// $Id: MainFrame.java,v 1.81 2010/10/02 21:34:07 cmzmasek Exp $
// FORESTER -- software libraries and applications
// for evolutionary biology research and applications.
//
// Copyright (C) 2008-2010 Christian M. Zmasek
// All rights reserved
//
// This library is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License as published by the Free Software Foundation; either
// version 2.1 of the License, or (at your option) any later version.
//
// This library is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
// Lesser General Public License for more details.
//
// You should have received a copy of the GNU Lesser General Public
// License along with this library; if not, write to the Free Software
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: cmzmasek at yahoo.com
// WWW: www.phylosoft.org/forester
package org.forester.archaeopteryx;
/**
* NOTE - The original file was obtained from SourceForge.net (Archaeopteryx Version 0.957 beta) on 2010.10.13
* and was modified by the LANL Influenza Sequence Database IT team (flu@lanl.gov)
*/
import gov.lanl.application.TPTD.applet.AppletParams;
import gov.lanl.application.TPTD.applet.AppletTerminate;
import gov.lanl.application.TPTD.applet.NewWindowSubtree;
import java.awt.Container;
import java.awt.Font;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.WindowAdapter;
import java.awt.event.WindowEvent;
import java.io.IOException;
import java.util.List;
import java.util.Locale;
import java.util.Map;
import javax.swing.JApplet;
import javax.swing.JCheckBoxMenuItem;
import javax.swing.JFrame;
import javax.swing.JMenu;
import javax.swing.JMenuBar;
import javax.swing.JMenuItem;
import javax.swing.JOptionPane;
import javax.swing.JRadioButtonMenuItem;
import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
import org.forester.phylogeny.Phylogeny;
import org.forester.util.ForesterConstants;
import org.forester.util.ForesterUtil;
public abstract class MainFrame extends JFrame implements ActionListener {
static final String USE_MOUSEWHEEL_SHIFT_TO_ROTATE = "In this display type, use mousewheel + Shift to rotate [or A and S]";
static final String PHYLOXML_REF_TOOL_TIP = Constants.PHYLOXML_REFERENCE; //TODO //FIXME
static final String APTX_REF_TOOL_TIP = Constants.APTX_REFERENCE;
private static final long serialVersionUID = 3655000897845508358L;
//******************************************START Chnaged**********************************************************//
public final static Font menu_font = new Font( Configuration.getDefaultFontFamilyName(),
Font.PLAIN,
10 ); //added public
//******************************************END**********************************************************//
static final String TYPE_MENU_HEADER = "Type";
static final String RECTANGULAR_TYPE_CBMI_LABEL = "Rectangular";
static final String EURO_TYPE_CBMI_LABEL = "Euro Type";
static final String CURVED_TYPE_CBMI_LABEL = "Curved";
static final String TRIANGULAR_TYPE_CBMI_LABEL = "Triangular";
static final String CONVEX_TYPE_CBMI_LABEL = "Convex";
static final String ROUNDED_TYPE_CBMI_LABEL = "Rounded";
static final String UNROOTED_TYPE_CBMI_LABEL = "Unrooted (alpha)"; //TODO
static final String CIRCULAR_TYPE_CBMI_LABEL = "Circular (alpha)"; //TODO
static final String OPTIONS_HEADER = "Options";
static final String SEARCH_SUBHEADER = "Search:";
static final String DISPLAY_SUBHEADER = "Display:";
static final String SEARCH_TERMS_ONLY_LABEL = "Match Complete Terms Only";
static final String SEARCH_CASE_SENSITIVE_LABEL = "Case Sensitive";
static final String INVERSE_SEARCH_RESULT_LABEL = "Negate Result";
static final String DISPLAY_BRANCH_LENGTH_VALUES_LABEL = "Display Branch Length Values";
static final String DISPLAY_SCALE_LABEL = "Display Scale";
static final String NON_LINED_UP_CLADOGRAMS_LABEL = "Non-Lined Up Cladograms";
static final String UNIFORM_CLADOGRAMS_LABEL = "Total Node Sum Dependent Cladograms";
static final String LABEL_DIRECTION_LABEL = "Radial Labels";
static final String LABEL_DIRECTION_TIP = "To use radial node labels in radial and unrooted display types";
static final String SCREEN_ANTIALIAS_LABEL = "Antialias";
static final String COLOR_LABELS_LABEL = "Colorize Labels Same as Parent Branch";
static final String BG_GRAD_LABEL = "Background Color Gradient";
static final String DISPLAY_NODE_BOXES_LABEL = "Display Node Boxes";
static final String SHOW_OVERVIEW_LABEL = "Show Overview";
static final String FONT_SIZE_MENU_LABEL = "Font Size";
static final String NONUNIFORM_CLADOGRAMS_LABEL = "External Node Sum Dependent Cladograms";
static final String SHOW_DOMAIN_LABELS_LABEL = "Show Domain Labels";
static final String COLOR_LABELS_TIP = "To use parent branch colors for node labels as well, need to turn off taxonomy dependent colorization and turn on branch colorization for this to become apparent";
JMenuBar _jmenubar;
JMenu _file_jmenu;
JMenu _tools_menu;
JMenu _view_jmenu;
JMenu _options_jmenu;
JMenu _font_size_menu;
JMenu _help_jmenu;
JMenuItem[] _load_phylogeny_from_webservice_menu_items;
// file menu:
JMenuItem _open_item;
JMenuItem _open_url_item;
JMenuItem _save_item;
JMenuItem _save_all_item;
JMenuItem _close_item;
JMenuItem _exit_item;
JMenuItem _new_item;
// tools menu:
JMenuItem _midpoint_root_item;
JMenuItem _taxcolor_item;
JMenuItem _confcolor_item;
JMenuItem _infer_common_sn_names_item;
