-// $Id:
-// FORESTER -- software libraries and applications
-// for evolutionary biology research and applications.
-//
-// Copyright (C) 2008-2010 Christian M. Zmasek
-// All rights reserved
-//
-// This library is free software; you can redistribute it and/or
-// modify it under the terms of the GNU Lesser General Public
-// License as published by the Free Software Foundation; either
-// version 2.1 of the License, or (at your option) any later version.
-//
-// This library is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
-// Lesser General Public License for more details.
-//
-// You should have received a copy of the GNU Lesser General Public
-// License along with this library; if not, write to the Free Software
-// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-//
-// Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
-
-package org.forester.archaeopteryx;
-
-import java.awt.Color;
-import java.awt.Component;
-import java.awt.Container;
-import java.awt.Font;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.io.IOException;
-import java.util.List;
-import java.util.Locale;
-import java.util.Map;
-
-import javax.swing.JApplet;
-import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JFrame;
-import javax.swing.JMenu;
-import javax.swing.JMenuBar;
-import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
-import javax.swing.JRadioButtonMenuItem;
-import javax.swing.SwingUtilities;
-
-import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
-import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
-import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
-import org.forester.archaeopteryx.tools.InferenceManager;
-import org.forester.archaeopteryx.tools.ProcessPool;
-import org.forester.archaeopteryx.tools.ProcessRunning;
-import org.forester.phylogeny.Phylogeny;
-import org.forester.phylogeny.PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE;
-import org.forester.phylogeny.data.NodeVisualization.NodeFill;
-import org.forester.phylogeny.data.NodeVisualization.NodeShape;
-import org.forester.util.ForesterConstants;
-import org.forester.util.ForesterUtil;
-
-public abstract class MainFrame extends JFrame implements ActionListener {
-
- static final String USE_MOUSEWHEEL_SHIFT_TO_ROTATE = "In this display type, use mousewheel + Shift to rotate [or A and S]";
- static final String PHYLOXML_REF_TOOL_TIP = Constants.PHYLOXML_REFERENCE; //TODO //FIXME
- static final String APTX_REF_TOOL_TIP = Constants.APTX_REFERENCE;
- private static final long serialVersionUID = 3655000897845508358L;
- final static Font menu_font = new Font( Configuration.getDefaultFontFamilyName(),
- Font.PLAIN,
- 10 );
- static final String TYPE_MENU_HEADER = "Type";
- static final String RECTANGULAR_TYPE_CBMI_LABEL = "Rectangular";
- static final String EURO_TYPE_CBMI_LABEL = "Euro Type";
- static final String CURVED_TYPE_CBMI_LABEL = "Curved";
- static final String TRIANGULAR_TYPE_CBMI_LABEL = "Triangular";
- static final String CONVEX_TYPE_CBMI_LABEL = "Convex";
- static final String ROUNDED_TYPE_CBMI_LABEL = "Rounded";
- static final String UNROOTED_TYPE_CBMI_LABEL = "Unrooted (alpha)"; //TODO
- static final String CIRCULAR_TYPE_CBMI_LABEL = "Circular (alpha)"; //TODO
- static final String OPTIONS_HEADER = "Options";
- static final String SEARCH_SUBHEADER = "Search:";
- static final String DISPLAY_SUBHEADER = "Display:";
- static final String SEARCH_TERMS_ONLY_LABEL = "Match Complete Terms Only";
- static final String SEARCH_CASE_SENSITIVE_LABEL = "Case Sensitive";
- static final String INVERSE_SEARCH_RESULT_LABEL = "Negate Result";
- static final String DISPLAY_BRANCH_LENGTH_VALUES_LABEL = "Display Branch Length Values";
- static final String DISPLAY_SCALE_LABEL = "Display Scale";
- static final String NON_LINED_UP_CLADOGRAMS_LABEL = "Non-Lined Up Cladograms";
- static final String UNIFORM_CLADOGRAMS_LABEL = "Total Node Sum Dependent Cladograms";
- static final String LABEL_DIRECTION_LABEL = "Radial Labels";
- static final String LABEL_DIRECTION_TIP = "To use radial node labels in radial and unrooted display types";
- static final String SCREEN_ANTIALIAS_LABEL = "Antialias";
- static final String COLOR_LABELS_LABEL = "Colorize Labels Same as Parent Branch";
- static final String BG_GRAD_LABEL = "Background Color Gradient";
- static final String DISPLAY_NODE_BOXES_LABEL = "Show Node Shapes";
- static final String SHOW_OVERVIEW_LABEL = "Show Overview";
- static final String FONT_SIZE_MENU_LABEL = "Font Size";
- static final String NONUNIFORM_CLADOGRAMS_LABEL = "External Node Sum Dependent Cladograms";
- static final String SHOW_DOMAIN_LABELS_LABEL = "Show Domain Labels";
- static final String COLOR_LABELS_TIP = "To use parent branch colors for node labels as well, need to turn off taxonomy dependent colorization and turn on branch colorization for this to become apparent";
- static final String ABBREV_SN_LABEL = "Abbreviate Scientific Taxonomic Names";
- static final String TAXONOMY_COLORIZE_NODE_SHAPES_LABEL = "Colorize Node Shapes According to Taxonomy";
- static final String CYCLE_NODE_SHAPE_LABEL = "Cycle Node Shapes";
- static final String CYCLE_NODE_FILL_LABEL = "Cycle Node Fill Type";
- static final String CHOOSE_NODE_SIZE_LABEL = "Choose Node Shape Size";
- static final String SHOW_CONF_STDDEV_LABEL = "Show Confidence Standard Deviations";
- static final String USE_BRACKETS_FOR_CONF_IN_NH_LABEL = "Use Brackets for Confidence Values";
- static final String USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL = "Use Internal Node Names for Confidence Values";
- JMenuBar _jmenubar;
- JMenu _file_jmenu;
- JMenu _tools_menu;
- JMenu _view_jmenu;
- JMenu _options_jmenu;
- JMenu _font_size_menu;
- JMenu _help_jmenu;
- JMenuItem[] _load_phylogeny_from_webservice_menu_items;
- // file menu:
- JMenuItem _open_item;
- JMenuItem _open_url_item;
- JMenuItem _save_item;
- JMenuItem _save_all_item;
- JMenuItem _close_item;
- JMenuItem _exit_item;
- JMenuItem _new_item;
- // tools menu:
- JMenuItem _midpoint_root_item;
- JMenuItem _taxcolor_item;
- JMenuItem _confcolor_item;
- JMenuItem _color_rank_jmi;
- JMenuItem _infer_common_sn_names_item;
- JMenuItem _collapse_species_specific_subtrees;
- JMenuItem _collapse_below_threshold; //TODO implememt me
- JMenuItem _obtain_detailed_taxonomic_information_jmi;
- JMenuItem _obtain_detailed_taxonomic_information_deleting_jmi;
- JMenuItem _obtain_uniprot_seq_information_jmi;
- JMenuItem _move_node_names_to_tax_sn_jmi;
- JMenuItem _move_node_names_to_seq_names_jmi;
- JMenuItem _extract_tax_code_from_node_names_jmi;
- // font size menu:
- JMenuItem _super_tiny_fonts_item;
- JMenuItem _tiny_fonts_item;
- JMenuItem _small_fonts_item;
- JMenuItem _medium_fonts_item;
- JMenuItem _large_fonts_item;
- // options menu:
- // _ screen and print
- JMenuItem _choose_font_mi;
- JMenuItem _switch_colors_mi;
- JCheckBoxMenuItem _label_direction_cbmi;
- // _ screen display
- JCheckBoxMenuItem _screen_antialias_cbmi;
- JCheckBoxMenuItem _background_gradient_cbmi;
- JRadioButtonMenuItem _non_lined_up_cladograms_rbmi;
- JRadioButtonMenuItem _uniform_cladograms_rbmi;
- JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi;
- JCheckBoxMenuItem _show_branch_length_values_cbmi;
- JCheckBoxMenuItem _show_scale_cbmi; //TODO fix me
- JCheckBoxMenuItem _show_overview_cbmi;
- JCheckBoxMenuItem _show_domain_labels;
- JCheckBoxMenuItem _abbreviate_scientific_names;
- JCheckBoxMenuItem _color_labels_same_as_parent_branch;
- JMenuItem _overview_placment_mi;
- JMenuItem _choose_minimal_confidence_mi;
- JCheckBoxMenuItem _show_default_node_shapes_cbmi;
- JMenuItem _cycle_node_shape_mi;
- JMenuItem _cycle_node_fill_mi;
- JMenuItem _choose_node_size_mi;
- JCheckBoxMenuItem _taxonomy_colorize_node_shapes_cbmi;
- JCheckBoxMenuItem _show_confidence_stddev_cbmi;
- // _ print
- JCheckBoxMenuItem _graphics_export_visible_only_cbmi;
- JCheckBoxMenuItem _antialias_print_cbmi;
- JCheckBoxMenuItem _print_black_and_white_cbmi;
- JCheckBoxMenuItem _print_using_actual_size_cbmi;
- JCheckBoxMenuItem _graphics_export_using_actual_size_cbmi;
- JMenuItem _print_size_mi;
- JMenuItem _choose_pdf_width_mi;
- // _ parsing
- JCheckBoxMenuItem _internal_number_are_confidence_for_nh_parsing_cbmi;
- JCheckBoxMenuItem _extract_pfam_style_tax_codes_cbmi;
- JCheckBoxMenuItem _replace_underscores_cbmi;
- JCheckBoxMenuItem _use_brackets_for_conf_in_nh_export_cbmi;
- JCheckBoxMenuItem _use_internal_names_for_conf_in_nh_export_cbmi;
- // _ search
- JCheckBoxMenuItem _search_case_senstive_cbmi;
- JCheckBoxMenuItem _search_whole_words_only_cbmi;
- JCheckBoxMenuItem _inverse_search_result_cbmi;
- // type menu:
- JMenu _type_menu;
- JCheckBoxMenuItem _rectangular_type_cbmi;
- JCheckBoxMenuItem _triangular_type_cbmi;
- JCheckBoxMenuItem _curved_type_cbmi;
- JCheckBoxMenuItem _convex_type_cbmi;
- JCheckBoxMenuItem _euro_type_cbmi;
- JCheckBoxMenuItem _rounded_type_cbmi;
- JCheckBoxMenuItem _unrooted_type_cbmi;
- JCheckBoxMenuItem _circular_type_cbmi;
- // view as text menu:
- JMenuItem _view_as_NH_item;
- JMenuItem _view_as_NHX_item;
- JMenuItem _view_as_XML_item;
- JMenuItem _view_as_nexus_item;
- JMenuItem _display_basic_information_item;
- // help menu:
- JMenuItem _about_item;
- JMenuItem _help_item;
- JMenuItem _website_item;
- JMenuItem _phyloxml_website_item;
- JMenuItem _phyloxml_ref_item;
- JMenuItem _aptx_ref_item;
- // process menu:
- JMenu _process_menu;
- // Handy pointers to child components:
- MainPanel _mainpanel;
- Container _contentpane;
- TextFrame _textframe;
- Configuration _configuration;
- JMenuItem _remove_branch_color_item;
- Options _options;
- InferenceManager _inference_manager;
- final ProcessPool _process_pool;
-
- MainFrame() {
- _process_pool = ProcessPool.createInstance();
- }
-
- public ProcessPool getProcessPool() {
- return _process_pool;
- }
-
- /**
- * Action performed.
- */
- public void actionPerformed( final ActionEvent e ) {
- final Object o = e.getSource();
- boolean is_applet = false;
- JApplet applet = null;
- if ( getCurrentTreePanel() != null ) {
- is_applet = getCurrentTreePanel().isApplet();
- if ( is_applet ) {
- applet = getCurrentTreePanel().obtainApplet();
- }
- }
- if ( o == _open_url_item ) {
- readPhylogeniesFromURL();
- }
- else if ( o == _exit_item ) {
- close();
- }
- else if ( o == _taxcolor_item ) {
- taxColor();
- }
- else if ( o == _confcolor_item ) {
- confColor();
- }
- else if ( o == _color_rank_jmi ) {
- colorRank();
- }
- else if ( o == _infer_common_sn_names_item ) {
- if ( isSubtreeDisplayed() ) {
- return;
- }
- if ( getCurrentTreePanel() != null ) {
- getCurrentTreePanel().inferCommonPartOfScientificNames();
- }
- }
- else if ( o == _collapse_species_specific_subtrees ) {
- if ( isSubtreeDisplayed() ) {
- return;
- }
- if ( getCurrentTreePanel() != null ) {
- getCurrentTreePanel().collapseSpeciesSpecificSubtrees();
- }
- }
- else if ( o == _remove_branch_color_item ) {
- if ( isSubtreeDisplayed() ) {
- return;
- }
- removeBranchColors();
- }
- else if ( o == _midpoint_root_item ) {
- if ( isSubtreeDisplayed() ) {
- return;
- }
- midpointRoot();
- }
- else if ( o == _switch_colors_mi ) {
- switchColors();
- }
- else if ( o == _display_basic_information_item ) {
- displayBasicInformation();
- }
- else if ( o == _view_as_NH_item ) {
- viewAsNH();
- }
- else if ( o == _view_as_NHX_item ) {
- viewAsNHX();
- }
- else if ( o == _view_as_XML_item ) {
- viewAsXML();
- }
- else if ( o == _view_as_nexus_item ) {
- viewAsNexus();
- }
- else if ( o == _super_tiny_fonts_item ) {
- if ( getCurrentTreePanel() != null ) {
- getCurrentTreePanel().setSuperTinyFonts();
- getCurrentTreePanel().repaint();
- }
- }
- else if ( o == _tiny_fonts_item ) {
- if ( getCurrentTreePanel() != null ) {
- getCurrentTreePanel().setTinyFonts();
- getCurrentTreePanel().repaint();
- }
- }
- else if ( o == _small_fonts_item ) {
- if ( getCurrentTreePanel() != null ) {
- getCurrentTreePanel().setSmallFonts();
- getCurrentTreePanel().repaint();
- }
- }
- else if ( o == _medium_fonts_item ) {
- if ( getCurrentTreePanel() != null ) {
- getCurrentTreePanel().setMediumFonts();
- getCurrentTreePanel().repaint();
- }
- }
- else if ( o == _large_fonts_item ) {
- if ( getCurrentTreePanel() != null ) {
- getCurrentTreePanel().setLargeFonts();
- getCurrentTreePanel().repaint();
- }
- }
- else if ( o == _choose_font_mi ) {
- chooseFont();
- }
- else if ( o == _choose_minimal_confidence_mi ) {
- chooseMinimalConfidence();
- }
- else if ( o == _choose_node_size_mi ) {
- chooseNodeSize( getOptions(), this );
- }
- else if ( o == _overview_placment_mi ) {
- MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );
- }
- else if ( o == _cycle_node_fill_mi ) {
- MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() );
- }
- else if ( o == _cycle_node_shape_mi ) {
- MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() );
- }
- else if ( o == _screen_antialias_cbmi ) {
- updateOptions( getOptions() );
- updateScreenTextAntialias( getMainPanel().getTreePanels() );
- }
- else if ( o == _background_gradient_cbmi ) {
- updateOptions( getOptions() );
- }
- else if ( o == _show_domain_labels ) {
- updateOptions( getOptions() );
- }
- else if ( o == _abbreviate_scientific_names ) {
- updateOptions( getOptions() );
- }
- else if ( o == _color_labels_same_as_parent_branch ) {
- updateOptions( getOptions() );
