Merge branch 'develop' into features/JAL-2393customMatrices

diff --combined resources/lang/Messages.properties
index 9e3c98d,2e92717..2450be8
--- 1/resources/lang/Messages.properties
--- 2/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@@ -3,6 -3,9 +3,9 @@@ action.reset_services = Reset Service
  action.merge_results = Merge Results
  action.load_scheme = Load scheme
  action.save_scheme = Save scheme
+ label.scheme_changed = Changes to scheme {0} have not been saved<br>Save changes, or continue without saving to make a new colour scheme
+ label.save_changes = Save Changes
+ label.dont_save_changes = Don't Save
  action.save_image = Save Image
  action.paste = Paste
  action.show_html_source = Show HTML Source
@@@ -77,8 -80,7 +80,8 @@@ action.scale_left = Scale Lef
  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
@@@ -168,7 -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
@@@ -176,8 -177,6 +179,8 @@@ label.select_score_model = Select scor
  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
@@@ -333,7 -332,6 +336,7 @@@ label.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.
@@@ -900,7 -898,6 +903,7 @@@ label.choose_filename_for_param_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}