From e14f15b067fc014c878f765f4afa40470133c821 Mon Sep 17 00:00:00 2001 From: cmzmasek Date: Fri, 21 Oct 2016 16:38:37 -0700 Subject: [PATCH] keeping applet code in archive --- forester/archive/Applets/ArchaeopteryxA.txt | 247 ++++ forester/archive/Applets/ArchaeopteryxE.txt | 1793 +++++++++++++++++++++++++ forester/archive/Applets/MainFrameApplet.txt | 330 +++++ forester/archive/Applets/MainPanelApplets.txt | 90 ++ 4 files changed, 2460 insertions(+) create mode 100644 forester/archive/Applets/ArchaeopteryxA.txt create mode 100644 forester/archive/Applets/ArchaeopteryxE.txt create mode 100644 forester/archive/Applets/MainFrameApplet.txt create mode 100644 forester/archive/Applets/MainPanelApplets.txt diff --git a/forester/archive/Applets/ArchaeopteryxA.txt b/forester/archive/Applets/ArchaeopteryxA.txt new file mode 100644 index 0000000..6b4cdd7 --- /dev/null +++ b/forester/archive/Applets/ArchaeopteryxA.txt @@ -0,0 +1,247 @@ +// $Id: +// FORESTER -- software libraries and applications +// for evolutionary biology research and applications. +// +// Copyright (C) 2008-2009 Christian M. Zmasek +// Copyright (C) 2008-2009 Burnham Institute for Medical Research +// 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: https://sites.google.com/site/cmzmasek/home/software/forester + +package org.forester.archaeopteryx; + +import java.awt.Color; +import java.awt.Font; +import java.awt.Graphics; +import java.awt.KeyboardFocusManager; +import java.io.File; +import java.net.URL; + +import javax.swing.JApplet; +import javax.swing.UIManager; + +import org.forester.phylogeny.Phylogeny; +import org.forester.util.ForesterUtil; + +public class ArchaeopteryxA extends JApplet { + + private static final long serialVersionUID = 2314899014580484146L; + private final static Color background_color = new Color( 0, 0, 0 ); + private final static Color font_color = new Color( 0, 255, 0 ); + private final static Color ex_background_color = new Color( 0, 0, 0 ); + private final static Color ex_font_color = new Color( 255, 0, 0 ); + private final static Font font = new Font( Configuration.getDefaultFontFamilyName(), Font.BOLD, 9 ); + private MainFrameApplet _mainframe_applet; + private String _tree_url_str = ""; + private String _species_tree_url_str = ""; + private String _message_1 = ""; + private String _message_2 = ""; + public final static String NAME = "ArchaeopteryxA"; + + @Override + public void destroy() { + AptxUtil.printAppletMessage( NAME, "going to be destroyed" ); + if ( getMainFrameApplet() != null ) { + getMainFrameApplet().close(); + } + } + + /** + * This method returns the current external node data which + * has been selected by the user by clicking the "Return ..." + * menu item. This method is expected to be called from Javascript or + * something like it. + * + * @return current external node data as String + */ + public String getCurrentExternalNodesDataBuffer() { + return getMainFrameApplet().getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString(); + } + + public int getCurrentExternalNodesDataBufferChangeCounter() { + return getMainFrameApplet().getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter(); + } + + public int getCurrentExternalNodesDataBufferLength() { + return getMainFrameApplet().getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length(); + } + + public String getSpeciesTreeUrlStr() { + return _species_tree_url_str; + } + + public String getTreeUrlStr() { + return _tree_url_str; + } + + @Override + public void init() { + boolean has_exception = false; + setName( NAME ); + setTreeUrlStr( getParameter( AptxConstants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD ) ); + setSpeciesTreeUrlStr( getParameter( AptxConstants.APPLET_PARAM_NAME_FOR_URL_OF_SPECIES_TREE_TO_LOAD ) ); + if ( !ForesterUtil.isEmpty( getTreeUrlStr() ) ) { + AptxUtil.printAppletMessage( NAME, "URL of tree(s) to load: " + getTreeUrlStr() ); + } + else { + ForesterUtil.printErrorMessage( NAME, "no URL for tree(s) to load!" ); + setBackground( ex_background_color ); + setForeground( ex_font_color ); + has_exception = true; + setMessage1( "no URL for tree(s) to load" ); + repaint(); + } + if ( !ForesterUtil.isEmpty( getSpeciesTreeUrlStr() ) ) { + AptxUtil.printAppletMessage( NAME, "URL of species tree to load: " + getSpeciesTreeUrlStr() ); + } + setBackground( background_color ); + setForeground( font_color ); + setFont( font ); + repaint(); + String s = null; + try { + s = System.getProperty( "java.version" ); + } + catch ( final Exception e ) { + ForesterUtil.printWarningMessage( NAME, "minor error: " + e.getLocalizedMessage() ); + } + if ( ( s != null ) && ( s.length() > 0 ) ) { + setMessage2( "[Your Java version: " + s + "]" ); + repaint(); + } + final String config_filename = getParameter( AptxConstants.APPLET_PARAM_NAME_FOR_CONFIG_FILE_URL ); + AptxUtil.printAppletMessage( NAME, "URL for configuration file is: " + config_filename ); + final Configuration configuration = new Configuration( config_filename, true, true, true ); + try { + if ( configuration.isUseNativeUI() ) { + UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() ); + } + else { + UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() ); + } + setVisible( false ); + _mainframe_applet = new MainFrameApplet( this, configuration, getSpeciesTreeUrlStr() ); + final URL tree_url = new URL( getTreeUrlStr() ); + final Phylogeny[] phys = AptxUtil.readPhylogeniesFromUrl( tree_url, configuration + .isValidatePhyloXmlAgainstSchema(), configuration.isReplaceUnderscoresInNhParsing(), configuration + .isInternalNumberAreConfidenceForNhParsing(), configuration.getTaxonomyExtraction(), configuration + .isMidpointReroot() ); + if ( phys == null ) { + ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + tree_url + "] are null" ); + } + else if ( phys.length < 1 ) { + ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + tree_url + "] are empty" ); + } + else { + AptxUtil.printAppletMessage( NAME, "loaded " + phys.length + " phylogenies from: " + tree_url ); + } + AptxUtil.printAppletMessage( ArchaeopteryxA.NAME, "loaded " + phys.length + " phylogenies from: " + + tree_url ); + AptxUtil.addPhylogeniesToTabs( phys, + new File( tree_url.getFile() ).getName(), + getTreeUrlStr(), + getMainFrameApplet().getConfiguration(), + getMainFrameApplet().getMainPanel() ); + getMainFrameApplet().getMainPanel().getControlPanel().showWholeAll(); + getMainFrameApplet().getMainPanel().getControlPanel().showWhole(); + setVisible( true ); + } + catch ( final Exception e ) { + ForesterUtil.printErrorMessage( NAME, e.toString() ); + setBackground( ex_background_color ); + setForeground( ex_font_color ); + has_exception = true; + setMessage1( "Exception: " + e ); + e.printStackTrace(); + repaint(); + } + if ( !has_exception ) { + setMessage1( NAME + " is now ready!" ); + repaint(); + AptxUtil.printAppletMessage( NAME, "successfully initialized" ); + } + KeyboardFocusManager.getCurrentKeyboardFocusManager().clearGlobalFocusOwner(); + getMainFrameApplet().requestFocus(); + getMainFrameApplet().requestFocusInWindow(); + getMainFrameApplet().requestFocus(); + /* GUILHEM_BEG */ + final String default_relation = getParameter( AptxConstants.APPLET_PARAM_NAME_FOR_DEFAULT_SEQUENCE_RELATION_TYPE ); + if ( default_relation != null ) { + getMainFrameApplet().getMainPanel().getControlPanel().getSequenceRelationTypeBox() + .setSelectedItem( default_relation ); + } + final String default_sequence = getParameter( AptxConstants.APPLET_PARAM_NAME_FOR_DEFAULT_QUERY_SEQUENCE ); + if ( default_sequence != null ) { + getMainFrameApplet().getMainPanel().getControlPanel().getSequenceRelationBox() + .setSelectedItem( default_sequence ); + } + /* GUILHEM_END */ + } + + /** + * Prints message when initialization is finished. Called automatically. + * + * @param g + * Graphics + */ + @Override + public void paint( final Graphics g ) { + g.setColor( background_color ); + g.fillRect( 0, 0, 300, 60 ); + g.setColor( font_color ); + g.drawString( getMessage2(), 10, 20 ); + g.drawString( getMessage1(), 10, 40 ); + } + + @Override + public void start() { + getMainFrameApplet().getMainPanel().validate(); + getMainFrameApplet().requestFocus(); + getMainFrameApplet().requestFocusInWindow(); + getMainFrameApplet().requestFocus(); + AptxUtil.printAppletMessage( NAME, "started" ); + } + + private MainFrameApplet getMainFrameApplet() { + return _mainframe_applet; + } + + private String getMessage1() { + return _message_1; + } + + private String getMessage2() { + return _message_2; + } + + private void setMessage1( final String message_1 ) { + _message_1 = message_1; + } + + private void setMessage2( final String message_2 ) { + _message_2 = message_2; + } + + private void setSpeciesTreeUrlStr( final String url_string ) { + _species_tree_url_str = url_string; + } + + private void setTreeUrlStr( final String url_string ) { + _tree_url_str = url_string; + } +} diff --git a/forester/archive/Applets/ArchaeopteryxE.txt b/forester/archive/Applets/ArchaeopteryxE.txt new file mode 100644 index 0000000..694036b --- /dev/null +++ b/forester/archive/Applets/ArchaeopteryxE.txt @@ -0,0 +1,1793 @@ + +package org.forester.archaeopteryx; + +import java.awt.BorderLayout; +import java.awt.Container; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.ComponentAdapter; +import java.awt.event.ComponentEvent; +import java.io.ByteArrayOutputStream; +import java.io.File; +import java.io.IOException; +import java.net.URL; +import java.util.LinkedList; +import java.util.List; +import java.util.NoSuchElementException; + +import javax.swing.ButtonGroup; +import javax.swing.JApplet; +import javax.swing.JCheckBoxMenuItem; +import javax.swing.JFileChooser; +import javax.swing.JMenu; +import javax.swing.JMenuBar; +import javax.swing.JMenuItem; +import javax.swing.JOptionPane; +import javax.swing.JRadioButtonMenuItem; +import javax.swing.UIManager; +import javax.swing.UnsupportedLookAndFeelException; +import javax.swing.event.ChangeEvent; +import javax.swing.event.ChangeListener; + +import org.apache.commons.codec.binary.Base64; +import org.forester.archaeopteryx.AptxUtil.GraphicsExportType; +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.