JMenuItem _collapse_species_specific_subtrees;
JMenuItem _collapse_below_threshold; //TODO implememt me
JMenuItem _obtain_detailed_taxonomic_information_jmi;
JMenuItem _move_node_names_to_tax_sn_jmi;
JMenuItem _move_node_names_to_seq_names_jmi;
JMenuItem _extract_tax_code_from_node_names_jmi;
// font size menu:
JMenuItem _super_tiny_fonts_item;
JMenuItem _tiny_fonts_item;
JMenuItem _small_fonts_item;
JMenuItem _medium_fonts_item;
JMenuItem _large_fonts_item;
// options menu:
// _ screen and print
JMenuItem _choose_font_mi;
JMenuItem _switch_colors_mi;
JCheckBoxMenuItem _label_direction_cbmi;
// _ screen display
JCheckBoxMenuItem _screen_antialias_cbmi;
JCheckBoxMenuItem _background_gradient_cbmi;
JCheckBoxMenuItem _show_node_boxes_cbmi;
JRadioButtonMenuItem _non_lined_up_cladograms_rbmi;
JRadioButtonMenuItem _uniform_cladograms_rbmi;
JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi;
JCheckBoxMenuItem _show_branch_length_values_cbmi;
JCheckBoxMenuItem _show_scale_cbmi; //TODO fix me
JCheckBoxMenuItem _show_overview_cbmi;
JCheckBoxMenuItem _show_domain_labels;
JCheckBoxMenuItem _color_labels_same_as_parent_branch;
JMenuItem _overview_placment_mi;
JMenuItem _choose_minimal_confidence_mi;
// _ print
JCheckBoxMenuItem _graphics_export_visible_only_cbmi;
JCheckBoxMenuItem _antialias_print_cbmi;
JCheckBoxMenuItem _print_black_and_white_cbmi;
JCheckBoxMenuItem _print_using_actual_size_cbmi;
JCheckBoxMenuItem _graphics_export_using_actual_size_cbmi;
JMenuItem _print_size_mi;
JMenuItem _choose_pdf_width_mi;
// _ parsing
JCheckBoxMenuItem _internal_number_are_confidence_for_nh_parsing_cbmi;
JCheckBoxMenuItem _extract_pfam_style_tax_codes_cbmi;
JCheckBoxMenuItem _replace_underscores_cbmi;
// _ search
JCheckBoxMenuItem _search_case_senstive_cbmi;
JCheckBoxMenuItem _search_whole_words_only_cbmi;
JCheckBoxMenuItem _inverse_search_result_cbmi;
// type menu:
JMenu _type_menu;
JCheckBoxMenuItem _rectangular_type_cbmi;
JCheckBoxMenuItem _triangular_type_cbmi;
JCheckBoxMenuItem _curved_type_cbmi;
JCheckBoxMenuItem _convex_type_cbmi;
JCheckBoxMenuItem _euro_type_cbmi;
JCheckBoxMenuItem _rounded_type_cbmi;
JCheckBoxMenuItem _unrooted_type_cbmi;
JCheckBoxMenuItem _circular_type_cbmi;
// view as text menu:
JMenuItem _view_as_NH_item;
JMenuItem _view_as_NHX_item;
JMenuItem _view_as_XML_item;
JMenuItem _view_as_nexus_item;
// help menu:
JMenuItem _about_item;
JMenuItem _help_item;
JMenuItem _website_item;
JMenuItem _phyloxml_website_item;
JMenuItem _phyloxml_ref_item;
JMenuItem _aptx_ref_item;
// Handy pointers to child components:
MainPanel _mainpanel;
Container _contentpane;
TextFrame _textframe;
Configuration _configuration;
JMenuItem _remove_branch_color_item;
Options _options;
//******************************************START**********************************************************//
AppletTerminate appletTerminate = new AppletTerminate(this);
public WindowAdapter closeWindowAdapter = new WindowAdapter(){
@Override
public void windowClosing( final WindowEvent e ) {
close();
}
};
//********************************************END**********************************************************//
MainFrame() {
// Empty constructor.
}
/**
* Action performed.
*/
public void actionPerformed( final ActionEvent e ) {
final Object o = e.getSource();
boolean is_applet = false;
JApplet applet = null;
if ( getCurrentTreePanel() != null ) {
is_applet = getCurrentTreePanel().isApplet();
if ( is_applet ) {
applet = getCurrentTreePanel().obtainApplet();
}
}
if ( o == _open_url_item ) {
readPhylogeniesFromURL();
}
else if ( o == _exit_item ) {
close();
}
else if ( o == _taxcolor_item ) {
taxColor();
}
else if ( o == _confcolor_item ) {
confColor();
}
else if ( o == _infer_common_sn_names_item ) {
if ( getCurrentTreePanel() != null ) {
getCurrentTreePanel().inferCommonPartOfScientificNames();
}
}
else if ( o == _collapse_species_specific_subtrees ) {
if ( getCurrentTreePanel() != null ) {
getCurrentTreePanel().collapseSpeciesSpecificSubtrees();
}
}
else if ( o == _remove_branch_color_item ) {
removeBranchColors();
}
else if ( o == _midpoint_root_item ) {
midpointRoot();
}
else if ( o == _switch_colors_mi ) {
switchColors();
}
else if ( o == _view_as_NH_item ) {
viewAsNH();
}
else if ( o == _view_as_NHX_item ) {
viewAsNHX();
}
else if ( o == _view_as_XML_item ) {
viewAsXML();
}
else if ( o == _view_as_nexus_item ) {
viewAsNexus();
}
else if ( o == _super_tiny_fonts_item ) {
if ( getCurrentTreePanel() != null ) {
getCurrentTreePanel().setSuperTinyFonts();
getCurrentTreePanel().repaint();
}
}
else if ( o == _tiny_fonts_item ) {
if ( getCurrentTreePanel() != null ) {
getCurrentTreePanel().setTinyFonts();
getCurrentTreePanel().repaint();
}
}
else if ( o == _small_fonts_item ) {
if ( getCurrentTreePanel() != null ) {
getCurrentTreePanel().setSmallFonts();
getCurrentTreePanel().repaint();
}
}
else if ( o == _medium_fonts_item ) {
if ( getCurrentTreePanel() != null ) {
getCurrentTreePanel().setMediumFonts();
getCurrentTreePanel().repaint();
}
}
else if ( o == _large_fonts_item ) {
if ( getCurrentTreePanel() != null ) {
getCurrentTreePanel().setLargeFonts();
getCurrentTreePanel().repaint();
}
}
else if ( o == _choose_font_mi ) {
chooseFont();
}
else if ( o == _choose_minimal_confidence_mi ) {
chooseMinimalConfidence();
}
else if ( o == _overview_placment_mi ) {
MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );
}
else if ( o == _screen_antialias_cbmi ) {
updateOptions( getOptions() );
updateScreenTextAntialias( getMainPanel().getTreePanels() );
}
else if ( o == _background_gradient_cbmi ) {
updateOptions( getOptions() );
}
else if ( o == _show_domain_labels ) {
updateOptions( getOptions() );
}
else if ( o == _color_labels_same_as_parent_branch ) {
updateOptions( getOptions() );
}
else if ( o == _show_node_boxes_cbmi ) {
updateOptions( getOptions() );
}
else if ( o == _non_lined_up_cladograms_rbmi ) {
updateOptions( getOptions() );
showWhole();
}
else if ( o == _uniform_cladograms_rbmi ) {
updateOptions( getOptions() );
showWhole();
}
else if ( o == _ext_node_dependent_cladogram_rbmi ) {
updateOptions( getOptions() );
showWhole();
}
else if ( o == _search_case_senstive_cbmi ) {
updateOptions( getOptions() );
getMainPanel().getControlPanel().search();
}
else if ( o == _search_whole_words_only_cbmi ) {
updateOptions( getOptions() );
getMainPanel().getControlPanel().search();
}
else if ( o == _inverse_search_result_cbmi ) {
updateOptions( getOptions() );
getMainPanel().getControlPanel().search();
}
else if ( o == _show_scale_cbmi ) {
updateOptions( getOptions() );
}
else if ( o == _show_branch_length_values_cbmi ) {
updateOptions( getOptions() );
}
else if ( o == _label_direction_cbmi ) {
updateOptions( getOptions() );
}
else if ( o == _show_overview_cbmi ) {
updateOptions( getOptions() );
if ( getCurrentTreePanel() != null ) {
getCurrentTreePanel().updateOvSizes();
}
}
//******************************************START**********************************************************//
//TODO AAC Code Duplication from Main Frame Application
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 == _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() );
}
//********************************************END**********************************************************//
else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )
|| ( o == _convex_type_cbmi ) || ( o == _euro_type_cbmi ) || ( o == _rounded_type_cbmi )
|| ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {
typeChanged( o );
}
else if ( o == _about_item ) {
about();
}
else if ( o == _help_item ) {
help( getConfiguration().getWebLinks() );
}
else if ( o == _website_item ) {
try {
Util.openWebsite( Constants.APTX_WEB_SITE, is_applet, applet );
}
catch ( final IOException e1 ) {
ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
}
}
else if ( o == _phyloxml_website_item ) {
try {
Util.openWebsite( Constants.PHYLOXML_WEB_SITE, is_applet, applet );
}
catch ( final IOException e1 ) {
ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
}
}
else if ( o == _aptx_ref_item ) {
try {
Util.openWebsite( Constants.APTX_REFERENCE_URL, is_applet, applet );
}
catch ( final IOException e1 ) {
ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
}
}
else if ( o == _phyloxml_ref_item ) {
try {
Util.openWebsite( Constants.PHYLOXML_REFERENCE_URL, is_applet, applet );
}
catch ( final IOException e1 ) {
ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
}
}
else {
if ( _load_phylogeny_from_webservice_menu_items != null ) {
for( int i = 0; i < _load_phylogeny_from_webservice_menu_items.length; ++i ) {
if ( o == _load_phylogeny_from_webservice_menu_items[ i ] ) {
readPhylogeniesFromWebservice( i );
}
}
}
}
_contentpane.repaint();
}
void activateSaveAllIfNeeded() {
if ( ( getMainPanel().getTabbedPane() != null ) && ( getMainPanel().getTabbedPane().getTabCount() > 1 ) ) {
_save_all_item.setEnabled( true );
}
else {
_save_all_item.setEnabled( false );
}
}
void buildFileMenu() {
_file_jmenu = createMenu( "File", getConfiguration() );
_file_jmenu.add( _open_url_item = new JMenuItem( "Read tree from URL/webservice..." ) );
_file_jmenu.addSeparator();
_file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );
customizeJMenuItem( _open_url_item );
customizeJMenuItem( _exit_item );
_jmenubar.add( _file_jmenu );
}
void buildFontSizeMenu() {
_font_size_menu = createMenu( FONT_SIZE_MENU_LABEL, getConfiguration() );
_font_size_menu.add( _super_tiny_fonts_item = new JMenuItem( "Super Tiny Fonts" ) );
_font_size_menu.add( _tiny_fonts_item = new JMenuItem( "Tiny Fonts" ) );
_font_size_menu.add( _small_fonts_item = new JMenuItem( "Small Fonts" ) );
_font_size_menu.add( _medium_fonts_item = new JMenuItem( "Medium Fonts" ) );
_font_size_menu.add( _large_fonts_item = new JMenuItem( "Large Fonts" ) );
customizeJMenuItem( _super_tiny_fonts_item );
customizeJMenuItem( _tiny_fonts_item );
customizeJMenuItem( _small_fonts_item );
customizeJMenuItem( _medium_fonts_item );
customizeJMenuItem( _large_fonts_item );
_jmenubar.add( _font_size_menu );
}
void buildHelpMenu() {
_help_jmenu = createMenu( "Help", getConfiguration() );
_help_jmenu.add( _help_item = new JMenuItem( "Help" ) );
_help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );
_aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" );
_help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );
_help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );
_help_jmenu.addSeparator();
_help_jmenu.add( _about_item = new JMenuItem( "About" ) );
customizeJMenuItem( _help_item );
customizeJMenuItem( _website_item );
customizeJMenuItem( _phyloxml_website_item );
customizeJMenuItem( _aptx_ref_item );
