JAL-2629 choice of hmm profile now a parameter not a selection, apis simplified

[jalview.git] / resources / lang / Messages.properties

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index b3afc6a..4fe5ada 100644 (file)
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -885,7 +885,6 @@ label.error_unsupported_owwner_user_colour_scheme = Unsupported owner for User C
 label.save_alignment_to_file = Save Alignment to file
 label.save_features_to_file = Save Features to File
 label.save_annotation_to_file = Save Annotation to File
-label.no_features_on_alignment = No features found on alignment
 label.save_pdb_file = Save PDB File
 label.save_text_to_file = Save Text to File
 label.save_state = Save State
@@ -1373,21 +1372,16 @@ label.most_polymer_residues = Most Polymer Residues
 label.cached_structures = Cached Structures
 label.free_text_search = Free Text Search
 label.hmmalign = hmmalign
+label.use_hmm = HMM profile to use
 label.hmmbuild = hmmbuild
-label.hmmbuild_group = Build HMM from Selected Group
-label.group_hmmbuild = Build HMM from Group
 label.hmmsearch = hmmsearch
 label.installation = Installation
 label.hmmer_location = HMMER Binaries Installation Location
 label.cygwin_location = Cygwin Binaries Installation Location (Windows)
 label.information_annotation = Information Annotation
-warn.null_hmm = Please ensure the alignment contains a hidden Markov model
 label.ignore_below_background_frequency = Ignore Below Background Frequency
 label.information_description = Information content, measured in bits
-warn.no_selected_hmm = Please select a hidden Markov model sequence.
-label.select_hmm = Select HMM
-warn.no_sequence_data = No sequence data found.
-warn.empty_grp_or_alignment = An empty group or alignment was found.
+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
@@ -1395,14 +1389,11 @@ label.trim_termini_desc = If true, non-matching regions on either end of the res
 label.no_of_sequences = Number of sequences returned
 label.freq_alignment = Use alignment background frequencies
 label.freq_uniprot = Use Uniprot background frequencies
-label.hmmalign_label = hmmalign options
-label.hmmsearch_label = hmmsearch options
+label.hmmalign_options = hmmalign options
+label.hmmsearch_options = hmmsearch options
 label.executable_not_found = The ''{0}'' executable file was not found
-warn.hmm_command_failed = hmm command not found
+warn.command_failed = {0} failed
 label.invalid_folder = Invalid Folder
-label.folder_not_exists = HMMER binaries not found. \n Please enter the path to the HMMER binaries (if installed).
-label.hmmer_installed = HMMER installed
-label.hmmer_no_sequences_found = No sequences found
 label.number_of_results = Number of Results to Return
 label.auto_align_seqs = Automatically Align Fetched Sequences
 label.use_accessions = Return Accessions
@@ -1417,10 +1408,8 @@ label.seq_e_value_desc = The E-value cutoff for returned sequences (hmmsearch -E
 label.seq_score_desc = The score threshold for returned sequences
 label.dom_e_value_desc = The E-value cutoff for returned domains (hmmsearch -domE)
 label.dom_score_desc = The score threshold for returned domains
-label.not_enough_sequences = There are not enough sequences to run {0}
 label.add_database = Add Database
 label.this_alignment = This alignment
-warn.file_not_exists = File does not exist
 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