// $Id: MainFrameApplication.java,v 1.55 2009/12/09 20:13:50 cmzmasek Exp $
// 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: cmzmasek@yahoo.com
// WWW: www.phylosoft.org/forester
package org.forester.archaeopteryx;
import java.awt.BorderLayout;
import java.awt.event.ActionEvent;
import java.awt.event.ComponentAdapter;
import java.awt.event.ComponentEvent;
import java.awt.event.WindowAdapter;
import java.awt.event.WindowEvent;
import java.io.File;
import java.io.IOException;
import java.net.MalformedURLException;
import java.net.URL;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import javax.swing.ButtonGroup;
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.WindowConstants;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
import javax.swing.filechooser.FileFilter;
import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
import org.forester.archaeopteryx.Util.GraphicsExportType;
import org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient;
import org.forester.archaeopteryx.webservices.WebservicesManager;
import org.forester.io.parsers.PhylogenyParser;
import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
import org.forester.io.parsers.nhx.NHXParser;
import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
import org.forester.io.parsers.phyloxml.PhyloXmlParser;
import org.forester.io.parsers.tol.TolParser;
import org.forester.io.writers.PhylogenyWriter;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyNode;
import org.forester.phylogeny.data.Taxonomy;
import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
import org.forester.phylogeny.factories.PhylogenyFactory;
import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
import org.forester.sdi.GSDI;
import org.forester.sdi.SDI;
import org.forester.sdi.SDIR;
import org.forester.sdi.SDIse;
import org.forester.util.ForesterUtil;
import org.forester.util.WindowsUtils;
class DefaultFilter extends FileFilter {
@Override
public boolean accept( final File f ) {
final String file_name = f.getName().trim().toLowerCase();
return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )
|| file_name.endsWith( ".tr" ) || file_name.endsWith( ".dnd" ) || file_name.endsWith( ".tree" )
|| file_name.endsWith( ".nhx" ) || file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" )
|| file_name.endsWith( ".px" ) || file_name.endsWith( ".pxml" ) || file_name.endsWith( ".nexus" )
|| file_name.endsWith( ".nx" ) || file_name.endsWith( ".nex" ) || file_name.endsWith( ".tre" )
|| file_name.endsWith( ".zip" ) || file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" )
|| f.isDirectory();
}
@Override
public String getDescription() {
return "All supported files (*.xml, *.phyloxml, *.nhx, *.nh, *.newick, *.nex, *.nexus, *.phy, *.tre, *.tree, *.tol)";
}
}
class GraphicsFileFilter extends FileFilter {
@Override
public boolean accept( final File f ) {
final String file_name = f.getName().trim().toLowerCase();
return file_name.endsWith( ".jpg" ) || file_name.endsWith( ".jpeg" ) || file_name.endsWith( ".png" )
|| file_name.endsWith( ".gif" ) || file_name.endsWith( ".bmp" ) || f.isDirectory();
}
@Override
public String getDescription() {
return "Image files (*.jpg, *.jpeg, *.png, *.gif, *.bmp)";
}
}
public final class MainFrameApplication extends MainFrame {
private final static int FRAME_X_SIZE = 800;
private final static int FRAME_Y_SIZE = 800;
// Filters for the file-open dialog (classes defined in this file)
private final static NHFilter nhfilter = new NHFilter();
private final static NHXFilter nhxfilter = new NHXFilter();
private final static XMLFilter xmlfilter = new XMLFilter();
private final static TolFilter tolfilter = new TolFilter();
private final static NexusFilter nexusfilter = new NexusFilter();
private final static PdfFilter pdffilter = new PdfFilter();
private final static GraphicsFileFilter graphicsfilefilter = new GraphicsFileFilter();
private final static DefaultFilter defaultfilter = new DefaultFilter();
private static final long serialVersionUID = -799735726778865234L;
private final JFileChooser _open_filechooser;
private final JFileChooser _open_filechooser_for_species_tree;
private final JFileChooser _save_filechooser;
private final JFileChooser _writetopdf_filechooser;
private final JFileChooser _writetographics_filechooser;
// Analysis menu
private JMenu _analysis_menu;
private JMenuItem _load_species_tree_item;
private JMenuItem _sdi_item;
private JMenuItem _gsdi_item;
private JMenuItem _root_min_dups_item;
private JMenuItem _root_min_cost_l_item;
// Application-only print menu items
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 Phylogeny _species_tree;
private File _current_dir;
private ButtonGroup _radio_group_1;
private MainFrameApplication( final Phylogeny[] phys, final Configuration config, final String title ) {
_configuration = config;
if ( _configuration == null ) {
throw new IllegalArgumentException( "configuration is null" );
}
try {
if ( _configuration.isUseNativeUI() ) {
UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
}
else {
UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );
}
}
catch ( final UnsupportedLookAndFeelException e ) {
Util.dieWithSystemError( "UnsupportedLookAndFeelException: " + e.toString() );
}
catch ( final ClassNotFoundException e ) {
Util.dieWithSystemError( "ClassNotFoundException: " + e.toString() );
}
catch ( final InstantiationException e ) {
Util.dieWithSystemError( "InstantiationException: " + e.toString() );
}
catch ( final IllegalAccessException e ) {
Util.dieWithSystemError( "IllegalAccessException: " + e.toString() );
}
catch ( final Exception e ) {
Util.dieWithSystemError( e.toString() );
}
// hide until everything is ready
setVisible( false );
setOptions( Options.createInstance( _configuration ) );
_textframe = null;
_species_tree = null;
// set title
setTitle( Constants.PRG_NAME + " " + Constants.VERSION + " (" + Constants.PRG_DATE + ")" );
_mainpanel = new MainPanel( _configuration, this );
// The file dialogs
_open_filechooser = new JFileChooser();
_open_filechooser.setCurrentDirectory( new File( "." ) );
_open_filechooser.setMultiSelectionEnabled( false );
_open_filechooser.addChoosableFileFilter( MainFrameApplication.xmlfilter );
_open_filechooser.addChoosableFileFilter( MainFrameApplication.nhxfilter );
_open_filechooser.addChoosableFileFilter( MainFrameApplication.nhfilter );
_open_filechooser.addChoosableFileFilter( MainFrameApplication.nexusfilter );
_open_filechooser.addChoosableFileFilter( MainFrameApplication.tolfilter );
_open_filechooser.addChoosableFileFilter( _open_filechooser.getAcceptAllFileFilter() );
_open_filechooser.setFileFilter( MainFrameApplication.defaultfilter );
_open_filechooser_for_species_tree = new JFileChooser();
_open_filechooser_for_species_tree.setCurrentDirectory( new File( "." ) );
_open_filechooser_for_species_tree.setMultiSelectionEnabled( false );
_open_filechooser_for_species_tree.addChoosableFileFilter( MainFrameApplication.xmlfilter );
