X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=resources%2Flang%2FMessages.properties;fp=resources%2Flang%2FMessages.properties;h=b12891f7025b11c1fa47dbed6043959216b27a07;hb=36e7c887ef91f49f6065dea063180f7de146b3e1;hp=354dc9346d7fefdc8ca051f8824b28ecaf50ed1e;hpb=124aa4823768a2c745a5e41f2ebfe13ab77bbea4;p=jalview.git

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index 354dc93..b12891f 100644
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -68,7 +68,6 @@ action.user_defined = User Defined...
 action.by_conservation = By Conservation
 action.wrap = Wrap
 action.show_gaps = Show Gaps
-action.show_occupancy = Show Occupancy
 action.show_hidden_markers = Show Hidden Markers
 action.find = Find
 action.undefine_groups = Undefine Groups
@@ -81,7 +80,8 @@ action.scale_left = Scale Left
 action.scale_right = Scale Right
 action.by_tree_order = By Tree Order
 action.sort = Sort
-action.calculate_tree = Calculate Tree
+action.calculate_tree = Calculate Tree...
+action.calculate_tree_pca = Calculate Tree or PCA...
 action.help = Help
 action.by_annotation = By Annotation...
 action.invert_sequence_selection = Invert Sequence Selection
@@ -171,6 +171,7 @@ label.redo_command = Redo {0}
 label.principal_component_analysis = Principal Component Analysis
 label.average_distance_identity = Average Distance Using % Identity
 label.neighbour_joining_identity = Neighbour Joining Using % Identity
+label.choose_calculation = Choose Calculation
 label.treecalc_title = {0} Using {1}
 label.tree_calc_av = Average Distance
 label.tree_calc_nj = Neighbour Joining
@@ -178,6 +179,8 @@ label.select_score_model = Select score model
 label.score_model_pid = % Identity
 label.score_model_blosum62 = BLOSUM62
 label.score_model_pam250 = PAM 250
+label.score_model_smithwatermanscore = Score between two sequences aligned with Smith-Waterman with default Peptide/Nucleotide matrix
+label.score_model_sequencefeaturesimilarity = Distance measure of average number of features not shared at sequence positions 
 label.score_model_conservation = Physicochemical property conservation
 label.score_model_enhconservation = Physicochemical property conservation
 label.status_bar = Status bar
@@ -334,6 +337,7 @@ label.colour_residues_above_occurrence = Colour residues above % occurrence
 label.set_this_label_text = set this label text
 label.sequences_from = Sequences from {0}
 label.successfully_loaded_file  = Successfully loaded file {0}
+label.successfully_loaded_matrix  = Successfully loaded score matrix {0}
 label.successfully_saved_to_file_in_format = Successfully saved to file: {0} in {1} format.
 label.copied_sequences_to_clipboard = Copied {0} sequences to clipboard.
 label.check_file_matches_sequence_ids_alignment = Check that the file matches sequence IDs in the alignment.
@@ -377,14 +381,11 @@ label.remove_from_default_list = Remove from default list?
 label.remove_user_defined_colour = Remove user defined colour
 label.you_must_select_least_two_sequences = You must select at least 2 sequences.
 label.invalid_selection = Invalid Selection
-label.principal_component_analysis_must_take_least_four_input_sequences = Principal component analysis must take\nat least 4 input sequences.
 label.sequence_selection_insufficient = Sequence selection insufficient
-label.you_need_more_two_sequences_selected_build_tree = You need to have more than two sequences selected to build a tree!
+label.you_need_at_least_n_sequences = You need to select at least {0} sequences
 label.not_enough_sequences = Not enough sequences
 label.selected_region_to_tree_may_only_contain_residues_or_gaps =  The selected region to create a tree may\nonly contain residues or gaps.\nTry using the Pad function in the edit menu,\nor one of the multiple sequence alignment web services.
 label.sequences_selection_not_aligned = Sequences in selection are not aligned
-label.sequences_must_be_aligned_before_creating_tree = The sequences must be aligned before creating a tree.\nTry using the Pad function in the edit menu,\n or one of the multiple sequence alignment web services.
-label.sequences_not_aligned = Sequences not aligned
 label.problem_reading_tree_file =  Problem reading tree file
 label.possible_problem_with_tree_file = Possible problem with tree file
 label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation = Please select at least three bases in at least one sequence in order to perform a cDNA translation.
@@ -713,7 +714,6 @@ label.set_as_default = Set as Default
 label.show_labels = Show labels
 action.background_colour = Background Colour...
 label.associate_nodes_with = Associate Nodes With
-label.jalview_pca_calculation = Jalview PCA Calculation
 label.link_name = Link Name
 label.pdb_file = PDB file
 label.colour_with_jmol = Colour with Jmol
@@ -856,7 +856,6 @@ label.couldnt_save_project = Couldn't save project
 label.error_whilst_saving_current_state_to = Error whilst saving current state to {0}
 label.error_whilst_loading_project_from = Error whilst loading project from {0}
 label.couldnt_load_project = Couldn't load project
-label.pca_sequences_not_aligned = The sequences must be aligned before calculating PCA.\nTry using the Pad function in the edit menu,\nor one of the multiple sequence alignment web services.
 label.invalid_name_preset_exists = Invalid name - preset already exists.
 label.invalid_name = Invalid name
 label.set_proxy_settings = Please set up your proxy settings in the 'Connections' tab of the Preferences window
@@ -900,6 +899,7 @@ label.choose_filename_for_param_file = Choose a filename for this parameter file
 label.save_as_html = Save as HTML
 label.recently_opened = Recently Opened
 label.blasting_for_unidentified_sequence_jobs_running = BLASTing for unidentified sequences - {0}  jobs running.
+label.tree = Tree
 label.tree_from = Tree from {0}
 label.webservice_job_title = {0} using {1}
 label.select_visible_region_of = selected {0} region of {1}
@@ -1225,6 +1225,7 @@ label.configure_displayed_columns = Customise Displayed Options
 label.start_jalview = Start Jalview
 label.biojs_html_export = BioJS
 label.scale_as_cdna = Scale protein residues to codons
+label.font_as_cdna = Use same font for cDNA and peptide
 label.scale_protein_to_cdna = Scale Protein to cDNA
 label.scale_protein_to_cdna_tip = Make protein residues same width as codons in split frame views
 info.select_annotation_row = Select Annotation Row
@@ -1300,5 +1301,12 @@ warn.name_cannot_be_duplicate = User-defined URL names must be unique and cannot
 label.invalid_name = Invalid Name !
 label.output_seq_details = Output Sequence Details to list all database references
 label.urllinks = Links
+label.togglehidden = Show hidden regions
+label.quality_descr = Alignment Quality based on Blosum62 scores
+label.conservation_descr = Conservation of total alignment less than {0}% gaps
+label.consensus_descr = PID
+label.complement_consensus_descr = PID for cDNA
+label.strucconsensus_descr = PID for base pairs
+label.occupancy_descr = Number of aligned positions 
 label.show_experimental = Enable experimental features
-label.show_experimental_tip = Enable any new and currently 'experimental' features (see Latest Release Notes for details)
\ No newline at end of file
+label.show_experimental_tip = Enable any new and currently 'experimental' features (see Latest Release Notes for details)