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
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
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.link = Link
action.group_link = Group Link
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
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}
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}
label.free_text_search = Free Text Search
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.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.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.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.
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
git://source.jalview.org / jalview.git / blobdiff