_open_filechooser_for_species_tree.addChoosableFileFilter( MainFrameApplication.tolfilter );
_open_filechooser_for_species_tree.setFileFilter( MainFrameApplication.xmlfilter );
_save_filechooser = new JFileChooser();
_save_filechooser.setCurrentDirectory( new File( "." ) );
_save_filechooser.setMultiSelectionEnabled( false );
_save_filechooser.setFileFilter( MainFrameApplication.xmlfilter );
_save_filechooser.addChoosableFileFilter( MainFrameApplication.nhxfilter );
_save_filechooser.addChoosableFileFilter( MainFrameApplication.nhfilter );
_save_filechooser.addChoosableFileFilter( MainFrameApplication.nexusfilter );
_save_filechooser.addChoosableFileFilter( _save_filechooser.getAcceptAllFileFilter() );
_writetopdf_filechooser = new JFileChooser();
_writetopdf_filechooser.addChoosableFileFilter( MainFrameApplication.pdffilter );
_writetographics_filechooser = new JFileChooser();
_writetographics_filechooser.addChoosableFileFilter( MainFrameApplication.graphicsfilefilter );
// build the menu bar
_jmenubar = new JMenuBar();
if ( !_configuration.isUseNativeUI() ) {
_jmenubar.setBackground( Constants.MENU_BACKGROUND_COLOR_DEFAULT );
}
buildFileMenu();
buildToolsMenu();
buildViewMenu();
buildFontSizeMenu();
buildOptionsMenu();
buildTypeMenu();
buildAnalysisMenu();
buildHelpMenu();
setJMenuBar( _jmenubar );
_jmenubar.add( _help_jmenu );
_contentpane = getContentPane();
_contentpane.setLayout( new BorderLayout() );
_contentpane.add( _mainpanel, BorderLayout.CENTER );
// App is this big
setSize( MainFrameApplication.FRAME_X_SIZE, MainFrameApplication.FRAME_Y_SIZE );
// addWindowFocusListener( new WindowAdapter() {
//
// @Override
// public void windowGainedFocus( WindowEvent e ) {
// requestFocusInWindow();
// }
// } );
// The window listener
setDefaultCloseOperation( WindowConstants.DO_NOTHING_ON_CLOSE );
addWindowListener( new WindowAdapter() {
@Override
public void windowClosing( final WindowEvent e ) {
if ( isUnsavedDataPresent() ) {
final int r = JOptionPane.showConfirmDialog( null,
"Exit despite potentially unsaved changes?",
"Exit?",
JOptionPane.YES_NO_OPTION );
if ( r != JOptionPane.YES_OPTION ) {
return;
}
}
else {
final int r = JOptionPane.showConfirmDialog( null,
"Exit Archaeopteryx?",
"Exit?",
JOptionPane.YES_NO_OPTION );
if ( r != JOptionPane.YES_OPTION ) {
return;
}
}
exit();
}
} );
// The component listener
addComponentListener( new ComponentAdapter() {
@Override
public void componentResized( final ComponentEvent e ) {
if ( _mainpanel.getCurrentTreePanel() != null ) {
_mainpanel.getCurrentTreePanel().setParametersForPainting( _mainpanel.getCurrentTreePanel()
.getWidth(),
_mainpanel.getCurrentTreePanel()
.getHeight(),
false );
}
}
} );
requestFocusInWindow();
// addKeyListener( this );
setVisible( true );
if ( ( phys != null ) && ( phys.length > 0 ) ) {
Util.addPhylogeniesToTabs( phys, title, null, _configuration, _mainpanel );
validate();
getMainPanel().getControlPanel().showWholeAll();
getMainPanel().getControlPanel().showWhole();
}
activateSaveAllIfNeeded();
// ...and its children
_contentpane.repaint();
System.gc();
}
private MainFrameApplication( final Phylogeny[] phys, final String config_file, final String title ) {
// Reads the config file (false, false => not url, not applet):
this( phys, new Configuration( config_file, false, false ), title );
}
@Override
public void actionPerformed( final ActionEvent e ) {
try {
super.actionPerformed( e );
final Object o = e.getSource();
// Handle app-specific actions here:
if ( o == _open_item ) {
readPhylogeniesFromFile();
}
else if ( o == _save_item ) {
writeToFile( _mainpanel.getCurrentPhylogeny() );
// If subtree currently displayed, save it, instead of complete
// tree.
}
else if ( o == _new_item ) {
newTree();
}
else if ( o == _save_all_item ) {
writeAllToFile();
}
else if ( o == _close_item ) {
closeCurrentPane();
}
else if ( o == _write_to_pdf_item ) {
writeToPdf( _mainpanel.getCurrentPhylogeny() );
}
else if ( o == _write_to_jpg_item ) {
writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.JPG );
}
else if ( o == _write_to_png_item ) {
writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.PNG );
}
else if ( o == _write_to_gif_item ) {
writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.GIF );
}
else if ( o == _write_to_tif_item ) {
writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.TIFF );
}
else if ( o == _write_to_bmp_item ) {
writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.BMP );
}
else if ( o == _print_item ) {
print();
}
else if ( o == _load_species_tree_item ) {
readSpeciesTreeFromFile();
}
else if ( o == _sdi_item ) {
executeSDI();
}
else if ( o == _gsdi_item ) {
executeGSDI();
}
else if ( o == _root_min_dups_item ) {
executeSDIR( false );
}
else if ( o == _root_min_cost_l_item ) {
executeSDIR( true );
}
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 == _print_using_actual_size_cbmi ) {
updateOptions( getOptions() );
}
else if ( o == _graphics_export_using_actual_size_cbmi ) {
updateOptions( getOptions() );
}
else if ( o == _print_size_mi ) {
choosePrintSize();
}
else if ( o == _choose_pdf_width_mi ) {
choosePdfWidth();
}
else if ( o == _internal_number_are_confidence_for_nh_parsing_cbmi ) {
updateOptions( getOptions() );
}
else if ( o == _ignore_quotes_in_nh_parsing_cbmi ) {
updateOptions( getOptions() );
}
else if ( o == _replace_underscores_cbmi ) {
if ( ( _extract_pfam_style_tax_codes_cbmi != null ) && _replace_underscores_cbmi.isSelected() ) {
_extract_pfam_style_tax_codes_cbmi.setSelected( false );
}
updateOptions( getOptions() );
}
else if ( o == _extract_pfam_style_tax_codes_cbmi ) {
if ( ( _replace_underscores_cbmi != null ) && _extract_pfam_style_tax_codes_cbmi.isSelected() ) {
_replace_underscores_cbmi.setSelected( false );
}
updateOptions( getOptions() );
}
_contentpane.repaint();
}
catch ( final Exception ex ) {
Util.unexpectedException( ex );
}
catch ( final Error err ) {
Util.unexpectedError( err );
}
}
void buildAnalysisMenu() {
_analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );
_analysis_menu.add( _sdi_item = new JMenuItem( "SDI (Speciation Duplication Inference)" ) );
if ( !Constants.__RELEASE && !Constants.__SNAPSHOT_RELEASE ) {
_analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );
}
_analysis_menu.addSeparator();
_analysis_menu.add( _root_min_dups_item = new JMenuItem( "Root by Minimizing Duplications | Height (SDI)" ) );
_analysis_menu.add( _root_min_cost_l_item = new JMenuItem( "Root by Minimizing Cost L | Height (SDI)" ) );
_analysis_menu.addSeparator();
_analysis_menu.add( _load_species_tree_item = new JMenuItem( "Load Species Tree..." ) );
customizeJMenuItem( _sdi_item );
customizeJMenuItem( _gsdi_item );
customizeJMenuItem( _root_min_dups_item );
customizeJMenuItem( _root_min_cost_l_item );
customizeJMenuItem( _load_species_tree_item );
_jmenubar.add( _analysis_menu );
}
@Override
void buildFileMenu() {