customizeJMenuItem( _phyloxml_ref_item );
customizeJMenuItem( _about_item );
_phyloxml_ref_item.setToolTipText( PHYLOXML_REF_TOOL_TIP );
_aptx_ref_item.setToolTipText( APTX_REF_TOOL_TIP );
_jmenubar.add( _help_jmenu );
}
void buildTypeMenu() {
_type_menu = createMenu( TYPE_MENU_HEADER, getConfiguration() );
_type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );
_type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );
_type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );
_type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );
_type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );
_type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );
_type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );
_type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );
customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );
customizeCheckBoxMenuItem( _triangular_type_cbmi, false );
customizeCheckBoxMenuItem( _euro_type_cbmi, false );
customizeCheckBoxMenuItem( _rounded_type_cbmi, false );
customizeCheckBoxMenuItem( _curved_type_cbmi, false );
customizeCheckBoxMenuItem( _convex_type_cbmi, false );
customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );
customizeCheckBoxMenuItem( _circular_type_cbmi, false );
_unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
_circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
initializeTypeMenu( getOptions() );
_jmenubar.add( _type_menu );
}
void buildViewMenu() {
_view_jmenu = createMenu( "View as Text", getConfiguration() );
_view_jmenu.add( _view_as_XML_item = new JMenuItem( "View as phyloXML" ) );
_view_jmenu.add( _view_as_NH_item = new JMenuItem( "View as Newick" ) );
_view_jmenu.add( _view_as_NHX_item = new JMenuItem( "View as NHX" ) );
_view_jmenu.add( _view_as_nexus_item = new JMenuItem( "View as Nexus" ) );
customizeJMenuItem( _view_as_NH_item );
customizeJMenuItem( _view_as_NHX_item );
customizeJMenuItem( _view_as_XML_item );
customizeJMenuItem( _view_as_nexus_item );
_jmenubar.add( _view_jmenu );
}
private void chooseFont() {
final FontChooser fc = new FontChooser();
fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
fc.showDialog( this, "Select the Base Font" );
getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );
}
private void chooseMinimalConfidence() {
final String s = ( String ) JOptionPane
.showInputDialog( this,
"Please enter the minimum for confidence values to be displayed.\n"
+ "[current value: " + getOptions().getMinConfidenceValue() + "]\n",
"Minimal Confidence Value",
JOptionPane.QUESTION_MESSAGE,
null,
null,
getOptions().getMinConfidenceValue() );
if ( !ForesterUtil.isEmpty( s ) ) {
boolean success = true;
double m = 0.0;
final String m_str = s.trim();
if ( !ForesterUtil.isEmpty( m_str ) ) {
try {
m = Double.parseDouble( m_str );
}
catch ( final Exception ex ) {
success = false;
}
}
else {
success = false;
}
if ( success && ( m >= 0.0 ) ) {
getOptions().setMinConfidenceValue( m );
}
}
}
void close() {
//******************************************START**********************************************************//
if(AppletParams.isEitherTPorTDForAll() ){
if(appletTerminate.check_terminate(this)){
removeTextFrame();
if ( _mainpanel != null ) {
_mainpanel.terminate();
}
if ( _contentpane != null ) {
_contentpane.removeAll();
}
setVisible( false );
dispose();
NewWindowSubtree.handleBackToSubTreeButton();
NewWindowSubtree.handleCloseXButton();
AppletTerminate.extraTerminationActions(this);
}
else{
appletTerminate.closeAdditionalTasks();
}
}
else{
//********************************************END**********************************************************//
removeTextFrame();
if ( _mainpanel != null ) {
_mainpanel.terminate();
}
if ( _contentpane != null ) {
_contentpane.removeAll();
}
setVisible( false );
dispose();
//******************************************START**********************************************************//
} //end of else
//********************************************END**********************************************************//
}
void confColor() {
if ( _mainpanel.getCurrentTreePanel() != null ) {
_mainpanel.getCurrentTreePanel().confColor();
}
}
void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {
if ( item != null ) {
item.setFont( MainFrame.menu_font );
if ( !getConfiguration().isUseNativeUI() ) {
item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
item.setForeground( getConfiguration().getGuiMenuTextColor() );
}
item.setSelected( is_selected );
item.addActionListener( this );
}
}
void customizeJMenuItem( final JMenuItem jmi ) {
if ( jmi != null ) {
jmi.setFont( MainFrame.menu_font );
if ( !getConfiguration().isUseNativeUI() ) {
jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
jmi.setForeground( getConfiguration().getGuiMenuTextColor() );
}
jmi.addActionListener( this );
}
}
void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {
if ( item != null ) {
item.setFont( MainFrame.menu_font );
if ( !getConfiguration().isUseNativeUI() ) {
item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
item.setForeground( getConfiguration().getGuiMenuTextColor() );
}
item.setSelected( is_selected );
item.addActionListener( this );
}
}
void exceptionOccuredDuringOpenFile( final Exception e ) {
try {
_mainpanel.getCurrentTreePanel().setArrowCursor();
}
catch ( final Exception ex ) {
// Do nothing.