- }
- else if ( o == _show_default_node_shapes_cbmi ) {
- updateOptions( getOptions() );
- }
- else if ( o == _taxonomy_colorize_node_shapes_cbmi ) {
- updateOptions( getOptions() );
- }
- else if ( o == _non_lined_up_cladograms_rbmi ) {
- updateOptions( getOptions() );
- showWhole();
- }
- else if ( o == _uniform_cladograms_rbmi ) {
- updateOptions( getOptions() );
- showWhole();
- }
- else if ( o == _ext_node_dependent_cladogram_rbmi ) {
- updateOptions( getOptions() );
- showWhole();
- }
- else if ( o == _search_case_senstive_cbmi ) {
- updateOptions( getOptions() );
- getMainPanel().getControlPanel().search();
- }
- else if ( o == _search_whole_words_only_cbmi ) {
- updateOptions( getOptions() );
- getMainPanel().getControlPanel().search();
- }
- else if ( o == _inverse_search_result_cbmi ) {
- updateOptions( getOptions() );
- getMainPanel().getControlPanel().search();
- }
- else if ( o == _show_scale_cbmi ) {
- updateOptions( getOptions() );
- }
- else if ( o == _show_branch_length_values_cbmi ) {
- updateOptions( getOptions() );
- }
- else if ( o == _show_confidence_stddev_cbmi ) {
- updateOptions( getOptions() );
- }
- else if ( o == _use_brackets_for_conf_in_nh_export_cbmi ) {
- if ( _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {
- _use_internal_names_for_conf_in_nh_export_cbmi.setSelected( false );
- }
- updateOptions( getOptions() );
- }
- else if ( o == _use_internal_names_for_conf_in_nh_export_cbmi ) {
- if ( _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {
- _use_brackets_for_conf_in_nh_export_cbmi.setSelected( false );
- }
- updateOptions( getOptions() );
- }
- else if ( o == _label_direction_cbmi ) {
- updateOptions( getOptions() );
- }
- else if ( o == _show_overview_cbmi ) {
- updateOptions( getOptions() );
- if ( getCurrentTreePanel() != null ) {
- getCurrentTreePanel().updateOvSizes();
- }
- }
- else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )
- || ( o == _convex_type_cbmi ) || ( o == _euro_type_cbmi ) || ( o == _rounded_type_cbmi )
- || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {
- typeChanged( o );
- }
- else if ( o == _about_item ) {
- about();
- }
- else if ( o == _help_item ) {
- help( getConfiguration().getWebLinks() );
- }
- else if ( o == _website_item ) {
- try {
- AptxUtil.openWebsite( Constants.APTX_WEB_SITE, is_applet, applet );
- }
- catch ( final IOException e1 ) {
- ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
- }
- }
- else if ( o == _phyloxml_website_item ) {
- try {
- AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, is_applet, applet );
- }
- catch ( final IOException e1 ) {
- ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
- }
- }
- else if ( o == _aptx_ref_item ) {
- try {
- AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, is_applet, applet );
- }
- catch ( final IOException e1 ) {
- ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
- }
- }
- else if ( o == _phyloxml_ref_item ) {
- try {
- AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, is_applet, applet );
- }
- catch ( final IOException e1 ) {
- ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
- }
- }
- else {
- if ( _load_phylogeny_from_webservice_menu_items != null ) {
- for( int i = 0; i < _load_phylogeny_from_webservice_menu_items.length; ++i ) {
- if ( o == _load_phylogeny_from_webservice_menu_items[ i ] ) {
- readPhylogeniesFromWebservice( i );
- }
- }
- }
- }
- _contentpane.repaint();
- }
-
- boolean isSubtreeDisplayed() {
- if ( getCurrentTreePanel() != null ) {
- if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {
- JOptionPane
- .showMessageDialog( this,
- "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",
- "Operation can not be exectuted on a sub-tree",
- JOptionPane.WARNING_MESSAGE );
- return true;
- }
- }
- return false;
- }
-
- void activateSaveAllIfNeeded() {
- if ( ( getMainPanel().getTabbedPane() != null ) && ( getMainPanel().getTabbedPane().getTabCount() > 1 ) ) {
- _save_all_item.setEnabled( true );
- }
- else {
- _save_all_item.setEnabled( false );
- }
- }
-
- void buildFileMenu() {
- _file_jmenu = createMenu( "File", getConfiguration() );
- _file_jmenu.add( _open_url_item = new JMenuItem( "Read tree from URL/webservice..." ) );
- _file_jmenu.addSeparator();
- _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );
- customizeJMenuItem( _open_url_item );
- customizeJMenuItem( _exit_item );
- _jmenubar.add( _file_jmenu );
- }
-
- void buildFontSizeMenu() {
- _font_size_menu = createMenu( FONT_SIZE_MENU_LABEL, getConfiguration() );
- _font_size_menu.add( _super_tiny_fonts_item = new JMenuItem( "Super Tiny Fonts" ) );
- _font_size_menu.add( _tiny_fonts_item = new JMenuItem( "Tiny Fonts" ) );
- _font_size_menu.add( _small_fonts_item = new JMenuItem( "Small Fonts" ) );
- _font_size_menu.add( _medium_fonts_item = new JMenuItem( "Medium Fonts" ) );
- _font_size_menu.add( _large_fonts_item = new JMenuItem( "Large Fonts" ) );
- customizeJMenuItem( _super_tiny_fonts_item );
- customizeJMenuItem( _tiny_fonts_item );
- customizeJMenuItem( _small_fonts_item );
- customizeJMenuItem( _medium_fonts_item );
- customizeJMenuItem( _large_fonts_item );
- _jmenubar.add( _font_size_menu );
- }
-
- void buildHelpMenu() {
- _help_jmenu = createMenu( "Help", getConfiguration() );
- _help_jmenu.add( _help_item = new JMenuItem( "Help" ) );
- _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );
- _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" );
- _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );
- _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );
- _help_jmenu.addSeparator();
- _help_jmenu.add( _about_item = new JMenuItem( "About" ) );
- customizeJMenuItem( _help_item );
- customizeJMenuItem( _website_item );
- customizeJMenuItem( _phyloxml_website_item );
- customizeJMenuItem( _aptx_ref_item );
- customizeJMenuItem( _phyloxml_ref_item );
- customizeJMenuItem( _about_item );
- _phyloxml_ref_item.setToolTipText( PHYLOXML_REF_TOOL_TIP );
- _aptx_ref_item.setToolTipText( APTX_REF_TOOL_TIP );
- _jmenubar.add( _help_jmenu );
- }
-
- public void updateProcessMenu() {
- // In general Swing is not thread safe.
- // See "Swing's Threading Policy".
- SwingUtilities.invokeLater( new Runnable() {
-
- public void run() {
- doUpdateProcessMenu();
- }
- } );
- }
-
- private void doUpdateProcessMenu() {
- if ( _process_pool.size() > 0 ) {
- if ( _process_menu == null ) {
- _process_menu = createMenu( "", getConfiguration() );
- _process_menu.setForeground( Color.RED );
- }
- _process_menu.removeAll();
- final String text = "processes running: " + _process_pool.size();
- _process_menu.setText( text );
- _jmenubar.add( _process_menu );
- for( int i = 0; i < _process_pool.size(); ++i ) {
- final ProcessRunning p = _process_pool.getProcessByIndex( i );
- _process_menu.add( customizeJMenuItem( new JMenuItem( p.getName() + " [" + p.getStart() + "]" ) ) );
- }
- }
- else {
- if ( _process_menu != null ) {
- _process_menu.removeAll();
- _jmenubar.remove( _process_menu );
- }
- }
- _jmenubar.validate();
- _jmenubar.repaint();
- repaint();
- }
-
- void buildTypeMenu() {
- _type_menu = createMenu( TYPE_MENU_HEADER, getConfiguration() );
- _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );
- _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );
- _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );
- _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );
- _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );
- _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );
- _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );
- _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );
- customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );
- customizeCheckBoxMenuItem( _triangular_type_cbmi, false );
- customizeCheckBoxMenuItem( _euro_type_cbmi, false );
- customizeCheckBoxMenuItem( _rounded_type_cbmi, false );
- customizeCheckBoxMenuItem( _curved_type_cbmi, false );
- customizeCheckBoxMenuItem( _convex_type_cbmi, false );
- customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );
- customizeCheckBoxMenuItem( _circular_type_cbmi, false );
- _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
- _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
- initializeTypeMenu( getOptions() );
- _jmenubar.add( _type_menu );
- }
-
- void buildViewMenu() {
- _view_jmenu = createMenu( "View", getConfiguration() );
- _view_jmenu.add( _display_basic_information_item = new JMenuItem( "Display Basic Information" ) );
- _view_jmenu.addSeparator();
- _view_jmenu.add( _view_as_XML_item = new JMenuItem( "View as phyloXML" ) );
- _view_jmenu.add( _view_as_NH_item = new JMenuItem( "View as Newick" ) );
- _view_jmenu.add( _view_as_NHX_item = new JMenuItem( "View as NHX" ) );
- _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "View as Nexus" ) );
- customizeJMenuItem( _display_basic_information_item );
- customizeJMenuItem( _view_as_NH_item );
- customizeJMenuItem( _view_as_NHX_item );
- customizeJMenuItem( _view_as_XML_item );
- customizeJMenuItem( _view_as_nexus_item );
- _jmenubar.add( _view_jmenu );
- }
-
- private void chooseFont() {
- final FontChooser fc = new FontChooser();
- fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
- fc.showDialog( this, "Select the Base Font" );
- getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );
- }
-
- private void chooseMinimalConfidence() {
- final String s = ( String ) JOptionPane
- .showInputDialog( this,
- "Please enter the minimum for confidence values to be displayed.\n"
- + "[current value: " + getOptions().getMinConfidenceValue() + "]\n",
- "Minimal Confidence Value",
- JOptionPane.QUESTION_MESSAGE,
- null,
- null,
- getOptions().getMinConfidenceValue() );
- if ( !ForesterUtil.isEmpty( s ) ) {
- boolean success = true;
- double m = 0.0;
- final String m_str = s.trim();
- if ( !ForesterUtil.isEmpty( m_str ) ) {
- try {
- m = Double.parseDouble( m_str );
- }
- catch ( final Exception ex ) {
- success = false;
- }
- }
- else {
- success = false;
- }
- if ( success && ( m >= 0.0 ) ) {
- getOptions().setMinConfidenceValue( m );
- }
- }
- }
-
- static void chooseNodeSize( final Options options, final Component parent ) {
- final String s = ( String ) JOptionPane.showInputDialog( parent,
- "Please enter the default size for node shapes.\n"
- + "[current value: "
- + options.getDefaultNodeShapeSize() + "]\n",
- "Node Shape Size",
- JOptionPane.QUESTION_MESSAGE,
- null,
- null,
- options.getDefaultNodeShapeSize() );
- if ( !ForesterUtil.isEmpty( s ) ) {
- boolean success = true;
- double m = 0.0;
- final String m_str = s.trim();
- if ( !ForesterUtil.isEmpty( m_str ) ) {
- try {
- m = Double.parseDouble( m_str );
- }
- catch ( final Exception ex ) {
- success = false;
- }
- }
- else {
- success = false;
- }
- if ( success && ( m >= 0.0 ) ) {
- final short size = ForesterUtil.roundToShort( m );
- if ( size >= 0.0 ) {
- options.setDefaultNodeShapeSize( size );
- }
- }
- }
- }
-
- void close() {
- removeTextFrame();
- if ( _mainpanel != null ) {
- _mainpanel.terminate();
- }
- if ( _contentpane != null ) {
- _contentpane.removeAll();
- }
- setVisible( false );
- dispose();
- }
-
- void confColor() {
- if ( _mainpanel.getCurrentTreePanel() != null ) {
- _mainpanel.getCurrentTreePanel().confColor();
- }
- }
-
- void colorRank() {
- if ( _mainpanel.getCurrentTreePanel() != null ) {
- final String[] ranks = AptxUtil.getAllPossibleRanks();
- final String rank = ( String ) JOptionPane
- .showInputDialog( this,
- "What rank should the colorization be based on",
- "Rank Selection",
- JOptionPane.QUESTION_MESSAGE,
- null,
- ranks,
- null );
- if ( !ForesterUtil.isEmpty( rank ) ) {
- _mainpanel.getCurrentTreePanel().colorRank( rank );
- }
- }
- }
-
- void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {
- if ( item != null ) {
- item.setFont( MainFrame.menu_font );
- if ( !getConfiguration().isUseNativeUI() ) {
- item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
- item.setForeground( getConfiguration().getGuiMenuTextColor() );
- }
- item.setSelected( is_selected );
- item.addActionListener( this );
- }
- }
-
- JMenuItem customizeJMenuItem( final JMenuItem jmi ) {
- if ( jmi != null ) {
- jmi.setFont( MainFrame.menu_font );
- if ( !getConfiguration().isUseNativeUI() ) {
- jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
- jmi.setForeground( getConfiguration().getGuiMenuTextColor() );
- }
- jmi.addActionListener( this );
- }
- return jmi;
- }
-
- void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {
- if ( item != null ) {
- item.setFont( MainFrame.menu_font );
- if ( !getConfiguration().isUseNativeUI() ) {
- item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
- item.setForeground( getConfiguration().getGuiMenuTextColor() );
- }
- item.setSelected( is_selected );
- item.addActionListener( this );
- }
- }
-
- void exceptionOccuredDuringOpenFile( final Exception e ) {
- try {
- _mainpanel.getCurrentTreePanel().setArrowCursor();
- }
- catch ( final Exception ex ) {
- // Do nothing.
- }
- JOptionPane.showMessageDialog( this,
- ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
- "Error during File|Open",
- JOptionPane.ERROR_MESSAGE );
- }
-
- void exceptionOccuredDuringSaveAs( final Exception e ) {
- try {
- _mainpanel.getCurrentTreePanel().setArrowCursor();
- }
- catch ( final Exception ex ) {
- // Do nothing.