_file_jmenu = MainFrame.createMenu( "File", getConfiguration() );
_file_jmenu.add( _open_item = new JMenuItem( "Read Tree from File..." ) );
_file_jmenu.addSeparator();
_file_jmenu.add( _open_url_item = new JMenuItem( "Read Tree from URL/Webservice..." ) );
_file_jmenu.addSeparator();
final WebservicesManager webservices_manager = WebservicesManager.getInstance();
_load_phylogeny_from_webservice_menu_items = new JMenuItem[ webservices_manager
.getAvailablePhylogeniesWebserviceClients().size() ];
for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {
final PhylogeniesWebserviceClient client = webservices_manager.getAvailablePhylogeniesWebserviceClient( i );
_load_phylogeny_from_webservice_menu_items[ i ] = new JMenuItem( client.getMenuName() );
_file_jmenu.add( _load_phylogeny_from_webservice_menu_items[ i ] );
}
if ( getConfiguration().isEditable() ) {
_file_jmenu.addSeparator();
_file_jmenu.add( _new_item = new JMenuItem( "New" ) );
_new_item.setToolTipText( "to create a new tree with one node, as source for manual tree construction" );
}
_file_jmenu.addSeparator();
_file_jmenu.add( _save_item = new JMenuItem( "Save Tree As..." ) );
_file_jmenu.add( _save_all_item = new JMenuItem( "Save All Trees As..." ) );
_save_all_item.setToolTipText( "Write all phylogenies to one file." );
_save_all_item.setEnabled( false );
_file_jmenu.addSeparator();
_file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) );
if ( Util.canWriteFormat( "tif" ) || Util.canWriteFormat( "tiff" ) || Util.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 ( Util.canWriteFormat( "gif" ) ) {
_file_jmenu.add( _write_to_gif_item = new JMenuItem( "Export to GIF file..." ) );
}
if ( Util.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..." ) );
_file_jmenu.addSeparator();
_file_jmenu.add( _close_item = new JMenuItem( "Close Tab" ) );
_close_item.setToolTipText( "To close the current pane." );
_close_item.setEnabled( true );
_file_jmenu.addSeparator();
_file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );
// For print in color option item
customizeJMenuItem( _open_item );
customizeJMenuItem( _open_url_item );
for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {
customizeJMenuItem( _load_phylogeny_from_webservice_menu_items[ i ] );
}
customizeJMenuItem( _save_item );
if ( getConfiguration().isEditable() ) {
customizeJMenuItem( _new_item );
}
customizeJMenuItem( _close_item );
customizeJMenuItem( _save_all_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 );
customizeJMenuItem( _exit_item );
_jmenubar.add( _file_jmenu );
}
void buildOptionsMenu() {
_options_jmenu = MainFrame.createMenu( OPTIONS_HEADER, getConfiguration() );
_options_jmenu.addChangeListener( new ChangeListener() {
@Override
public void stateChanged( final ChangeEvent e ) {
MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getCurrentTreePanel() );
MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
MainFrame
.setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame
.createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );
setTextForGraphicsSizeChooserMenuItem( _print_size_mi, getOptions() );
setTextForPdfLineWidthChooserMenuItem( _choose_pdf_width_mi, getOptions() );
MainFrame.updateOptionsMenuDependingOnPhylogenyType( getMainPanel(),
_show_scale_cbmi,
_show_branch_length_values_cbmi,
_non_lined_up_cladograms_rbmi,
_uniform_cladograms_rbmi,
_ext_node_dependent_cladogram_rbmi,
_label_direction_cbmi );
}
} );
_options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( DISPLAY_SUBHEADER ), getConfiguration() ) );
_options_jmenu
.add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
_options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_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( _uniform_cladograms_rbmi );
_radio_group_1.add( _non_lined_up_cladograms_rbmi );
_options_jmenu.add( _show_node_boxes_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL ) );
_options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( DISPLAY_SCALE_LABEL ) );
_options_jmenu
.add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );
_options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( SHOW_OVERVIEW_LABEL ) );
_options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( LABEL_DIRECTION_LABEL ) );
_label_direction_cbmi.setToolTipText( LABEL_DIRECTION_TIP );
_options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( SCREEN_ANTIALIAS_LABEL ) );
_options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( BG_GRAD_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( customizeMenuItemAsLabel( new JMenuItem( SEARCH_SUBHEADER ), getConfiguration() ) );
_options_jmenu.add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( SEARCH_CASE_SENSITIVE_LABEL ) );
_options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( SEARCH_TERMS_ONLY_LABEL ) );
_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( _print_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PDF export and Printing" ) );
_options_jmenu
.add( _graphics_export_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PNG, JPG, and GIF export" ) );
_options_jmenu
.add( _graphics_export_visible_only_cbmi = new JCheckBoxMenuItem( "Limit to Visible ('Screenshot') for PNG, JPG, and GIF export" ) );
_options_jmenu.add( _print_size_mi = new JMenuItem( "" ) );
_options_jmenu.add( _choose_pdf_width_mi = new JMenuItem( "" ) );
_options_jmenu.addSeparator();
_options_jmenu
.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/NHX/Nexus Parsing:" ), getConfiguration() ) );
_options_jmenu
.add( _internal_number_are_confidence_for_nh_parsing_cbmi = new JCheckBoxMenuItem( "Internal Numbers Are Confidence Values" ) );
_options_jmenu.add( _replace_underscores_cbmi = new JCheckBoxMenuItem( "Replace Underscores with Spaces" ) );
_options_jmenu
.add( _ignore_quotes_in_nh_parsing_cbmi = new JCheckBoxMenuItem( "Ignore Quotation Marks and Spaces in Labels" ) );
_options_jmenu
.add( _extract_pfam_style_tax_codes_cbmi = new JCheckBoxMenuItem( "Extract Taxonomy Codes from Pfam-style Labels" ) );
customizeJMenuItem( _choose_font_mi );
customizeJMenuItem( _choose_minimal_confidence_mi );
customizeJMenuItem( _switch_colors_mi );
customizeJMenuItem( _print_size_mi );
customizeJMenuItem( _choose_pdf_width_mi );
customizeJMenuItem( _overview_placment_mi );
customizeCheckBoxMenuItem( _show_node_boxes_cbmi, getOptions().isShowNodeBoxes() );
customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
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( _uniform_cladograms_rbmi,
getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
customizeCheckBoxMenuItem( _show_branch_length_values_cbmi, getOptions().isShowBranchLengthValues() );
customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
customizeCheckBoxMenuItem( _label_direction_cbmi,
getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
customizeCheckBoxMenuItem( _antialias_print_cbmi, getOptions().isAntialiasPrint() );