}
JOptionPane.showMessageDialog( this,
ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
"Error during File|Open",
JOptionPane.ERROR_MESSAGE );
}
void exceptionOccuredDuringSaveAs( final Exception e ) {
try {
_mainpanel.getCurrentTreePanel().setArrowCursor();
}
catch ( final Exception ex ) {
// Do nothing.
}
JOptionPane.showMessageDialog( this, "Exception" + e, "Error during File|SaveAs", JOptionPane.ERROR_MESSAGE );
}
boolean GAndSDoHaveMoreThanOneSpeciesInComman( final Phylogeny gene_tree ) {
if ( ( gene_tree == null ) || gene_tree.isEmpty() ) {
JOptionPane.showMessageDialog( this,
"Gene tree and species tree have no species in common.",
"Error during SDI",
JOptionPane.ERROR_MESSAGE );
return false;
}
else if ( gene_tree.getNumberOfExternalNodes() < 2 ) {
JOptionPane.showMessageDialog( this,
"Gene tree and species tree have only one species in common.",
"Error during SDI",
JOptionPane.ERROR_MESSAGE );
return false;
}
else {
return true;
}
}
Configuration getConfiguration() {
return _configuration;
}
TreePanel getCurrentTreePanel() {
return getMainPanel().getCurrentTreePanel();
}
JMenu getHelpMenu() {
return _help_jmenu;
}
JCheckBoxMenuItem getlabelDirectionCbmi() {
return _label_direction_cbmi;
}
MainPanel getMainPanel() {
return _mainpanel;
}
JMenuBar getMenuBarOfMainFrame() {
return _jmenubar;
}
Options getOptions() {
return _options;
}
void initializeTypeMenu( final Options options ) {
setTypeMenuToAllUnselected();
switch ( options.getPhylogenyGraphicsType() ) {
case CONVEX:
_convex_type_cbmi.setSelected( true );
break;
case CURVED:
_curved_type_cbmi.setSelected( true );
break;
case EURO_STYLE:
_euro_type_cbmi.setSelected( true );
break;
case ROUNDED:
_rounded_type_cbmi.setSelected( true );
break;
case TRIANGULAR:
_triangular_type_cbmi.setSelected( true );
break;
case UNROOTED:
_unrooted_type_cbmi.setSelected( true );
break;
case CIRCULAR:
_circular_type_cbmi.setSelected( true );
break;
default:
_rectangular_type_cbmi.setSelected( true );
break;
}
}
void midpointRoot() {
if ( _mainpanel.getCurrentTreePanel() != null ) {
_mainpanel.getCurrentTreePanel().midpointRoot();
}
}
abstract void readPhylogeniesFromURL();
void readPhylogeniesFromWebservice( final int i ) {
final UrlTreeReader reader = new UrlTreeReader( this, i );
new Thread( reader ).start();
}
private void removeBranchColors() {
if ( getMainPanel().getCurrentPhylogeny() != null ) {
Util.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
}
}
void removeTextFrame() {
if ( _textframe != null ) {
_textframe.close();
_textframe = null;
}
}
void setConfiguration( final Configuration configuration ) {
_configuration = configuration;
}
void setOptions( final Options options ) {
_options = options;
}
void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {
setTypeMenuToAllUnselected();
switch ( type ) {
case CIRCULAR:
_circular_type_cbmi.setSelected( true );
break;
case CONVEX:
_convex_type_cbmi.setSelected( true );
break;
case CURVED:
_curved_type_cbmi.setSelected( true );
break;
case EURO_STYLE:
_euro_type_cbmi.setSelected( true );
break;
case ROUNDED:
_rounded_type_cbmi.setSelected( true );
break;
case RECTANGULAR:
_rectangular_type_cbmi.setSelected( true );
break;
case TRIANGULAR:
_triangular_type_cbmi.setSelected( true );
break;
case UNROOTED:
_unrooted_type_cbmi.setSelected( true );
break;
default:
throw new IllegalArgumentException( "unknown type: " + type );
}
}
void setTypeMenuToAllUnselected() {
_convex_type_cbmi.setSelected( false );
_curved_type_cbmi.setSelected( false );
_euro_type_cbmi.setSelected( false );
_rounded_type_cbmi.setSelected( false );
_triangular_type_cbmi.setSelected( false );
_rectangular_type_cbmi.setSelected( false );
_unrooted_type_cbmi.setSelected( false );
_circular_type_cbmi.setSelected( false );
}
void showWhole() {
_mainpanel.getControlPanel().showWhole();
}
void switchColors() {
final TreeColorSet colorset = _mainpanel.getTreeColorSet();
final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );
csc.setVisible( true );
}
void taxColor() {
if ( _mainpanel.getCurrentTreePanel() != null ) {
_mainpanel.getCurrentTreePanel().taxColor();
}
}
void typeChanged( final Object o ) {
updateTypeCheckboxes( getOptions(), o );
updateOptions( getOptions() );
if ( getCurrentTreePanel() != null ) {
final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();
final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();
if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
|| ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )
|| ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
|| ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {
getCurrentTreePanel().getControlPanel().showWhole();
}
if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );
}
else {
getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );
}
getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );
updateScreenTextAntialias( getMainPanel().getTreePanels() );
if ( getCurrentTreePanel().getControlPanel().getDynamicallyHideData() != null ) {
if ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( false );
}
else {
getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( true );
}
}
}
}
void updateOptions( final Options options ) {
options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );
options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
&& _background_gradient_cbmi.isSelected() );
options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
&& _color_labels_same_as_parent_branch.isSelected() );
options.setShowNodeBoxes( ( _show_node_boxes_cbmi != null ) && _show_node_boxes_cbmi.isSelected() );
if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
}
else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {
options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
}
else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {
options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
}
options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )
&& _search_case_senstive_cbmi.isSelected() );
if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {
options.setShowScale( _show_scale_cbmi.isSelected() );
}
if ( _label_direction_cbmi != null ) {
if ( _label_direction_cbmi.isSelected() ) {
options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