- }
- JOptionPane.showMessageDialog( this, "Exception" + e, "Error during File|SaveAs", JOptionPane.ERROR_MESSAGE );
- }
-
- boolean GAndSDoHaveMoreThanOneSpeciesInComman( final Phylogeny gene_tree ) {
- if ( ( gene_tree == null ) || gene_tree.isEmpty() ) {
- JOptionPane.showMessageDialog( this,
- "Gene tree and species tree have no species in common.",
- "Error during SDI",
- JOptionPane.ERROR_MESSAGE );
- return false;
- }
- else if ( gene_tree.getNumberOfExternalNodes() < 2 ) {
- JOptionPane.showMessageDialog( this,
- "Gene tree and species tree have only one species in common.",
- "Error during SDI",
- JOptionPane.ERROR_MESSAGE );
- return false;
- }
- else {
- return true;
- }
- }
-
- public Configuration getConfiguration() {
- return _configuration;
- }
-
- TreePanel getCurrentTreePanel() {
- return getMainPanel().getCurrentTreePanel();
- }
-
- JMenu getHelpMenu() {
- return _help_jmenu;
- }
-
- JCheckBoxMenuItem getlabelDirectionCbmi() {
- return _label_direction_cbmi;
- }
-
- public MainPanel getMainPanel() {
- return _mainpanel;
- }
-
- JMenuBar getMenuBarOfMainFrame() {
- return _jmenubar;
- }
-
- public Options getOptions() {
- return _options;
- }
-
- void initializeTypeMenu( final Options options ) {
- setTypeMenuToAllUnselected();
- switch ( options.getPhylogenyGraphicsType() ) {
- case CONVEX:
- _convex_type_cbmi.setSelected( true );
- break;
- case CURVED:
- _curved_type_cbmi.setSelected( true );
- break;
- case EURO_STYLE:
- _euro_type_cbmi.setSelected( true );
- break;
- case ROUNDED:
- _rounded_type_cbmi.setSelected( true );
- break;
- case TRIANGULAR:
- _triangular_type_cbmi.setSelected( true );
- break;
- case UNROOTED:
- _unrooted_type_cbmi.setSelected( true );
- break;
- case CIRCULAR:
- _circular_type_cbmi.setSelected( true );
- break;
- default:
- _rectangular_type_cbmi.setSelected( true );
- break;
- }
- }
-
- void midpointRoot() {
- if ( _mainpanel.getCurrentTreePanel() != null ) {
- _mainpanel.getCurrentTreePanel().midpointRoot();
- }
- }
-
- abstract void readPhylogeniesFromURL();
-
- void readPhylogeniesFromWebservice( final int i ) {
- final UrlTreeReader reader = new UrlTreeReader( this, i );
- new Thread( reader ).start();
- }
-
- private void removeBranchColors() {
- if ( getMainPanel().getCurrentPhylogeny() != null ) {
- AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
- }
- }
-
- void removeTextFrame() {
- if ( _textframe != null ) {
- _textframe.close();
- _textframe = null;
- }
- }
-
- void setConfiguration( final Configuration configuration ) {
- _configuration = configuration;
- }
-
- void setOptions( final Options options ) {
- _options = options;
- }
-
- void setInferenceManager( final InferenceManager i ) {
- _inference_manager = i;
- }
-
- InferenceManager getInferenceManager() {
- return _inference_manager;
- }
-
-
- void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {
- setTypeMenuToAllUnselected();
- switch ( type ) {
- case CIRCULAR:
- _circular_type_cbmi.setSelected( true );
- break;
- case CONVEX:
- _convex_type_cbmi.setSelected( true );
- break;
- case CURVED:
- _curved_type_cbmi.setSelected( true );
- break;
- case EURO_STYLE:
- _euro_type_cbmi.setSelected( true );
- break;
- case ROUNDED:
- _rounded_type_cbmi.setSelected( true );
- break;
- case RECTANGULAR:
- _rectangular_type_cbmi.setSelected( true );
- break;
- case TRIANGULAR:
- _triangular_type_cbmi.setSelected( true );
- break;
- case UNROOTED:
- _unrooted_type_cbmi.setSelected( true );
- break;
- default:
- throw new IllegalArgumentException( "unknown type: " + type );
- }
- }
-
- void setTypeMenuToAllUnselected() {
- _convex_type_cbmi.setSelected( false );
- _curved_type_cbmi.setSelected( false );
- _euro_type_cbmi.setSelected( false );
- _rounded_type_cbmi.setSelected( false );
- _triangular_type_cbmi.setSelected( false );
- _rectangular_type_cbmi.setSelected( false );
- _unrooted_type_cbmi.setSelected( false );
- _circular_type_cbmi.setSelected( false );
- }
-
- public void showWhole() {
- _mainpanel.getControlPanel().showWhole();
- }
-
- void switchColors() {
- final TreeColorSet colorset = _mainpanel.getTreeColorSet();
- final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );
- csc.setVisible( true );
- }
-
- void taxColor() {
- if ( _mainpanel.getCurrentTreePanel() != null ) {
- _mainpanel.getCurrentTreePanel().taxColor();
- }
- }
-
- void typeChanged( final Object o ) {
- updateTypeCheckboxes( getOptions(), o );
- updateOptions( getOptions() );
- if ( getCurrentTreePanel() != null ) {
- final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();
- final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();
- if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
- || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )
- || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
- || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {
- getCurrentTreePanel().getControlPanel().showWhole();
- }
- if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
- getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );
- }
- else {
- getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );
- }
- getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );
- updateScreenTextAntialias( getMainPanel().getTreePanels() );
- if ( getCurrentTreePanel().getControlPanel().getDynamicallyHideData() != null ) {
- if ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
- getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( false );
- }
- else {
- getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( true );
- }
- }
- }
- }
-
- void updateOptions( final Options options ) {
- options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );
- options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
- && _background_gradient_cbmi.isSelected() );
- options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
- options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
- && _abbreviate_scientific_names.isSelected() );
- options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
- && _color_labels_same_as_parent_branch.isSelected() );
- options.setShowDefaultNodeShapes( ( _show_default_node_shapes_cbmi != null )
- && _show_default_node_shapes_cbmi.isSelected() );
- options.setTaxonomyColorizeNodeShapes( ( _taxonomy_colorize_node_shapes_cbmi != null )
- && _taxonomy_colorize_node_shapes_cbmi.isSelected() );
- if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
- options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
- }
- else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {
- options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
- }
- else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {
- options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
- }
- options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )
- && _search_case_senstive_cbmi.isSelected() );
- if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {
- options.setShowScale( _show_scale_cbmi.isSelected() );
- }
- if ( _label_direction_cbmi != null ) {
- if ( _label_direction_cbmi.isSelected() ) {
- options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
- }
- else {
- options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
- }
- }
- options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
- options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )
- && _show_confidence_stddev_cbmi.isSelected() );
- if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) {
- options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() );
- }
- options.setPrintUsingActualSize( ( _print_using_actual_size_cbmi != null )
- && ( _print_using_actual_size_cbmi.isSelected() ) );
- options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null )
- && ( _graphics_export_using_actual_size_cbmi.isSelected() ) );
- options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() );
- if ( ( _use_brackets_for_conf_in_nh_export_cbmi != null )
- && _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {
- options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );
- }
- else if ( ( _use_internal_names_for_conf_in_nh_export_cbmi != null )
- && _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {
- options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );
- }
- else {
- options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );
- }
- options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null )
- && _print_black_and_white_cbmi.isSelected() );
- options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null )
- && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );
- options.setExtractPfamTaxonomyCodesInNhParsing( ( _extract_pfam_style_tax_codes_cbmi != null )
- && _extract_pfam_style_tax_codes_cbmi.isSelected() );
- options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )
- && _replace_underscores_cbmi.isSelected() );
- options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
- && _search_whole_words_only_cbmi.isSelected() );
- options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
- && _inverse_search_result_cbmi.isSelected() );
- if ( _graphics_export_visible_only_cbmi != null ) {
- options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_cbmi.isSelected() );
- if ( _graphics_export_visible_only_cbmi.isSelected() && ( _graphics_export_using_actual_size_cbmi != null ) ) {
- _graphics_export_using_actual_size_cbmi.setSelected( true );
- _graphics_export_using_actual_size_cbmi.setEnabled( false );
- }
- else {
- _graphics_export_using_actual_size_cbmi.setEnabled( true );
- }
- }
- if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {
- options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
- }
- else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {
- options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
- }
- else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {
- options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
- }
- else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {
- options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
- }
- else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {
- options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
- }
- else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {
- options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
- }
- else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {
- options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
- }
- else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {
- options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
- }
- }
-
- void updateTypeCheckboxes( final Options options, final Object o ) {
- setTypeMenuToAllUnselected();
- ( ( JCheckBoxMenuItem ) o ).setSelected( true );
- }
-
- void displayBasicInformation() {
- if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {
- return;
- }
- _textframe = TextFrame.instantiate( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny() ) );
- }
-
- void viewAsNexus() {
- removeTextFrame();
- if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty()
- || ( _mainpanel.getCurrentPhylogeny().getNumberOfExternalNodes() > 20000 ) ) {
- return;
- }
- _textframe = TextFrame.instantiate( _mainpanel.getCurrentPhylogeny().toNexus( getOptions()
- .getNhConversionSupportValueStyle() ) );
- }
-
- void viewAsNH() {
- removeTextFrame();
- if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty()
- || ( _mainpanel.getCurrentPhylogeny().getNumberOfExternalNodes() > 20000 ) ) {
- return;
- }
- _textframe = TextFrame.instantiate( _mainpanel.getCurrentPhylogeny()
- .toNewHampshire( false, getOptions().getNhConversionSupportValueStyle() ) );
- }
-
- void viewAsNHX() {
- removeTextFrame();
- if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty()
- || ( _mainpanel.getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
- return;
- }
- _textframe = TextFrame.instantiate( _mainpanel.getCurrentPhylogeny().toNewHampshireX() );
- }
-
- void viewAsXML() {
- removeTextFrame();
- if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty()
- && ( _mainpanel.getCurrentPhylogeny().getNumberOfExternalNodes() <= 10000 ) ) {
- _textframe = TextFrame.instantiate( _mainpanel.getCurrentPhylogeny().toPhyloXML( 0 ) );
- }
- }
-
- /**
- * Display the about box.
- */
- static void about() {
- final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + Constants.VERSION + "\n" );
- about.append( "Copyright (C) 2007-2012 Christian M. Zmasek\n" );
- about.append( "All Rights Reserved\n" );
- about.append( "License: GNU Lesser General Public License (LGPL)\n" );
- about.append( "Last modified: " + Constants.PRG_DATE + "\n" );
- about.append( "Based on: " + ForesterUtil.getForesterLibraryInformation() + "\n" );
- about.append( "phyloXML version : " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
- about.append( "phyloXML location: " + ForesterConstants.PHYLO_XML_LOCATION + "\n" );
- if ( !ForesterUtil.isEmpty( ForesterUtil.JAVA_VERSION ) && !ForesterUtil.isEmpty( ForesterUtil.JAVA_VENDOR ) ) {
- about.append( "[your Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]\n" );
- }
- if ( !ForesterUtil.isEmpty( ForesterUtil.OS_NAME ) && !ForesterUtil.isEmpty( ForesterUtil.OS_ARCH )
- && !ForesterUtil.isEmpty( ForesterUtil.OS_VERSION ) ) {
- about.append( "[your OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " "
- + ForesterUtil.OS_VERSION + "]\n" );
- }
- final Runtime rt = java.lang.Runtime.getRuntime();
- final long free_memory = rt.freeMemory() / 1000000;
- final long total_memory = rt.totalMemory() / 1000000;
- about.append( "[free memory: " + free_memory + "MB, total memory: " + total_memory + "MB]\n" );
- about.append( "[locale: " + Locale.getDefault() + "]\n" );
- about.append( "References:\n" );
- about.append( Constants.PHYLOXML_REFERENCE_SHORT + "\n" );
- about.append( "For more information & download:\n" );
- about.append( Constants.APTX_WEB_SITE + "\n" );
- about.append( "Comments: " + Constants.AUTHOR_EMAIL );
- JOptionPane.showMessageDialog( null, about, Constants.PRG_NAME, JOptionPane.PLAIN_MESSAGE );
- }
-
- static String createCurrentFontDesc( final TreeFontSet tree_font_set ) {
- return tree_font_set.getLargeFont().getFamily() + " " + tree_font_set.getLargeFont().getSize();
- }
-
- static JMenu createMenu( final String title, final Configuration conf ) {
- final JMenu jmenu = new JMenu( title );
- if ( !conf.isUseNativeUI() ) {
- jmenu.setFont( MainFrame.menu_font );
- jmenu.setBackground( conf.getGuiMenuBackgroundColor() );
- jmenu.setForeground( conf.getGuiMenuTextColor() );
- }
- return jmenu;
- }
-
- static JMenuItem customizeMenuItemAsLabel( final JMenuItem label, final Configuration configuration ) {
- label.setFont( MainFrame.menu_font.deriveFont( Font.BOLD ) );
- if ( !configuration.isUseNativeUI() ) {
- label.setBackground( configuration.getGuiMenuBackgroundColor() );
- label.setForeground( configuration.getGuiMenuTextColor() );
- label.setOpaque( true );
- }
- label.setSelected( false );
- label.setEnabled( false );
- return label;
- }
-
- static void cycleOverview( final Options op, final TreePanel tree_panel ) {
- switch ( op.getOvPlacement() ) {
- case LOWER_LEFT:
- op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
- break;
- case LOWER_RIGHT:
- op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );
- break;
- case UPPER_LEFT:
- op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );
- break;
- case UPPER_RIGHT:
- op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );
- break;
- default:
- throw new RuntimeException( "unknown placement: " + op.getOvPlacement() );
- }
- if ( tree_panel != null ) {
- tree_panel.updateOvSettings();
- }
- }
-
- static void cycleNodeFill( final Options op, final TreePanel tree_panel ) {
- switch ( op.getDefaultNodeFill() ) {
- case GRADIENT:
- op.setDefaultNodeFill( NodeFill.SOLID );
- break;
- case NONE:
- op.setDefaultNodeFill( NodeFill.GRADIENT );
- break;
- case SOLID:
- op.setDefaultNodeFill( NodeFill.NONE );
- break;
- default:
- throw new RuntimeException( "unknown fill: " + op.getDefaultNodeFill() );
- }
- }
-
- static void cycleNodeShape( final Options op, final TreePanel tree_panel ) {