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION; +import org.forester.phylogeny.Phylogeny; +import org.forester.phylogeny.PhylogenyMethods; +import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY; +import org.forester.phylogeny.data.SequenceRelation; +import org.forester.sdi.GSDI; +import org.forester.sdi.GSDIR; +import org.forester.sdi.SDIException; +import org.forester.util.ForesterConstants; +import org.forester.util.ForesterUtil; +import org.forester.util.WindowsUtils; + +// Use like this: +// +// +// +// +public class ArchaeopteryxE extends JApplet implements ActionListener { + + private final static String NAME = "ArchaeopteryxE"; + private static final long serialVersionUID = -1220055577935759443L; + private Configuration _configuration; + private MainPanel _mainpanel; + private JMenuBar _jmenubar; + private JMenu _options_jmenu; + private JMenu _font_size_menu; + private JMenuItem _super_tiny_fonts_mi; + private JMenuItem _tiny_fonts_mi; + private JMenuItem _small_fonts_mi; + private JMenuItem _medium_fonts_mi; + private JMenuItem _large_fonts_mi; + private JMenu _tools_menu; + private JMenuItem _taxcolor_item; + private JMenuItem _confcolor_item; + private JMenuItem _midpoint_root_item; + private JMenu _view_jmenu; + private JMenuItem _view_as_XML_item; + private JMenuItem _view_as_NH_item; + private JMenuItem _view_as_nexus_item; + private JMenuItem _display_basic_information_item; + private JMenu _type_menu; + private JCheckBoxMenuItem _rectangular_type_cbmi; + private JCheckBoxMenuItem _triangular_type_cbmi; + private JCheckBoxMenuItem _curved_type_cbmi; + private JCheckBoxMenuItem _convex_type_cbmi; + private JCheckBoxMenuItem _euro_type_cbmi; + private JCheckBoxMenuItem _rounded_type_cbmi; + private JCheckBoxMenuItem _unrooted_type_cbmi; + private JCheckBoxMenuItem _circular_type_cbmi; + private JMenuItem _help_item; + private JMenuItem _about_item; + private JMenu _help_jmenu; + private JMenuItem _website_item; + private JMenuItem _phyloxml_website_item; + private JMenuItem _phyloxml_ref_item; + private JMenuItem _aptx_ref_item; + private JMenuItem _remove_branch_color_item; + private JMenuItem _remove_visual_styles_item; + private JCheckBoxMenuItem _show_domain_labels; + private JCheckBoxMenuItem _show_annotation_ref_source; + private JCheckBoxMenuItem _color_labels_same_as_parent_branch; + private JCheckBoxMenuItem _abbreviate_scientific_names; + private JCheckBoxMenuItem _screen_antialias_cbmi; + private JCheckBoxMenuItem _background_gradient_cbmi; + private JCheckBoxMenuItem _color_by_taxonomic_group_cbmi; + private JRadioButtonMenuItem _non_lined_up_cladograms_rbmi; + private JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi; + private Options _options; + private JMenuItem _choose_font_mi; + private JMenuItem _switch_colors_mi; + JCheckBoxMenuItem _label_direction_cbmi; + private JCheckBoxMenuItem _show_scale_cbmi; + private JCheckBoxMenuItem _search_case_senstive_cbmi; + private JCheckBoxMenuItem _search_whole_words_only_cbmi; + private JCheckBoxMenuItem _inverse_search_result_cbmi; + private JCheckBoxMenuItem _search_with_regex_cbmi; + private JCheckBoxMenuItem _show_overview_cbmi; + private JMenuItem _choose_minimal_confidence_mi; + private JMenuItem _collapse_species_specific_subtrees; + private JMenuItem _overview_placment_mi; + private ButtonGroup _radio_group_1; + private JCheckBoxMenuItem _show_default_node_shapes_internal_cbmi; + private JCheckBoxMenuItem _show_default_node_shapes_external_cbmi; + private JCheckBoxMenuItem _show_default_node_shapes_for_marked_cbmi; + private JMenuItem _cycle_node_shape_mi; + private JMenuItem _cycle_node_fill_mi; + private JMenuItem _choose_node_size_mi; + private JCheckBoxMenuItem _show_confidence_stddev_cbmi; + private final LinkedList _textframes = new LinkedList(); + private JMenu _analysis_menu; + private JMenuItem _gsdi_item; + private JMenuItem _gsdir_item; + private Phylogeny _species_tree; + private JCheckBoxMenuItem _right_line_up_domains_cbmi; + private JCheckBoxMenuItem _line_up_renderable_data_cbmi; + // file menu: + private JMenuItem _save_item; + private JMenuItem _print_item; + private JMenuItem _write_to_pdf_item; + private JMenuItem _write_to_jpg_item; + private JMenuItem _write_to_gif_item; + private JMenuItem _write_to_tif_item; + private JMenuItem _write_to_png_item; + private JMenuItem _write_to_bmp_item; + private JMenu _file_jmenu; + private JFileChooser _writetopdf_filechooser; + private File _current_dir; + private JFileChooser _save_filechooser; + private JFileChooser _writetographics_filechooser; + private JCheckBoxMenuItem _graphics_export_visible_only_cbmi; + private JCheckBoxMenuItem _antialias_print_cbmi; + private JCheckBoxMenuItem _print_black_and_white_cbmi; + private JMenuItem _choose_pdf_width_mi; + + @Override + public void actionPerformed( final ActionEvent e ) { + final Object o = e.getSource(); + if ( o == _midpoint_root_item ) { + getMainPanel().getCurrentTreePanel().midpointRoot(); + } + else if ( o == _gsdi_item ) { + if ( isSubtreeDisplayed() ) { + return; + } + executeGSDI(); + } + else if ( o == _gsdir_item ) { + if ( isSubtreeDisplayed() ) { + return; + } + executeGSDIR(); + } + else if ( o == _taxcolor_item ) { + getMainPanel().getCurrentTreePanel().taxColor(); + } + else if ( o == _confcolor_item ) { + getMainPanel().getCurrentTreePanel().confColor(); + } + else if ( o == _collapse_species_specific_subtrees ) { + if ( getCurrentTreePanel() != null ) { + getCurrentTreePanel().collapseSpeciesSpecificSubtrees(); + } + } + else if ( o == _remove_branch_color_item ) { + removeBranchColors(); + } + else if ( o == _remove_visual_styles_item ) { + removeVisualStyles(); + } + 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_XML_item ) { + viewAsXML(); + } + else if ( o == _view_as_nexus_item ) { + viewAsNexus(); + } + else if ( o == _super_tiny_fonts_mi ) { + if ( getCurrentTreePanel() != null ) { + getCurrentTreePanel().setSuperTinyFonts(); + getCurrentTreePanel().repaint(); + } + } + else if ( o == _tiny_fonts_mi ) { + if ( getCurrentTreePanel() != null ) { + getCurrentTreePanel().setTinyFonts(); + getCurrentTreePanel().repaint(); + } + } + else if ( o == _small_fonts_mi ) { + if ( getCurrentTreePanel() != null ) { + getCurrentTreePanel().setSmallFonts(); + getCurrentTreePanel().repaint(); + } + } + else if ( o == _medium_fonts_mi ) { + if ( getCurrentTreePanel() != null ) { + getCurrentTreePanel().setMediumFonts(); + getCurrentTreePanel().repaint(); + } + } + else if ( o == _large_fonts_mi ) { + 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 ) { + MainFrame.chooseNodeSize( getOptions(), this ); + } + else if ( o == _overview_placment_mi ) { + MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() ); + } + else if ( o == _cycle_node_fill_mi ) { + MainFrame.cycleNodeFill( getOptions() ); + } + else if ( o == _cycle_node_shape_mi ) { + MainFrame.cycleNodeShape( getOptions() ); + } + else if ( o == _non_lined_up_cladograms_rbmi ) { + updateOptions( getOptions() ); + _mainpanel.getControlPanel().showWhole(); + } + else if ( o == _ext_node_dependent_cladogram_rbmi ) { + updateOptions( getOptions() ); + _mainpanel.getControlPanel().showWhole(); + } + else if ( o == _search_case_senstive_cbmi ) { + updateOptions( getOptions() ); + getMainPanel().getControlPanel().search0(); + getMainPanel().getControlPanel().search1(); + } + else if ( o == _search_whole_words_only_cbmi ) { + if ( ( _search_with_regex_cbmi != null ) && _search_whole_words_only_cbmi.isSelected() ) { + _search_with_regex_cbmi.setSelected( false ); + } + updateOptions( getOptions() ); + getMainPanel().getControlPanel().search0(); + getMainPanel().getControlPanel().search1(); + } + else if ( o == _inverse_search_result_cbmi ) { + updateOptions( getOptions() ); + getMainPanel().getControlPanel().search0(); + getMainPanel().getControlPanel().search1(); + } + else if ( o == _search_with_regex_cbmi ) { + if ( ( _search_whole_words_only_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) { + _search_whole_words_only_cbmi.setSelected( false ); + } + if ( ( _search_case_senstive_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) { + _search_case_senstive_cbmi.setSelected( true ); + } + updateOptions( getOptions() ); + getMainPanel().getControlPanel().search0(); + getMainPanel().getControlPanel().search1(); + } + else if ( o == _show_scale_cbmi ) { + updateOptions( getOptions() ); + } + else if ( o == _show_confidence_stddev_cbmi ) { + updateOptions( getOptions() ); + } + else if ( o == _label_direction_cbmi ) { + updateOptions( getOptions() ); + } + else if ( o == _abbreviate_scientific_names ) { + 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 == _rounded_type_cbmi ) || ( o == _euro_type_cbmi ) + || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) { + typeChanged( o ); + } + else if ( o == _screen_antialias_cbmi ) { + updateOptions( getOptions() ); + setupScreenTextAntialias( getMainPanel().getTreePanels(), isScreenAntialias() ); + } + else if ( o == _background_gradient_cbmi ) { + updateOptions( getOptions() ); + } + else if ( o == _show_domain_labels ) { + updateOptions( getOptions() ); + } + else if ( o == _color_labels_same_as_parent_branch ) { + updateOptions( getOptions() ); + } + else if ( o == _show_default_node_shapes_internal_cbmi ) { + updateOptions( getOptions() ); + } + else if ( o == _show_default_node_shapes_external_cbmi ) { + updateOptions( getOptions() ); + } + else if ( o == _about_item ) { + getMainPanel().getMainFrame().about(); + } + else if ( o == _help_item ) { + try { + AptxUtil.openWebsite( AptxConstants.APTX_DOC_SITE, true, this ); + } + catch ( final IOException e1 ) { + ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() ); + } + } + else if ( o == _website_item ) { + try { + AptxUtil.openWebsite( AptxConstants.APTX_WEB_SITE, true, this ); + } + catch ( final IOException e1 ) { + ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() ); + } + } + else if ( o == _phyloxml_website_item ) { + try { + AptxUtil.openWebsite( AptxConstants.PHYLOXML_WEB_SITE, true, this ); + } + catch ( final IOException e1 ) { + ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() ); + } + } + else if ( o == _aptx_ref_item ) { + try { + AptxUtil.openWebsite( AptxConstants.APTX_REFERENCE_URL, true, this ); + } + catch ( final IOException e1 ) { + ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() ); + } + } + else if ( o == _phyloxml_ref_item ) { + try { + AptxUtil.openWebsite( AptxConstants.PHYLOXML_REFERENCE_URL, true, this ); + } + catch ( final IOException e1 ) { + ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() ); + } + } + else if ( o == _color_by_taxonomic_group_cbmi ) { + updateOptions( getOptions() ); + } + else if ( o == _line_up_renderable_data_cbmi ) { + if ( !