customizeCheckBoxMenuItem( _print_black_and_white_cbmi, getOptions().isPrintBlackAndWhite() );
customizeCheckBoxMenuItem( _internal_number_are_confidence_for_nh_parsing_cbmi, getOptions()
.isInternalNumberAreConfidenceForNhParsing() );
customizeCheckBoxMenuItem( _extract_pfam_style_tax_codes_cbmi, getOptions()
.isExtractPfamTaxonomyCodesInNhParsing() );
customizeCheckBoxMenuItem( _replace_underscores_cbmi, getOptions().isReplaceUnderscoresInNhParsing() );
customizeCheckBoxMenuItem( _ignore_quotes_in_nh_parsing_cbmi, getOptions().isNhParsingIgnoreQuotes() );
customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
customizeCheckBoxMenuItem( _graphics_export_visible_only_cbmi, getOptions().isGraphicsExportVisibleOnly() );
customizeCheckBoxMenuItem( _print_using_actual_size_cbmi, getOptions().isPrintUsingActualSize() );
customizeCheckBoxMenuItem( _graphics_export_using_actual_size_cbmi, getOptions()
.isGraphicsExportUsingActualSize() );
_jmenubar.add( _options_jmenu );
}
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 choosePrintSize() {
final String s = ( String ) JOptionPane.showInputDialog( this,
"Please enter values for width and height,\nseparated by a comma.\n"
+ "[current values: "
+ getOptions().getPrintSizeX() + ", "
+ getOptions().getPrintSizeY() + "]\n"
+ "[A4: " + Constants.A4_SIZE_X + ", "
+ Constants.A4_SIZE_Y + "]\n" + "[US Letter: "
+ Constants.US_LETTER_SIZE_X + ", "
+ Constants.US_LETTER_SIZE_Y + "]",
"Default Size for Graphics Export",
JOptionPane.QUESTION_MESSAGE,
null,
null,
getOptions().getPrintSizeX() + ", "
+ getOptions().getPrintSizeY() );
if ( !ForesterUtil.isEmpty( s ) && ( s.indexOf( ',' ) > 0 ) ) {
boolean success = true;
int x = 0;
int y = 0;
final String[] str_ary = s.split( "," );
if ( str_ary.length == 2 ) {
final String x_str = str_ary[ 0 ].trim();
final String y_str = str_ary[ 1 ].trim();
if ( !ForesterUtil.isEmpty( x_str ) && !ForesterUtil.isEmpty( y_str ) ) {
try {
x = Integer.parseInt( x_str );
y = Integer.parseInt( y_str );
}
catch ( final Exception ex ) {
success = false;
}
}
else {
success = false;
}
}
else {
success = false;
}
if ( success && ( x > 1 ) && ( y > 1 ) ) {
getOptions().setPrintSizeX( x );
getOptions().setPrintSizeY( y );
}
}
}
@Override
void close() {
if ( isUnsavedDataPresent() ) {
final int r = JOptionPane.showConfirmDialog( this,
"Exit despite potentially unsaved changes?",
"Exit?",
JOptionPane.YES_NO_OPTION );
if ( r != JOptionPane.YES_OPTION ) {
return;
}
}
exit();
}
private void closeCurrentPane() {
if ( getMainPanel().getCurrentTreePanel() != null ) {
if ( getMainPanel().getCurrentTreePanel().isEdited() ) {
final int r = JOptionPane.showConfirmDialog( this,
"Close tab despite potentially unsaved changes?",
"Close Tab?",
JOptionPane.YES_NO_OPTION );
if ( r != JOptionPane.YES_OPTION ) {
return;
}
}
getMainPanel().closeCurrentPane();
activateSaveAllIfNeeded();
}
}
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;
int duplications = -1;
try {
gsdi = new GSDI( gene_tree, _species_tree.copy(), true );
duplications = gsdi.getDuplicationsSum();
}
catch ( final Exception e ) {
JOptionPane.showMessageDialog( this, e.toString(), "Error during GSDI", JOptionPane.ERROR_MESSAGE );
}
gene_tree.setRerootable( false );
_mainpanel.getCurrentTreePanel().setTree( gene_tree );
getControlPanel().setShowEvents( true );
showWhole();
JOptionPane.showMessageDialog( this,
"Number of duplications: " + duplications,
"GSDI successfully completed",
JOptionPane.INFORMATION_MESSAGE );
}
void executeSDI() {
if ( !isOKforSDI( true, true ) ) {
return;
}
if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
JOptionPane.showMessageDialog( this,
"Gene tree is not rooted",
"Cannot execute SDI",
JOptionPane.ERROR_MESSAGE );
return;
}
final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
gene_tree.setAllNodesToNotCollapse();
gene_tree.recalculateNumberOfExternalDescendants( false );
SDI sdi = null;
int duplications = -1;
try {
sdi = new SDIse( gene_tree, _species_tree.copy() );
duplications = sdi.getDuplicationsSum();
}
catch ( final Exception e ) {
JOptionPane.showMessageDialog( this, e.toString(), "Error during SDI", JOptionPane.ERROR_MESSAGE );
}
gene_tree.setRerootable( false );
_mainpanel.getCurrentTreePanel().setTree( gene_tree );
getControlPanel().setShowEvents( true );
showWhole();
JOptionPane.showMessageDialog( this,
"Number of duplications: " + duplications,
"SDI successfully completed",
JOptionPane.INFORMATION_MESSAGE );
}
void executeSDIR( final boolean minimize_cost ) {
if ( !isOKforSDI( true, true ) ) {
return;
}
Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
final SDIR sdiunrooted = new SDIR();
gene_tree.setAllNodesToNotCollapse();
gene_tree.recalculateNumberOfExternalDescendants( false );
try {
gene_tree = sdiunrooted.infer( gene_tree, _species_tree, minimize_cost, // minimize cost
!minimize_cost, // minimize sum of dups
true, // minimize height
true, // return tree(s)
1 )[ 0 ]; // # of trees to return
}
catch ( final Exception e ) {
JOptionPane.showMessageDialog( this, e.toString(), "Error during SDIR", JOptionPane.ERROR_MESSAGE );
return;
}
final int duplications = sdiunrooted.getMinimalDuplications();
gene_tree.setRerootable( false );
_mainpanel.getCurrentTreePanel().setTree( gene_tree );
getControlPanel().setShowEvents( true );
showWhole();
JOptionPane.showMessageDialog( this,
"Number of duplications: " + duplications,
"SDIR successfully completed",
JOptionPane.INFORMATION_MESSAGE );
}
void exit() {
removeTextFrame();
_mainpanel.terminate();
_contentpane.removeAll();
setVisible( false );
dispose();
System.exit( 0 );
}
private ControlPanel getControlPanel() {
return getMainPanel().getControlPanel();
}
private File getCurrentDir() {
if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
if ( ForesterUtil.OS_NAME.toLowerCase().indexOf( "win" ) > -1 ) {
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;
}
@Override
MainPanel getMainPanel() {
return _mainpanel;
}
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 SDI",
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 SDI",
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 SDI",
JOptionPane.ERROR_MESSAGE );
return false;
}
else {
return true;
}
}
private boolean isUnsavedDataPresent() {
final List<TreePanel> tps = getMainPanel().getTreePanels();
for( final TreePanel tp : tps ) {
if ( tp.isEdited() ) {
return true;
}
}
return false;
}
private void newTree() {
final Phylogeny[] phys = new Phylogeny[ 1 ];
final Phylogeny phy = new Phylogeny();
final PhylogenyNode node = new PhylogenyNode();
phy.setRoot( node );
phy.setRooted( true );
phys[ 0 ] = phy;
Util.addPhylogeniesToTabs( phys, "", "", getConfiguration(), getMainPanel() );
_mainpanel.getControlPanel().showWhole();
_mainpanel.getCurrentTreePanel().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
_mainpanel.getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
if ( getMainPanel().getMainFrame() == null ) {
// Must be "E" applet version.
( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() )
.setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
}
else {
getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
}
activateSaveAllIfNeeded();
System.gc();
}
private void print() {
if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null )
|| getCurrentTreePanel().getPhylogeny().isEmpty() ) {
return;
}
if ( !getOptions().isPrintUsingActualSize() ) {
getCurrentTreePanel().setParametersForPainting( getOptions().getPrintSizeX() - 80,
getOptions().getPrintSizeY() - 140,
true );
getCurrentTreePanel().resetPreferredSize();
getCurrentTreePanel().repaint();
}
final String job_name = Constants.PRG_NAME;
boolean error = false;
String printer_name = null;
try {
printer_name = Printer.print( getCurrentTreePanel(), job_name );
}
catch ( final Exception e ) {
error = true;
JOptionPane.showMessageDialog( this, e.getMessage(), "Printing Error", JOptionPane.ERROR_MESSAGE );
}
if ( !error && ( printer_name != null ) ) {
String msg = "Printing data sent to printer";
if ( printer_name.length() > 1 ) {
msg += " [" + printer_name + "]";
}
JOptionPane.showMessageDialog( this, msg, "Printing...", JOptionPane.INFORMATION_MESSAGE );
}
if ( !getOptions().isPrintUsingActualSize() ) {
getControlPanel().showWhole();
}
}
private void printPhylogenyToPdf( final String file_name ) {
if ( !getOptions().isPrintUsingActualSize() ) {
getCurrentTreePanel().setParametersForPainting( getOptions().getPrintSizeX(),
getOptions().getPrintSizeY(),
true );
getCurrentTreePanel().resetPreferredSize();
getCurrentTreePanel().repaint();
}
String pdf_written_to = "";
boolean error = false;
try {
if ( getOptions().isPrintUsingActualSize() ) {
pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name,
getCurrentTreePanel(),
getCurrentTreePanel().getWidth(),
getCurrentTreePanel().getHeight() );
}
else {
pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name, getCurrentTreePanel(), getOptions()
.getPrintSizeX(), getOptions().getPrintSizeY() );
}
}
catch ( final IOException e ) {
error = true;
JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );
}
if ( !error ) {
if ( !ForesterUtil.isEmpty( pdf_written_to ) ) {
JOptionPane.showMessageDialog( this,
"Wrote PDF to: " + pdf_written_to,
"Information",
JOptionPane.INFORMATION_MESSAGE );
}
else {
JOptionPane.showMessageDialog( this,
"There was an unknown problem when attempting to write to PDF file: \""
+ file_name + "\"",
"Error",
JOptionPane.ERROR_MESSAGE );
}
}
if ( !getOptions().isPrintUsingActualSize() ) {
getControlPanel().showWhole();
}
}
private void readPhylogeniesFromFile() {
boolean exception = false;
Phylogeny[] phys = null;
// Set an initial directory if none set yet
final File my_dir = getCurrentDir();
_open_filechooser.setMultiSelectionEnabled( true );
// Open file-open dialog and set current directory
if ( my_dir != null ) {
_open_filechooser.setCurrentDirectory( my_dir );
}
final int result = _open_filechooser.showOpenDialog( _contentpane );
// All done: get the file
final File[] files = _open_filechooser.getSelectedFiles();
setCurrentDir( _open_filechooser.getCurrentDirectory() );
boolean nhx_or_nexus = false;
if ( ( files != null ) && ( files.length > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
for( final File file : files ) {
if ( ( file != null ) && !file.isDirectory() ) {
if ( _mainpanel.getCurrentTreePanel() != null ) {
_mainpanel.getCurrentTreePanel().setWaitCursor();
}
else {
_mainpanel.setWaitCursor();
}
if ( ( _open_filechooser.getFileFilter() == MainFrameApplication.nhfilter )
|| ( _open_filechooser.getFileFilter() == MainFrameApplication.nhxfilter ) ) {
try {
final NHXParser nhx = new NHXParser();
setSpecialOptionsForNhxParser( nhx );
phys = Util.readPhylogenies( nhx, file );
nhx_or_nexus = true;
}
catch ( final Exception e ) {
exception = true;
exceptionOccuredDuringOpenFile( e );
}
}
else if ( _open_filechooser.getFileFilter() == MainFrameApplication.xmlfilter ) {
warnIfNotPhyloXmlValidation( getConfiguration() );
try {
final PhyloXmlParser xml_parser = createPhyloXmlParser();
phys = Util.readPhylogenies( xml_parser, file );
}
catch ( final Exception e ) {
exception = true;
exceptionOccuredDuringOpenFile( e );
}
}
else if ( _open_filechooser.getFileFilter() == MainFrameApplication.tolfilter ) {
try {
phys = Util.readPhylogenies( new TolParser(), file );
}
catch ( final Exception e ) {
exception = true;
exceptionOccuredDuringOpenFile( e );
}
}
else if ( _open_filechooser.getFileFilter() == MainFrameApplication.nexusfilter ) {
try {
final NexusPhylogeniesParser nex = new NexusPhylogeniesParser();
setSpecialOptionsForNexParser( nex );
phys = Util.readPhylogenies( nex, file );
nhx_or_nexus = true;
}
catch ( final Exception e ) {
exception = true;
exceptionOccuredDuringOpenFile( e );
}
}
// "*.*":
else {
try {
final PhylogenyParser parser = ForesterUtil
.createParserDependingOnFileType( file, getConfiguration()
.isValidatePhyloXmlAgainstSchema() );
if ( parser instanceof NexusPhylogeniesParser ) {
final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) parser;
setSpecialOptionsForNexParser( nex );
nhx_or_nexus = true;
}
else if ( parser instanceof NHXParser ) {
final NHXParser nhx = ( NHXParser ) parser;
setSpecialOptionsForNhxParser( nhx );
nhx_or_nexus = true;
}
else if ( parser instanceof PhyloXmlParser ) {
warnIfNotPhyloXmlValidation( getConfiguration() );
}
phys = Util.readPhylogenies( parser, file );
}
catch ( final Exception e ) {
exception = true;
exceptionOccuredDuringOpenFile( e );
}
}
if ( _mainpanel.getCurrentTreePanel() != null ) {
_mainpanel.getCurrentTreePanel().setArrowCursor();
}
else {
_mainpanel.setArrowCursor();
}
if ( !exception && ( phys != null ) && ( phys.length > 0 ) ) {
if ( nhx_or_nexus && getOptions().isInternalNumberAreConfidenceForNhParsing() ) {
for( final Phylogeny phy : phys ) {
ForesterUtil.transferInternalNodeNamesToConfidence( phy );
}
}
Util.addPhylogeniesToTabs( phys,
file.getName(),
file.getAbsolutePath(),
getConfiguration(),
getMainPanel() );
_mainpanel.getControlPanel().showWhole();
}
}
}
}
activateSaveAllIfNeeded();
System.gc();
}