- switch ( op.getDefaultNodeShape() ) {
- case CIRCLE:
- op.setDefaultNodeShape( NodeShape.RECTANGLE );
- break;
- case RECTANGLE:
- op.setDefaultNodeShape( NodeShape.CIRCLE );
- break;
- default:
- throw new RuntimeException( "unknown shape: " + op.getDefaultNodeShape() );
- }
- }
-
- static void help( final Map<String, WebLink> weblinks ) {
- final StringBuilder sb = new StringBuilder();
- sb.append( "Display options\n" );
- sb.append( "-------------------\n" );
- sb.append( "Use the checkboxes to select types of information to display on the tree.\n\n" );
- sb.append( "Clickable tree nodes\n" );
- sb.append( "--------------------\n" );
- sb.append( "Tree nodes can be clicked, the action is determined by the 'click on node to' menu\n" );
- sb.append( "or by right clicking:\n" );
- sb.append( "o Display Node Data -- display information for a node\n" );
- sb.append( "o Collapse/Uncollapse -- collapse and uncollapse subtree from clicked node\n" );
- sb.append( "o Root/Reroot -- change tree root to clicked node\n" );
- sb.append( "o Sub/Super Tree -- toggle between subtree from clicked node and whole tree\n" );
- sb.append( "o Swap Descendants -- switch descendant on either side of clicked node\n" );
- sb.append( "o Colorize Subtree -- color a subtree\n" );
- sb.append( "o Open Sequence Web -- launch a web browser to display sequence information\n" );
- sb.append( "o Open Taxonomy Web -- launch a web browser to display taxonomy information\n" );
- sb.append( "- there may be additional choices depending on this particular setup\n\n" );
- sb.append( "Right clicking on a node always displays the information of a node.\n\n" );
- sb.append( "Zooming\n" );
- sb.append( "---------\n" );
- sb.append( "The mouse wheel and the plus and minus keys control zooming.\n" );
- sb.append( "Mouse wheel+Ctrl changes the text size.\n" );
- sb.append( "Mouse wheel+Shift controls zooming in vertical direction only.\n" );
- sb.append( "Use the buttons on the control panel to zoom the tree in and out, horizontally or vertically.\n" );
- sb.append( "The entire tree can be fitted into the window by clicking the \"F\" button, or by pressing F, Delete, or Home.\n" );
- sb.append( "The up, down, left, and right keys can be used to move the visible part (if zoomed in).\n" );
- sb.append( "Up, down, left, and right+Shift can be used to control zooming horizontally and vertically.\n" );
- sb.append( "Plus and minus keys+Ctrl change the text size; F+Ctrl, Delete+Ctrl, or Home+Ctrl resets it.\n\n" );
- sb.append( "Quick tree manipulation:\n" );
- sb.append( "------------------------\n" );
- sb.append( "Order Subtrees -- order the tree by branch length\n" );
- sb.append( "Uncollapse All -- uncollapse any and all collapsed branches\n\n" );
- sb.append( "Memory problems (Java heap space error)\n" );
- sb.append( "---------------------------------------\n" );
- sb.append( "Since the Java default memory allocation is quite small, it might by necessary (for trees\n" );
- sb.append( "with more than approximately 5000 external nodes) to increase the memory which Java can use, with\n" );
- sb.append( "the '-Xmx' Java command line option. For example:\n" );
- sb.append( "java -Xms32m -Xmx256m -cp path\\to\\forester.jar org.forester.archaeopteryx.Archaeopteryx\n\n" );
- if ( ( weblinks != null ) && ( weblinks.size() > 0 ) ) {
- sb.append( "Active web links\n" );
- sb.append( "--------------------\n" );
- for( final String key : weblinks.keySet() ) {
- sb.append( " " + weblinks.get( key ).toString() + "\n" );
- }
- }
- // + "General remarks\n"
- // + "---------------\n"
- // +
- // "o The application version permits copying to the clipboard \n"
- // +
- // " in the \"View\"|\"View as ...\" frame (either by control-c or button press).\n"
- // +
- // "o Changes made to a subtree affect this subtree and its subtrees,\n"
- // + " but not any of its parent tree(s).\n"
- // +
- // "o Archaeopteryx tries to detect whether the numerical values in a NH tree\n"
- // +
- // " are likely to be bootstrap values instead of branch length values.\n\n"
- // +
- // " Remarks regarding SDI (Speciation Duplication Inference):\n"
- // +
- // "o Each external node of the gene tree (in display) needs to be associated with\n"
- // +
- // " a species: either directly through the \"Species\" field, or the species\n"
- // +
- // " is part of the sequence name in the form \"XXXX_SPECIES\"\n"
- // +
- // " (e.g. \"ACON_DROME\" or \"ACON_DROME/123-4489\" which is also acceptable).\n"
- // +
- // "o A species tree for each species of the gene tree needs to be loaded with\n"
- // +
- // " \"SDI\"|\"Load species tree\" prior the SDI execution.\n"
- // +
- // "o !External nodes of the gene tree associated with species not present in\n"
- // +
- // " the species tree are REMOVED prior to SDI execution!\n"
- // +
- // "o Both the gene tree and the species tree must be completely binary.\n"
- // +
- // "o Duplications and speciations are a function of the position of the root.\n"
- // +
- // " Hence, after each manual \"Root/Reroot\"ing some duplications will be\n"
- // + " incorrect and need to be inferred again\n"
- // +
- // " with: \"SDI\"|\"SDI (Speciation Duplication Inference)\n\n"
- sb.append( "\n" );
- sb.append( "phyloXML\n" );
- sb.append( "-------------------\n" );
- sb.append( "Reference: " + Constants.PHYLOXML_REFERENCE + "\n" );
- sb.append( "Website: " + Constants.PHYLOXML_WEB_SITE + "\n" );
- sb.append( "Version: " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
- sb.append( "\n" );
- sb.append( "For more information: http://www.phylosoft.org/archaeopteryx/\n" );
- sb.append( "Email: " + Constants.AUTHOR_EMAIL + "\n\n" );
- TextFrame.instantiate( sb.toString() );
- }
-
- static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) {
- if ( ( options != null ) && ( options.getOvPlacement() != null ) ) {
- mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" );
- }
- else {
- mi.setText( "Cycle Overview Placement..." );
- }
- }
-
- static void setCycleNodeFillMenuItem( final JMenuItem mi, final Options options ) {
- if ( ( options != null ) && ( options.getDefaultNodeFill() != null ) ) {
- mi.setText( "Cycle Node Shape Fill Type... (current: "
- + options.getDefaultNodeFill().toString().toLowerCase() + ")" );
- }
- else {
- mi.setText( "Cycle Node Shape Fill Type..." );
- }
- }
-
- static void setCycleNodeShapeMenuItem( final JMenuItem mi, final Options options ) {
- if ( ( options != null ) && ( options.getDefaultNodeShape() != null ) ) {
- mi.setText( "Cycle Node Shape Fill Type... (current: "
- + options.getDefaultNodeShape().toString().toLowerCase() + ")" );
- }
- else {
- mi.setText( "Cycle Node Shape Fill Type..." );
- }
- }
-
- static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) {
- if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) {
- mi.setText( "Select Colors... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName() + ")" );
- }
- else {
- mi.setText( "Select Colors..." );
- }
- }
-
- static void setTextForFontChooserMenuItem( final JMenuItem mi, final String font_desc ) {
- mi.setText( "Select Font... (current: " + font_desc + ")" );
- }
-
- static void setTextMinSupportMenuItem( final JMenuItem mi, final Options options, final TreePanel current_tree_panel ) {
- if ( ( current_tree_panel == null ) || ( current_tree_panel.getPhylogeny() == null ) ) {
- mi.setEnabled( true );
- }
- else if ( AptxUtil.isHasAtLeastOneBranchWithSupportValues( current_tree_panel.getPhylogeny() ) ) {
- mi.setEnabled( true );
- }
- else {
- mi.setEnabled( false );
- }
- mi.setText( "Enter Min Confidence Value... (current: " + options.getMinConfidenceValue() + ")" );
- }
-
- static void setTextNodeSizeMenuItem( final JMenuItem mi, final Options options ) {
- mi.setText( "Enter Default Node Shape Size... (current: " + options.getDefaultNodeShapeSize() + ")" );
- }
-
- static void updateOptionsMenuDependingOnPhylogenyType( final MainPanel main_panel,
- final JCheckBoxMenuItem scale,
- final JCheckBoxMenuItem branch_lengths,
- final JRadioButtonMenuItem non_lined_up,
- final JRadioButtonMenuItem uniform_clado,
- final JRadioButtonMenuItem nonuniform_clado,
- final JCheckBoxMenuItem label_direction_cbmi ) {
- final TreePanel tree_panel = main_panel.getCurrentTreePanel();
- final ControlPanel control = main_panel.getControlPanel();
- final Options options = main_panel.getOptions();
- scale.setSelected( options.isShowScale() );
- branch_lengths.setSelected( options.isShowBranchLengthValues() );
- // non_lined_up.setSelected( options.isNonLinedUpCladogram() );
- if ( ( tree_panel != null ) && ( !tree_panel.isPhyHasBranchLengths() ) ) {
- scale.setSelected( false );
- scale.setEnabled( false );
- branch_lengths.setSelected( false );
- branch_lengths.setEnabled( false );
- }
- else if ( ( tree_panel != null ) && !control.isDrawPhylogram() ) {
- scale.setSelected( false );
- scale.setEnabled( false );
- branch_lengths.setEnabled( true );
- }
- else {
- scale.setEnabled( true );
- branch_lengths.setEnabled( true );
- }
- if ( ( tree_panel != null )
- && ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.ROUNDED )
- && ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) && ( tree_panel
- .getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) ) ) {
- branch_lengths.setSelected( false );
- branch_lengths.setEnabled( false );
- }
- if ( tree_panel != null ) {
- if ( ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR )
- || ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) {
- non_lined_up.setEnabled( false );
- uniform_clado.setEnabled( false );
- nonuniform_clado.setEnabled( false );
- }
- else {
- non_lined_up.setEnabled( true );
- uniform_clado.setEnabled( true );
- nonuniform_clado.setEnabled( true );
- }
- }
- else {
- if ( ( tree_panel != null )
- && ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) && ( tree_panel
- .getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) ) ) {
- branch_lengths.setSelected( false );
- branch_lengths.setEnabled( false );
- }
- if ( ( tree_panel != null )
- && ( ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) || ( tree_panel
- .getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) ) {
- non_lined_up.setEnabled( false );
- }
- else {
- // non_lined_up.setSelected( options.isNonLinedUpCladogram() );
- non_lined_up.setEnabled( true );
- }
- }
- label_direction_cbmi.setEnabled( true );
- if ( tree_panel != null ) {
- if ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
- && ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
- label_direction_cbmi.setEnabled( false );
- }
- if ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
- scale.setSelected( false );
- scale.setEnabled( false );
- }
- }
- }
-
- static void updateScreenTextAntialias( final List<TreePanel> treepanels ) {
- for( final TreePanel tree_panel : treepanels ) {
- tree_panel.setTextAntialias();
- }
- }
-}
+// $Id:\r
+// FORESTER -- software libraries and applications\r
+// for evolutionary biology research and applications.\r
+//\r
+// Copyright (C) 2008-2010 Christian M. Zmasek\r
+// All rights reserved\r
+//\r
+// This library is free software; you can redistribute it and/or\r
+// modify it under the terms of the GNU Lesser General Public\r
+// License as published by the Free Software Foundation; either\r
+// version 2.1 of the License, or (at your option) any later version.\r
+//\r
+// This library is distributed in the hope that it will be useful,\r
+// but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU\r
+// Lesser General Public License for more details.\r
+//\r
+// You should have received a copy of the GNU Lesser General Public\r
+// License along with this library; if not, write to the Free Software\r
+// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+//\r
+// Contact: phylosoft @ gmail . com\r
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester\r
+\r
+package org.forester.archaeopteryx;\r
+\r
+import java.awt.Color;\r
+import java.awt.Component;\r
+import java.awt.Container;\r
+import java.awt.Font;\r
+import java.awt.event.ActionEvent;\r
+import java.awt.event.ActionListener;\r
+import java.io.File;\r
+import java.io.IOException;\r
+import java.util.ArrayList;\r
+import java.util.LinkedList;\r
+import java.util.List;\r
+import java.util.Locale;\r
+import java.util.NoSuchElementException;\r
+\r
+import javax.swing.Box;\r
+import javax.swing.JApplet;\r
+import javax.swing.JCheckBoxMenuItem;\r
+import javax.swing.JFrame;\r
+import javax.swing.JLabel;\r
+import javax.swing.JMenu;\r
+import javax.swing.JMenuBar;\r
+import javax.swing.JMenuItem;\r
+import javax.swing.JOptionPane;\r
+import javax.swing.JPanel;\r
+import javax.swing.JRadioButtonMenuItem;\r
+import javax.swing.JTextField;\r
+import javax.swing.SwingUtilities;\r
+\r
+import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;\r
+import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;\r
+import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;\r
+import org.forester.archaeopteryx.tools.InferenceManager;\r
+import org.forester.archaeopteryx.tools.ProcessPool;\r
+import org.forester.archaeopteryx.tools.ProcessRunning;\r
+import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;\r
+import org.forester.phylogeny.Phylogeny;\r
+import org.forester.phylogeny.PhylogenyMethods;\r
+import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;\r
+import org.forester.phylogeny.PhylogenyNode;\r
+import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;\r
+import org.forester.phylogeny.data.Annotation;\r
+import org.forester.phylogeny.data.NodeDataField;\r
+import org.forester.phylogeny.data.NodeVisualData.NodeFill;\r
+import org.forester.phylogeny.data.NodeVisualData.NodeShape;\r
+import org.forester.phylogeny.iterators.PhylogenyNodeIterator;\r
+import org.forester.sdi.GSDI;\r
+import org.forester.sdi.GSDIR;\r
+import org.forester.sdi.SDIException;\r
+import org.forester.util.ForesterConstants;\r
+import org.forester.util.ForesterUtil;\r
+\r
+public abstract class MainFrame extends JFrame implements ActionListener {\r
+\r
+ static final String USE_MOUSEWHEEL_SHIFT_TO_ROTATE = "In this display type, use mousewheel + Shift to rotate [or A and S]";\r
+ static final String PHYLOXML_REF_TOOL_TIP = Constants.PHYLOXML_REFERENCE; //TODO //FIXME\r
+ static final String APTX_REF_TOOL_TIP = Constants.APTX_REFERENCE;\r
+ private static final long serialVersionUID = 3655000897845508358L;\r
+ final static Font menu_font = new Font( Configuration.getDefaultFontFamilyName(),\r
+ Font.PLAIN,\r
+ 10 );\r
+ static final String TYPE_MENU_HEADER = "Type";\r
+ static final String RECTANGULAR_TYPE_CBMI_LABEL = "Rectangular";\r
+ static final String EURO_TYPE_CBMI_LABEL = "Euro Type";\r
+ static final String CURVED_TYPE_CBMI_LABEL = "Curved";\r
+ static final String TRIANGULAR_TYPE_CBMI_LABEL = "Triangular";\r
+ static final String CONVEX_TYPE_CBMI_LABEL = "Convex";\r
+ static final String ROUNDED_TYPE_CBMI_LABEL = "Rounded";\r
+ static final String UNROOTED_TYPE_CBMI_LABEL = "Unrooted (alpha)"; //TODO\r
+ static final String CIRCULAR_TYPE_CBMI_LABEL = "Circular (alpha)"; //TODO\r
+ static final String OPTIONS_HEADER = "Options";\r
+ static final String SEARCH_SUBHEADER = "Search:";\r
+ static final String DISPLAY_SUBHEADER = "Display:";\r
+ static final String SEARCH_TERMS_ONLY_LABEL = "Match Complete Terms Only";\r
+ static final String SEARCH_REGEX_LABEL = "Search with Regular Expressions";\r
+ static final String SEARCH_CASE_SENSITIVE_LABEL = "Case Sensitive";\r
+ static final String INVERSE_SEARCH_RESULT_LABEL = "Negate Result";\r
+ static final String COLOR_BY_TAXONOMIC_GROUP = "Colorize by Taxonomic Group";\r
+ static final String DISPLAY_SCALE_LABEL = "Scale";\r
+ static final String NON_LINED_UP_CLADOGRAMS_LABEL = "Non-Lined Up Cladograms";\r
+ static final String UNIFORM_CLADOGRAMS_LABEL = "Total Node Sum Dependent Cladograms";\r
+ static final String LABEL_DIRECTION_LABEL = "Radial Labels";\r
+ static final String LABEL_DIRECTION_TIP = "To use radial node labels in radial and unrooted display types";\r