_line_up_renderable_data_cbmi.isSelected() ) { + _right_line_up_domains_cbmi.setSelected( false ); + } + updateOptions( getOptions() ); + } + else if ( o == _right_line_up_domains_cbmi ) { + if ( _right_line_up_domains_cbmi.isSelected() ) { + _line_up_renderable_data_cbmi.setSelected( true ); + } + updateOptions( getOptions() ); + } + else if ( o == _write_to_pdf_item ) { + final File curr_dir = MainFrame.writeToPdf( _mainpanel.getCurrentPhylogeny(), + getMainPanel(), + _writetopdf_filechooser, + _current_dir, + getContentPane(), + this ); + if ( curr_dir != null ) { + setCurrentDir( curr_dir ); + } + } + else if ( o == _write_to_jpg_item ) { + final File curr_dir = MainFrame.writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), + GraphicsExportType.JPG, + _mainpanel, + _writetographics_filechooser, + this, + getContentPane(), + _current_dir ); + if ( curr_dir != null ) { + setCurrentDir( curr_dir ); + } + } + else if ( o == _write_to_gif_item ) { + final File curr_dir = MainFrame.writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), + GraphicsExportType.GIF, + _mainpanel, + _writetographics_filechooser, + this, + getContentPane(), + _current_dir ); + if ( curr_dir != null ) { + setCurrentDir( curr_dir ); + } + } + else if ( o == _write_to_tif_item ) { + final File curr_dir = MainFrame.writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), + GraphicsExportType.TIFF, + _mainpanel, + _writetographics_filechooser, + this, + getContentPane(), + _current_dir ); + if ( curr_dir != null ) { + setCurrentDir( curr_dir ); + } + } + else if ( o == _write_to_bmp_item ) { + final File curr_dir = MainFrame.writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), + GraphicsExportType.BMP, + _mainpanel, + _writetographics_filechooser, + this, + getContentPane(), + _current_dir ); + if ( curr_dir != null ) { + setCurrentDir( curr_dir ); + } + } + else if ( o == _write_to_png_item ) { + final File curr_dir = MainFrame.writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), + GraphicsExportType.PNG, + _mainpanel, + _writetographics_filechooser, + this, + getContentPane(), + _current_dir ); + if ( curr_dir != null ) { + setCurrentDir( curr_dir ); + } + } + else if ( o == _print_item ) { + MainFrame.print( getCurrentTreePanel(), getOptions(), this ); + } + else if ( o == _save_item ) { + final File new_dir = MainFrame.writeToFile( _mainpanel.getCurrentPhylogeny(), + getMainPanel(), + _save_filechooser, + _current_dir, + getContentPane(), + this ); + if ( new_dir != null ) { + setCurrentDir( new_dir ); + } + } + else if ( o == _graphics_export_visible_only_cbmi ) { + updateOptions( getOptions() ); + } + else if ( o == _antialias_print_cbmi ) { + updateOptions( getOptions() ); + } + else if ( o == _print_black_and_white_cbmi ) { + updateOptions( getOptions() ); + } + else if ( o == _choose_pdf_width_mi ) { + choosePdfWidth(); + } + repaint(); + } + + @Override + public void destroy() { + AptxUtil.printAppletMessage( NAME, "going to be destroyed " ); + removeAllTextFrames(); + if ( getMainPanel() != null ) { + getMainPanel().terminate(); + } + } + + /** + * This method returns the current external node data which + * has been selected by the user by clicking the "Return ..." + * menu item. This method is expected to be called from Javascript or + * something like it. + * + * @return current external node data as String + */ + public String getCurrentExternalNodesDataBuffer() { + return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString(); + } + + public int getCurrentExternalNodesDataBufferChangeCounter() { + return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter(); + } + + public int getCurrentExternalNodesDataBufferLength() { + return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length(); + } + + /** + * This method returns the current phylogeny as a string in the chosen format + * + * @param format must be NH, NHX, NEXUS or PHYLOXML + * @return the phylogeny string + * @author Herve Menager + */ + public String getCurrentPhylogeny( final String format ) { + removeAllTextFrames(); + if ( ( getMainPanel().getCurrentPhylogeny() == null ) || getMainPanel().getCurrentPhylogeny().isEmpty() + || ( getMainPanel().getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) { + return new String(); + } + switch ( ForesterConstants.PhylogeneticTreeFormats.valueOf( format ) ) { + case NH: + return getMainPanel().getCurrentPhylogeny().toNewHampshire(); + case NHX: + return getMainPanel().getCurrentPhylogeny().toNewHampshireX(); + case NEXUS: + return getMainPanel().getCurrentPhylogeny().toNexus(); + case PHYLOXML: + return getMainPanel().getCurrentPhylogeny().toPhyloXML( -1 ); + default: + break; + } + return new String(); + } + + /** + * This method returns a view of the current phylogeny in a chosen + * graphics format, base64-encoded in a string so that in can be used + * from javascript. + * + * @param format must be GraphicsExportType (gif, jpg, pdf, png, tif, bmp) + * @return the phylogeny string + * @author Herve Menager + */ + public String getCurrentPhylogenyGraphicsAsBase64EncodedString( final String format ) { + final ByteArrayOutputStream baos = new ByteArrayOutputStream(); + try { + AptxUtil.writePhylogenyToGraphicsByteArrayOutputStream( baos, + _mainpanel.getWidth(), + _mainpanel.getHeight(), + getCurrentTreePanel(), + getCurrentTreePanel().getControlPanel(), + GraphicsExportType.valueOf( format ), + getOptions() ); + } + catch ( final IOException ioe ) { + ForesterUtil.printErrorMessage( NAME, ioe.toString() ); + ioe.printStackTrace(); + JOptionPane.showMessageDialog( this, + NAME + ": Failed to generate graphics: " + "\nException: " + ioe, + "Failed to generate graphics", + JOptionPane.ERROR_MESSAGE ); + return null; + } + final byte[] bytes = baos.toByteArray(); + final String dataImg = Base64.encodeBase64String( bytes ); + return dataImg; + } + + public Options getOptions() { + return _options; + } + + @Override + public void init() { + _writetopdf_filechooser = new JFileChooser(); + _writetopdf_filechooser.setMultiSelectionEnabled( false ); + _writetopdf_filechooser.addChoosableFileFilter( MainFrame.pdffilter ); + _writetographics_filechooser = new JFileChooser(); + _writetographics_filechooser.setMultiSelectionEnabled( false ); + _writetographics_filechooser.addChoosableFileFilter( MainFrame.graphicsfilefilter ); + _save_filechooser = new JFileChooser(); + _save_filechooser.setMultiSelectionEnabled( false ); + _save_filechooser.setFileFilter( MainFrame.xmlfilter ); + _save_filechooser.addChoosableFileFilter( MainFrame.nhfilter ); + _save_filechooser.addChoosableFileFilter( MainFrame.nexusfilter ); + _save_filechooser.addChoosableFileFilter( _save_filechooser.getAcceptAllFileFilter() ); + try { + final String home_dir = System.getProperty( "user.home" ); + _save_filechooser.setCurrentDirectory( new File( home_dir ) ); + _writetopdf_filechooser.setCurrentDirectory( new File( home_dir ) ); + _writetographics_filechooser.setCurrentDirectory( new File( home_dir ) ); + } + catch ( final Exception e ) { + e.printStackTrace(); + // Do nothing. Not important. + } + final String config_filename = getParameter( AptxConstants.APPLET_PARAM_NAME_FOR_CONFIG_FILE_URL ); + AptxUtil.printAppletMessage( NAME, "URL for configuration file is: " + config_filename ); + final Configuration configuration = new Configuration( config_filename, true, true, true ); + setConfiguration( configuration ); + setOptions( Options.createInstance( configuration ) ); + setupUI(); + final String tree_url_str = getParameter( AptxConstants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD ); + if ( ForesterUtil.isEmpty( tree_url_str ) ) { + ForesterUtil.printErrorMessage( NAME, "could not get tree URL from " + + AptxConstants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD ); + JOptionPane.showMessageDialog( this, NAME + ": could not get tree URL from " + + AptxConstants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD, "Failed get URL", JOptionPane.ERROR_MESSAGE ); + return; + } + AptxUtil.printAppletMessage( NAME, "URL for phylogenies is " + tree_url_str ); + // Get URL to tree file + URL phys_url = null; + try { + phys_url = new URL( tree_url_str ); + } + catch ( final Exception e ) { + ForesterUtil.printErrorMessage( NAME, "error: " + e ); + e.printStackTrace(); + JOptionPane.showMessageDialog( this, NAME + ": Could not create URL from: \"" + tree_url_str + + "\"\nException: " + e, "Failed to create URL", JOptionPane.ERROR_MESSAGE ); + } + if ( phys_url == null ) { + ForesterUtil.printErrorMessage( NAME, "failed to get tree URL from " + + AptxConstants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD ); + JOptionPane.showMessageDialog( this, + NAME + ": Could not create URL from: \"" + tree_url_str, + "Failed to create URL", + JOptionPane.ERROR_MESSAGE ); + return; + } + // Load the tree from URL + Phylogeny[] phys = null; + try { + phys = AptxUtil.readPhylogeniesFromUrl( phys_url, + getConfiguration().isValidatePhyloXmlAgainstSchema(), + getConfiguration().isReplaceUnderscoresInNhParsing(), + getConfiguration().isInternalNumberAreConfidenceForNhParsing(), + getConfiguration().getTaxonomyExtraction(), + getConfiguration().isMidpointReroot() ); + } + catch ( final Exception e ) { + ForesterUtil.printErrorMessage( NAME, e.toString() ); + e.printStackTrace(); + JOptionPane.showMessageDialog( this, + NAME + ": Failed to read phylogenies: " + "\nException: " + e, + "Failed to read