}
else {
options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
}
}
options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) {
options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() );
}
options.setPrintUsingActualSize( ( _print_using_actual_size_cbmi != null )
&& ( _print_using_actual_size_cbmi.isSelected() ) );
options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null )
&& ( _graphics_export_using_actual_size_cbmi.isSelected() ) );
options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() );
options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null )
&& _print_black_and_white_cbmi.isSelected() );
options
.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null )
&& _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );
options.setExtractPfamTaxonomyCodesInNhParsing( ( _extract_pfam_style_tax_codes_cbmi != null )
&& _extract_pfam_style_tax_codes_cbmi.isSelected() );
options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )
&& _replace_underscores_cbmi.isSelected() );
options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
&& _search_whole_words_only_cbmi.isSelected() );
options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
&& _inverse_search_result_cbmi.isSelected() );
if ( _graphics_export_visible_only_cbmi != null ) {
options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_cbmi.isSelected() );
if ( _graphics_export_visible_only_cbmi.isSelected() && ( _graphics_export_using_actual_size_cbmi != null ) ) {
_graphics_export_using_actual_size_cbmi.setSelected( true );
_graphics_export_using_actual_size_cbmi.setEnabled( false );
}
else {
_graphics_export_using_actual_size_cbmi.setEnabled( true );
}
}
if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {
options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
}
else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {
options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
}
else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {
options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
}
else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {
options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
}
else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {
options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
}
else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {
options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
}
else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {
options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
}
else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {
options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
}
}
void updateTypeCheckboxes( final Options options, final Object o ) {
setTypeMenuToAllUnselected();
( ( JCheckBoxMenuItem ) o ).setSelected( true );
}
void viewAsNexus() {
removeTextFrame();
if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty()
|| ( _mainpanel.getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
return;
}
_textframe = TextFrame.instantiate( _mainpanel.getCurrentPhylogeny().toNexus() );
}
void viewAsNH() {
removeTextFrame();
if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty()
|| ( _mainpanel.getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
return;
}
_textframe = TextFrame.instantiate( _mainpanel.getCurrentPhylogeny().toNewHampshire( false ) );
}
void viewAsNHX() {
removeTextFrame();
if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty()
|| ( _mainpanel.getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
return;
}
_textframe = TextFrame.instantiate( _mainpanel.getCurrentPhylogeny().toNewHampshireX() );
}
void viewAsXML() {
removeTextFrame();
if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty()
&& ( _mainpanel.getCurrentPhylogeny().getNumberOfExternalNodes() <= 10000 ) ) {
_textframe = TextFrame.instantiate( _mainpanel.getCurrentPhylogeny().toPhyloXML( 0 ) );
}
}
/**
* Display the about box.
*/
static void about() {
final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + Constants.VERSION + "\n" );
about.append( "Copyright (C) 2007-2009 Christian M Zmasek\n" );
about.append( "Copyright (C) 2007-2009 Ethalinda KS Cannon\n" );
about.append( "All Rights Reserved\n" );
about.append( "License: GNU Lesser General Public License (LGPL)\n" );
about.append( "Last modified: " + Constants.PRG_DATE + "\n" );
about.append( "phyloXML version : " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
about.append( "phyloXML location: " + ForesterConstants.PHYLO_XML_LOCATION + "\n" );
if ( !ForesterUtil.isEmpty( ForesterUtil.JAVA_VERSION ) && !ForesterUtil.isEmpty( ForesterUtil.JAVA_VENDOR ) ) {
about.append( "[your Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]\n" );
}
if ( !ForesterUtil.isEmpty( ForesterUtil.OS_NAME ) && !ForesterUtil.isEmpty( ForesterUtil.OS_ARCH )
&& !ForesterUtil.isEmpty( ForesterUtil.OS_VERSION ) ) {
about.append( "[your OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " "
+ ForesterUtil.OS_VERSION + "]\n" );
}
final Runtime rt = java.lang.Runtime.getRuntime();
final long free_memory = rt.freeMemory() / 1000000;
final long total_memory = rt.totalMemory() / 1000000;
about.append( "[free memory: " + free_memory + "MB, total memory: " + total_memory + "MB]\n" );
about.append( "[locale: " + Locale.getDefault() + "]\n" );
about.append( "References:\n" );
about.append( Constants.PHYLOXML_REFERENCE_SHORT + "\n" );
about.append( "Zmasek CM and Eddy SR (2001), Bioinformatics, 17, 383\n" );
about.append( "For more information & download:\n" );
about.append( Constants.APTX_WEB_SITE + "\n" );
about.append( "Comments: " + Constants.AUTHOR_EMAIL );
JOptionPane.showMessageDialog( null, about, Constants.PRG_NAME, JOptionPane.PLAIN_MESSAGE );
}
static String createCurrentFontDesc( final TreeFontSet tree_font_set ) {
return tree_font_set.getLargeFont().getFamily() + " " + tree_font_set.getLargeFont().getSize();
}
static JMenu createMenu( final String title, final Configuration conf ) {
final JMenu jmenu = new JMenu( title );
if ( !conf.isUseNativeUI() ) {
jmenu.setFont( MainFrame.menu_font );
jmenu.setBackground( conf.getGuiMenuBackgroundColor() );
jmenu.setForeground( conf.getGuiMenuTextColor() );
}
return jmenu;
}