+ static final String SEARCH_WITH_REGEX_TIP = "To search using regular expressions (~Java/Perl syntax). For example, use \"^B.+\\d{2,}$\" to search for everything starting with a B and ending with at least two digits.";\r
+ static final String SCREEN_ANTIALIAS_LABEL = "Antialias";\r
+ static final String COLOR_LABELS_LABEL = "Colorize Labels Same as Parent Branch";\r
+ static final String BG_GRAD_LABEL = "Background Color Gradient";\r
+ static final String DISPLAY_NODE_BOXES_LABEL_EXT = "Shapes for External Nodes";\r
+ static final String DISPLAY_NODE_BOXES_LABEL_INT = "Shapes for Internal Nodes";\r
+ static final String DISPLAY_NODE_BOXES_LABEL_MARKED = "Shapes for Nodes with Visual Data";\r
+ static final String SHOW_OVERVIEW_LABEL = "Overview";\r
+ static final String FONT_SIZE_MENU_LABEL = "Font Size";\r
+ static final String NONUNIFORM_CLADOGRAMS_LABEL = "External Node Sum Dependent Cladograms";\r
+ static final String SHOW_DOMAIN_LABELS_LABEL = "Domain Labels";\r
+ static final String SHOW_ANN_REF_SOURCE_LABEL = "Seq Annotation Ref Sources";\r
+ static final String COLOR_LABELS_TIP = "To use parent branch colors for node labels as well, need to turn off taxonomy dependent colorization and turn on branch colorization for this to become apparent";\r
+ static final String ABBREV_SN_LABEL = "Abbreviate Scientific Taxonomic Names";\r
+ static final String TAXONOMY_COLORIZE_NODE_SHAPES_LABEL = "Colorize Node Shapes According to Taxonomy";\r
+ static final String CYCLE_NODE_SHAPE_LABEL = "Cycle Node Shapes";\r
+ static final String CYCLE_NODE_FILL_LABEL = "Cycle Node Fill Type";\r
+ static final String CHOOSE_NODE_SIZE_LABEL = "Choose Node Shape Size";\r
+ static final String SHOW_CONF_STDDEV_LABEL = "Confidence Standard Deviations";\r
+ static final String USE_BRACKETS_FOR_CONF_IN_NH_LABEL = "Use Brackets for Confidence Values";\r
+ static final String USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL = "Use Internal Node Names for Confidence Values";\r
+ static final String SHOW_BASIC_TREE_INFORMATION_LABEL = "Basic Tree Information";\r
+ static final String RIGHT_LINE_UP_DOMAINS = "Right-align Domain Architectures";\r
+ static final String LINE_UP_RENDERABLE_DATA = "Line Up Diagrams (such as Domain Architectures)";\r
+ JMenuBar _jmenubar;\r
+ JMenu _file_jmenu;\r
+ JMenu _tools_menu;\r
+ JMenu _view_jmenu;\r
+ JMenu _options_jmenu;\r
+ JMenu _font_size_menu;\r
+ JMenu _help_jmenu;\r
+ JMenuItem[] _load_phylogeny_from_webservice_menu_items;\r
+ // Analysis menu\r
+ JMenu _analysis_menu;\r
+ JMenuItem _load_species_tree_item;\r
+ JMenuItem _gsdi_item;\r
+ JMenuItem _gsdir_item;\r
+ JMenuItem _lineage_inference;\r
+ // file menu:\r
+ JMenuItem _open_item;\r
+ JMenuItem _open_url_item;\r
+ JMenuItem _save_item;\r
+ JMenuItem _save_all_item;\r
+ JMenuItem _close_item;\r
+ JMenuItem _exit_item;\r
+ JMenuItem _new_item;\r
+ // tools menu:\r
+ JMenuItem _midpoint_root_item;\r
+ JMenuItem _taxcolor_item;\r
+ JMenuItem _confcolor_item;\r
+ JMenuItem _color_rank_jmi;\r
+ JMenuItem _collapse_species_specific_subtrees;\r
+ JMenuItem _obtain_detailed_taxonomic_information_jmi;\r
+ JMenuItem _obtain_detailed_taxonomic_information_deleting_jmi;\r
+ JMenuItem _obtain_seq_information_jmi;\r
+ JMenuItem _move_node_names_to_tax_sn_jmi;\r
+ JMenuItem _move_node_names_to_seq_names_jmi;\r
+ JMenuItem _extract_tax_code_from_node_names_jmi;\r
+ JMenuItem _annotate_item;\r
+ JMenuItem _remove_branch_color_item;\r
+ JMenuItem _remove_visual_styles_item;\r
+ JMenuItem _delete_selected_nodes_item;\r
+ JMenuItem _delete_not_selected_nodes_item;\r
+ // font size menu:\r
+ JMenuItem _super_tiny_fonts_item;\r
+ JMenuItem _tiny_fonts_item;\r
+ JMenuItem _small_fonts_item;\r
+ JMenuItem _medium_fonts_item;\r
+ JMenuItem _large_fonts_item;\r
+ // options menu:\r
+ // _ screen and print\r
+ JMenuItem _choose_font_mi;\r
+ JMenuItem _switch_colors_mi;\r
+ JCheckBoxMenuItem _label_direction_cbmi;\r
+ // _ screen display\r
+ JCheckBoxMenuItem _screen_antialias_cbmi;\r
+ JCheckBoxMenuItem _background_gradient_cbmi;\r
+ JRadioButtonMenuItem _non_lined_up_cladograms_rbmi;\r
+ JRadioButtonMenuItem _uniform_cladograms_rbmi;\r
+ JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi;\r
+ JCheckBoxMenuItem _color_by_taxonomic_group_cbmi;\r
+ JCheckBoxMenuItem _show_scale_cbmi; //TODO fix me\r
+ JCheckBoxMenuItem _show_overview_cbmi;\r
+ JCheckBoxMenuItem _show_domain_labels;\r
+ JCheckBoxMenuItem _show_annotation_ref_source;\r
+ JCheckBoxMenuItem _abbreviate_scientific_names;\r
+ JCheckBoxMenuItem _color_labels_same_as_parent_branch;\r
+ JMenuItem _overview_placment_mi;\r
+ JMenuItem _choose_minimal_confidence_mi;\r
+ JCheckBoxMenuItem _show_default_node_shapes_internal_cbmi;\r
+ JCheckBoxMenuItem _show_default_node_shapes_external_cbmi;\r
+ JCheckBoxMenuItem _show_default_node_shapes_for_marked_cbmi;\r
+ JMenuItem _cycle_node_shape_mi;\r
+ JMenuItem _cycle_node_fill_mi;\r
+ JMenuItem _choose_node_size_mi;\r
+ JMenuItem _cycle_data_return;\r
+ JCheckBoxMenuItem _show_confidence_stddev_cbmi;\r
+ JCheckBoxMenuItem _right_line_up_domains_cbmi;\r
+ JCheckBoxMenuItem _line_up_renderable_data_cbmi;\r
+ // _ print\r
+ JCheckBoxMenuItem _graphics_export_visible_only_cbmi;\r
+ JCheckBoxMenuItem _antialias_print_cbmi;\r
+ JCheckBoxMenuItem _print_black_and_white_cbmi;\r
+ JCheckBoxMenuItem _print_using_actual_size_cbmi;\r
+ JCheckBoxMenuItem _graphics_export_using_actual_size_cbmi;\r
+ JMenuItem _print_size_mi;\r
+ JMenuItem _choose_pdf_width_mi;\r
+ // _ parsing\r
+ JCheckBoxMenuItem _internal_number_are_confidence_for_nh_parsing_cbmi;\r
+ JRadioButtonMenuItem _extract_taxonomy_no_rbmi;\r
+ JRadioButtonMenuItem _extract_taxonomy_agressive_rbmi;\r
+ JRadioButtonMenuItem _extract_taxonomy_pfam_strict_rbmi;\r
+ JRadioButtonMenuItem _extract_taxonomy_pfam_relaxed_rbmi;\r
+ JCheckBoxMenuItem _replace_underscores_cbmi;\r
+ JCheckBoxMenuItem _allow_errors_in_distance_to_parent_cbmi;\r
+ JCheckBoxMenuItem _use_brackets_for_conf_in_nh_export_cbmi;\r
+ JCheckBoxMenuItem _use_internal_names_for_conf_in_nh_export_cbmi;\r
+ // _ search\r
+ JCheckBoxMenuItem _search_case_senstive_cbmi;\r
+ JCheckBoxMenuItem _search_whole_words_only_cbmi;\r
+ JCheckBoxMenuItem _inverse_search_result_cbmi;\r
+ JCheckBoxMenuItem _search_with_regex_cbmi;\r
+ // type menu:\r
+ JMenu _type_menu;\r
+ JCheckBoxMenuItem _rectangular_type_cbmi;\r
+ JCheckBoxMenuItem _triangular_type_cbmi;\r
+ JCheckBoxMenuItem _curved_type_cbmi;\r
+ JCheckBoxMenuItem _convex_type_cbmi;\r
+ JCheckBoxMenuItem _euro_type_cbmi;\r
+ JCheckBoxMenuItem _rounded_type_cbmi;\r
+ JCheckBoxMenuItem _unrooted_type_cbmi;\r
+ JCheckBoxMenuItem _circular_type_cbmi;\r
+ // view as text menu:\r
+ JMenuItem _view_as_NH_item;\r
+ JMenuItem _view_as_XML_item;\r
+ JMenuItem _view_as_nexus_item;\r
+ JMenuItem _display_basic_information_item;\r
+ // help menu:\r
+ JMenuItem _about_item;\r
+ JMenuItem _help_item;\r
+ JMenuItem _website_item;\r
+ JMenuItem _phyloxml_website_item;\r
+ JMenuItem _phyloxml_ref_item;\r
+ JMenuItem _aptx_ref_item;\r
+ // process menu:\r
+ JMenu _process_menu;\r
+ // Handy pointers to child components:\r
+ MainPanel _mainpanel;\r
+ Container _contentpane;\r
+ final LinkedList<TextFrame> _textframes = new LinkedList<TextFrame>(); ;\r
+ Configuration _configuration;\r
+ Options _options;\r
+ private Phylogeny _species_tree;\r
+ InferenceManager _inference_manager;\r
+ final ProcessPool _process_pool;\r
+ private String _previous_node_annotation_ref;\r
+\r
+ MainFrame() {\r
+ _process_pool = ProcessPool.createInstance();\r
+ }\r
+\r
+ /**\r
+ * Action performed.\r
+ */\r
+ @Override\r
+ public void actionPerformed( final ActionEvent e ) {\r
+ final Object o = e.getSource();\r
+ boolean is_applet = false;\r
+ JApplet applet = null;\r
+ if ( getCurrentTreePanel() != null ) {\r
+ is_applet = getCurrentTreePanel().isApplet();\r
+ if ( is_applet ) {\r
+ applet = getCurrentTreePanel().obtainApplet();\r
+ }\r
+ }\r
+ if ( o == _exit_item ) {\r
+ close();\r
+ }\r
+ else if ( o == _gsdi_item ) {\r
+ if ( isSubtreeDisplayed() ) {\r
+ return;\r
+ }\r
+ executeGSDI();\r
+ }\r
+ else if ( o == _gsdir_item ) {\r
+ if ( isSubtreeDisplayed() ) {\r
+ return;\r
+ }\r
+ executeGSDIR();\r
+ }\r
+ else if ( o == _taxcolor_item ) {\r
+ taxColor();\r
+ }\r
+ else if ( o == _confcolor_item ) {\r
+ confColor();\r
+ }\r
+ else if ( o == _color_rank_jmi ) {\r
+ colorRank();\r
+ }\r
+ else if ( o == _collapse_species_specific_subtrees ) {\r
+ if ( isSubtreeDisplayed() ) {\r
+ return;\r
+ }\r
+ if ( getCurrentTreePanel() != null ) {\r
+ getCurrentTreePanel().collapseSpeciesSpecificSubtrees();\r
+ }\r
+ }\r
+ else if ( o == _remove_branch_color_item ) {\r
+ if ( isSubtreeDisplayed() ) {\r
+ return;\r
+ }\r
+ removeBranchColors();\r
+ }\r
+ else if ( o == _remove_visual_styles_item ) {\r
+ if ( isSubtreeDisplayed() ) {\r
+ return;\r
+ }\r
+ removeVisualStyles();\r
+ }\r
+ else if ( o == _midpoint_root_item ) {\r
+ if ( isSubtreeDisplayed() ) {\r
+ return;\r
+ }\r
+ midpointRoot();\r
+ }\r
+ else if ( o == _delete_selected_nodes_item ) {\r
+ if ( isSubtreeDisplayed() ) {\r
+ return;\r
+ }\r
+ deleteSelectedNodes( true );\r
+ }\r
+ else if ( o == _delete_not_selected_nodes_item ) {\r
+ if ( isSubtreeDisplayed() ) {\r
+ return;\r
+ }\r
+ deleteSelectedNodes( false );\r
+ }\r
+ else if ( o == _annotate_item ) {\r
+ annotateSequences();\r
+ }\r
+ else if ( o == _switch_colors_mi ) {\r
+ switchColors();\r
+ }\r
+ else if ( o == _display_basic_information_item ) {\r
+ if ( getCurrentTreePanel() != null ) {\r
+ displayBasicInformation( getCurrentTreePanel().getTreeFile() );\r
+ }\r
+ }\r
+ else if ( o == _view_as_NH_item ) {\r
+ viewAsNH();\r
+ }\r
+ else if ( o == _view_as_XML_item ) {\r
+ viewAsXML();\r
+ }\r
+ else if ( o == _view_as_nexus_item ) {\r
+ viewAsNexus();\r
+ }\r
+ else if ( o == _super_tiny_fonts_item ) {\r
+ if ( getCurrentTreePanel() != null ) {\r
+ getCurrentTreePanel().setSuperTinyFonts();\r
+ getCurrentTreePanel().repaint();\r
+ }\r
+ }\r
+ else if ( o == _tiny_fonts_item ) {\r
+ if ( getCurrentTreePanel() != null ) {\r
+ getCurrentTreePanel().setTinyFonts();\r
+ getCurrentTreePanel().repaint();\r
+ }\r
+ }\r
+ else if ( o == _small_fonts_item ) {\r
+ if ( getCurrentTreePanel() != null ) {\r
+ getCurrentTreePanel().setSmallFonts();\r
+ getCurrentTreePanel().repaint();\r
+ }\r
+ }\r
+ else if ( o == _medium_fonts_item ) {\r
+ if ( getCurrentTreePanel() != null ) {\r
+ getCurrentTreePanel().setMediumFonts();\r
+ getCurrentTreePanel().repaint();\r
+ }\r
+ }\r
+ else if ( o == _large_fonts_item ) {\r
+ if ( getCurrentTreePanel() != null ) {\r
+ getCurrentTreePanel().setLargeFonts();\r
+ getCurrentTreePanel().repaint();\r
+ }\r
+ }\r
+ else if ( o == _choose_font_mi ) {\r
+ chooseFont();\r
+ }\r
+ else if ( o == _choose_minimal_confidence_mi ) {\r
+ chooseMinimalConfidence();\r
+ }\r
+ else if ( o == _choose_node_size_mi ) {\r
+ chooseNodeSize( getOptions(), this );\r
+ }\r
+ else if ( o == _overview_placment_mi ) {\r
+ MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );\r
+ }\r
+ else if ( o == _cycle_node_fill_mi ) {\r
+ MainFrame.cycleNodeFill( getOptions() );\r
+ }\r
+ else if ( o == _cycle_node_shape_mi ) {\r
+ MainFrame.cycleNodeShape( getOptions() );\r
+ }\r
+ else if ( o == _cycle_data_return ) {\r
+ MainFrame.cycleNodeDataReturn( getOptions(), getConfiguration() );\r
+ }\r
+ else if ( o == _screen_antialias_cbmi ) {\r
+ updateOptions( getOptions() );\r
+ updateScreenTextAntialias( getMainPanel().getTreePanels() );\r
+ }\r
+ else if ( o == _background_gradient_cbmi ) {\r
+ updateOptions( getOptions() );\r
+ }\r
+ else if ( o == _show_domain_labels ) {\r
+ updateOptions( getOptions() );\r
+ }\r
+ else if ( o == _show_annotation_ref_source ) {\r
+ updateOptions( getOptions() );\r
+ }\r
+ else if ( o == _abbreviate_scientific_names ) {\r
+ updateOptions( getOptions() );\r
+ }\r
+ else if ( o == _color_labels_same_as_parent_branch ) {\r
+ updateOptions( getOptions() );\r
+ }\r
+ else if ( o == _show_default_node_shapes_internal_cbmi ) {\r
+ updateOptions( getOptions() );\r
+ }\r
+ else if ( o == _show_default_node_shapes_external_cbmi ) {\r
+ updateOptions( getOptions() );\r
+ }\r
+ else if ( o == _show_default_node_shapes_for_marked_cbmi ) {\r
+ updateOptions( getOptions() );\r
+ }\r
+ else if ( o == _non_lined_up_cladograms_rbmi ) {\r
+ updateOptions( getOptions() );\r
+ showWhole();\r
+ }\r
+ else if ( o == _uniform_cladograms_rbmi ) {\r
+ updateOptions( getOptions() );\r
+ showWhole();\r
+ }\r
+ else if ( o == _ext_node_dependent_cladogram_rbmi ) {\r
+ updateOptions( getOptions() );\r
+ showWhole();\r
+ }\r
+ else if ( o == _search_case_senstive_cbmi ) {\r
+ updateOptions( getOptions() );\r
+ getMainPanel().getControlPanel().search0();\r
+ getMainPanel().getControlPanel().search1();\r
+ }\r
+ else if ( o == _search_whole_words_only_cbmi ) {\r
+ if ( ( _search_with_regex_cbmi != null ) && _search_whole_words_only_cbmi.isSelected() ) {\r
+ _search_with_regex_cbmi.setSelected( false );\r
+ }\r
+ updateOptions( getOptions() );\r
+ getMainPanel().getControlPanel().search0();\r
+ getMainPanel().getControlPanel().search1();\r
+ }\r
+ else if ( o == _inverse_search_result_cbmi ) {\r
+ updateOptions( getOptions() );\r
+ getMainPanel().getControlPanel().search0();\r
+ getMainPanel().getControlPanel().search1();\r
+ }\r
+ else if ( o == _search_with_regex_cbmi ) {\r
+ if ( ( _search_whole_words_only_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) {\r
+ _search_whole_words_only_cbmi.setSelected( false );\r
+ }\r
+ if ( ( _search_case_senstive_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) {\r
+ _search_case_senstive_cbmi.setSelected( true );\r
+ }\r
+ updateOptions( getOptions() );\r
+ getMainPanel().getControlPanel().search0();\r
+ getMainPanel().getControlPanel().search1();\r
+ }\r
+ else if ( o == _show_scale_cbmi ) {\r
+ updateOptions( getOptions() );\r
+ }\r
+ else if ( o == _color_by_taxonomic_group_cbmi ) {\r
+ updateOptions( getOptions() );\r
+ }\r
+ else if ( o == _show_confidence_stddev_cbmi ) {\r
+ updateOptions( getOptions() );\r
+ }\r
+ else if ( o == _use_brackets_for_conf_in_nh_export_cbmi ) {\r
+ if ( _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {\r
+ _use_internal_names_for_conf_in_nh_export_cbmi.setSelected( false );\r
+ }\r
+ updateOptions( getOptions() );\r
+ }\r
+ else if ( o == _use_internal_names_for_conf_in_nh_export_cbmi ) {\r
+ if ( _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {\r
+ _use_brackets_for_conf_in_nh_export_cbmi.setSelected( false );\r
+ }\r
+ updateOptions( getOptions() );\r
+ }\r
+ else if ( o == _label_direction_cbmi ) {\r
+ updateOptions( getOptions() );\r
+ }\r
+ else if ( o == _show_overview_cbmi ) {\r
+ updateOptions( getOptions() );\r
+ if ( getCurrentTreePanel() != null ) {\r
+ getCurrentTreePanel().updateOvSizes();\r
+ }\r
+ }\r
+ else if ( o == _line_up_renderable_data_cbmi ) {\r
+ if ( !_line_up_renderable_data_cbmi.isSelected() ) {\r
+ _right_line_up_domains_cbmi.setSelected( false );\r
+ }\r
+ updateOptions( getOptions() );\r
+ }\r
+ else if ( o == _right_line_up_domains_cbmi ) {\r
+ if ( _right_line_up_domains_cbmi.isSelected() ) {\r
+ _line_up_renderable_data_cbmi.setSelected( true );\r
+ }\r
+ updateOptions( getOptions() );\r
+ }\r
+ else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )\r
+ || ( o == _convex_type_cbmi ) || ( o == _euro_type_cbmi ) || ( o == _rounded_type_cbmi )\r
+ || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {\r
+ typeChanged( o );\r
+ }\r
+ else if ( o == _about_item ) {\r
+ about();\r
+ }\r
+ else if ( o == _help_item ) {\r
+ try {\r
+ AptxUtil.openWebsite( Constants.APTX_DOC_SITE, is_applet, applet );\r
+ }\r
+ catch ( final IOException e1 ) {\r
+ ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
+ }\r
+ }\r
+ else if ( o == _website_item ) {\r
+ try {\r
+ AptxUtil.openWebsite( Constants.APTX_WEB_SITE, is_applet, applet );\r
+ }\r
+ catch ( final IOException e1 ) {\r
+ ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
+ }\r
+ }\r
+ else if ( o == _phyloxml_website_item ) {\r
+ try {\r
+ AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, is_applet, applet );\r
