.fts_server_unreachable = Jalview is unable to reach the {0} server. \n
 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
@@ -1313,7 +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
@@ -1334,6 +1346,86 @@ 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)
+label.information_annotation = Information Annotation
+label.ignore_below_background_frequency = Ignore Below Background Frequency
+label.information_description = Information content, measured in bits
+warn.no_hmm = No Hidden Markov model found.\nRun hmmbuild or load an HMM file first.
+label.no_sequences_found = No matching sequences, or an error occurred.
+label.hmmer = HMMER
+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.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.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.
+label.database_for_hmmsearch = The database hmmsearch will search through
+label.use_reference = Use Reference Annotation
+label.use_reference_desc = If true, hmmbuild will keep all columns defined as a reference position by the reference annotation
+label.hmm_name = Alignment HMM Name
+label.hmm_name_desc = The name given to the HMM for the alignment
+warn.no_reference_annotation = No reference annotation found
+label.hmmbuild_for = Build HMM for
+label.hmmbuild_for_desc = Build an HMM for the selected sets of sequences
+label.alignment = Alignment
+label.groups_and_alignment = All groups and alignment
+label.groups = All groups
+label.selected_group = Selected group
+label.use_info_for_height = Use Information Content as Letter Height
+action.search = Search
 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
@@ -1401,7 +1493,9 @@ 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
 label.show_linked_features = Show {0} features
-label.show_linked_feature_settings = Open {0} settings
 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
\ No newline at end of file
+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
+