// $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.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 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.phylogeny.Phylogeny; 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 = "Display 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"; 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 _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_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; // _ 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; // _ 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; // Handy pointers to child components: MainPanel _mainpanel; Container _contentpane; TextFrame _textframe; Configuration _configuration; JMenuItem _remove_branch_color_item; Options _options; MainFrame() { // Empty constructor. } /** * 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 == _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 == _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 { Util.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 { Util.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 { Util.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 { Util.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 ); } 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 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 ); } } void 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 ); } } 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; } MainPanel getMainPanel() { return _mainpanel; } JMenuBar getMenuBarOfMainFrame() { return _jmenubar; } 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 ) { Util.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 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() ); 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() ); 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( Util.crateBasicInformation( _mainpanel.getCurrentPhylogeny() ) ); } void viewAsNexus() { removeTextFrame(); if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() || ( _mainpanel.getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) { return; } _textframe = TextFrame.instantiate( _mainpanel.getCurrentPhylogeny().toNexus() ); } void viewAsNH() { removeTextFrame(); if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() || ( _mainpanel.getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) { return; } _textframe = TextFrame.instantiate( _mainpanel.getCurrentPhylogeny().toNewHampshire( false ) ); } 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) 2007-2011 Christian 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( "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 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 ( ForesterUtil.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 treepanels ) { for( final TreePanel tree_panel : treepanels ) { tree_panel.setTextAntialias(); } } }