+ }\r
+ catch ( final IOException e1 ) {\r
+ ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
+ }\r
+ }\r
+ else if ( o == _aptx_ref_item ) {\r
+ try {\r
+ AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, is_applet, applet );\r
+ }\r
+ catch ( final IOException e1 ) {\r
+ ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
+ }\r
+ }\r
+ else if ( o == _phyloxml_ref_item ) {\r
+ try {\r
+ AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, is_applet, applet );\r
+ }\r
+ catch ( final IOException e1 ) {\r
+ ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
+ }\r
+ }\r
+ else {\r
+ if ( _load_phylogeny_from_webservice_menu_items != null ) {\r
+ for( int i = 0; i < _load_phylogeny_from_webservice_menu_items.length; ++i ) {\r
+ if ( o == _load_phylogeny_from_webservice_menu_items[ i ] ) {\r
+ readPhylogeniesFromWebservice( i );\r
+ }\r
+ }\r
+ }\r
+ }\r
+ _contentpane.repaint();\r
+ }\r
+\r
+ private void deleteSelectedNodes( final boolean delete ) {\r
+ final Phylogeny phy = getMainPanel().getCurrentPhylogeny();\r
+ if ( ( phy == null ) || ( phy.getNumberOfExternalNodes() < 2 ) ) {\r
+ return;\r
+ }\r
+ final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();\r
+ if ( ( getCurrentTreePanel().getFoundNodes0() != null ) || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {\r
+ final List<PhylogenyNode> all_selected_nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();\r
+ for( final PhylogenyNode n : all_selected_nodes ) {\r
+ if ( n.isExternal() ) {\r
+ nodes.add( n );\r
+ }\r
+ }\r
+ }\r
+ String function = "Retain";\r
+ if ( delete ) {\r
+ function = "Delete";\r
+ }\r
+ if ( ( nodes == null ) || nodes.isEmpty() ) {\r
+ JOptionPane\r
+ .showMessageDialog( this,\r
+ "Need to select external nodes, either via direct selection or via the \"Search\" function",\r
+ "No external nodes selected to " + function.toLowerCase(),\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ final int todo = nodes.size();\r
+ final int ext = phy.getNumberOfExternalNodes();\r
+ int res = todo;\r
+ if ( delete ) {\r
+ res = ext - todo;\r
+ }\r
+ if ( res < 1 ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Cannot delete all nodes",\r
+ "Attempt to delete all nodes ",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ final int result = JOptionPane.showConfirmDialog( null, function + " " + todo\r
+ + " external node(s), from a total of " + ext + " external nodes," + "\nresulting in tree with " + res\r
+ + " nodes?", function + " external nodes", JOptionPane.OK_CANCEL_OPTION );\r
+ if ( result == JOptionPane.OK_OPTION ) {\r
+ if ( !delete ) {\r
+ final List<PhylogenyNode> to_delete = new ArrayList<PhylogenyNode>();\r
+ for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {\r
+ final PhylogenyNode n = it.next();\r
+ if ( !nodes.contains( n ) ) {\r
+ to_delete.add( n );\r
+ }\r
+ }\r
+ for( final PhylogenyNode n : to_delete ) {\r
+ phy.deleteSubtree( n, true );\r
+ }\r
+ }\r
+ else {\r
+ for( final PhylogenyNode n : nodes ) {\r
+ phy.deleteSubtree( n, true );\r
+ }\r
+ }\r
+ resetSearch();\r
+ getCurrentTreePanel().setNodeInPreorderToNull();\r
+ phy.externalNodesHaveChanged();\r
+ phy.clearHashIdToNodeMap();\r
+ phy.recalculateNumberOfExternalDescendants( true );\r
+ getCurrentTreePanel().resetNodeIdToDistToLeafMap();\r
+ getCurrentTreePanel().setEdited( true );\r
+ repaint();\r
+ }\r
+ }\r
+\r
+ void resetSearch() {\r
+ getMainPanel().getCurrentTreePanel().setFoundNodes0( null );\r
+ getMainPanel().getCurrentTreePanel().setFoundNodes1( null );\r
+ getMainPanel().getControlPanel().setSearchFoundCountsOnLabel0( 0 );\r
+ getMainPanel().getControlPanel().getSearchFoundCountsLabel0().setVisible( false );\r
+ getMainPanel().getControlPanel().getSearchTextField0().setText( "" );\r
+ getMainPanel().getControlPanel().getSearchResetButton0().setEnabled( false );\r
+ getMainPanel().getControlPanel().getSearchResetButton0().setVisible( false );\r
+ getMainPanel().getControlPanel().setSearchFoundCountsOnLabel1( 0 );\r
+ getMainPanel().getControlPanel().getSearchFoundCountsLabel1().setVisible( false );\r
+ getMainPanel().getControlPanel().getSearchTextField1().setText( "" );\r
+ getMainPanel().getControlPanel().getSearchResetButton1().setEnabled( false );\r
+ getMainPanel().getControlPanel().getSearchResetButton1().setVisible( false );\r
+ }\r
+\r
+ public Configuration getConfiguration() {\r
+ return _configuration;\r
+ }\r
+\r
+ /**\r
+ * This method returns the current external node data which\r
+ * has been selected by the user by clicking the "Return ..."\r
+ * menu item. This method is expected to be called from Javascript or\r
+ * something like it.\r
+ *\r
+ * @return current external node data as String\r
+ */\r
+ public String getCurrentExternalNodesDataBuffer() {\r
+ return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();\r
+ }\r
+\r
+ public int getCurrentExternalNodesDataBufferChangeCounter() {\r
+ return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();\r
+ }\r
+\r
+ public int getCurrentExternalNodesDataBufferLength() {\r
+ return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();\r
+ }\r
+\r
+ public InferenceManager getInferenceManager() {\r
+ return _inference_manager;\r
+ }\r
+\r
+ public MainPanel getMainPanel() {\r
+ return _mainpanel;\r
+ }\r
+\r
+ public Options getOptions() {\r
+ return _options;\r
+ }\r
+\r
+ public ProcessPool getProcessPool() {\r
+ return _process_pool;\r
+ }\r
+\r
+ public void showTextFrame( final String s, final String title ) {\r
+ checkTextFrames();\r
+ _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );\r
+ }\r
+\r
+ public void showWhole() {\r
+ _mainpanel.getControlPanel().showWhole();\r
+ }\r
+\r
+ public void updateProcessMenu() {\r
+ // In general Swing is not thread safe.\r
+ // See "Swing's Threading Policy".\r
+ SwingUtilities.invokeLater( new Runnable() {\r
+\r
+ @Override\r
+ public void run() {\r
+ doUpdateProcessMenu();\r
+ }\r
+ } );\r
+ }\r
+\r
+ void activateSaveAllIfNeeded() {\r
+ if ( ( getMainPanel().getTabbedPane() != null ) && ( getMainPanel().getTabbedPane().getTabCount() > 1 ) ) {\r
+ _save_all_item.setEnabled( true );\r
+ }\r
+ else {\r
+ _save_all_item.setEnabled( false );\r
+ }\r
+ }\r
+\r
+ void buildFileMenu() {\r
+ _file_jmenu = createMenu( "File", getConfiguration() );\r
+ _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );\r
+ customizeJMenuItem( _exit_item );\r
+ _jmenubar.add( _file_jmenu );\r
+ }\r
+\r
+ void buildFontSizeMenu() {\r
+ _font_size_menu = createMenu( FONT_SIZE_MENU_LABEL, getConfiguration() );\r
+ _font_size_menu.add( _super_tiny_fonts_item = new JMenuItem( "Super Tiny Fonts" ) );\r
+ _font_size_menu.add( _tiny_fonts_item = new JMenuItem( "Tiny Fonts" ) );\r
+ _font_size_menu.add( _small_fonts_item = new JMenuItem( "Small Fonts" ) );\r
+ _font_size_menu.add( _medium_fonts_item = new JMenuItem( "Medium Fonts" ) );\r
+ _font_size_menu.add( _large_fonts_item = new JMenuItem( "Large Fonts" ) );\r
+ customizeJMenuItem( _super_tiny_fonts_item );\r
+ customizeJMenuItem( _tiny_fonts_item );\r
+ customizeJMenuItem( _small_fonts_item );\r
+ customizeJMenuItem( _medium_fonts_item );\r
+ customizeJMenuItem( _large_fonts_item );\r
+ _jmenubar.add( _font_size_menu );\r
+ }\r
+\r
+ void buildHelpMenu() {\r
+ _help_jmenu = createMenu( "Help", getConfiguration() );\r
+ _help_jmenu.add( _help_item = new JMenuItem( "Documentation" ) );\r
+ _help_jmenu.addSeparator();\r
+ _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );\r
+ _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" ); //TODO need to add this...\r
+ _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );\r
+ _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );\r
+ _help_jmenu.addSeparator();\r
+ _help_jmenu.add( _about_item = new JMenuItem( "About" ) );\r
+ customizeJMenuItem( _help_item );\r
+ customizeJMenuItem( _website_item );\r
+ customizeJMenuItem( _phyloxml_website_item );\r
+ customizeJMenuItem( _aptx_ref_item );\r
+ customizeJMenuItem( _phyloxml_ref_item );\r
+ customizeJMenuItem( _about_item );\r
+ _phyloxml_ref_item.setToolTipText( PHYLOXML_REF_TOOL_TIP );\r
+ _aptx_ref_item.setToolTipText( APTX_REF_TOOL_TIP );\r
+ _jmenubar.add( _help_jmenu );\r
+ }\r
+\r
+ void buildTypeMenu() {\r
+ _type_menu = createMenu( TYPE_MENU_HEADER, getConfiguration() );\r
+ _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );\r
+ _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );\r
+ _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );\r
+ _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );\r
+ _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );\r
+ _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );\r
+ _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );\r
+ _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );\r
+ customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );\r
+ customizeCheckBoxMenuItem( _triangular_type_cbmi, false );\r
+ customizeCheckBoxMenuItem( _euro_type_cbmi, false );\r
+ customizeCheckBoxMenuItem( _rounded_type_cbmi, false );\r
+ customizeCheckBoxMenuItem( _curved_type_cbmi, false );\r
+ customizeCheckBoxMenuItem( _convex_type_cbmi, false );\r
+ customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );\r
+ customizeCheckBoxMenuItem( _circular_type_cbmi, false );\r
+ _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );\r
+ _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );\r
+ initializeTypeMenu( getOptions() );\r
+ _jmenubar.add( _type_menu );\r
+ }\r
+\r
+ void buildViewMenu() {\r
+ _view_jmenu = createMenu( "View", getConfiguration() );\r
+ _view_jmenu.add( _display_basic_information_item = new JMenuItem( SHOW_BASIC_TREE_INFORMATION_LABEL ) );\r
+ _view_jmenu.addSeparator();\r
+ _view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) );\r
+ _view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) );\r
+ _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "as Nexus" ) );\r
+ customizeJMenuItem( _display_basic_information_item );\r
+ customizeJMenuItem( _view_as_NH_item );\r
+ customizeJMenuItem( _view_as_XML_item );\r
+ customizeJMenuItem( _view_as_nexus_item );\r
+ _jmenubar.add( _view_jmenu );\r
+ }\r
+\r
+ void checkTextFrames() {\r
+ if ( _textframes.size() > 5 ) {\r
+ try {\r
+ if ( _textframes.getFirst() != null ) {\r
+ _textframes.getFirst().removeMe();\r
+ }\r
+ else {\r
+ _textframes.removeFirst();\r
+ }\r
+ }\r
+ catch ( final NoSuchElementException e ) {\r
+ // Ignore.\r
+ }\r
+ }\r
+ }\r
+\r
+ void close() {\r
+ removeAllTextFrames();\r
+ if ( _mainpanel != null ) {\r
+ _mainpanel.terminate();\r
+ }\r
+ if ( _contentpane != null ) {\r
+ _contentpane.removeAll();\r
+ }\r
+ setVisible( false );\r
+ dispose();\r
+ }\r
+\r
+ void colorRank() {\r
+ if ( _mainpanel.getCurrentTreePanel() != null ) {\r
+ final String[] ranks = AptxUtil.getAllPossibleRanks();\r
+ final String rank = ( String ) JOptionPane\r
+ .showInputDialog( this,\r
+ "What rank should the colorization be based on",\r
+ "Rank Selection",\r
+ JOptionPane.QUESTION_MESSAGE,\r
+ null,\r
+ ranks,\r
+ null );\r
+ if ( !ForesterUtil.isEmpty( rank ) ) {\r
+ _mainpanel.getCurrentTreePanel().colorRank( rank );\r
+ }\r
+ }\r
+ }\r
+\r
+ void confColor() {\r
+ if ( _mainpanel.getCurrentTreePanel() != null ) {\r
+ _mainpanel.getCurrentTreePanel().confColor();\r
+ }\r
+ }\r
+\r
+ void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {\r
+ if ( item != null ) {\r
+ item.setFont( MainFrame.menu_font );\r
+ if ( !getConfiguration().isUseNativeUI() ) {\r
+ item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
+ item.setForeground( getConfiguration().getGuiMenuTextColor() );\r
+ }\r
+ item.setSelected( is_selected );\r
+ item.addActionListener( this );\r
+ }\r
+ }\r
+\r
+ JMenuItem customizeJMenuItem( final JMenuItem jmi ) {\r
+ if ( jmi != null ) {\r
+ jmi.setFont( MainFrame.menu_font );\r
+ if ( !getConfiguration().isUseNativeUI() ) {\r
+ jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
+ jmi.setForeground( getConfiguration().getGuiMenuTextColor() );\r
+ }\r
+ jmi.addActionListener( this );\r
+ }\r
+ return jmi;\r
+ }\r
+\r
+ void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {\r
+ if ( item != null ) {\r
+ item.setFont( MainFrame.menu_font );\r
+ if ( !getConfiguration().isUseNativeUI() ) {\r
+ item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
+ item.setForeground( getConfiguration().getGuiMenuTextColor() );\r
+ }\r
+ item.setSelected( is_selected );\r
+ item.addActionListener( this );\r
+ }\r
+ }\r
+\r
+ void displayBasicInformation( final File treefile ) {\r
+ if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
+ String title = "Basic Information";\r
+ if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
+ title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\"";\r
+ }\r
+ showTextFrame( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny(), treefile ), title );\r
+ }\r
+ }\r
+\r
+ void exceptionOccuredDuringOpenFile( final Exception e ) {\r
+ try {\r
+ _mainpanel.getCurrentTreePanel().setArrowCursor();\r
+ }\r
+ catch ( final Exception ex ) {\r
+ // Do nothing.\r
+ }\r
+ JOptionPane.showMessageDialog( this,\r
+ ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),\r
+ "Error during File|Open",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ }\r
+\r
+ void exceptionOccuredDuringSaveAs( final Exception e ) {\r
+ try {\r
+ _mainpanel.getCurrentTreePanel().setArrowCursor();\r
+ }\r
+ catch ( final Exception ex ) {\r
+ // Do nothing.\r
+ }\r
+ JOptionPane.showMessageDialog( this, "Exception" + e, "Error during File|SaveAs", JOptionPane.ERROR_MESSAGE );\r
+ }\r
+\r
+ void executeGSDI() {\r
+ if ( !isOKforSDI( false, true ) ) {\r
+ return;\r
+ }\r
+ if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Gene tree is not rooted.",\r
+ "Cannot execute GSDI",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();\r
+ gene_tree.setAllNodesToNotCollapse();\r
+ gene_tree.recalculateNumberOfExternalDescendants( false );\r
+ GSDI gsdi = null;\r
+ final Phylogeny species_tree = getSpeciesTree().copy();\r
+ try {\r
+ gsdi = new GSDI( gene_tree, species_tree, false, true, true, true );\r
+ }\r
+ catch ( final SDIException e ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ e.getLocalizedMessage(),\r
+ "Error during GSDI",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ catch ( final Exception e ) {\r
+ AptxUtil.unexpectedException( e );\r
+ return;\r
+ }\r
+ gene_tree.setRerootable( false );\r
+ gene_tree.clearHashIdToNodeMap();\r
+ gene_tree.recalculateNumberOfExternalDescendants( true );\r
+ _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null );\r
+ getMainPanel().getControlPanel().setShowEvents( true );\r
+ showWhole();\r
+ final int selected = _mainpanel.getTabbedPane().getSelectedIndex();\r
+ _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );\r
+ showWhole();\r
+ _mainpanel.getTabbedPane().setSelectedIndex( selected );\r
+ showWhole();\r
+ _mainpanel.getCurrentTreePanel().setEdited( true );\r
+ final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );\r
+ if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Duplications: " + gsdi.getDuplicationsSum() + "\n"\r
+ + "Potential duplications: "\r
+ + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"\r
+ + "Speciations: " + gsdi.getSpeciationsSum() + "\n"\r
+ + "Stripped gene tree nodes: "\r
+ + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"\r
+ + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"\r
+ + "Number of polytomies in species tree used: " + poly + "\n",\r
+ "GSDI successfully completed",\r
+ JOptionPane.WARNING_MESSAGE );\r
+ }\r
+ else {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Duplications: " + gsdi.getDuplicationsSum() + "\n"\r
+ + "Potential duplications: "\r
+ + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"\r
+ + "Speciations: " + gsdi.getSpeciationsSum() + "\n"\r
+ + "Stripped gene tree nodes: "\r
+ + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"\r
+ + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"\r
+ + "Number of polytomies in species tree used: " + poly + "\n",\r
+ "GSDI successfully completed",\r
