X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=resources%2Flang%2FMessages.properties;h=2c0fbb91952bc2cff4d4afa50af486186f213552;hb=933e28e48b4f3bf98851cedd99ef345d45bf25a3;hp=33d93595fc3f48896419bc4279d9193319b8b0ad;hpb=b5667f39acdf309cd92881b73edfda591e0acaf4;p=jalview.git

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index 33d9359..2c0fbb9 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 
@@ -99,6 +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
@@ -132,6 +135,8 @@ 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.link = Link
 action.group_link = Group Link
@@ -201,6 +206,7 @@ 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
@@ -1053,6 +1059,7 @@ 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}
@@ -1128,7 +1135,7 @@ 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}
@@ -1346,8 +1353,10 @@ label.cached_structures = Cached Structures
 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)
@@ -1361,27 +1370,41 @@ 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.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.
@@ -1399,8 +1422,6 @@ 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