phylogenies", + JOptionPane.ERROR_MESSAGE ); + } + if ( phys == null ) { + ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + phys_url + "] are null" ); + JOptionPane.showMessageDialog( this, + NAME + ": phylogenies from [" + phys_url + "] are null", + "Failed to read phylogenies", + JOptionPane.ERROR_MESSAGE ); + return; + } + else if ( phys.length < 1 ) { + ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + phys_url + "] are empty" ); + JOptionPane.showMessageDialog( this, + NAME + ": phylogenies from [" + phys_url + "] are empty", + "Failed to read phylogenies", + JOptionPane.ERROR_MESSAGE ); + return; + } + else { + AptxUtil.printAppletMessage( NAME, "loaded " + phys.length + " phylogenies from: " + phys_url ); + } + // + final String species_tree_url_str = getParameter( AptxConstants.APPLET_PARAM_NAME_FOR_URL_OF_SPECIES_TREE_TO_LOAD ); + if ( !ForesterUtil.isEmpty( species_tree_url_str ) ) { + AptxUtil.printAppletMessage( NAME, "URL of species tree to load: \"" + species_tree_url_str + "\"" ); + Phylogeny[] species_trees = null; + try { + final URL species_tree_url = new URL( species_tree_url_str ); + species_trees = AptxUtil.readPhylogeniesFromUrl( species_tree_url, + configuration.isValidatePhyloXmlAgainstSchema(), + configuration.isReplaceUnderscoresInNhParsing(), + false, + TAXONOMY_EXTRACTION.NO, + false ); + } + catch ( final IOException e ) { + ForesterUtil.printErrorMessage( NAME, "could not read species tree from [" + species_tree_url_str + + "]" ); + JOptionPane.showMessageDialog( this, NAME + ": could not read species tree from [" + + species_tree_url_str + "]", "Failed to read species tree", JOptionPane.ERROR_MESSAGE ); + } + if ( ( species_trees != null ) && ( species_trees.length > 0 ) ) { + AptxUtil.printAppletMessage( NAME, "successfully read species tree" ); + if ( species_trees[ 0 ].isEmpty() ) { + ForesterUtil.printErrorMessage( NAME, "species tree is empty" ); + } + else if ( !species_trees[ 0 ].isRooted() ) { + ForesterUtil.printErrorMessage( NAME, "species tree is not rooted" ); + } + else { + setSpeciesTree( species_trees[ 0 ] ); + AptxUtil.printAppletMessage( NAME, "species tree OK" ); + } + } + } + try { + setVisible( false ); + setMainPanel( new MainPanelApplets( getConfiguration(), this ) ); + _jmenubar = new JMenuBar(); + if ( !getConfiguration().isHideControlPanelAndMenubar() ) { + buildFileMenu(); + if ( !getConfiguration().isUseNativeUI() ) { + _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() ); + } + if ( getSpeciesTree() != null ) { + buildAnalysisMenu(); + } + buildToolsMenu(); + buildViewMenu(); + buildFontSizeMenu(); + buildOptionsMenu(); + buildTypeMenu(); + buildHelpMenu(); + setJMenuBar( _jmenubar ); + } + final Container contentpane = getContentPane(); + contentpane.setLayout( new BorderLayout() ); + contentpane.add( getMainPanel(), BorderLayout.CENTER ); + addComponentListener( new ComponentAdapter() { + + @Override + public void componentResized( final ComponentEvent e ) { + if ( getMainPanel().getCurrentTreePanel() != null ) { + getMainPanel().getCurrentTreePanel().calcParametersForPainting( getMainPanel() + .getCurrentTreePanel() + .getWidth(), + getMainPanel() + .getCurrentTreePanel() + .getHeight() ); + } + } + } ); + if ( getConfiguration().isUseTabbedDisplay() ) { + try { + AptxUtil.printAppletMessage( NAME, "using tabbed display" ); + AptxUtil.addPhylogeniesToTabs( phys, + new File( phys_url.getFile() ).getName(), + phys_url.toString(), + getConfiguration(), + getMainPanel() ); + } + catch ( final Exception e ) { + ForesterUtil.printErrorMessage( NAME, e.toString() ); + e.printStackTrace(); + } + } + else { + AptxUtil.printAppletMessage( NAME, "not using tabbed display" ); + if ( getSpeciesTree() != null ) { + AptxUtil.printAppletMessage( NAME, + "Warning: gsdi (gene duplication inference) only available tabbed display" ); + } + AptxUtil.addPhylogenyToPanel( phys, getConfiguration(), getMainPanel() ); + } + validate(); + setName( NAME ); + getMainPanel().getControlPanel().showWholeAll(); + getMainPanel().getControlPanel().showWhole(); + /* GUILHEM_BEG */ + getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().removeAllItems(); + for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : getMainPanel().getCurrentPhylogeny() + .getRelevantSequenceRelationTypes() ) { + getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().addItem( type ); + } + final String default_relation = getParameter( AptxConstants.APPLET_PARAM_NAME_FOR_DEFAULT_SEQUENCE_RELATION_TYPE ); + if ( default_relation != null ) { + getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().setSelectedItem( default_relation ); + } + final String default_sequence = getParameter( AptxConstants.APPLET_PARAM_NAME_FOR_DEFAULT_QUERY_SEQUENCE ); + if ( default_sequence != null ) { + getCurrentTreePanel().getControlPanel().getSequenceRelationBox().setSelectedItem( default_sequence ); + } + /* GUILHEM_END */ + System.gc(); + AptxUtil.printAppletMessage( NAME, "successfully initialized" ); + setVisible( true ); + } + catch ( final Exception e ) { + ForesterUtil.printErrorMessage( NAME, e.toString() ); + e.printStackTrace(); + } + } + + public void showTextFrame( final String s, final String title ) { + checkTextFrames(); + _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) ); + } + + @Override + public void start() { + if ( getMainPanel() != null ) { + getMainPanel().validate(); + } + requestFocus(); + requestFocusInWindow(); + requestFocus(); + AptxUtil.printAppletMessage( NAME, "started" ); + } + + 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 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 ); + } + } + } + + private void choosePdfWidth() { + final String s = ( String ) JOptionPane.showInputDialog( this, + "Please enter the default line width for PDF export.\n" + + "[current value: " + + getOptions().getPrintLineWidth() + "]\n", + "Line Width for PDF Export", + JOptionPane.QUESTION_MESSAGE, + null, + null, + getOptions().getPrintLineWidth() ); + if ( !ForesterUtil.isEmpty( s ) ) { + boolean success = true; + float f = 0.0f; + final String m_str = s.trim(); + if ( !ForesterUtil.isEmpty( m_str ) ) { + try { + f = Float.parseFloat( m_str ); + } + catch ( final Exception ex ) { + success = false; + } + } + else { + success = false; + } + if ( success && ( f > 0.0 ) ) { + getOptions().setPrintLineWidth( f ); + } + } + } + + private 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 ); + } + } + + private Phylogeny getSpeciesTree() { + return _species_tree; + } + + private boolean isScreenAntialias() { + return true; + } + + private void removeBranchColors() { + if ( getMainPanel().getCurrentPhylogeny() != null ) { + AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() ); + } + } + + private void removeVisualStyles() { + if ( getMainPanel().getCurrentPhylogeny() != null ) { + AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() ); + } + } + + private void setMainPanel( final MainPanelApplets main_panel ) { + _mainpanel = main_panel; + } + + private void setSpeciesTree( final Phylogeny species_tree ) { + _species_tree = species_tree; + } + + private void setupUI() { + try { + if ( getConfiguration().isUseNativeUI() ) { + UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() ); + } + else { + UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() ); + } + } + catch ( final UnsupportedLookAndFeelException e ) { + AptxUtil.dieWithSystemError( "UnsupportedLookAndFeelException: " + e.toString() ); + } + catch ( final ClassNotFoundException e ) { + AptxUtil.dieWithSystemError( "ClassNotFoundException: " + e.toString() ); + } + catch ( final InstantiationException e ) { + AptxUtil.dieWithSystemError( "InstantiationException: " + e.toString() ); + } + catch ( final IllegalAccessException e ) { + AptxUtil.dieWithSystemError( "IllegalAccessException: " + e.toString() ); + } + catch ( final Exception e ) { + AptxUtil.dieWithSystemError( e.toString() ); + } + } + + void buildAnalysisMenu() { + _analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() ); + _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) ); + _analysis_menu.add( _gsdir_item = new JMenuItem( "GSDIR (GSDI with re-rooting)" ) ); + customizeJMenuItem( _gsdi_item ); + customizeJMenuItem( _gsdir_item ); + _analysis_menu.addSeparator(); + _jmenubar.add( _analysis_menu ); + } + + void buildFileMenu() { + _file_jmenu = MainFrame.createMenu( "File", getConfiguration() ); + _file_jmenu.add( _save_item = new JMenuItem( "Save Tree As..." ) ); + _file_jmenu.addSeparator(); + _file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) ); + if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" ) || AptxUtil.canWriteFormat( "TIF" ) ) { + _file_jmenu.add( _write_to_tif_item = new JMenuItem( "Export to TIFF file..." ) ); + } + _file_jmenu.add( _write_to_png_item = new JMenuItem( "Export to PNG file..." ) ); + _file_jmenu.add( _write_to_jpg_item = new JMenuItem( "Export to JPG file..." ) ); + if ( AptxUtil.canWriteFormat( "gif" ) ) { + _file_jmenu.add( _write_to_gif_item = new JMenuItem( "Export to GIF file..." ) ); + } + if ( AptxUtil.canWriteFormat( "bmp" ) ) { + _file_jmenu.add( _write_to_bmp_item = new JMenuItem( "Export to BMP file..." ) ); + } + _file_jmenu.addSeparator(); + _file_jmenu.add( _print_item = new JMenuItem( "Print..." ) ); + customizeJMenuItem( _save_item ); + customizeJMenuItem( _write_to_pdf_item ); + customizeJMenuItem( _write_to_png_item ); + customizeJMenuItem( _write_to_jpg_item ); + customizeJMenuItem( _write_to_gif_item ); + customizeJMenuItem( _write_to_tif_item ); + customizeJMenuItem( _write_to_bmp_item ); + customizeJMenuItem( _print_item ); + _jmenubar.add( _file_jmenu ); + } + + void buildFontSizeMenu() { + _font_size_menu = MainFrame.createMenu( MainFrame.FONT_SIZE_MENU_LABEL, getConfiguration() ); + _font_size_menu.add( _super_tiny_fonts_mi = new JMenuItem( "Super tiny fonts" ) ); + _font_size_menu.add( _tiny_fonts_mi = new JMenuItem( "Tiny fonts" ) ); + _font_size_menu.add( _small_fonts_mi = new JMenuItem( "Small fonts" ) ); + _font_size_menu.add( _medium_fonts_mi = new JMenuItem( "Medium fonts" ) ); + _font_size_menu.add( _large_fonts_mi = new JMenuItem( "Large fonts" ) ); + customizeJMenuItem( _super_tiny_fonts_mi ); + customizeJMenuItem( _tiny_fonts_mi ); + customizeJMenuItem( _small_fonts_mi ); + customizeJMenuItem( _medium_fonts_mi ); + customizeJMenuItem( _large_fonts_mi ); + _jmenubar.add( _font_size_menu ); + } + + void buildHelpMenu() { + _help_jmenu = MainFrame.createMenu( "Help", getConfiguration() ); + _help_jmenu.add( _help_item = new JMenuItem( "Documentation" ) ); + _help_jmenu.addSeparator(); + _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( MainFrame.PHYLOXML_REF_TOOL_TIP ); + _aptx_ref_item.setToolTipText( MainFrame.APTX_REF_TOOL_TIP ); + _jmenubar.add( _help_jmenu ); + } + + void buildOptionsMenu() { + _options_jmenu = MainFrame.createMenu( MainFrame.OPTIONS_HEADER, getConfiguration() ); + _options_jmenu.addChangeListener( new ChangeListener() { + + @Override + public void stateChanged( final ChangeEvent e ) { + MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() ); + MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() ); + MainFrame + .