+ JOptionPane.INFORMATION_MESSAGE );\r
+ }\r
+ }\r
+\r
+ void executeGSDIR() {\r
+ if ( !isOKforSDI( false, false ) ) {\r
+ return;\r
+ }\r
+ final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() );\r
+ if ( ( p > 0 )\r
+ && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Gene tree is not completely binary",\r
+ "Cannot execute GSDI",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();\r
+ gene_tree.setAllNodesToNotCollapse();\r
+ gene_tree.recalculateNumberOfExternalDescendants( false );\r
+ GSDIR gsdir = null;\r
+ final Phylogeny species_tree = getSpeciesTree().copy();\r
+ try {\r
+ gsdir = new GSDIR( gene_tree, species_tree, true, true, true );\r
+ }\r
+ catch ( final SDIException e ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ e.getLocalizedMessage(),\r
+ "Error during GSDIR",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ catch ( final Exception e ) {\r
+ AptxUtil.unexpectedException( e );\r
+ return;\r
+ }\r
+ final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree();\r
+ result_gene_tree.setRerootable( false );\r
+ result_gene_tree.clearHashIdToNodeMap();\r
+ result_gene_tree.recalculateNumberOfExternalDescendants( true );\r
+ PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );\r
+ _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );\r
+ getMainPanel().getControlPanel().setShowEvents( true );\r
+ showWhole();\r
+ final int selected = _mainpanel.getTabbedPane().getSelectedIndex();\r
+ _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );\r
+ showWhole();\r
+ _mainpanel.getTabbedPane().setSelectedIndex( selected );\r
+ showWhole();\r
+ _mainpanel.getCurrentTreePanel().setEdited( true );\r
+ final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );\r
+ if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"\r
+ + "Speciations: " + gsdir.getSpeciationsSum() + "\n"\r
+ + "Stripped gene tree nodes: "\r
+ + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"\r
+ + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"\r
+ + "Number of polytomies in species tree used: " + poly + "\n",\r
+ "GSDIR successfully completed",\r
+ JOptionPane.WARNING_MESSAGE );\r
+ }\r
+ else {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"\r
+ + "Speciations: " + gsdir.getSpeciationsSum() + "\n"\r
+ + "Stripped gene tree nodes: "\r
+ + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"\r
+ + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"\r
+ + "Number of polytomies in species tree used: " + poly + "\n",\r
+ "GSDIR successfully completed",\r
+ JOptionPane.INFORMATION_MESSAGE );\r
+ }\r
+ }\r
+\r
+ boolean GAndSDoHaveMoreThanOneSpeciesInComman( final Phylogeny gene_tree ) {\r
+ if ( ( gene_tree == null ) || gene_tree.isEmpty() ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Gene tree and species tree have no species in common.",\r
+ "Error during SDI",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return false;\r
+ }\r
+ else if ( gene_tree.getNumberOfExternalNodes() < 2 ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Gene tree and species tree have only one species in common.",\r
+ "Error during SDI",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return false;\r
+ }\r
+ else {\r
+ return true;\r
+ }\r
+ }\r
+\r
+ TreePanel getCurrentTreePanel() {\r
+ return getMainPanel().getCurrentTreePanel();\r
+ }\r
+\r
+ JMenu getHelpMenu() {\r
+ return _help_jmenu;\r
+ }\r
+\r
+ JCheckBoxMenuItem getlabelDirectionCbmi() {\r
+ return _label_direction_cbmi;\r
+ }\r
+\r
+ JMenuBar getMenuBarOfMainFrame() {\r
+ return _jmenubar;\r
+ }\r
+\r
+ final Phylogeny getSpeciesTree() {\r
+ return _species_tree;\r
+ }\r
+\r
+ void initializeTypeMenu( final Options options ) {\r
+ setTypeMenuToAllUnselected();\r
+ switch ( options.getPhylogenyGraphicsType() ) {\r
+ case CONVEX:\r
+ _convex_type_cbmi.setSelected( true );\r
+ break;\r
+ case CURVED:\r
+ _curved_type_cbmi.setSelected( true );\r
+ break;\r
+ case EURO_STYLE:\r
+ _euro_type_cbmi.setSelected( true );\r
+ break;\r
+ case ROUNDED:\r
+ _rounded_type_cbmi.setSelected( true );\r
+ break;\r
+ case TRIANGULAR:\r
+ _triangular_type_cbmi.setSelected( true );\r
+ break;\r
+ case UNROOTED:\r
+ _unrooted_type_cbmi.setSelected( true );\r
+ break;\r
+ case CIRCULAR:\r
+ _circular_type_cbmi.setSelected( true );\r
+ break;\r
+ default:\r
+ _rectangular_type_cbmi.setSelected( true );\r
+ break;\r
+ }\r
+ }\r
+\r
+ boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {\r
+ if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
+ return false;\r
+ }\r
+ else if ( ( getSpeciesTree() == null ) || getSpeciesTree().isEmpty() ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "No species tree loaded",\r
+ "Cannot execute GSDI",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return false;\r
+ }\r
+ else if ( species_tree_has_to_binary && !getSpeciesTree().isCompletelyBinary() ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Species tree is not completely binary",\r
+ "Cannot execute GSDI",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return false;\r
+ }\r
+ else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Gene tree is not completely binary",\r
+ "Cannot execute GSDI",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return false;\r
+ }\r
+ else {\r
+ return true;\r
+ }\r
+ }\r
+\r
+ boolean isSubtreeDisplayed() {\r
+ if ( getCurrentTreePanel() != null ) {\r
+ if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {\r
+ JOptionPane\r
+ .showMessageDialog( this,\r
+ "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",\r
+ "Operation can not be exectuted on a sub-tree",\r
+ JOptionPane.WARNING_MESSAGE );\r
+ return true;\r
+ }\r
+ }\r
+ return false;\r
+ }\r
+\r
+ void midpointRoot() {\r
+ if ( _mainpanel.getCurrentTreePanel() != null ) {\r
+ _mainpanel.getCurrentTreePanel().midpointRoot();\r
+ }\r
+ }\r
+\r
+ void readPhylogeniesFromWebservice( final int i ) {\r
+ final UrlTreeReader reader = new UrlTreeReader( this, i );\r
+ new Thread( reader ).start();\r
+ }\r
+\r
+ void removeAllTextFrames() {\r
+ for( final TextFrame tf : _textframes ) {\r
+ if ( tf != null ) {\r
+ tf.close();\r
+ }\r
+ }\r
+ _textframes.clear();\r
+ }\r
+\r
+ void setConfiguration( final Configuration configuration ) {\r
+ _configuration = configuration;\r
+ }\r
+\r
+ void setInferenceManager( final InferenceManager i ) {\r
+ _inference_manager = i;\r
+ }\r
+\r
+ void setOptions( final Options options ) {\r
+ _options = options;\r
+ }\r
+\r
+ void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {\r
+ setTypeMenuToAllUnselected();\r
+ switch ( type ) {\r
+ case CIRCULAR:\r
+ _circular_type_cbmi.setSelected( true );\r
+ break;\r
+ case CONVEX:\r
+ _convex_type_cbmi.setSelected( true );\r
+ break;\r
+ case CURVED:\r
+ _curved_type_cbmi.setSelected( true );\r
+ break;\r
+ case EURO_STYLE:\r
+ _euro_type_cbmi.setSelected( true );\r
+ break;\r
+ case ROUNDED:\r
+ _rounded_type_cbmi.setSelected( true );\r
+ break;\r
+ case RECTANGULAR:\r
+ _rectangular_type_cbmi.setSelected( true );\r
+ break;\r
+ case TRIANGULAR:\r
+ _triangular_type_cbmi.setSelected( true );\r
+ break;\r
+ case UNROOTED:\r
+ _unrooted_type_cbmi.setSelected( true );\r
+ break;\r
+ default:\r
+ throw new IllegalArgumentException( "unknown type: " + type );\r
+ }\r
+ }\r
+\r
+ final void setSpeciesTree( final Phylogeny species_tree ) {\r
+ _species_tree = species_tree;\r
+ }\r
+\r
+ void setTypeMenuToAllUnselected() {\r
+ _convex_type_cbmi.setSelected( false );\r
+ _curved_type_cbmi.setSelected( false );\r
+ _euro_type_cbmi.setSelected( false );\r
+ _rounded_type_cbmi.setSelected( false );\r
+ _triangular_type_cbmi.setSelected( false );\r
+ _rectangular_type_cbmi.setSelected( false );\r
+ _unrooted_type_cbmi.setSelected( false );\r
+ _circular_type_cbmi.setSelected( false );\r
+ }\r
+\r
+ void switchColors() {\r
+ final TreeColorSet colorset = _mainpanel.getTreeColorSet();\r
+ final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );\r
+ csc.setVisible( true );\r
+ }\r
+\r
+ void taxColor() {\r
+ if ( _mainpanel.getCurrentTreePanel() != null ) {\r
+ _mainpanel.getCurrentTreePanel().taxColor();\r
+ }\r
+ }\r
+\r
+ void typeChanged( final Object o ) {\r
+ updateTypeCheckboxes( getOptions(), o );\r
+ updateOptions( getOptions() );\r
+ if ( getCurrentTreePanel() != null ) {\r
+ final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();\r
+ final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();\r
+ if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )\r
+ || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )\r
+ || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )\r
+ || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {\r
+ getCurrentTreePanel().getControlPanel().showWhole();\r
+ }\r
+ if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {\r
+ getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );\r
+ }\r
+ else {\r
+ getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );\r
+ }\r
+ getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );\r
+ updateScreenTextAntialias( getMainPanel().getTreePanels() );\r
+ if ( getCurrentTreePanel().getControlPanel().getDynamicallyHideData() != null ) {\r
+ if ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {\r
+ getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( false );\r
+ }\r
+ else {\r
+ getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( true );\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ void updateOptions( final Options options ) {\r
+ options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );\r
+ options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )\r
+ && _background_gradient_cbmi.isSelected() );\r
+ options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );\r
+ options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null )\r
+ && _show_annotation_ref_source.isSelected() );\r
+ options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )\r
+ && _abbreviate_scientific_names.isSelected() );\r
+ options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )\r
+ && _color_labels_same_as_parent_branch.isSelected() );\r
+ options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )\r
+ && _show_default_node_shapes_internal_cbmi.isSelected() );\r
+ options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )\r
+ && _show_default_node_shapes_external_cbmi.isSelected() );\r
+ options.setShowDefaultNodeShapesForMarkedNodes( ( _show_default_node_shapes_for_marked_cbmi != null )\r
+ && _show_default_node_shapes_for_marked_cbmi.isSelected() );\r
+ if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {\r
+ options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );\r
+ }\r
+ else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {\r
+ options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );\r
+ }\r
+ else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {\r
+ options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );\r
+ }\r
+ options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )\r
+ && _search_case_senstive_cbmi.isSelected() );\r
+ if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {\r
+ options.setShowScale( _show_scale_cbmi.isSelected() );\r
+ }\r
+ if ( _label_direction_cbmi != null ) {\r
+ if ( _label_direction_cbmi.isSelected() ) {\r
+ options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );\r
+ }\r
+ else {\r
+ options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );\r
+ }\r
+ }\r
+ options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );\r
+ options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )\r
+ && _show_confidence_stddev_cbmi.isSelected() );\r
+ if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) {\r
+ options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() );\r
+ }\r
+ options.setPrintUsingActualSize( ( _print_using_actual_size_cbmi != null )\r
+ && ( _print_using_actual_size_cbmi.isSelected() ) );\r
+ options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null )\r
+ && ( _graphics_export_using_actual_size_cbmi.isSelected() ) );\r
+ options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() );\r
+ if ( ( _use_brackets_for_conf_in_nh_export_cbmi != null )\r
+ && _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {\r
+ options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );\r
+ }\r
+ else if ( ( _use_internal_names_for_conf_in_nh_export_cbmi != null )\r
+ && _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {\r
+ options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );\r
+ }\r
+ else {\r
+ options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );\r
+ }\r
+ options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null )\r
+ && _print_black_and_white_cbmi.isSelected() );\r
+ options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null )\r
+ && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );\r
+ if ( ( _extract_taxonomy_pfam_strict_rbmi != null ) && _extract_taxonomy_pfam_strict_rbmi.isSelected() ) {\r
+ options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );\r
+ }\r
+ else if ( ( _extract_taxonomy_pfam_relaxed_rbmi != null ) && _extract_taxonomy_pfam_relaxed_rbmi.isSelected() ) {\r
+ options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );\r
+ }\r
+ else if ( ( _extract_taxonomy_agressive_rbmi != null ) && _extract_taxonomy_agressive_rbmi.isSelected() ) {\r
+ options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );\r
+ }\r
+ else if ( ( _extract_taxonomy_no_rbmi != null ) && _extract_taxonomy_no_rbmi.isSelected() ) {\r
+ options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );\r
+ }\r
+ options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )\r
+ && _replace_underscores_cbmi.isSelected() );\r
+ options.setAllowErrorsInDistanceToParent( ( _allow_errors_in_distance_to_parent_cbmi != null )\r
+ && _allow_errors_in_distance_to_parent_cbmi.isSelected() );\r
+ options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )\r
+ && _search_whole_words_only_cbmi.isSelected() );\r
+ options.setSearchWithRegex( ( _search_with_regex_cbmi != null ) && _search_with_regex_cbmi.isSelected() );\r
+ options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )\r
+ && _inverse_search_result_cbmi.isSelected() );\r
+ if ( _graphics_export_visible_only_cbmi != null ) {\r
+ options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_cbmi.isSelected() );\r
+ if ( _graphics_export_visible_only_cbmi.isSelected() && ( _graphics_export_using_actual_size_cbmi != null ) ) {\r
+ _graphics_export_using_actual_size_cbmi.setSelected( true );\r
+ _graphics_export_using_actual_size_cbmi.setEnabled( false );\r
+ }\r
+ else {\r
+ _graphics_export_using_actual_size_cbmi.setEnabled( true );\r
+ }\r
+ }\r
+ if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {\r
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );\r
+ }\r
+ else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {\r
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );\r
+ }\r
+ else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {\r
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );\r
+ }\r
+ else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {\r
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );\r
+ }\r
+ else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {\r
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );\r
+ }\r
+ else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {\r
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );\r
+ }\r
+ else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {\r
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );\r
+ }\r
+ else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {\r
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );\r
+ }\r
+ if ( ( _right_line_up_domains_cbmi != null ) && _right_line_up_domains_cbmi.isEnabled() ) {\r
+ options.setRightLineUpDomains( _right_line_up_domains_cbmi.isSelected() );\r
+ }\r
+ if ( ( _line_up_renderable_data_cbmi != null ) && _line_up_renderable_data_cbmi.isEnabled() ) {\r
+ options.setLineUpRendarableNodeData( _line_up_renderable_data_cbmi.isSelected() );\r
+ }\r
+ }\r
+\r
+ void updateTypeCheckboxes( final Options options, final Object o ) {\r