static void warnIfNotPhyloXmlValidation( final Configuration c ) {
if ( !c.isValidatePhyloXmlAgainstSchema() ) {
JOptionPane
.showMessageDialog( null,
ForesterUtil
.wordWrap( "phyloXML XSD-based validation is turned off [enable with line 'validate_against_phyloxml_xsd_schem: true' in configuration file]",
80 ),
"Warning",
JOptionPane.WARNING_MESSAGE );
}
}
private PhyloXmlParser createPhyloXmlParser() {
PhyloXmlParser xml_parser = null;
if ( getConfiguration().isValidatePhyloXmlAgainstSchema() ) {
try {
xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
}
catch ( final Exception e ) {
JOptionPane.showMessageDialog( this,
e.getLocalizedMessage(),
"failed to create validating XML parser",
JOptionPane.WARNING_MESSAGE );
}
}
if ( xml_parser == null ) {
xml_parser = new PhyloXmlParser();
}
return xml_parser;
}
@Override
void readPhylogeniesFromURL() {
URL url = null;
Phylogeny[] phys = null;
final String message = "Please enter a complete URL, for example \"http://www.phyloxml.org/examples/apaf.xml\"";
final String url_string = JOptionPane.showInputDialog( this,
message,
"Use URL/webservice to obtain a phylogeny",
JOptionPane.QUESTION_MESSAGE );
boolean nhx_or_nexus = false;
if ( ( url_string != null ) && ( url_string.length() > 0 ) ) {
try {
url = new URL( url_string );
PhylogenyParser parser = null;
if ( url.getHost().toLowerCase().indexOf( "tolweb" ) >= 0 ) {
parser = new TolParser();
}
else {
parser = ForesterUtil.createParserDependingOnUrlContents( url, getConfiguration()
.isValidatePhyloXmlAgainstSchema() );
}
if ( parser instanceof NexusPhylogeniesParser ) {
nhx_or_nexus = true;
}
else if ( parser instanceof NHXParser ) {
nhx_or_nexus = true;
}
if ( _mainpanel.getCurrentTreePanel() != null ) {
_mainpanel.getCurrentTreePanel().setWaitCursor();
}
else {
_mainpanel.setWaitCursor();
}
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
phys = factory.create( url.openStream(), parser );
}
catch ( final MalformedURLException e ) {
JOptionPane.showMessageDialog( this,
"Malformed URL: " + url + "\n" + e.getLocalizedMessage(),
"Malformed URL",
JOptionPane.ERROR_MESSAGE );
}
catch ( final IOException e ) {
JOptionPane.showMessageDialog( this,
"Could not read from " + url + "\n"
+ ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
"Failed to read URL",
JOptionPane.ERROR_MESSAGE );
}
catch ( final Exception e ) {
JOptionPane.showMessageDialog( this,
ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
"Unexpected Exception",
JOptionPane.ERROR_MESSAGE );
}
finally {
if ( _mainpanel.getCurrentTreePanel() != null ) {
_mainpanel.getCurrentTreePanel().setArrowCursor();
}
else {
_mainpanel.setArrowCursor();
}
}
if ( ( phys != null ) && ( phys.length > 0 ) ) {
if ( nhx_or_nexus && getOptions().isInternalNumberAreConfidenceForNhParsing() ) {
for( final Phylogeny phy : phys ) {
ForesterUtil.transferInternalNodeNamesToConfidence( phy );
}
}
Util.addPhylogeniesToTabs( phys, new File( url.getFile() ).getName(), new File( url.getFile() )
.toString(), getConfiguration(), getMainPanel() );
_mainpanel.getControlPanel().showWhole();
}
}
activateSaveAllIfNeeded();
System.gc();
}
private void readSpeciesTreeFromFile() {
Phylogeny t = null;
boolean exception = false;
final File my_dir = getCurrentDir();
_open_filechooser_for_species_tree.setSelectedFile( new File( "" ) );
if ( my_dir != null ) {
_open_filechooser_for_species_tree.setCurrentDirectory( my_dir );
}
final int result = _open_filechooser_for_species_tree.showOpenDialog( _contentpane );
final File file = _open_filechooser_for_species_tree.getSelectedFile();
if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrameApplication.xmlfilter ) {
try {
final Phylogeny[] trees = Util.readPhylogenies( new PhyloXmlParser(), file );
t = trees[ 0 ];
}
catch ( final Exception e ) {
exception = true;
exceptionOccuredDuringOpenFile( e );
}
}
else if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrameApplication.tolfilter ) {
try {
final Phylogeny[] trees = Util.readPhylogenies( new TolParser(), file );
t = trees[ 0 ];
}
catch ( final Exception e ) {
exception = true;
exceptionOccuredDuringOpenFile( e );
}
}
// "*.*":
else {
try {
final Phylogeny[] trees = Util.readPhylogenies( new PhyloXmlParser(), file );
t = trees[ 0 ];
}
catch ( final Exception e ) {
exception = true;
exceptionOccuredDuringOpenFile( e );
}
}
if ( !exception && ( t != null ) && !t.isRooted() ) {
exception = true;
t = null;
JOptionPane.showMessageDialog( this,
"Species tree is not rooted",
"Species tree not loaded",
JOptionPane.ERROR_MESSAGE );
}
if ( !exception && ( t != null ) ) {
final Set<Taxonomy> tax_set = new HashSet<Taxonomy>();
for( final PhylogenyNodeIterator it = t.iteratorExternalForward(); it.hasNext(); ) {
final PhylogenyNode node = it.next();
if ( !node.getNodeData().isHasTaxonomy() ) {
exception = true;
t = null;
JOptionPane
.showMessageDialog( this,
"Species tree contains external node(s) without taxonomy information",
"Species tree not loaded",
JOptionPane.ERROR_MESSAGE );
break;
}
else {
if ( tax_set.contains( node.getNodeData().getTaxonomy() ) ) {
exception = true;
t = null;
JOptionPane.showMessageDialog( this,
"Taxonomy ["
+ node.getNodeData().getTaxonomy().asSimpleText()
+ "] is not unique in species tree",
"Species tree not loaded",
JOptionPane.ERROR_MESSAGE );
break;
}
else {
tax_set.add( node.getNodeData().getTaxonomy() );
}
}
}
}
if ( !exception && ( t != null ) ) {
_species_tree = t;
JOptionPane.showMessageDialog( this,
"Species tree successfully loaded",
"Species tree loaded",
JOptionPane.INFORMATION_MESSAGE );
}
_contentpane.repaint();
System.gc();
}
}
private void setCurrentDir( final File current_dir ) {
_current_dir = current_dir;
}
private void setSpecialOptionsForNexParser( final NexusPhylogeniesParser nex ) {
nex.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );
nex.setIgnoreQuotes( getOptions().isNhParsingIgnoreQuotes() );
}
private void setSpecialOptionsForNhxParser( final NHXParser nhx ) {
nhx.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );
nhx.setIgnoreQuotes( getOptions().isNhParsingIgnoreQuotes() );
TAXONOMY_EXTRACTION te = TAXONOMY_EXTRACTION.NO;