static JMenuItem customizeMenuItemAsLabel( final JMenuItem label, final Configuration configuration ) {
label.setFont( MainFrame.menu_font.deriveFont( Font.BOLD ) );
if ( !configuration.isUseNativeUI() ) {
label.setBackground( configuration.getGuiMenuBackgroundColor() );
label.setForeground( configuration.getGuiMenuTextColor() );
label.setOpaque( true );
}
label.setSelected( false );
label.setEnabled( false );
return label;
}
static void cycleOverview( final Options op, final TreePanel tree_panel ) {
switch ( op.getOvPlacement() ) {
case LOWER_LEFT:
op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
break;
case LOWER_RIGHT:
op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );
break;
case UPPER_LEFT:
op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );
break;
case UPPER_RIGHT:
op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );
break;
default:
throw new IllegalStateException( "unknown placement: " + op.getOvPlacement() );
}
tree_panel.updateOvSettings();
}
static void help( final Map<String, WebLink> weblinks ) {
final StringBuilder sb = new StringBuilder();
sb.append( "Display options\n" );
sb.append( "-------------------\n" );
sb.append( "Use the checkboxes to select types of information to display on the tree.\n\n" );
sb.append( "Clickable tree nodes\n" );
sb.append( "--------------------\n" );
sb.append( "Tree nodes can be clicked, the action is determined by the 'click on node to' menu\n" );
sb.append( "or by right clicking:\n" );
sb.append( "o Display Node Data -- display information for a node\n" );
sb.append( "o Collapse/Uncollapse -- collapse and uncollapse subtree from clicked node\n" );
sb.append( "o Root/Reroot -- change tree root to clicked node\n" );
sb.append( "o Sub/Super Tree -- toggle between subtree from clicked node and whole tree\n" );
sb.append( "o Swap Descendants -- switch descendant on either side of clicked node\n" );
sb.append( "o Colorize Subtree -- color a subtree\n" );
sb.append( "o Open Sequence Web -- launch a web browser to display sequence information\n" );
sb.append( "o Open Taxonomy Web -- launch a web browser to display taxonomy information\n" );
sb.append( "- there may be additional choices depending on this particular setup\n\n" );
sb.append( "Right clicking on a node always displays the information of a node.\n\n" );
sb.append( "Zooming\n" );
sb.append( "---------\n" );
sb.append( "The mouse wheel and the plus and minus keys control zooming.\n" );
sb.append( "Mouse wheel+Ctrl changes the text size.\n" );
sb.append( "Mouse wheel+Shift controls zooming in vertical direction only.\n" );
sb.append( "Use the buttons on the control panel to zoom the tree in and out, horizontally or vertically.\n" );
sb
.append( "The entire tree can be fitted into the window by clicking the \"F\" button, or by pressing F, Delete, or Home.\n" );
sb.append( "The up, down, left, and right keys can be used to move the visible part (if zoomed in).\n" );
sb.append( "Up, down, left, and right+Shift can be used to control zooming horizontally and vertically.\n" );
sb.append( "Plus and minus keys+Ctrl change the text size; F+Ctrl, Delete+Ctrl, or Home+Ctrl resets it.\n\n" );
sb.append( "Quick tree manipulation:\n" );
sb.append( "------------------------\n" );
sb.append( "Order Subtrees -- order the tree by branch length\n" );
sb.append( "Uncollapse All -- uncollapse any and all collapsed branches\n\n" );
sb.append( "Memory problems (Java heap space error)\n" );
sb.append( "---------------------------------------\n" );
sb.append( "Since the Java default memory allocation is quite small, it might by necessary (for trees\n" );
sb
.append( "with more than approximately 5000 external nodes) to increase the memory which Java can use, with\n" );
sb.append( "the '-Xmx' Java command line option. For example:\n" );
sb.append( "java -Xms32m -Xmx256m -cp path\\to\\forester.jar org.forester.archaeopteryx.Archaeopteryx\n\n" );
if ( ( weblinks != null ) && ( weblinks.size() > 0 ) ) {
sb.append( "Active web links\n" );
sb.append( "--------------------\n" );
for( final String key : weblinks.keySet() ) {
sb.append( " " + weblinks.get( key ).toString() + "\n" );
}
}
// + "General remarks\n"
// + "---------------\n"
// +
// "o The application version permits copying to the clipboard \n"
// +
// " in the \"View\"|\"View as ...\" frame (either by control-c or button press).\n"
// +
// "o Changes made to a subtree affect this subtree and its subtrees,\n"
// + " but not any of its parent tree(s).\n"
// +
// "o Archaeopteryx tries to detect whether the numerical values in a NH tree\n"
// +
// " are likely to be bootstrap values instead of branch length values.\n\n"
// +
// " Remarks regarding SDI (Speciation Duplication Inference):\n"
// +
// "o Each external node of the gene tree (in display) needs to be associated with\n"
// +
// " a species: either directly through the \"Species\" field, or the species\n"
// +
// " is part of the sequence name in the form \"XXXX_SPECIES\"\n"
// +
// " (e.g. \"ACON_DROME\" or \"ACON_DROME/123-4489\" which is also acceptable).\n"
// +
// "o A species tree for each species of the gene tree needs to be loaded with\n"
// +
// " \"SDI\"|\"Load species tree\" prior the SDI execution.\n"
// +
// "o !External nodes of the gene tree associated with species not present in\n"
// +
// " the species tree are REMOVED prior to SDI execution!\n"
// +
// "o Both the gene tree and the species tree must be completely binary.\n"
// +
// "o Duplications and speciations are a function of the position of the root.\n"
// +
// " Hence, after each manual \"Root/Reroot\"ing some duplications will be\n"
// + " incorrect and need to be inferred again\n"
// +
// " with: \"SDI\"|\"SDI (Speciation Duplication Inference)\n\n"
sb.append( "\n" );
sb.append( "phyloXML\n" );
sb.append( "-------------------\n" );
sb.append( "Reference: " + Constants.PHYLOXML_REFERENCE + "\n" );
sb.append( "Website: " + Constants.PHYLOXML_WEB_SITE + "\n" );
sb.append( "Version: " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
sb.append( "\n" );
sb.append( "For more information: http://www.phylosoft.org/archaeopteryx/\n" );
sb.append( "Email: " + Constants.AUTHOR_EMAIL + "\n\n" );
TextFrame.instantiate( sb.toString() );
}
static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) {
