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 _uniform_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 JCheckBoxMenuItem _print_using_actual_size_cbmi;
private JCheckBoxMenuItem _graphics_export_using_actual_size_cbmi;
private JMenuItem _print_size_mi;
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 == _uniform_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 ) {
MainFrame.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 == _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();
}
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 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: " + AptxConstants.A4_SIZE_X + ", "
+ AptxConstants.A4_SIZE_Y + "]\n" + "[US Letter: "
+ AptxConstants.US_LETTER_SIZE_X + ", "
+ AptxConstants.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 );
}
}
}
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() ) );
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( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_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( _uniform_cladograms_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( _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( "" ) );
//
customizeCheckBoxMenuItem( _antialias_print_cbmi, getOptions().isAntialiasPrint() );
customizeCheckBoxMenuItem( _print_black_and_white_cbmi, getOptions().isPrintBlackAndWhite() );
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() );
customizeJMenuItem( _print_size_mi );
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( _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_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 ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {
options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
}
else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {
options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
}
options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )
&& _search_case_senstive_cbmi.isSelected() );
if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {
options.setShowScale( _show_scale_cbmi.isSelected() );
}
if ( _label_direction_cbmi != null ) {
if ( _label_direction_cbmi.isSelected() ) {
options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
}
else {
options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
}
}
options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )
&& _show_confidence_stddev_cbmi.isSelected() );
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.setPrintUsingActualSize( ( _print_using_actual_size_cbmi != null )
&& ( _print_using_actual_size_cbmi.isSelected() ) );
options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null )
&& ( _graphics_export_using_actual_size_cbmi.isSelected() ) );
options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() );
options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null )
&& _print_black_and_white_cbmi.isSelected() );
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() );
if ( _graphics_export_visible_only_cbmi.isSelected() && ( _graphics_export_using_actual_size_cbmi != null ) ) {
_graphics_export_using_actual_size_cbmi.setSelected( true );
_graphics_export_using_actual_size_cbmi.setEnabled( false );
}
else {
_graphics_export_using_actual_size_cbmi.setEnabled( true );
}
}
}
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 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() + ")" );
}
static void setupScreenTextAntialias( final List treepanels, final boolean antialias ) {
for( final TreePanel tree_panel : treepanels ) {
tree_panel.setTextAntialias();
}
}
}