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() ); + MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame + .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) ); + setTextForPdfLineWidthChooserMenuItem( _choose_pdf_width_mi, getOptions() ); + MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() ); + MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() ); + MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() ); + try { + getMainPanel().getControlPanel().setVisibilityOfDomainStrucureCB(); + getMainPanel().getControlPanel().setVisibilityOfX(); + } + catch ( final Exception ignore ) { + // do nothing, not important. + } + } + } ); + _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.DISPLAY_SUBHEADER ), + getConfiguration() ) ); + _options_jmenu + .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) ); + _options_jmenu + .add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.NON_LINED_UP_CLADOGRAMS_LABEL ) ); + _radio_group_1 = new ButtonGroup(); + _radio_group_1.add( _ext_node_dependent_cladogram_rbmi ); + _radio_group_1.add( _non_lined_up_cladograms_rbmi ); + _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) ); + _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) ); + _options_jmenu + .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_INT ) ); + _options_jmenu + .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) ); + _options_jmenu + .add( _show_default_node_shapes_for_marked_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_MARKED ) ); + _options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) ); + if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) { + _options_jmenu.add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) ); + _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) ); + } + _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( MainFrame.SHOW_ANN_REF_SOURCE_LABEL ) ); + _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_CONF_STDDEV_LABEL ) ); + _options_jmenu + .add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( MainFrame.COLOR_BY_TAXONOMIC_GROUP ) ); + _options_jmenu + .add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) ); + _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP ); + _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( MainFrame.ABBREV_SN_LABEL ) ); + _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( MainFrame.LABEL_DIRECTION_LABEL ) ); + _label_direction_cbmi.setToolTipText( MainFrame.LABEL_DIRECTION_TIP ); + _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( MainFrame.SCREEN_ANTIALIAS_LABEL ) ); + _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( MainFrame.BG_GRAD_LABEL ) ); + _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) ); + _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) ); + _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) ); + _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) ); + _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) ); + _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) ); + _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) ); + _options_jmenu.addSeparator(); + _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.SEARCH_SUBHEADER ), + getConfiguration() ) ); + _options_jmenu + .add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_CASE_SENSITIVE_LABEL ) ); + _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_TERMS_ONLY_LABEL ) ); + _options_jmenu.add( _search_with_regex_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_REGEX_LABEL ) ); + _search_with_regex_cbmi.setToolTipText( MainFrame.SEARCH_WITH_REGEX_TIP ); + _options_jmenu + .add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( MainFrame.INVERSE_SEARCH_RESULT_LABEL ) ); + // + _options_jmenu.addSeparator(); + _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( "Graphics Export & Printing:" ), + getConfiguration() ) ); + _options_jmenu.add( _antialias_print_cbmi = new JCheckBoxMenuItem( "Antialias" ) ); + _options_jmenu.add( _print_black_and_white_cbmi = new JCheckBoxMenuItem( "Export in Black and White" ) ); + _options_jmenu + .add( _graphics_export_visible_only_cbmi = new JCheckBoxMenuItem( "Limit to Visible ('Screenshot') for PNG, JPG, and GIF export" ) ); + _options_jmenu.add( _choose_pdf_width_mi = new JMenuItem( "" ) ); + // + customizeCheckBoxMenuItem( _antialias_print_cbmi, getOptions().isAntialiasPrint() ); + customizeCheckBoxMenuItem( _print_black_and_white_cbmi, getOptions().isPrintBlackAndWhite() ); + customizeCheckBoxMenuItem( _graphics_export_visible_only_cbmi, getOptions().isGraphicsExportVisibleOnly() ); + customizeJMenuItem( _choose_pdf_width_mi ); + // + customizeJMenuItem( _choose_font_mi ); + customizeJMenuItem( _choose_minimal_confidence_mi ); + customizeJMenuItem( _switch_colors_mi ); + customizeJMenuItem( _overview_placment_mi ); + customizeCheckBoxMenuItem( _color_by_taxonomic_group_cbmi, getOptions().isColorByTaxonomicGroup() ); + customizeCheckBoxMenuItem( _label_direction_cbmi, + getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL ); + customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() ); + customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() ); + customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() ); + customizeCheckBoxMenuItem( _show_annotation_ref_source, getOptions().isShowAnnotationRefSource() ); + customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() ); + customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions() + .isShowDefaultNodeShapesExternal() ); + customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions() + .isShowDefaultNodeShapesInternal() ); + customizeCheckBoxMenuItem( _show_default_node_shapes_for_marked_cbmi, getOptions() + .isShowDefaultNodeShapesForMarkedNodes() ); + customizeJMenuItem( _cycle_node_shape_mi ); + customizeJMenuItem( _cycle_node_fill_mi ); + customizeJMenuItem( _choose_node_size_mi ); + customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() ); + customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() ); + customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() ); + customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi, + getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP ); + customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi, + getOptions().getCladogramType() == CLADOGRAM_TYPE.LINED_UP ); + customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() ); + customizeCheckBoxMenuItem( _search_with_regex_cbmi, getOptions().isSearchWithRegex() ); + customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() ); + customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() ); + customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() ); + customizeCheckBoxMenuItem( _line_up_renderable_data_cbmi, getOptions().isLineUpRendarableNodeData() ); + customizeCheckBoxMenuItem( _right_line_up_domains_cbmi, getOptions().isRightLineUpDomains() ); + _jmenubar.add( _options_jmenu ); + } + + void buildToolsMenu() { + _tools_menu = MainFrame.createMenu( "Tools", getConfiguration() ); + _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) ); + customizeJMenuItem( _confcolor_item ); + _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) ); + customizeJMenuItem( _taxcolor_item ); + _tools_menu.addSeparator(); + _tools_menu.add( _remove_visual_styles_item = new JMenuItem( "Delete All Visual Styles From Nodes" ) ); + _remove_visual_styles_item + .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny." ); + customizeJMenuItem( _remove_visual_styles_item ); + _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete All Colors From Branches" ) ); + _remove_branch_color_item.setToolTipText( "To remove all branch color values from the current phylogeny." ); + customizeJMenuItem( _remove_branch_color_item ); + _tools_menu.addSeparator(); + _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) ); + customizeJMenuItem( _midpoint_root_item ); + _tools_menu.addSeparator(); + _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) ); + customizeJMenuItem( _collapse_species_specific_subtrees ); + _jmenubar.add( _tools_menu ); + } + + void buildTypeMenu() { + _type_menu = MainFrame.createMenu( MainFrame.