if ( getOptions().isExtractPfamTaxonomyCodesInNhParsing() ) {
te = TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY;
}
nhx.setTaxonomyExtraction( te );
}
private void writeAllToFile() {
if ( ( getMainPanel().getTabbedPane() == null ) || ( getMainPanel().getTabbedPane().getTabCount() < 1 ) ) {
return;
}
final File my_dir = getCurrentDir();
if ( my_dir != null ) {
_save_filechooser.setCurrentDirectory( my_dir );
}
_save_filechooser.setSelectedFile( new File( "" ) );
final int result = _save_filechooser.showSaveDialog( _contentpane );
final File file = _save_filechooser.getSelectedFile();
setCurrentDir( _save_filechooser.getCurrentDirectory() );
if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
if ( file.exists() ) {
final int i = JOptionPane.showConfirmDialog( this,
file + " already exists. Overwrite?",
"Warning",
JOptionPane.OK_CANCEL_OPTION,
JOptionPane.WARNING_MESSAGE );
if ( i != JOptionPane.OK_OPTION ) {
return;
}
else {
try {
file.delete();
}
catch ( final Exception e ) {
JOptionPane.showMessageDialog( this,
"Failed to delete: " + file,
"Error",
JOptionPane.WARNING_MESSAGE );
}
}
}
final int count = getMainPanel().getTabbedPane().getTabCount();
final List<Phylogeny> trees = new ArrayList<Phylogeny>();
for( int i = 0; i < count; ++i ) {
trees.add( getMainPanel().getPhylogeny( i ) );
getMainPanel().getTreePanels().get( i ).setEdited( false );
}
final PhylogenyWriter writer = new PhylogenyWriter();
try {
writer.toPhyloXML( file, trees, 0, ForesterUtil.LINE_SEPARATOR );
}
catch ( final IOException e ) {
JOptionPane.showMessageDialog( this,
"Failed to write to: " + file,
"Error",
JOptionPane.WARNING_MESSAGE );
}
}
}
private boolean writeAsNewHampshire( final Phylogeny t, boolean exception, final File file ) {
try {
final PhylogenyWriter writer = new PhylogenyWriter();
writer.toNewHampshire( t, false, true, file );
}
catch ( final Exception e ) {
exception = true;
exceptionOccuredDuringSaveAs( e );
}
return exception;
}
private boolean writeAsNexus( final Phylogeny t, boolean exception, final File file ) {
try {
final PhylogenyWriter writer = new PhylogenyWriter();
writer.toNexus( file, t );
}
catch ( final Exception e ) {
exception = true;
exceptionOccuredDuringSaveAs( e );
}
return exception;
}
private boolean writeAsNHX( final Phylogeny t, boolean exception, final File file ) {
try {
final PhylogenyWriter writer = new PhylogenyWriter();
writer.toNewHampshireX( t, file );
}
catch ( final Exception e ) {
exception = true;
exceptionOccuredDuringSaveAs( e );
}
return exception;
}
private boolean writeAsPhyloXml( final Phylogeny t, boolean exception, final File file ) {
try {
final PhylogenyWriter writer = new PhylogenyWriter();
writer.toPhyloXML( file, t, 0 );
}
catch ( final Exception e ) {
exception = true;
exceptionOccuredDuringSaveAs( e );
}
return exception;
}
private void writePhylogenyToGraphicsFile( final String file_name, final GraphicsExportType type ) {
_mainpanel.getCurrentTreePanel().setParametersForPainting( _mainpanel.getCurrentTreePanel().getWidth(),
_mainpanel.getCurrentTreePanel().getHeight(),
true );
String file_written_to = "";
boolean error = false;
try {
file_written_to = Util.writePhylogenyToGraphicsFile( file_name,
_mainpanel.getCurrentTreePanel().getWidth(),
_mainpanel.getCurrentTreePanel().getHeight(),
_mainpanel.getCurrentTreePanel(),
_mainpanel.getControlPanel(),
type,
getOptions() );
}
catch ( final IOException e ) {
error = true;
JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );
}
if ( !error ) {
if ( ( file_written_to != null ) && ( file_written_to.length() > 0 ) ) {
JOptionPane.showMessageDialog( this,
"Wrote image to: " + file_written_to,
"Graphics Export",
JOptionPane.INFORMATION_MESSAGE );
}
else {
JOptionPane.showMessageDialog( this,
"There was an unknown problem when attempting to write to an image file: \""
+ file_name + "\"",
"Error",
JOptionPane.ERROR_MESSAGE );
}
}
_contentpane.repaint();
}
private void writeToFile( final Phylogeny t ) {
if ( t == null ) {
return;
}
String initial_filename = null;
if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {
try {
initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().getCanonicalPath();
}
catch ( final IOException e ) {
initial_filename = null;
}
}
if ( !ForesterUtil.isEmpty( initial_filename ) ) {
_save_filechooser.setSelectedFile( new File( initial_filename ) );
}
else {
_save_filechooser.setSelectedFile( new File( "" ) );
}
final File my_dir = getCurrentDir();
if ( my_dir != null ) {
_save_filechooser.setCurrentDirectory( my_dir );
}
final int result = _save_filechooser.showSaveDialog( _contentpane );
final File file = _save_filechooser.getSelectedFile();
setCurrentDir( _save_filechooser.getCurrentDirectory() );
boolean exception = false;
if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
if ( file.exists() ) {
final int i = JOptionPane.showConfirmDialog( this,
file + " already exists. Overwrite?",
"Overwrite?",
JOptionPane.OK_CANCEL_OPTION,
JOptionPane.WARNING_MESSAGE );
if ( i != JOptionPane.OK_OPTION ) {
return;
}
else {
try {
file.delete();
}
catch ( final Exception e ) {
JOptionPane.showMessageDialog( this,
"Failed to delete: " + file,
"Error",
JOptionPane.WARNING_MESSAGE );
}
}
}
if ( _save_filechooser.getFileFilter() == MainFrameApplication.nhfilter ) {
exception = writeAsNewHampshire( t, exception, file );
}
else if ( _save_filechooser.getFileFilter() == MainFrameApplication.nhxfilter ) {
exception = writeAsNHX( t, exception, file );
}
else if ( _save_filechooser.getFileFilter() == MainFrameApplication.xmlfilter ) {
exception = writeAsPhyloXml( t, exception, file );
}
else if ( _save_filechooser.getFileFilter() == MainFrameApplication.nexusfilter ) {
exception = writeAsNexus( t, exception, file );
}
// "*.*":
else {
final String file_name = file.getName().trim().toLowerCase();
if ( file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )
|| file_name.endsWith( ".tree" ) ) {
exception = writeAsNewHampshire( t, exception, file );
}
else if ( file_name.endsWith( ".nhx" ) ) {
exception = writeAsNHX( t, exception, file );
}
else if ( file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) ) {