if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) {
mi.setText( "Overview Placement... (current: " + tree_panel.getOptions().getOvPlacement() + ")" );
}
else {
mi.setText( "Overview Placement..." );
}
}
static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) {
if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) {
mi.setText( "Select Colors... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName() + ")" );
}
else {
mi.setText( "Select Colors..." );
}
}
static void setTextForFontChooserMenuItem( final JMenuItem mi, final String font_desc ) {
mi.setText( "Select Font... (current: " + font_desc + ")" );
}
static void setTextMinSupportMenuItem( final JMenuItem mi, final Options options, final TreePanel current_tree_panel ) {
if ( ( current_tree_panel == null ) || ( current_tree_panel.getPhylogeny() == null ) ) {
mi.setEnabled( true );
}
else if ( ForesterUtil.isHasAtLeastOneBranchWithSupportValues( current_tree_panel.getPhylogeny() ) ) {
mi.setEnabled( true );
}
else {
mi.setEnabled( false );
}
mi.setText( "Enter Min Confidence Value... (current: " + options.getMinConfidenceValue() + ")" );
}
static void updateOptionsMenuDependingOnPhylogenyType( final MainPanel main_panel,
final JCheckBoxMenuItem scale,
final JCheckBoxMenuItem branch_lengths,
final JRadioButtonMenuItem non_lined_up,
final JRadioButtonMenuItem uniform_clado,
final JRadioButtonMenuItem nonuniform_clado,
final JCheckBoxMenuItem label_direction_cbmi ) {
final TreePanel tree_panel = main_panel.getCurrentTreePanel();
final ControlPanel control = main_panel.getControlPanel();
final Options options = main_panel.getOptions();
scale.setSelected( options.isShowScale() );
branch_lengths.setSelected( options.isShowBranchLengthValues() );
// non_lined_up.setSelected( options.isNonLinedUpCladogram() );
if ( ( tree_panel != null ) && ( !tree_panel.isPhyHasBranchLengths() ) ) {
scale.setSelected( false );
scale.setEnabled( false );
branch_lengths.setSelected( false );
branch_lengths.setEnabled( false );
}
else if ( ( tree_panel != null ) && !control.isDrawPhylogram() ) {
scale.setSelected( false );
scale.setEnabled( false );
branch_lengths.setEnabled( true );
}
else {
scale.setEnabled( true );
branch_lengths.setEnabled( true );
}
if ( ( tree_panel != null )
&& ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.ROUNDED )
&& ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) && ( tree_panel
.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) ) ) {
branch_lengths.setSelected( false );
branch_lengths.setEnabled( false );
}
if ( tree_panel != null ) {
if ( ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR )
|| ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) {
non_lined_up.setEnabled( false );
uniform_clado.setEnabled( false );
nonuniform_clado.setEnabled( false );
}
else {
non_lined_up.setEnabled( true );
uniform_clado.setEnabled( true );
nonuniform_clado.setEnabled( true );
}
}
else {
if ( ( tree_panel != null )
&& ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) && ( tree_panel
.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) ) ) {
branch_lengths.setSelected( false );
branch_lengths.setEnabled( false );
}
if ( ( tree_panel != null )
&& ( ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) || ( tree_panel
.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) ) {
non_lined_up.setEnabled( false );
}
else {
// non_lined_up.setSelected( options.isNonLinedUpCladogram() );
non_lined_up.setEnabled( true );
}
}
label_direction_cbmi.setEnabled( true );
if ( tree_panel != null ) {
if ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
&& ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
label_direction_cbmi.setEnabled( false );
}
if ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
scale.setSelected( false );
scale.setEnabled( false );
}
}
}
static void updateScreenTextAntialias( final List<TreePanel> treepanels ) {
for( final TreePanel tree_panel : treepanels ) {
tree_panel.setTextAntialias();
}
}
//******************************************START**********************************************************//
//TODO AAC Code Duplication from Main Frame Application
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 );
}
}
}
//TODO AAC Code Duplication from Main Frame Application
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 );
}
}
}
public void closeOnDelete() {
removeTextFrame();
if ( _mainpanel != null ) {
_mainpanel.terminateOnDelete();
}
if ( _contentpane != null ) {
_contentpane.removeAll();
}
setVisible( false );
dispose();
AppletTerminate.extraTerminationActions(this);
}
public MainPanel get_main_panel() {
return _mainpanel;
}
public void repaintPanel(){
this.getMainPanel().repaint();
}
public Configuration get_configuration() {
return _configuration;
}
public void close_() {
/**
* NOTE TO PROGRAMMER
* CHANGES MADE IN THIS METHOD WILL ALSO AFFECT void close(){...}. Hence whenever you make any changes here, also make changes in
* void close(){...}
*/
//******************************************START**********************************************************//
if(AppletParams.isEitherTPorTDForAll() ){
if(appletTerminate.check_terminate(this)){
removeTextFrame();
if ( _mainpanel != null ) {
_mainpanel.terminate();
}
if ( _contentpane != null ) {
_contentpane.removeAll();
}
setVisible( false );
dispose();
NewWindowSubtree.handleBackToSubTreeButton();
NewWindowSubtree.handleCloseXButton();
AppletTerminate.extraTerminationActions(this);
}
else{
appletTerminate.closeAdditionalTasks();
}
}
else{
//********************************************END**********************************************************//
removeTextFrame();
if ( _mainpanel != null ) {
_mainpanel.terminate();
}
if ( _contentpane != null ) {
_contentpane.removeAll();
}
setVisible( false );
dispose();
//******************************************START**********************************************************//
} //end of else
//********************************************END**********************************************************//
}
public Options get_options() {
return _options;
}
public Container get_content_pane(){
return _contentpane;
}
//********************************************END**********************************************************//
}