Merge branch 'develop' of https://source.jalview.org/git/jalview.git into kjvdh/featu...

diff --combined resources/lang/Messages.properties
index b0d4b68,f526699..d159e81
--- 1/resources/lang/Messages.properties
--- 2/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@@ -173,8 -173,6 +173,8 @@@ label.average_distance_identity = Avera
  label.neighbour_joining_identity = Neighbour Joining Using % Identity
  label.choose_calculation = Choose Calculation
  label.treecalc_title = {0} Using {1}
 +label.aptx_title = Archaeopteryx Tree View 
 +label.aptx_title_append = of {0}
  label.tree_calc_av = Average Distance
  label.tree_calc_nj = Neighbour Joining
  label.select_score_model = Select score model
@@@ -301,11 -299,7 +301,11 @@@ label.show_distances = Show distance
  label.mark_unassociated_leaves = Mark Unassociated Leaves
  label.fit_to_window = Fit To Window
  label.newick_format = Newick Format
 -label.select_newick_like_tree_file = Select a newick-like tree file
 +label.select_tree_file = Select a tree file
 +label.treebase_study = TreeBASE Study
 +label.treebase = TreeBASE
 +label.treefam = TreeFam
 +label.tree_of_life = Tree of Life
  label.colours = Colours
  label.view_mapping = View Mapping
  label.wireframe = Wireframe
@@@ -393,12 -387,7 +393,12 @@@ label.not_enough_sequences = Not enoug
  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.problem_reading_tree_file =  Problem reading tree file
 +label.tabs_detected_archaeopteryx = Warning, multiple trees detected in a single tree viewer instance. This will cause problems!
  label.possible_problem_with_tree_file = Possible problem with tree file
 +label.aptx_config_not_found = Warning: tree viewer configuration file not found, continue anyway? (this WILL cause the viewer to look different)
 +label.tree_url_example = Please enter a complete URL, for example \"http://www.jalview.org/examples/ferredoxin.nw\"
 +label.from_database = From Database...
 +label.load_tree_url = Tree from URL
  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.
  label.translation_failed = Translation Failed
  label.error_when_translating_sequences_submit_bug_report = Unfortunately, something went wrong when translating your sequences.\nPlease take a look in the Jalview java console\nand submit a bug report including the stacktrace.
@@@ -428,7 -417,7 +428,7 @@@ label.input_alignment_from_url = Input 
  label.input_alignment = Input Alignment
  label.couldnt_import_as_vamsas_session = Couldn't import {0} as a new vamsas session.
  label.vamsas_document_import_failed = Vamsas Document Import Failed
 -label.couldnt_locate = Couldn't locate {0}
 +label.couldnt_locate = Could not locate {0}
  label.url_not_found = URL not found
  label.new_sequence_url_link = New sequence URL link
  label.cannot_edit_annotations_in_wrapped_view = Cannot edit annotations in wrapped view
@@@ -570,10 -559,10 +570,10 @@@ label.select_copy_raw_html = Select thi
  label.share_data_vamsas_applications = Share data with other vamsas applications
  label.connect_to = Connect to
  label.join_existing_vamsas_session = Join an existing vamsas session
 -label.from_url = from URL
 +label.from_url = From URL
  label.any_trees_calculated_or_loaded_alignment_automatically_sort = When selected, any trees calculated or loaded onto the alignment will automatically sort the alignment
  label.sort_with_new_tree = Sort With New Tree
 -label.from_textbox = from Textbox
 +label.from_textbox = From Textbox
  label.window = Window
  label.preferences = Preferences
  label.tools = Tools
@@@ -684,7 -673,8 +684,8 @@@ label.2d_rna_structure_line = 2D RNA {0
  label.2d_rna_sequence_name = 2D RNA - {0}
  label.edit_name_and_description_current_group = Edit name and description of current group
  label.from_file = From File
- label.enter_pdb_id = Enter PDB Id (or pdbid:chaincode)
+ label.enter_pdb_id = Enter PDB Id
+ label.enter_pdb_id_tip = Enter PDB Id (or pdbid:chaincode)
  label.text_colour = Text Colour...
  label.structure = Structure
  label.show_pdbstruct_dialog = 3D Structure Data...
@@@ -921,8 -911,6 +922,8 @@@ label.updating_vamsas_session = Updatin
  label.loading_file = Loading File: {0}
  label.edit_params = Edit {0}
  label.as_percentage = As Percentage
 +error.database_id_has_letters = Database identifier ({0}) should contain only digits
 +error.phyloxml_validation = phyloXML XSD-based validation is turned off (enable with line 'validate_against_phyloxml_xsd_schem: true' in configuration file)
  error.not_implemented = Not implemented
  error.no_such_method_as_clone1_for = No such method as clone1 for {0}
  error.null_from_clone1 = Null from clone1!
@@@ -1080,7 -1068,6 +1081,7 @@@ exception.couldnt_parse_sequence_line 
  exception.unknown_annotation_detected = Unknown annotation detected: {0} {1}
  exception.couldnt_store_sequence_mappings = Couldn't store sequence mappings for {0}
  exception.matrix_too_many_iteration = Too many iterations in {0} (max is {1})
 +exception.invalid_matrix_identifier = Sequence identifier {0} not found in distance matrix.
  exception.browser_not_found = Exception in finding browser: {0}
  exception.browser_unable_to_locate = Unable to locate browser: {0}
  exception.invocation_target_exception_creating_aedesc = InvocationTargetException while creating AEDesc: {0}
@@@ -1333,6 -1320,13 +1334,13 @@@ label.select_hidden_colour = Select hid
  label.overview = Overview
  label.reset_to_defaults = Reset to defaults
  label.oview_calc = Recalculating overview...
- option.enable_disable_autosearch = When ticked, search is performed automatically.
+ option.enable_disable_autosearch = When ticked, search is performed automatically
  option.autosearch = Autosearch
- label.retrieve_ids = Retrieve IDs
+ label.retrieve_ids = Retrieve IDs
+ label.best_quality = Best Quality
+ label.best_resolution = Best Resolution
+ label.most_protein_chain = Most Protein Chain
+ label.most_bound_molecules = Most Bound Molecules
+ label.most_polymer_residues = Most Polymer Residues
+ label.cached_structures = Cached Structures
+ label.free_text_search = Free Text Search

diff --combined src/jalview/fts/core/GFTSPanel.java
index fbeeee8,86710e1..0d0cce6
--- 1/src/jalview/fts/core/GFTSPanel.java
--- 2/src/jalview/fts/core/GFTSPanel.java
+++ b/src/jalview/fts/core/GFTSPanel.java
@@@ -681,7 -681,8 +681,8 @@@ public abstract class GFTSPanel extend
      if (tabs != null)
      {
        tabs.setOpaque(true);
-       tabs.insertTab("Free Text Search", null, this, "", 0);
+       tabs.insertTab(MessageManager.getString("label.free_text_search"),
+               null, this, "", 0);
        mainFrame.setContentPane(tabs);
        tabs.setVisible(true);
      }
@@@ -900,7 -901,7 +901,7 @@@
    public void transferToSequenceFetcher(String ids)
    {
      seqFetcher.getTextArea().setText(ids);
 -    Thread worker = new Thread(seqFetcher);
 +    Thread worker = new Thread(seqFetcher, "GFTSSeqFetcher");
      worker.start();
    }