X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=resources%2Flang%2FMessages.properties;h=2647c431e1325685e63a97a65211c3707326b3c3;hb=857348180124be7ab86d7de1e4d3f780e65b1fdd;hp=3b22f2e423efe4f9e01ae02b4d6d544c8e5a6dc3;hpb=ed581b841fe9361bfe80bb006df190a29df264fb;p=jalview.git

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index 3b22f2e..2647c43 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 
@@ -1236,9 +1238,6 @@ 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
@@ -1255,8 +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
@@ -1368,6 +1365,7 @@ 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
@@ -1377,19 +1375,33 @@ 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.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.
@@ -1473,4 +1485,7 @@ 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