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 = MainFrame.createMenu( "View", getConfiguration() ); + _view_jmenu + .add( _display_basic_information_item = new JMenuItem( MainFrame.SHOW_BASIC_TREE_INFORMATION_LABEL ) ); + _view_jmenu.addSeparator(); + _view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) ); + _view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) ); + _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "as Nexus" ) ); + customizeJMenuItem( _display_basic_information_item ); + customizeJMenuItem( _view_as_NH_item ); + customizeJMenuItem( _view_as_XML_item ); + customizeJMenuItem( _view_as_nexus_item ); + _jmenubar.add( _view_jmenu ); + } + + void checkTextFrames() { + if ( _textframes.size() > 5 ) { + try { + if ( _textframes.getFirst() != null ) { + _textframes.getFirst().removeMe(); + } + else { + _textframes.removeFirst(); + } + } + catch ( final NoSuchElementException e ) { + // Ignore. + } + } + } + + void clearCurrentExternalNodesDataBuffer() { + getCurrentTreePanel().clearCurrentExternalNodesDataBuffer(); + } + + 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 displayBasicInformation() { + if ( ( getMainPanel() != null ) && ( getMainPanel().getCurrentPhylogeny() != null ) + && !getMainPanel().getCurrentPhylogeny().isEmpty() ) { + String title = "Basic Information"; + if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) { + title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\""; + } + showTextFrame( AptxUtil.createBasicInformation( getMainPanel().getCurrentPhylogeny(), null ), title ); + } + } + + void executeGSDI() { + if ( !isOKforSDI( false, true ) ) { + return; + } + if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) { + JOptionPane.showMessageDialog( this, + "Gene tree is not rooted.", + "Cannot execute GSDI", + JOptionPane.ERROR_MESSAGE ); + return; + } + final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy(); + gene_tree.setAllNodesToNotCollapse(); + gene_tree.recalculateNumberOfExternalDescendants( false ); + GSDI gsdi = null; + final Phylogeny species_tree = _species_tree.copy(); + try { + gsdi = new GSDI( gene_tree, species_tree, false, true, true, true ); + } + catch ( final SDIException e ) { + JOptionPane.showMessageDialog( this, + e.getLocalizedMessage(), + "Error during GSDI", + JOptionPane.ERROR_MESSAGE ); + return; + } + catch ( final Exception e ) { + AptxUtil.unexpectedException( e ); + return; + } + gene_tree.setRerootable( false ); + gene_tree.clearHashIdToNodeMap(); + gene_tree.recalculateNumberOfExternalDescendants( true ); + _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null ); + getMainPanel().getControlPanel().setShowEvents( true ); + showWhole(); + final int selected = _mainpanel.getTabbedPane().getSelectedIndex(); + _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null ); + showWhole(); + _mainpanel.getTabbedPane().setSelectedIndex( selected ); + showWhole(); + _mainpanel.getCurrentTreePanel().setEdited( true ); + final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree ); + if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) { + JOptionPane.showMessageDialog( this, + "Duplications: " + gsdi.getDuplicationsSum() + "\n" + + "Potential duplications: " + + gsdi.getSpeciationOrDuplicationEventsSum() + "\n" + + "Speciations: " + gsdi.getSpeciationsSum() + "\n" + + "Stripped gene tree nodes: " + + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n" + + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n" + + "Number of polytomies in species tree used: " + poly + "\n", + "GSDI successfully completed", + JOptionPane.WARNING_MESSAGE ); + } + else { + JOptionPane.showMessageDialog( this, + "Duplications: " + gsdi.getDuplicationsSum() + "\n" + + "Potential duplications: " + + gsdi.getSpeciationOrDuplicationEventsSum() + "\n" + + "Speciations: " + gsdi.getSpeciationsSum() + "\n" + + "Stripped gene tree nodes: " + + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n" + + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n" + + "Number of polytomies in species tree used: " + poly + "\n", + "GSDI successfully completed", + JOptionPane.INFORMATION_MESSAGE ); + } + } + + void executeGSDIR() { + if ( !isOKforSDI( false, false ) ) { + return; + } + final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() ); + if ( ( p > 0 ) + && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) { + JOptionPane.showMessageDialog( this, + "Gene tree is not completely binary", + "Cannot execute GSDI", + JOptionPane.ERROR_MESSAGE ); + return; + } + final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy(); + gene_tree.setAllNodesToNotCollapse(); + gene_tree.recalculateNumberOfExternalDescendants( false ); + GSDIR gsdir = null; + final Phylogeny species_tree = _species_tree.copy(); + try { + gsdir = new GSDIR( gene_tree, species_tree, true, true, true ); + } + catch ( final SDIException e ) { + JOptionPane.showMessageDialog( this, + e.getLocalizedMessage(), + "Error during GSDIR", + JOptionPane.ERROR_MESSAGE ); + return; + } + catch ( final Exception e ) { + AptxUtil.unexpectedException( e ); + return; + } + final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree(); + result_gene_tree.setRerootable( false ); + result_gene_tree.clearHashIdToNodeMap(); + result_gene_tree.recalculateNumberOfExternalDescendants( true ); + PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME ); + _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null ); + getMainPanel().getControlPanel().setShowEvents( true ); + showWhole(); + final int selected = _mainpanel.getTabbedPane().getSelectedIndex(); + _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null ); + showWhole(); + _mainpanel.getTabbedPane().setSelectedIndex( selected ); + showWhole(); + _mainpanel.getCurrentTreePanel().setEdited( true ); + final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree ); + if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) { + JOptionPane.showMessageDialog( this, + "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n" + + "Speciations: " + gsdir.getSpeciationsSum() + "\n" + + "Stripped gene tree nodes: " + + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n" + + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n" + + "Number of polytomies in species tree used: " + poly + "\n", + "GSDIR successfully completed", + JOptionPane.WARNING_MESSAGE ); + } + else { + JOptionPane.showMessageDialog( this, + "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n" + + "Speciations: " + gsdir.getSpeciationsSum() + "\n" + + "Stripped gene tree nodes: " + + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n" + + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n" + + "Number of polytomies in species tree used: " + poly + "\n", + "GSDIR successfully completed", + JOptionPane.INFORMATION_MESSAGE ); + } + } + + Configuration getConfiguration() { + return _configuration; + } + + File getCurrentDir() { + if ( ( _current_dir == null ) || !_current_dir.canRead() ) { + if ( ForesterUtil.isWindows() ) { + try { + _current_dir = new File( WindowsUtils.getCurrentUserDesktopPath() ); + } + catch ( final Exception e ) { + _current_dir = null; + } + } + } + if ( ( _current_dir == null ) || !_current_dir.canRead() ) { + if ( System.getProperty( "user.home" ) != null ) { + _current_dir = new File( System.getProperty( "user.home" ) ); + } + else if ( System.getProperty( "user.dir" ) != null ) { + _current_dir = new File( System.getProperty( "user.dir" ) ); + } + } + return _current_dir; + } + + TreePanel getCurrentTreePanel() { + return getMainPanel().getCurrentTreePanel(); + } + + JCheckBoxMenuItem getlabelDirectionCbmi() { + return _label_direction_cbmi; + } + + MainPanel getMainPanel() { + return _mainpanel; + } + + Options getOtions() { + return _options; + } + + void initializeTypeMenu( final Options options ) { + setTypeMenuToAllUnselected(); + try { + 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; + } + } + catch ( final NullPointerException np ) { + // In all likelihood, this is caused by menu-less display. + } + } + + boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) { + if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) { + return false; + } + else if ( ( _species_tree == null ) || _species_tree.isEmpty() ) { + JOptionPane.showMessageDialog( this, + "No species tree loaded", + "Cannot execute GSDI", + JOptionPane.ERROR_MESSAGE ); + return false; + } + else if ( species_tree_has_to_binary && !_species_tree.isCompletelyBinary() ) { + JOptionPane.showMessageDialog( this, + "Species tree is not completely binary", + "Cannot execute GSDI", + JOptionPane.ERROR_MESSAGE ); + return false; + } + else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) { + JOptionPane.showMessageDialog( this, + "Gene tree is not completely binary", + "Cannot execute GSDI", + JOptionPane.ERROR_MESSAGE ); + return false; + } + else { + return true; + } + } + + 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 removeAllTextFrames() { + for( final TextFrame tf : _textframes ) { + if ( tf != null ) { + tf.close(); + } + } + _textframes.clear(); + } + + void setConfiguration( final Configuration configuration ) { + _configuration = configuration; + } + + void setCurrentDir( final File current_dir ) { + _current_dir = current_dir; + } + + void setOptions( final Options options ) { + _options = options; + } + + void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) { + setTypeMenuToAllUnselected(); + try { + 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 ); + } + } + catch ( final NullPointerException np ) { + // In all likelihood, this is caused by menu-less display. + } + } + + void setTypeMenuToAllUnselected() { + if ( _convex_type_cbmi != null ) { + _convex_type_cbmi.setSelected( false ); + } + if ( _curved_type_cbmi != null ) { + _curved_type_cbmi.setSelected( false ); + } + if ( _euro_type_cbmi != null ) { + _euro_type_cbmi.setSelected( false ); + } + if ( _rounded_type_cbmi != null ) { + _rounded_type_cbmi.setSelected( false ); + } + if ( _triangular_type_cbmi != null ) { + _triangular_type_cbmi.setSelected( false ); + } + if ( _rectangular_type_cbmi != null ) { + _rectangular_type_cbmi.setSelected( false ); + } + if ( _unrooted_type_cbmi != null ) { + _unrooted_type_cbmi.setSelected( false ); + } + if ( _circular_type_cbmi != null ) { + _circular_type_cbmi.setSelected( false ); + } + } + + void showWhole() { + _mainpanel.getControlPanel().showWhole(); + } + + void switchColors() { + final TreeColorSet colorset = getMainPanel().getCurrentTreePanel().getTreeColorSet(); + final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset ); + csc.setVisible( true ); + getMainPanel().setTreeColorSet( colorset ); + } + + 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() ); + MainFrame.updateScreenTextAntialias( getMainPanel().getTreePanels() ); + } + } + + 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.setShowAnnotationRefSource( ( _show_annotation_ref_source != null ) + && _show_annotation_ref_source.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.