+ setTypeMenuToAllUnselected();\r
+ ( ( JCheckBoxMenuItem ) o ).setSelected( true );\r
+ }\r
+\r
+ void viewAsNexus() {\r
+ if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
+ String title = "Nexus";\r
+ if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
+ title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
+ }\r
+ showTextFrame( _mainpanel.getCurrentPhylogeny().toNexus( getOptions().getNhConversionSupportValueStyle() ),\r
+ title );\r
+ }\r
+ }\r
+\r
+ void viewAsNH() {\r
+ if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
+ String title = "New Hampshire";\r
+ if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
+ title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
+ }\r
+ showTextFrame( _mainpanel.getCurrentPhylogeny().toNewHampshire( getOptions()\r
+ .getNhConversionSupportValueStyle() ),\r
+ title );\r
+ }\r
+ }\r
+\r
+ void viewAsXML() {\r
+ if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
+ String title = "phyloXML";\r
+ if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
+ title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
+ }\r
+ showTextFrame( _mainpanel.getCurrentPhylogeny().toPhyloXML( 0 ), title );\r
+ }\r
+ }\r
+\r
+ private void annotateSequences() {\r
+ if ( getCurrentTreePanel() != null ) {\r
+ List<PhylogenyNode> nodes = null;\r
+ if ( ( getCurrentTreePanel().getFoundNodes0() != null )\r
+ || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {\r
+ nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();\r
+ }\r
+ if ( ( nodes == null ) || nodes.isEmpty() ) {\r
+ JOptionPane\r
+ .showMessageDialog( this,\r
+ "Need to select nodes, either via direct selection or via the \"Search\" function",\r
+ "No nodes selected for annotation",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ final Phylogeny phy = getMainPanel().getCurrentPhylogeny();\r
+ if ( ( phy != null ) && !phy.isEmpty() ) {\r
+ final JTextField ref_field = new JTextField( 10 );\r
+ final JTextField desc_filed = new JTextField( 20 );\r
+ ref_field.setText( ForesterUtil.isEmpty( getPreviousNodeAnnotationReference() ) ? ""\r
+ : getPreviousNodeAnnotationReference() );\r
+ final JPanel my_panel = new JPanel();\r
+ my_panel.add( new JLabel( "Reference " ) );\r
+ my_panel.add( ref_field );\r
+ my_panel.add( Box.createHorizontalStrut( 15 ) );\r
+ my_panel.add( new JLabel( "Description " ) );\r
+ my_panel.add( desc_filed );\r
+ final int result = JOptionPane.showConfirmDialog( null,\r
+ my_panel,\r
+ "Enter the sequence annotation(s) for the "\r
+ + nodes.size() + " selected nodes",\r
+ JOptionPane.OK_CANCEL_OPTION );\r
+ if ( result == JOptionPane.OK_OPTION ) {\r
+ String ref = ref_field.getText();\r
+ String desc = desc_filed.getText();\r
+ if ( !ForesterUtil.isEmpty( ref ) ) {\r
+ ref = ref.trim();\r
+ ref = ref.replaceAll( "\\s+", " " );\r
+ if ( ( ref.indexOf( ':' ) < 1 ) || ( ref.indexOf( ':' ) > ( ref.length() - 2 ) )\r
+ || ( ref.length() < 3 ) ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Reference needs to be in the form of \"GO:1234567\"",\r
+ "Illegal Format for Annotation Reference",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ }\r
+ if ( ref != null ) {\r
+ setPreviousNodeAnnotationReference( ref );\r
+ }\r
+ if ( desc != null ) {\r
+ desc = desc.trim();\r
+ desc = desc.replaceAll( "\\s+", " " );\r
+ }\r
+ if ( !ForesterUtil.isEmpty( ref ) || !ForesterUtil.isEmpty( desc ) ) {\r
+ for( final PhylogenyNode n : nodes ) {\r
+ ForesterUtil.ensurePresenceOfSequence( n );\r
+ final Annotation ann = ForesterUtil.isEmpty( ref ) ? new Annotation()\r
+ : new Annotation( ref );\r
+ if ( !ForesterUtil.isEmpty( desc ) ) {\r
+ ann.setDesc( desc );\r
+ }\r
+ n.getNodeData().getSequence().addAnnotation( ann );\r
+ }\r
+ }\r
+ getMainPanel().getControlPanel().showAnnotations();\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ private void chooseFont() {\r
+ final FontChooser fc = new FontChooser();\r
+ fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );\r
+ fc.showDialog( this, "Select the Base Font" );\r
+ getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );\r
+ }\r
+\r
+ private void chooseMinimalConfidence() {\r
+ final String s = ( String ) JOptionPane\r
+ .showInputDialog( this,\r
+ "Please enter the minimum for confidence values to be displayed.\n"\r
+ + "[current value: " + getOptions().getMinConfidenceValue() + "]\n",\r
+ "Minimal Confidence Value",\r
+ JOptionPane.QUESTION_MESSAGE,\r
+ null,\r
+ null,\r
+ getOptions().getMinConfidenceValue() );\r
+ if ( !ForesterUtil.isEmpty( s ) ) {\r
+ boolean success = true;\r
+ double m = 0.0;\r
+ final String m_str = s.trim();\r
+ if ( !ForesterUtil.isEmpty( m_str ) ) {\r
+ try {\r
+ m = Double.parseDouble( m_str );\r
+ }\r
+ catch ( final Exception ex ) {\r
+ success = false;\r
+ }\r
+ }\r
+ else {\r
+ success = false;\r
+ }\r
+ if ( success && ( m >= 0.0 ) ) {\r
+ getOptions().setMinConfidenceValue( m );\r
+ }\r
+ }\r
+ }\r
+\r
+ private void doUpdateProcessMenu() {\r
+ if ( _process_pool.size() > 0 ) {\r
+ if ( _process_menu == null ) {\r
+ _process_menu = createMenu( "", getConfiguration() );\r
+ _process_menu.setForeground( Color.RED );\r
+ }\r
+ _process_menu.removeAll();\r
+ final String text = "processes running: " + _process_pool.size();\r
+ _process_menu.setText( text );\r
+ _jmenubar.add( _process_menu );\r
+ for( int i = 0; i < _process_pool.size(); ++i ) {\r
+ final ProcessRunning p = _process_pool.getProcessByIndex( i );\r
+ _process_menu.add( customizeJMenuItem( new JMenuItem( p.getName() + " [" + p.getStart() + "]" ) ) );\r
+ }\r
+ }\r
+ else {\r
+ if ( _process_menu != null ) {\r
+ _process_menu.removeAll();\r
+ _jmenubar.remove( _process_menu );\r
+ }\r
+ }\r
+ _jmenubar.validate();\r
+ _jmenubar.repaint();\r
+ repaint();\r
+ }\r
+\r
+ private String getPreviousNodeAnnotationReference() {\r
+ return _previous_node_annotation_ref;\r
+ }\r
+\r
+ private void removeBranchColors() {\r
+ if ( getMainPanel().getCurrentPhylogeny() != null ) {\r
+ AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );\r
+ }\r
+ }\r
+\r
+ private void removeVisualStyles() {\r
+ if ( getMainPanel().getCurrentPhylogeny() != null ) {\r
+ AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() );\r
+ }\r
+ }\r
+\r
+ private void setPreviousNodeAnnotationReference( final String previous_node_annotation_ref ) {\r
+ _previous_node_annotation_ref = previous_node_annotation_ref;\r
+ }\r
+\r
+ /**\r
+ * Display the about box.\r
+ */\r
+ static void about() {\r
+ final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + Constants.VERSION + "\n" );\r
+ about.append( "Copyright (C) 2014 Christian M Zmasek\n" );\r
+ about.append( "All Rights Reserved\n" );\r
+ about.append( "License: GNU Lesser General Public License (LGPL)\n" );\r
+ about.append( "Last modified: " + Constants.PRG_DATE + "\n" );\r
+ about.append( "Based on: " + ForesterUtil.getForesterLibraryInformation() + "\n" );\r
+ about.append( "phyloXML version : " + ForesterConstants.PHYLO_XML_VERSION + "\n" );\r
+ about.append( "phyloXML location: " + ForesterConstants.PHYLO_XML_LOCATION + "\n" );\r
+ if ( !ForesterUtil.isEmpty( ForesterUtil.JAVA_VERSION ) && !ForesterUtil.isEmpty( ForesterUtil.JAVA_VENDOR ) ) {\r
+ about.append( "[your Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]\n" );\r
+ }\r
+ if ( !ForesterUtil.isEmpty( ForesterUtil.OS_NAME ) && !ForesterUtil.isEmpty( ForesterUtil.OS_ARCH )\r
+ && !ForesterUtil.isEmpty( ForesterUtil.OS_VERSION ) ) {\r
+ about.append( "[your OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " "\r
+ + ForesterUtil.OS_VERSION + "]\n" );\r
+ }\r
+ final Runtime rt = java.lang.Runtime.getRuntime();\r
+ final long free_memory = rt.freeMemory() / 1000000;\r
+ final long total_memory = rt.totalMemory() / 1000000;\r
+ about.append( "[free memory: " + free_memory + "MB, total memory: " + total_memory + "MB]\n" );\r
+ about.append( "[locale: " + Locale.getDefault() + "]\n" );\r
+ about.append( "References:\n" );\r
+ about.append( Constants.PHYLOXML_REFERENCE_SHORT + "\n" );\r
+ about.append( "For more information & download:\n" );\r
+ about.append( Constants.APTX_WEB_SITE + "\n" );\r
+ about.append( "Documentation:\n" );\r
+ about.append( Constants.APTX_DOC_SITE + "\n" );\r
+ about.append( "Comments: " + Constants.AUTHOR_EMAIL );\r
+ JOptionPane.showMessageDialog( null, about, Constants.PRG_NAME, JOptionPane.PLAIN_MESSAGE );\r
+ }\r
+\r
+ static void chooseNodeSize( final Options options, final Component parent ) {\r
+ final String s = ( String ) JOptionPane.showInputDialog( parent,\r
+ "Please enter the default size for node shapes.\n"\r
+ + "[current value: "\r
+ + options.getDefaultNodeShapeSize() + "]\n",\r
+ "Node Shape Size",\r
+ JOptionPane.QUESTION_MESSAGE,\r
+ null,\r
+ null,\r
+ options.getDefaultNodeShapeSize() );\r
+ if ( !ForesterUtil.isEmpty( s ) ) {\r
+ boolean success = true;\r
+ double m = 0.0;\r
+ final String m_str = s.trim();\r
+ if ( !ForesterUtil.isEmpty( m_str ) ) {\r
+ try {\r
+ m = Double.parseDouble( m_str );\r
+ }\r
+ catch ( final Exception ex ) {\r
+ success = false;\r
+ }\r
+ }\r
+ else {\r
+ success = false;\r
+ }\r
+ if ( success && ( m >= 0.0 ) ) {\r
+ final short size = ForesterUtil.roundToShort( m );\r
+ if ( size >= 0.0 ) {\r
+ options.setDefaultNodeShapeSize( size );\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ static String createCurrentFontDesc( final TreeFontSet tree_font_set ) {\r
+ return tree_font_set.getLargeFont().getFamily() + " " + tree_font_set.getLargeFont().getSize();\r
+ }\r
+\r
+ static JMenu createMenu( final String title, final Configuration conf ) {\r
+ final JMenu jmenu = new JMenu( title );\r
+ if ( !conf.isUseNativeUI() ) {\r
+ jmenu.setFont( MainFrame.menu_font );\r
+ jmenu.setBackground( conf.getGuiMenuBackgroundColor() );\r
+ jmenu.setForeground( conf.getGuiMenuTextColor() );\r
+ }\r
+ return jmenu;\r
+ }\r
+\r
+ static JMenuItem customizeMenuItemAsLabel( final JMenuItem label, final Configuration configuration ) {\r
+ label.setFont( MainFrame.menu_font.deriveFont( Font.BOLD ) );\r
+ if ( !configuration.isUseNativeUI() ) {\r
+ label.setBackground( configuration.getGuiMenuBackgroundColor() );\r
+ label.setForeground( configuration.getGuiMenuTextColor() );\r
+ label.setOpaque( true );\r
+ }\r
+ label.setSelected( false );\r
+ label.setEnabled( false );\r
+ return label;\r
+ }\r
+\r
+ static void cycleNodeFill( final Options op ) {\r
+ switch ( op.getDefaultNodeFill() ) {\r
+ case GRADIENT:\r
+ op.setDefaultNodeFill( NodeFill.SOLID );\r
+ break;\r
+ case NONE:\r
+ op.setDefaultNodeFill( NodeFill.GRADIENT );\r
+ break;\r
+ case SOLID:\r
+ op.setDefaultNodeFill( NodeFill.NONE );\r
+ break;\r
+ default:\r
+ throw new RuntimeException( "unknown fill: " + op.getDefaultNodeFill() );\r
+ }\r
+ }\r
+\r
+ static void cycleNodeShape( final Options op ) {\r
+ switch ( op.getDefaultNodeShape() ) {\r
+ case CIRCLE:\r
+ op.setDefaultNodeShape( NodeShape.RECTANGLE );\r
+ break;\r
+ case RECTANGLE:\r
+ op.setDefaultNodeShape( NodeShape.CIRCLE );\r
+ break;\r
+ default:\r
+ throw new RuntimeException( "unknown shape: " + op.getDefaultNodeShape() );\r
+ }\r
+ }\r
+\r
+ private static void cycleNodeDataReturn( final Options op, Configuration conf ) {\r
+ switch ( op.getExtDescNodeDataToReturn() ) {\r
+ case UNKNOWN:\r
+ op.setExtDescNodeDataToReturn( NodeDataField.DOMAINS_ALL );\r
+ break;\r
+ case DOMAINS_ALL:\r
+ op.setExtDescNodeDataToReturn( NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN );\r
+ break;\r
+ case DOMAINS_COLLAPSED_PER_PROTEIN:\r
+ op.setExtDescNodeDataToReturn( NodeDataField.SEQ_ANNOTATIONS );\r
+ break;\r
+ case SEQ_ANNOTATIONS:\r
+ op.setExtDescNodeDataToReturn( NodeDataField.GO_TERM_IDS );\r
+ break;\r
+ case GO_TERM_IDS:\r
+ op.setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_MOL_SEQ_FASTA );\r
+ break;\r
+ case SEQUENCE_MOL_SEQ_FASTA:\r
+ if ( conf != null && conf.getExtDescNodeDataToReturn() != null\r
+ && conf.getExtDescNodeDataToReturn() != NodeDataField.DOMAINS_ALL\r
+ && conf.getExtDescNodeDataToReturn() != NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN\r
+ && conf.getExtDescNodeDataToReturn() != NodeDataField.SEQ_ANNOTATIONS\r
+ && conf.getExtDescNodeDataToReturn() != NodeDataField.GO_TERM_IDS\r
+ && conf.getExtDescNodeDataToReturn() != NodeDataField.SEQUENCE_MOL_SEQ_FASTA\r
+ ) {\r
+ op.setExtDescNodeDataToReturn( conf.getExtDescNodeDataToReturn() );\r
+ }\r
+ else {\r
+ op.setExtDescNodeDataToReturn( NodeDataField.UNKNOWN );\r
+ }\r
+ break; \r
+ default:\r
+ op.setExtDescNodeDataToReturn( NodeDataField.UNKNOWN );\r
+ }\r
+ }\r
+\r
+ static void cycleOverview( final Options op, final TreePanel tree_panel ) {\r
+ switch ( op.getOvPlacement() ) {\r
+ case LOWER_LEFT:\r
+ op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );\r
+ break;\r
+ case LOWER_RIGHT:\r
+ op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );\r
+ break;\r
+ case UPPER_LEFT:\r
+ op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );\r
+ break;\r
+ case UPPER_RIGHT:\r
+ op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );\r
+ break;\r
+ default:\r
+ throw new RuntimeException( "unknown placement: " + op.getOvPlacement() );\r
+ }\r
+ if ( tree_panel != null ) {\r
+ tree_panel.updateOvSettings();\r
+ }\r
+ }\r
+\r
+ static void setCycleNodeFillMenuItem( final JMenuItem mi, final Options options ) {\r
+ if ( ( options != null ) && ( options.getDefaultNodeFill() != null ) ) {\r
+ mi.setText( "Cycle Node Shape Fill Type... (current: "\r
+ + options.getDefaultNodeFill().toString().toLowerCase() + ")" );\r
+ }\r
+ else {\r
+ mi.setText( "Cycle Node Shape Fill Type..." );\r
+ }\r
+ }\r
+\r
+ static void setCycleNodeShapeMenuItem( final JMenuItem mi, final Options options ) {\r
+ if ( ( options != null ) && ( options.getDefaultNodeShape() != null ) ) {\r
+ mi.setText( "Cycle Node Shape Fill Type... (current: "\r
+ + options.getDefaultNodeShape().toString().toLowerCase() + ")" );\r
+ }\r
+ else {\r
+ mi.setText( "Cycle Node Shape Fill Type..." );\r
+ }\r
+ }\r
+\r
+ static void setCycleDataReturnMenuItem( final JMenuItem mi, final Options options ) {\r
+ if ( ( options != null ) && ( options.getExtDescNodeDataToReturn() != null ) ) {\r
+ mi.setText( "Cycle Node Return Data... (current: "\r
+ + options.getExtDescNodeDataToReturn().toString() + ")" );\r
+ }\r
+ else {\r
+ mi.setText( "Cycle Node Return Data..." );\r
+ }\r
+ }\r
+\r
+ static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) {\r
+ if ( ( options != null ) && ( options.getOvPlacement() != null ) ) {\r
+ mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" );\r
+ }\r
+ else {\r
+ mi.setText( "Cycle Overview Placement..." );\r
+ }\r
+ }\r
+\r
+ static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) {\r
+ if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) {\r
+ mi.setText( "Select Color Scheme... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName()\r
+ + ")" );\r
+ }\r
+ else {\r
+ mi.setText( "Select Color Scheme..." );\r
+ }\r
+ }\r
+\r
+ static void setTextForFontChooserMenuItem( final JMenuItem mi, final String font_desc ) {\r
+ mi.setText( "Select Default Font... (current: " + font_desc + ")" );\r
+ }\r
+\r
+ static void setTextMinSupportMenuItem( final JMenuItem mi, final Options options, final TreePanel current_tree_panel ) {\r
+ if ( ( current_tree_panel == null ) || ( current_tree_panel.getPhylogeny() == null ) ) {\r
+ mi.setEnabled( true );\r
+ }\r
+ else if ( AptxUtil.isHasAtLeastOneBranchWithSupportValues( current_tree_panel.getPhylogeny() ) ) {\r
+ mi.setEnabled( true );\r
+ }\r
+ else {\r
+ mi.setEnabled( false );\r
+ }\r
+ mi.setText( "Enter Min Confidence Value... (current: " + options.getMinConfidenceValue() + ")" );\r
+ }\r
+\r
+ static void setTextNodeSizeMenuItem( final JMenuItem mi, final Options options ) {\r
+ mi.setText( "Enter Default Node Shape Size... (current: " + options.getDefaultNodeShapeSize() + ")" );\r
+ }\r
+\r
+ static void updateScreenTextAntialias( final List<TreePanel> treepanels ) {\r
+ for( final TreePanel tree_panel : treepanels ) {\r
+ tree_panel.setTextAntialias();\r
+ }\r
+ }\r
+}\r