X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=resources%2Flang%2FMessages.properties;h=e63752d376a8ee9a80ddaf9ef157e91437dba693;hp=922f48269b5acb02383cad658d7d5fcf502366ca;hb=0288494d034d48dd8ce0c5a8654ac2ee695b4573;hpb=7451c6419c9c94627f79d044228db55b90e9b4cf

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index 922f482..e63752d 100644
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -80,7 +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
@@ -170,6 +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
@@ -177,6 +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
@@ -333,6 +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.
@@ -379,11 +384,10 @@ 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_more_than_n_sequences = You need to have more than {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.
@@ -712,7 +716,6 @@ 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
@@ -855,7 +858,6 @@ 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
@@ -899,6 +901,7 @@ 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}