X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=resources%2Flang%2FMessages.properties;h=b627ac84db89801574c6e736c5e3b86f3971440e;hb=5cb4c1540eaca054c26ff42a8319f0dbffb1f8e6;hp=4ff30d402e2052c173bd5f7e7b73b8df174e3942;hpb=dd2b17330673faf79c5e239afd163668fdb3fe0a;p=jalview.git

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index 4ff30d4..b627ac8 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 
@@ -1368,6 +1370,7 @@ 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
@@ -1377,23 +1380,33 @@ 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.seq_evalue = Sequence E-value Cut-off
 label.evalue = E-Value
-label.seq_score = Sequence Score Threshold
-label.dom_evalue = Domain E-value Cut-off
-label.dom_score = Domain Score Threshold
+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.