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null ) + && _show_default_node_shapes_internal_cbmi.isSelected() ); + options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null ) + && _show_default_node_shapes_external_cbmi.isSelected() ); + options.setShowDefaultNodeShapesForMarkedNodes( ( _show_default_node_shapes_for_marked_cbmi != null ) + && _show_default_node_shapes_for_marked_cbmi.isSelected() ); + if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) { + options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP ); + } + + else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) { + options.setCladogramType( CLADOGRAM_TYPE.LINED_UP ); + } + 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() ); + options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null ) + && _search_whole_words_only_cbmi.isSelected() ); + options.setSearchWithRegex( ( _search_with_regex_cbmi != null ) && _search_with_regex_cbmi.isSelected() ); + options.setInverseSearchResult( ( _inverse_search_result_cbmi != null ) + && _inverse_search_result_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() ); + 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 ); + } + if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) { + options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() ); + } + if ( ( _right_line_up_domains_cbmi != null ) && _right_line_up_domains_cbmi.isEnabled() ) { + options.setRightLineUpDomains( _right_line_up_domains_cbmi.isSelected() ); + } + if ( ( _line_up_renderable_data_cbmi != null ) && _line_up_renderable_data_cbmi.isEnabled() ) { + options.setLineUpRendarableNodeData( _line_up_renderable_data_cbmi.isSelected() ); + } + if ( _graphics_export_visible_only_cbmi != null ) { + options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_cbmi.isSelected() ); + } + } + + void updateTypeCheckboxes( final Options options, final Object o ) { + setTypeMenuToAllUnselected(); + ( ( JCheckBoxMenuItem ) o ).setSelected( true ); + } + + void viewAsNexus() { + if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) { + String title = "Nexus"; + if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) { + title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title; + } + showTextFrame( getMainPanel().getCurrentPhylogeny().toNexus( getOptions() + .getNhConversionSupportValueStyle() ), + title ); + } + } + + void viewAsNH() { + if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) { + String title = "New Hampshire"; + if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) { + title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title; + } + showTextFrame( getMainPanel().getCurrentPhylogeny().toNewHampshire( getOptions() + .getNhConversionSupportValueStyle() ), + title ); + } + } + + void viewAsXML() { + if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) { + String title = "phyloXML"; + if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) { + title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title; + } + showTextFrame( getMainPanel().getCurrentPhylogeny().toPhyloXML( 0 ), title ); + } + } + + static void setTextForPdfLineWidthChooserMenuItem( final JMenuItem mi, final Options o ) { + mi.setText( "Enter Default Line Width for PDF Export... (current: " + o.getPrintLineWidth() + ")" ); + } + + static void setupScreenTextAntialias( final List treepanels, final boolean antialias ) { + for( final TreePanel tree_panel : treepanels ) { + tree_panel.setTextAntialias(); + } + } +} \ No newline at end of file diff --git a/forester/archive/Applets/MainFrameApplet.txt b/forester/archive/Applets/MainFrameApplet.txt new file mode 100644 index 0000000..c44a75c --- /dev/null +++ b/forester/archive/Applets/MainFrameApplet.txt @@ -0,0 +1,330 @@ +// $Id: +// FORESTER -- software libraries and applications +// for evolutionary biology research and applications. +// +// Copyright (C) 2008-2009 Christian M. Zmasek +// Copyright (C) 2008-2009 Burnham Institute for Medical Research +// Copyright (C) 2000-2001 Washington University School of Medicine +// and Howard Hughes Medical Institute +// Copyright (C) 2003-2007 Ethalinda K.S. Cannon +// 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: https://sites.google.com/site/cmzmasek/home/software/forester + +package org.forester.archaeopteryx; + +import java.awt.BorderLayout; +import java.awt.event.ComponentAdapter; +import java.awt.event.ComponentEvent; +import java.awt.event.WindowAdapter; +import java.awt.event.WindowEvent; +import java.io.FileNotFoundException; +import java.io.IOException; +import java.net.MalformedURLException; +import java.net.URL; + +import javax.swing.ButtonGroup; +import javax.swing.JApplet; +import javax.swing.JCheckBoxMenuItem; +import javax.swing.JMenuBar; +import javax.swing.JMenuItem; +import javax.swing.JRadioButtonMenuItem; +import javax.swing.event.ChangeEvent; +import javax.swing.event.ChangeListener; + +import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE; +import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION; +import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION; +import org.forester.phylogeny.Phylogeny; +import org.forester.util.ForesterUtil; + +public final class MainFrameApplet extends MainFrame { + + private static final long serialVersionUID = 1941019292746717053L; + private final static int DEFAULT_FRAME_X_SIZE = 640; + private final static int DEFAULT_FRAME_Y_SIZE = 580; + private final ArchaeopteryxA _applet; + private ButtonGroup _radio_group_1; + + MainFrameApplet( final ArchaeopteryxA parent_applet, + final Configuration configuration, + final String species_tree_url_str ) { + setTitle( ArchaeopteryxA.NAME ); + _applet = parent_applet; + setConfiguration( configuration ); + setOptions( Options.createInstance( configuration ) ); + _mainpanel = new MainPanelApplets( _configuration, this ); + if ( !ForesterUtil.isEmpty( species_tree_url_str ) ) { + try { + readSpeciesTree( configuration, species_tree_url_str ); + } + catch ( final Exception e ) { + ForesterUtil.printErrorMessage( ArchaeopteryxA.NAME, "failed to read species tree from " + + species_tree_url_str ); + ForesterUtil.printErrorMessage( ArchaeopteryxA.NAME, e.toString() ); + } + } + // build the menu bar + _jmenubar = new JMenuBar(); + buildFileMenu(); + if ( !_configuration.isUseNativeUI() ) { + _jmenubar.setBackground( _configuration.getGuiMenuBackgroundColor() ); + } + buildAnalysisMenu(); + buildToolsMenu(); + buildViewMenu(); + buildFontSizeMenu(); + buildOptionsMenu(); + buildTypeMenu(); + buildHelpMenu(); + setJMenuBar( _jmenubar ); + _contentpane = getContentPane(); + _contentpane.setLayout( new BorderLayout() ); + _contentpane.add( _mainpanel, BorderLayout.CENTER ); + setSize( getConfiguration().getFrameXSize() > 40 ? getConfiguration().getFrameXSize() : DEFAULT_FRAME_X_SIZE, + getConfiguration().getFrameYSize() > 40 ? getConfiguration().getFrameYSize() : DEFAULT_FRAME_Y_SIZE ); + addWindowListener( new WindowAdapter() { + + @Override + public void windowClosing( final WindowEvent e ) { + close(); + } + } ); + addComponentListener( new ComponentAdapter() { + + @Override + public void componentResized( final ComponentEvent e ) { + if ( _mainpanel.getCurrentTreePanel() != null ) { + _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel() + .getWidth(), + _mainpanel.getCurrentTreePanel() + .getHeight() ); + } + } + } ); + setFocusable( true ); + requestFocus(); + requestFocusInWindow(); + setVisible( true ); + System.gc(); + } + + @Override + public MainPanel getMainPanel() { + return _mainpanel; + } + + private void readSpeciesTree( final Configuration configuration, final String species_tree_url_str ) + throws MalformedURLException, FileNotFoundException, IOException { + final URL species_tree_url = new URL( species_tree_url_str ); + final Phylogeny[] species_trees = AptxUtil.readPhylogeniesFromUrl( species_tree_url, + configuration + .isValidatePhyloXmlAgainstSchema(), + configuration + .isReplaceUnderscoresInNhParsing(), + false, + TAXONOMY_EXTRACTION.NO, + false ); + if ( ( species_trees != null ) && ( species_trees.length > 0 ) ) { + AptxUtil.printAppletMessage( ArchaeopteryxA.NAME, "successfully read species tree" ); + if ( species_trees[ 0 ].isEmpty() ) { + ForesterUtil.printErrorMessage( ArchaeopteryxA.NAME, "species tree is empty" ); + } + else if ( !species_trees[ 0 ].isRooted() ) { + ForesterUtil.printErrorMessage( ArchaeopteryxA.NAME, "species tree is not rooted" ); + } + else { + setSpeciesTree( species_trees[ 0 ] ); + AptxUtil.printAppletMessage( ArchaeopteryxA.NAME, "species tree OK" ); + } + } + else { + ForesterUtil.printErrorMessage( ArchaeopteryxA.NAME, "failed to read species tree from " + + species_tree_url_str ); + } + } + + void buildAnalysisMenu() { + _analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() ); + if ( getSpeciesTree() != null ) { + _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) ); + _analysis_menu.add( _gsdir_item = new JMenuItem( "GSDIR (GSDI with re-rooting)" ) ); + customizeJMenuItem( _gsdi_item ); + customizeJMenuItem( _gsdir_item ); + _analysis_menu.addSeparator(); + } + _analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) ); + customizeJMenuItem( _lineage_inference ); + _lineage_inference.setToolTipText( "Inference of ancestor taxonomies/lineages" ); + _jmenubar.add( _analysis_menu ); + } + + void buildOptionsMenu() { + _options_jmenu = MainFrame.createMenu( MainFrame.OPTIONS_HEADER, getConfiguration() ); + _options_jmenu.addChangeListener( new ChangeListener() { + + @Override + public void stateChanged( final ChangeEvent e ) { + MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() ); + MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() ); + MainFrame + .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() ); + MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, createCurrentFontDesc( getMainPanel() + .getTreeFontSet() ) ); + // setTextForGraphicsSizeChooserMenuItem( _print_size_mi, getOptions() ); + setTextForPdfLineWidthChooserMenuItem( _choose_pdf_width_mi, getOptions() ); + MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() ); + MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() ); + MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() ); + try { + getMainPanel().getControlPanel().setVisibilityOfDomainStrucureCB(); + getMainPanel().getControlPanel().setVisibilityOfX(); + } + catch ( final Exception ignore ) { + // do nothing, not important. + } + } + } ); + _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.DISPLAY_SUBHEADER ), + getConfiguration() ) ); + _options_jmenu + .