From: Jim Procter Date: Wed, 17 May 2017 13:31:54 +0000 (+0100) Subject: Merge branch 'features/JAL-2447experimentalFlag' into develop X-Git-Tag: Release_2_10_2~3^2~82 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;ds=inline;h=36e7c887ef91f49f6065dea063180f7de146b3e1;hp=-c;p=jalview.git Merge branch 'features/JAL-2447experimentalFlag' into develop --- 36e7c887ef91f49f6065dea063180f7de146b3e1 diff --combined resources/lang/Messages.properties index f6eeb26,354dc93..b12891f --- a/resources/lang/Messages.properties +++ b/resources/lang/Messages.properties @@@ -68,6 -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 @@@ -80,8 -81,7 +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 @@@ -171,7 -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 @@@ -179,8 -178,6 +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 @@@ -337,7 -334,6 +337,7 @@@ 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. @@@ -381,11 -377,14 +381,11 @@@ label.remove_from_default_list = Remov 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. @@@ -714,6 -713,7 +714,6 @@@ label.set_as_default = Set as Defaul 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 @@@ -856,6 -856,7 +856,6 @@@ label.couldnt_save_project = Couldn't s 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 @@@ -899,7 -900,6 +899,7 @@@ 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} @@@ -1225,7 -1225,6 +1225,7 @@@ label.configure_displayed_columns = Cus 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 @@@ -1301,10 -1300,5 +1301,12 @@@ warn.name_cannot_be_duplicate = User-de 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) ++label.show_experimental_tip = Enable any new and currently 'experimental' features (see Latest Release Notes for details) diff --combined src/jalview/gui/Desktop.java index d6c25a8,b8f8399..4877d7f --- a/src/jalview/gui/Desktop.java +++ b/src/jalview/gui/Desktop.java @@@ -129,10 -129,8 +129,12 @@@ public class Desktop extends jalview.jb DropTargetListener, ClipboardOwner, IProgressIndicator, jalview.api.StructureSelectionManagerProvider { + private static int DEFAULT_MIN_WIDTH = 300; + + private static int DEFAULT_MIN_HEIGHT = 250; + + private static final String EXPERIMENTAL_FEATURES = "EXPERIMENTAL_FEATURES"; + private JalviewChangeSupport changeSupport = new JalviewChangeSupport(); /** @@@ -330,19 -328,6 +332,6 @@@ instance = this; doVamsasClientCheck(); - groovyShell = new JMenuItem(); - groovyShell.setText(MessageManager.getString("label.groovy_console")); - groovyShell.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - groovyShell_actionPerformed(); - } - }); - toolsMenu.add(groovyShell); - groovyShell.setVisible(true); - doConfigureStructurePrefs(); setTitle("Jalview " + jalview.bin.Cache.getProperty("VERSION")); setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE); @@@ -397,6 -382,8 +386,8 @@@ showConsole(showjconsole); showNews.setVisible(false); + + experimentalFeatures.setSelected(showExperimental()); getIdentifiersOrgData(); @@@ -493,6 -480,19 +484,19 @@@ }); } + /** + * Answers true if user preferences to enable experimental features is True + * (on), else false + * + * @return + */ + public boolean showExperimental() + { + String experimental = Cache.getDefault(EXPERIMENTAL_FEATURES, + Boolean.FALSE.toString()); + return Boolean.valueOf(experimental).booleanValue(); + } + public void doConfigureStructurePrefs() { // configure services @@@ -836,8 -836,6 +840,8 @@@ openFrameCount++; + frame.setMinimumSize(new Dimension(DEFAULT_MIN_WIDTH, + DEFAULT_MIN_HEIGHT)); frame.setVisible(makeVisible); frame.setClosable(true); frame.setResizable(resizable); @@@ -2497,8 -2495,6 +2501,6 @@@ } - protected JMenuItem groovyShell; - /** * Accessor method to quickly get all the AlignmentFrames loaded. * @@@ -2584,6 -2580,7 +2586,7 @@@ /** * Add Groovy Support to Jalview */ + @Override public void groovyShell_actionPerformed() { try @@@ -3398,4 -3395,14 +3401,14 @@@ } } } + + /** + * Sets the Preferences property for experimental features to True or False + * depending on the state of the controlling menu item + */ + @Override + protected void showExperimental_actionPerformed(boolean selected) + { + Cache.setProperty(EXPERIMENTAL_FEATURES, Boolean.toString(selected)); + } }