exception = writeAsNexus( t, exception, file );
}
// XML is default:
else {
exception = writeAsPhyloXml( t, exception, file );
}
}
if ( !exception ) {
getMainPanel().getCurrentTreePanel().setTreeFile( file );
getMainPanel().getCurrentTreePanel().setEdited( false );
}
}
}
private void writeToGraphicsFile( final Phylogeny t, final GraphicsExportType type ) {
if ( ( t == null ) || t.isEmpty() ) {
return;
}
String initial_filename = "";
if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {
initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().toString();
}
if ( initial_filename.indexOf( '.' ) > 0 ) {
initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );
}
initial_filename = initial_filename + "." + type;
_writetographics_filechooser.setSelectedFile( new File( initial_filename ) );
final File my_dir = getCurrentDir();
if ( my_dir != null ) {
_writetographics_filechooser.setCurrentDirectory( my_dir );
}
final int result = _writetographics_filechooser.showSaveDialog( _contentpane );
File file = _writetographics_filechooser.getSelectedFile();
setCurrentDir( _writetographics_filechooser.getCurrentDirectory() );
if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
if ( !file.toString().toLowerCase().endsWith( type.toString() ) ) {
file = new File( file.toString() + "." + type );
}
if ( file.exists() ) {
final int i = JOptionPane.showConfirmDialog( this,
file + " already exists. Overwrite?",
"Warning",
JOptionPane.OK_CANCEL_OPTION,
JOptionPane.WARNING_MESSAGE );
if ( i != JOptionPane.OK_OPTION ) {
return;
}
else {
try {
file.delete();
}
catch ( final Exception e ) {
JOptionPane.showMessageDialog( this,
"Failed to delete: " + file,
"Error",
JOptionPane.WARNING_MESSAGE );
}
}
}
writePhylogenyToGraphicsFile( file.toString(), type );
}
}
private void writeToPdf( final Phylogeny t ) {
if ( ( t == null ) || t.isEmpty() ) {
return;
}
String initial_filename = "";
if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {
initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().toString();
}
if ( initial_filename.indexOf( '.' ) > 0 ) {
initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );
}
initial_filename = initial_filename + ".pdf";
_writetopdf_filechooser.setSelectedFile( new File( initial_filename ) );
final File my_dir = getCurrentDir();
if ( my_dir != null ) {
_writetopdf_filechooser.setCurrentDirectory( my_dir );
}
final int result = _writetopdf_filechooser.showSaveDialog( _contentpane );
File file = _writetopdf_filechooser.getSelectedFile();
setCurrentDir( _writetopdf_filechooser.getCurrentDirectory() );
if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
if ( !file.toString().toLowerCase().endsWith( ".pdf" ) ) {
file = new File( file.toString() + ".pdf" );
}
if ( file.exists() ) {
final int i = JOptionPane.showConfirmDialog( this,
file + " already exists. Overwrite?",
"WARNING",
JOptionPane.OK_CANCEL_OPTION,
JOptionPane.WARNING_MESSAGE );
if ( i != JOptionPane.OK_OPTION ) {
return;
}
}
printPhylogenyToPdf( file.toString() );
}
}
static MainFrame createInstance( final Phylogeny[] phys, final Configuration config, final String title ) {
return new MainFrameApplication( phys, config, title );
}
static MainFrame createInstance( final Phylogeny[] phys, final String config_file_name, final String title ) {
return new MainFrameApplication( phys, config_file_name, title );
}
static void setTextForGraphicsSizeChooserMenuItem( final JMenuItem mi, final Options o ) {
mi.setText( "Enter Default Size for Graphics Export... (current: " + o.getPrintSizeX() + ", "
+ o.getPrintSizeY() + ")" );
}
static void setTextForPdfLineWidthChooserMenuItem( final JMenuItem mi, final Options o ) {
mi.setText( "Enter Default Line Width for PDF Export... (current: " + o.getPrintLineWidth() + ")" );
}
} // MainFrameApplication.
class NexusFilter extends FileFilter {
@Override
public boolean accept( final File f ) {
final String file_name = f.getName().trim().toLowerCase();
return file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) || file_name.endsWith( ".nx" )
|| file_name.endsWith( ".tre" ) || f.isDirectory();
}
@Override
public String getDescription() {
return "Nexus files (*.nex, *.nexus, *.nx, *.tre)";
}
} // NexusFilter
class NHFilter extends FileFilter {
@Override
public boolean accept( final File f ) {
final String file_name = f.getName().trim().toLowerCase();
return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )
|| file_name.endsWith( ".tr" ) || file_name.endsWith( ".tree" ) || file_name.endsWith( ".dnd" )
|| f.isDirectory();
}
@Override
public String getDescription() {
return "New Hampshire - Newick files (*.nh, *.newick, *.phy, *.tree, *.dnd, *.tr)";
}
} // NHFilter
class NHXFilter extends FileFilter {
@Override
public boolean accept( final File f ) {
final String file_name = f.getName().trim().toLowerCase();
return file_name.endsWith( ".nhx" ) || f.isDirectory();
}
@Override
public String getDescription() {
return "NHX files (*.nhx)";
}
}
class PdfFilter extends FileFilter {
@Override
public boolean accept( final File f ) {
return f.getName().trim().toLowerCase().endsWith( ".pdf" ) || f.isDirectory();
}
@Override
public String getDescription() {
return "PDF files (*.pdf)";
}
} // PdfFilter
class TolFilter extends FileFilter {
@Override
public boolean accept( final File f ) {
final String file_name = f.getName().trim().toLowerCase();
return ( file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" ) || file_name.endsWith( ".zip" ) || f
.isDirectory() )
&& ( !file_name.endsWith( ".xml.zip" ) );
}
@Override
public String getDescription() {
return "Tree of Life files (*.tol, *.tolxml)";
}
} // TolFilter
class XMLFilter extends FileFilter {
@Override
public boolean accept( final File f ) {
final String file_name = f.getName().trim().toLowerCase();
return file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" ) || file_name.endsWith( ".px" )
|| file_name.endsWith( ".pxml" ) || file_name.endsWith( ".zip" ) || f.isDirectory();
}
@Override
public String getDescription() {
return "phyloXML files (*.xml, *.phyloxml, *.phylo.xml)";
}
} // XMLFilter