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) ); + _options_jmenu.add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( NON_LINED_UP_CLADOGRAMS_LABEL ) ); + _radio_group_1 = new ButtonGroup(); + _radio_group_1.add( _ext_node_dependent_cladogram_rbmi ); + _radio_group_1.add( _non_lined_up_cladograms_rbmi ); + _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) ); + _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) ); + _options_jmenu + .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_INT ) ); + _options_jmenu + .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) ); + _options_jmenu + .add( _show_default_node_shapes_for_marked_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_MARKED ) ); + _options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) ); + if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) { + _options_jmenu.add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) ); + _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) ); + } + _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( MainFrame.SHOW_ANN_REF_SOURCE_LABEL ) ); + _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_CONF_STDDEV_LABEL ) ); + _options_jmenu + .add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( MainFrame.COLOR_BY_TAXONOMIC_GROUP ) ); + _options_jmenu + .add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) ); + _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP ); + _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( MainFrame.ABBREV_SN_LABEL ) ); + _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( MainFrame.LABEL_DIRECTION_LABEL ) ); + _label_direction_cbmi.setToolTipText( MainFrame.LABEL_DIRECTION_TIP ); + _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( MainFrame.SCREEN_ANTIALIAS_LABEL ) ); + _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( MainFrame.BG_GRAD_LABEL ) ); + _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) ); + _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) ); + _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) ); + _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) ); + _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) ); + _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) ); + _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) ); + _options_jmenu.addSeparator(); + _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.SEARCH_SUBHEADER ), + getConfiguration() ) ); + _options_jmenu + .add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_CASE_SENSITIVE_LABEL ) ); + _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_TERMS_ONLY_LABEL ) ); + _options_jmenu.add( _search_with_regex_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_REGEX_LABEL ) ); + _search_with_regex_cbmi.setToolTipText( MainFrame.SEARCH_WITH_REGEX_TIP ); + _options_jmenu.add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( INVERSE_SEARCH_RESULT_LABEL ) ); + + _options_jmenu.addSeparator(); + _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Graphics Export & Printing:" ), + getConfiguration() ) ); + _options_jmenu.add( _antialias_print_cbmi = new JCheckBoxMenuItem( "Antialias" ) ); + _options_jmenu.add( _print_black_and_white_cbmi = new JCheckBoxMenuItem( "Export in Black and White" ) ); + _options_jmenu + .add( _graphics_export_visible_only_cbmi = new JCheckBoxMenuItem( "Limit to Visible ('Screenshot') for PNG, JPG, and GIF export" ) ); + _options_jmenu.add( _choose_pdf_width_mi = new JMenuItem( "" ) ); + + customizeCheckBoxMenuItem( _antialias_print_cbmi, getOptions().isAntialiasPrint() ); + customizeCheckBoxMenuItem( _print_black_and_white_cbmi, getOptions().isPrintBlackAndWhite() ); + customizeJMenuItem( _choose_pdf_width_mi ); + + customizeJMenuItem( _choose_font_mi ); + customizeJMenuItem( _switch_colors_mi ); + customizeJMenuItem( _choose_minimal_confidence_mi ); + customizeJMenuItem( _overview_placment_mi ); + customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions() + .isShowDefaultNodeShapesInternal() ); + customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions() + .isShowDefaultNodeShapesExternal() ); + customizeCheckBoxMenuItem( _show_default_node_shapes_for_marked_cbmi, getOptions() + .isShowDefaultNodeShapesForMarkedNodes() ); + customizeJMenuItem( _cycle_node_shape_mi ); + customizeJMenuItem( _cycle_node_fill_mi ); + customizeJMenuItem( _choose_node_size_mi ); + customizeCheckBoxMenuItem( _color_by_taxonomic_group_cbmi, getOptions().isColorByTaxonomicGroup() ); + customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() ); + customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() ); + customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() ); + customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() ); + customizeCheckBoxMenuItem( _show_annotation_ref_source, getOptions().isShowAnnotationRefSource() ); + customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() ); + customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() ); + customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() ); + customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi, + getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP ); + customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi, + getOptions().getCladogramType() == CLADOGRAM_TYPE.LINED_UP ); + customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() ); + customizeCheckBoxMenuItem( _label_direction_cbmi, + getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL ); + customizeCheckBoxMenuItem( _search_with_regex_cbmi, getOptions().isSearchWithRegex() ); + customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() ); + customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() ); + customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() ); + customizeCheckBoxMenuItem( _line_up_renderable_data_cbmi, getOptions().isLineUpRendarableNodeData() ); + customizeCheckBoxMenuItem( _right_line_up_domains_cbmi, getOptions().isRightLineUpDomains() ); + _jmenubar.add( _options_jmenu ); + } + + void buildToolsMenu() { + _tools_menu = MainFrame.createMenu( "Tools", getConfiguration() ); + _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) ); + customizeJMenuItem( _confcolor_item ); + _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) ); + customizeJMenuItem( _taxcolor_item ); + _tools_menu.addSeparator(); + _tools_menu.add( _remove_visual_styles_item = new JMenuItem( "Delete All Visual Styles From Nodes" ) ); + _remove_visual_styles_item + .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny." ); + customizeJMenuItem( _remove_visual_styles_item ); + _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete All Colors From Branches" ) ); + _remove_branch_color_item.setToolTipText( "To remove all branch color values from the current phylogeny." ); + customizeJMenuItem( _remove_branch_color_item ); + _tools_menu.addSeparator(); + _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) ); + customizeJMenuItem( _midpoint_root_item ); + _tools_menu.addSeparator(); + _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) ); + customizeJMenuItem( _collapse_species_specific_subtrees ); + _jmenubar.add( _tools_menu ); + } + + JApplet getApplet() { + return _applet; + } +} diff --git a/forester/archive/Applets/MainPanelApplets.txt b/forester/archive/Applets/MainPanelApplets.txt new file mode 100644 index 0000000..cfd54d7 --- /dev/null +++ b/forester/archive/Applets/MainPanelApplets.txt @@ -0,0 +1,90 @@ +// $Id: +// FORESTER -- software libraries and applications +// for evolutionary biology research and applications. +// +// Copyright (C) 2008-2009 Christian M. Zmasek +// Copyright (C) 2008-2009 Burnham Institute for Medical Research +// Copyright (C) 2000-2001 Washington University School of Medicine +// and Howard Hughes Medical Institute +// Copyright (C) 2003-2007 Ethalinda K.S. Cannon +// 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: https://sites.google.com/site/cmzmasek/home/software/forester + +package org.forester.archaeopteryx; + +import java.awt.BorderLayout; +import java.util.ArrayList; + +import javax.swing.JApplet; + +final class MainPanelApplets extends MainPanel { + + private static final long serialVersionUID = -7142615479464963140L; + private final JApplet _applet; + + public MainPanelApplets( final Configuration configuration, final ArchaeopteryxE em_applet ) { + if ( configuration == null ) { + throw new IllegalArgumentException( "configuration is null" ); + } + addComponentListener( this ); + _configuration = configuration; + _mainframe = null; + _treepanels = new ArrayList(); + _applet = em_applet; + initialize(); + _control_panel = new ControlPanel( this, configuration ); + if ( !configuration.isHideControlPanelAndMenubar() ) { + add( _control_panel, BorderLayout.WEST ); + } + setupTreeGraphic( configuration, getControlPanel() ); + } + + public MainPanelApplets( final Configuration configuration, final MainFrameApplet aaf ) { + if ( configuration == null ) { + throw new IllegalArgumentException( "configuration is null" ); + } + addComponentListener( this ); + _configuration = configuration; + _mainframe = aaf; + _treepanels = new ArrayList(); + _applet = aaf.getApplet(); + initialize(); + _control_panel = new ControlPanel( this, configuration ); + add( _control_panel, BorderLayout.WEST ); + setupTreeGraphic( configuration, getControlPanel() ); + } + + @Override + public Options getOptions() { + if ( _mainframe != null ) { + return _mainframe.getOptions(); + } + else { + return ( ( ArchaeopteryxE ) _applet ).getOptions(); + } + } + + JApplet getApplet() { + return _applet; + } + + MainFrameApplet getAppletFrame() { + return ( MainFrameApplet ) _mainframe; + } +} \ No newline at end of file -- 1.7.10.2