From: cmzmasek Date: Fri, 21 Oct 2016 23:36:33 +0000 (-0700) Subject: removed applet code X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=42d56879faae998a9616c130dd6907e8f9c03134;p=jalview.git removed applet code --- diff --git a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java index d683f29..ec258ba 100644 --- a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java +++ b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java @@ -59,7 +59,6 @@ import javax.imageio.ImageIO; import javax.imageio.ImageWriteParam; import javax.imageio.ImageWriter; import javax.imageio.stream.ImageOutputStream; -import javax.swing.JApplet; import javax.swing.JOptionPane; import javax.swing.text.MaskFormatter; @@ -245,13 +244,8 @@ public final class AptxUtil { } final public static void launchWebBrowser( final URI uri, - final boolean is_applet, - final JApplet applet, - final String frame_name ) throws IOException { - if ( is_applet ) { - applet.getAppletContext().showDocument( uri.toURL(), frame_name ); - } - else { + final String frame_name ) throws IOException { + // This requires Java 1.6: // ======================= // boolean no_desktop = false; @@ -282,7 +276,7 @@ public final class AptxUtil { throw new IOException( e ); } // } - } + } public static Set obtainAllDistinctTaxonomies( final PhylogenyNode node ) { @@ -880,9 +874,9 @@ public final class AptxUtil { } } - final static void openWebsite( final String url, final boolean is_applet, final JApplet applet ) throws IOException { + final static void openWebsite( final String url ) throws IOException { try { - AptxUtil.launchWebBrowser( new URI( url ), is_applet, applet, AptxConstants.PRG_NAME ); + AptxUtil.launchWebBrowser( new URI( url ), AptxConstants.PRG_NAME ); } catch ( final Exception e ) { throw new IOException( e ); diff --git a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxA.java b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxA.java deleted file mode 100644 index 6b4cdd7..0000000 --- a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxA.java +++ /dev/null @@ -1,247 +0,0 @@ -// $Id: -// FORESTER -- software libraries and applications -// for evolutionary biology research and applications. -// -// Copyright (C) 2008-2009 Christian M. Zmasek -// Copyright (C) 2008-2009 Burnham Institute for Medical Research -// All rights reserved -// -// This library is free software; you can redistribute it and/or -// modify it under the terms of the GNU Lesser General Public -// License as published by the Free Software Foundation; either -// version 2.1 of the License, or (at your option) any later version. -// -// This library is distributed in the hope that it will be useful, -// but WITHOUT ANY WARRANTY; without even the implied warranty of -// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU -// Lesser General Public License for more details. -// -// You should have received a copy of the GNU Lesser General Public -// License along with this library; if not, write to the Free Software -// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA -// -// Contact: phylosoft @ gmail . com -// WWW: https://sites.google.com/site/cmzmasek/home/software/forester - -package org.forester.archaeopteryx; - -import java.awt.Color; -import java.awt.Font; -import java.awt.Graphics; -import java.awt.KeyboardFocusManager; -import java.io.File; -import java.net.URL; - -import javax.swing.JApplet; -import javax.swing.UIManager; - -import org.forester.phylogeny.Phylogeny; -import org.forester.util.ForesterUtil; - -public class ArchaeopteryxA extends JApplet { - - private static final long serialVersionUID = 2314899014580484146L; - private final static Color background_color = new Color( 0, 0, 0 ); - private final static Color font_color = new Color( 0, 255, 0 ); - private final static Color ex_background_color = new Color( 0, 0, 0 ); - private final static Color ex_font_color = new Color( 255, 0, 0 ); - private final static Font font = new Font( Configuration.getDefaultFontFamilyName(), Font.BOLD, 9 ); - private MainFrameApplet _mainframe_applet; - private String _tree_url_str = ""; - private String _species_tree_url_str = ""; - private String _message_1 = ""; - private String _message_2 = ""; - public final static String NAME = "ArchaeopteryxA"; - - @Override - public void destroy() { - AptxUtil.printAppletMessage( NAME, "going to be destroyed" ); - if ( getMainFrameApplet() != null ) { - getMainFrameApplet().close(); - } - } - - /** - * This method returns the current external node data which - * has been selected by the user by clicking the "Return ..." - * menu item. This method is expected to be called from Javascript or - * something like it. - * - * @return current external node data as String - */ - public String getCurrentExternalNodesDataBuffer() { - return getMainFrameApplet().getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString(); - } - - public int getCurrentExternalNodesDataBufferChangeCounter() { - return getMainFrameApplet().getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter(); - } - - public int getCurrentExternalNodesDataBufferLength() { - return getMainFrameApplet().getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length(); - } - - public String getSpeciesTreeUrlStr() { - return _species_tree_url_str; - } - - public String getTreeUrlStr() { - return _tree_url_str; - } - - @Override - public void init() { - boolean has_exception = false; - setName( NAME ); - setTreeUrlStr( getParameter( AptxConstants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD ) ); - setSpeciesTreeUrlStr( getParameter( AptxConstants.APPLET_PARAM_NAME_FOR_URL_OF_SPECIES_TREE_TO_LOAD ) ); - if ( !ForesterUtil.isEmpty( getTreeUrlStr() ) ) { - AptxUtil.printAppletMessage( NAME, "URL of tree(s) to load: " + getTreeUrlStr() ); - } - else { - ForesterUtil.printErrorMessage( NAME, "no URL for tree(s) to load!" ); - setBackground( ex_background_color ); - setForeground( ex_font_color ); - has_exception = true; - setMessage1( "no URL for tree(s) to load" ); - repaint(); - } - if ( !ForesterUtil.isEmpty( getSpeciesTreeUrlStr() ) ) { - AptxUtil.printAppletMessage( NAME, "URL of species tree to load: " + getSpeciesTreeUrlStr() ); - } - setBackground( background_color ); - setForeground( font_color ); - setFont( font ); - repaint(); - String s = null; - try { - s = System.getProperty( "java.version" ); - } - catch ( final Exception e ) { - ForesterUtil.printWarningMessage( NAME, "minor error: " + e.getLocalizedMessage() ); - } - if ( ( s != null ) && ( s.length() > 0 ) ) { - setMessage2( "[Your Java version: " + s + "]" ); - repaint(); - } - final String config_filename = getParameter( AptxConstants.APPLET_PARAM_NAME_FOR_CONFIG_FILE_URL ); - AptxUtil.printAppletMessage( NAME, "URL for configuration file is: " + config_filename ); - final Configuration configuration = new Configuration( config_filename, true, true, true ); - try { - if ( configuration.isUseNativeUI() ) { - UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() ); - } - else { - UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() ); - } - setVisible( false ); - _mainframe_applet = new MainFrameApplet( this, configuration, getSpeciesTreeUrlStr() ); - final URL tree_url = new URL( getTreeUrlStr() ); - final Phylogeny[] phys = AptxUtil.readPhylogeniesFromUrl( tree_url, configuration - .isValidatePhyloXmlAgainstSchema(), configuration.isReplaceUnderscoresInNhParsing(), configuration - .isInternalNumberAreConfidenceForNhParsing(), configuration.getTaxonomyExtraction(), configuration - .isMidpointReroot() ); - if ( phys == null ) { - ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + tree_url + "] are null" ); - } - else if ( phys.length < 1 ) { - ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + tree_url + "] are empty" ); - } - else { - AptxUtil.printAppletMessage( NAME, "loaded " + phys.length + " phylogenies from: " + tree_url ); - } - AptxUtil.printAppletMessage( ArchaeopteryxA.NAME, "loaded " + phys.length + " phylogenies from: " - + tree_url ); - AptxUtil.addPhylogeniesToTabs( phys, - new File( tree_url.getFile() ).getName(), - getTreeUrlStr(), - getMainFrameApplet().getConfiguration(), - getMainFrameApplet().getMainPanel() ); - getMainFrameApplet().getMainPanel().getControlPanel().showWholeAll(); - getMainFrameApplet().getMainPanel().getControlPanel().showWhole(); - setVisible( true ); - } - catch ( final Exception e ) { - ForesterUtil.printErrorMessage( NAME, e.toString() ); - setBackground( ex_background_color ); - setForeground( ex_font_color ); - has_exception = true; - setMessage1( "Exception: " + e ); - e.printStackTrace(); - repaint(); - } - if ( !has_exception ) { - setMessage1( NAME + " is now ready!" ); - repaint(); - AptxUtil.printAppletMessage( NAME, "successfully initialized" ); - } - KeyboardFocusManager.getCurrentKeyboardFocusManager().clearGlobalFocusOwner(); - getMainFrameApplet().requestFocus(); - getMainFrameApplet().requestFocusInWindow(); - getMainFrameApplet().requestFocus(); - /* GUILHEM_BEG */ - final String default_relation = getParameter( AptxConstants.APPLET_PARAM_NAME_FOR_DEFAULT_SEQUENCE_RELATION_TYPE ); - if ( default_relation != null ) { - getMainFrameApplet().getMainPanel().getControlPanel().getSequenceRelationTypeBox() - .setSelectedItem( default_relation ); - } - final String default_sequence = getParameter( AptxConstants.APPLET_PARAM_NAME_FOR_DEFAULT_QUERY_SEQUENCE ); - if ( default_sequence != null ) { - getMainFrameApplet().getMainPanel().getControlPanel().getSequenceRelationBox() - .setSelectedItem( default_sequence ); - } - /* GUILHEM_END */ - } - - /** - * Prints message when initialization is finished. Called automatically. - * - * @param g - * Graphics - */ - @Override - public void paint( final Graphics g ) { - g.setColor( background_color ); - g.fillRect( 0, 0, 300, 60 ); - g.setColor( font_color ); - g.drawString( getMessage2(), 10, 20 ); - g.drawString( getMessage1(), 10, 40 ); - } - - @Override - public void start() { - getMainFrameApplet().getMainPanel().validate(); - getMainFrameApplet().requestFocus(); - getMainFrameApplet().requestFocusInWindow(); - getMainFrameApplet().requestFocus(); - AptxUtil.printAppletMessage( NAME, "started" ); - } - - private MainFrameApplet getMainFrameApplet() { - return _mainframe_applet; - } - - private String getMessage1() { - return _message_1; - } - - private String getMessage2() { - return _message_2; - } - - private void setMessage1( final String message_1 ) { - _message_1 = message_1; - } - - private void setMessage2( final String message_2 ) { - _message_2 = message_2; - } - - private void setSpeciesTreeUrlStr( final String url_string ) { - _species_tree_url_str = url_string; - } - - private void setTreeUrlStr( final String url_string ) { - _tree_url_str = url_string; - } -} diff --git a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java deleted file mode 100644 index 694036b..0000000 --- a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java +++ /dev/null @@ -1,1793 +0,0 @@ - -package org.forester.archaeopteryx; - -import java.awt.BorderLayout; -import java.awt.Container; -import java.awt.event.ActionEvent; -import java.awt.event.ActionListener; -import java.awt.event.ComponentAdapter; -import java.awt.event.ComponentEvent; -import java.io.ByteArrayOutputStream; -import java.io.File; -import java.io.IOException; -import java.net.URL; -import java.util.LinkedList; -import java.util.List; -import java.util.NoSuchElementException; - -import javax.swing.ButtonGroup; -import javax.swing.JApplet; -import javax.swing.JCheckBoxMenuItem; -import javax.swing.JFileChooser; -import javax.swing.JMenu; -import javax.swing.JMenuBar; -import javax.swing.JMenuItem; -import javax.swing.JOptionPane; -import javax.swing.JRadioButtonMenuItem; -import javax.swing.UIManager; -import javax.swing.UnsupportedLookAndFeelException; -import javax.swing.event.ChangeEvent; -import javax.swing.event.ChangeListener; - -import org.apache.commons.codec.binary.Base64; -import org.forester.archaeopteryx.AptxUtil.GraphicsExportType; -import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE; -import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION; -import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE; -import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION; -import org.forester.phylogeny.Phylogeny; -import org.forester.phylogeny.PhylogenyMethods; -import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY; -import org.forester.phylogeny.data.SequenceRelation; -import org.forester.sdi.GSDI; -import org.forester.sdi.GSDIR; -import org.forester.sdi.SDIException; -import org.forester.util.ForesterConstants; -import org.forester.util.ForesterUtil; -import org.forester.util.WindowsUtils; - -// Use like this: -// -// -// -// -public class ArchaeopteryxE extends JApplet implements ActionListener { - - private final static String NAME = "ArchaeopteryxE"; - private static final long serialVersionUID = -1220055577935759443L; - private Configuration _configuration; - private MainPanel _mainpanel; - private JMenuBar _jmenubar; - private JMenu _options_jmenu; - private JMenu _font_size_menu; - private JMenuItem _super_tiny_fonts_mi; - private JMenuItem _tiny_fonts_mi; - private JMenuItem _small_fonts_mi; - private JMenuItem _medium_fonts_mi; - private JMenuItem _large_fonts_mi; - private JMenu _tools_menu; - private JMenuItem _taxcolor_item; - private JMenuItem _confcolor_item; - private JMenuItem _midpoint_root_item; - private JMenu _view_jmenu; - private JMenuItem _view_as_XML_item; - private JMenuItem _view_as_NH_item; - private JMenuItem _view_as_nexus_item; - private JMenuItem _display_basic_information_item; - private JMenu _type_menu; - private JCheckBoxMenuItem _rectangular_type_cbmi; - private JCheckBoxMenuItem _triangular_type_cbmi; - private JCheckBoxMenuItem _curved_type_cbmi; - private JCheckBoxMenuItem _convex_type_cbmi; - private JCheckBoxMenuItem _euro_type_cbmi; - private JCheckBoxMenuItem _rounded_type_cbmi; - private JCheckBoxMenuItem _unrooted_type_cbmi; - private JCheckBoxMenuItem _circular_type_cbmi; - private JMenuItem _help_item; - private JMenuItem _about_item; - private JMenu _help_jmenu; - private JMenuItem _website_item; - private JMenuItem _phyloxml_website_item; - private JMenuItem _phyloxml_ref_item; - private JMenuItem _aptx_ref_item; - private JMenuItem _remove_branch_color_item; - private JMenuItem _remove_visual_styles_item; - private JCheckBoxMenuItem _show_domain_labels; - private JCheckBoxMenuItem _show_annotation_ref_source; - private JCheckBoxMenuItem _color_labels_same_as_parent_branch; - private JCheckBoxMenuItem _abbreviate_scientific_names; - private JCheckBoxMenuItem _screen_antialias_cbmi; - private JCheckBoxMenuItem _background_gradient_cbmi; - private JCheckBoxMenuItem _color_by_taxonomic_group_cbmi; - private JRadioButtonMenuItem _non_lined_up_cladograms_rbmi; - private JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi; - private Options _options; - private JMenuItem _choose_font_mi; - private JMenuItem _switch_colors_mi; - JCheckBoxMenuItem _label_direction_cbmi; - private JCheckBoxMenuItem _show_scale_cbmi; - private JCheckBoxMenuItem _search_case_senstive_cbmi; - private JCheckBoxMenuItem _search_whole_words_only_cbmi; - private JCheckBoxMenuItem _inverse_search_result_cbmi; - private JCheckBoxMenuItem _search_with_regex_cbmi; - private JCheckBoxMenuItem _show_overview_cbmi; - private JMenuItem _choose_minimal_confidence_mi; - private JMenuItem _collapse_species_specific_subtrees; - private JMenuItem _overview_placment_mi; - private ButtonGroup _radio_group_1; - private JCheckBoxMenuItem _show_default_node_shapes_internal_cbmi; - private JCheckBoxMenuItem _show_default_node_shapes_external_cbmi; - private JCheckBoxMenuItem _show_default_node_shapes_for_marked_cbmi; - private JMenuItem _cycle_node_shape_mi; - private JMenuItem _cycle_node_fill_mi; - private JMenuItem _choose_node_size_mi; - private JCheckBoxMenuItem _show_confidence_stddev_cbmi; - private final LinkedList _textframes = new LinkedList(); - private JMenu _analysis_menu; - private JMenuItem _gsdi_item; - private JMenuItem _gsdir_item; - private Phylogeny _species_tree; - private JCheckBoxMenuItem _right_line_up_domains_cbmi; - private JCheckBoxMenuItem _line_up_renderable_data_cbmi; - // file menu: - private JMenuItem _save_item; - private JMenuItem _print_item; - private JMenuItem _write_to_pdf_item; - private JMenuItem _write_to_jpg_item; - private JMenuItem _write_to_gif_item; - private JMenuItem _write_to_tif_item; - private JMenuItem _write_to_png_item; - private JMenuItem _write_to_bmp_item; - private JMenu _file_jmenu; - private JFileChooser _writetopdf_filechooser; - private File _current_dir; - private JFileChooser _save_filechooser; - private JFileChooser _writetographics_filechooser; - private JCheckBoxMenuItem _graphics_export_visible_only_cbmi; - private JCheckBoxMenuItem _antialias_print_cbmi; - private JCheckBoxMenuItem _print_black_and_white_cbmi; - private JMenuItem _choose_pdf_width_mi; - - @Override - public void actionPerformed( final ActionEvent e ) { - final Object o = e.getSource(); - if ( o == _midpoint_root_item ) { - getMainPanel().getCurrentTreePanel().midpointRoot(); - } - else if ( o == _gsdi_item ) { - if ( isSubtreeDisplayed() ) { - return; - } - executeGSDI(); - } - else if ( o == _gsdir_item ) { - if ( isSubtreeDisplayed() ) { - return; - } - executeGSDIR(); - } - else if ( o == _taxcolor_item ) { - getMainPanel().getCurrentTreePanel().taxColor(); - } - else if ( o == _confcolor_item ) { - getMainPanel().getCurrentTreePanel().confColor(); - } - else if ( o == _collapse_species_specific_subtrees ) { - if ( getCurrentTreePanel() != null ) { - getCurrentTreePanel().collapseSpeciesSpecificSubtrees(); - } - } - else if ( o == _remove_branch_color_item ) { - removeBranchColors(); - } - else if ( o == _remove_visual_styles_item ) { - removeVisualStyles(); - } - else if ( o == _switch_colors_mi ) { - switchColors(); - } - else if ( o == _display_basic_information_item ) { - displayBasicInformation(); - } - else if ( o == _view_as_NH_item ) { - viewAsNH(); - } - else if ( o == _view_as_XML_item ) { - viewAsXML(); - } - else if ( o == _view_as_nexus_item ) { - viewAsNexus(); - } - else if ( o == _super_tiny_fonts_mi ) { - if ( getCurrentTreePanel() != null ) { - getCurrentTreePanel().setSuperTinyFonts(); - getCurrentTreePanel().repaint(); - } - } - else if ( o == _tiny_fonts_mi ) { - if ( getCurrentTreePanel() != null ) { - getCurrentTreePanel().setTinyFonts(); - getCurrentTreePanel().repaint(); - } - } - else if ( o == _small_fonts_mi ) { - if ( getCurrentTreePanel() != null ) { - getCurrentTreePanel().setSmallFonts(); - getCurrentTreePanel().repaint(); - } - } - else if ( o == _medium_fonts_mi ) { - if ( getCurrentTreePanel() != null ) { - getCurrentTreePanel().setMediumFonts(); - getCurrentTreePanel().repaint(); - } - } - else if ( o == _large_fonts_mi ) { - if ( getCurrentTreePanel() != null ) { - getCurrentTreePanel().setLargeFonts(); - getCurrentTreePanel().repaint(); - } - } - else if ( o == _choose_font_mi ) { - chooseFont(); - } - else if ( o == _choose_minimal_confidence_mi ) { - chooseMinimalConfidence(); - } - else if ( o == _choose_node_size_mi ) { - MainFrame.chooseNodeSize( getOptions(), this ); - } - else if ( o == _overview_placment_mi ) { - MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() ); - } - else if ( o == _cycle_node_fill_mi ) { - MainFrame.cycleNodeFill( getOptions() ); - } - else if ( o == _cycle_node_shape_mi ) { - MainFrame.cycleNodeShape( getOptions() ); - } - else if ( o == _non_lined_up_cladograms_rbmi ) { - updateOptions( getOptions() ); - _mainpanel.getControlPanel().showWhole(); - } - else if ( o == _ext_node_dependent_cladogram_rbmi ) { - updateOptions( getOptions() ); - _mainpanel.getControlPanel().showWhole(); - } - else if ( o == _search_case_senstive_cbmi ) { - updateOptions( getOptions() ); - getMainPanel().getControlPanel().search0(); - getMainPanel().getControlPanel().search1(); - } - else if ( o == _search_whole_words_only_cbmi ) { - if ( ( _search_with_regex_cbmi != null ) && _search_whole_words_only_cbmi.isSelected() ) { - _search_with_regex_cbmi.setSelected( false ); - } - updateOptions( getOptions() ); - getMainPanel().getControlPanel().search0(); - getMainPanel().getControlPanel().search1(); - } - else if ( o == _inverse_search_result_cbmi ) { - updateOptions( getOptions() ); - getMainPanel().getControlPanel().search0(); - getMainPanel().getControlPanel().search1(); - } - else if ( o == _search_with_regex_cbmi ) { - if ( ( _search_whole_words_only_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) { - _search_whole_words_only_cbmi.setSelected( false ); - } - if ( ( _search_case_senstive_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) { - _search_case_senstive_cbmi.setSelected( true ); - } - updateOptions( getOptions() ); - getMainPanel().getControlPanel().search0(); - getMainPanel().getControlPanel().search1(); - } - else if ( o == _show_scale_cbmi ) { - updateOptions( getOptions() ); - } - else if ( o == _show_confidence_stddev_cbmi ) { - updateOptions( getOptions() ); - } - else if ( o == _label_direction_cbmi ) { - updateOptions( getOptions() ); - } - else if ( o == _abbreviate_scientific_names ) { - updateOptions( getOptions() ); - } - else if ( o == _show_overview_cbmi ) { - updateOptions( getOptions() ); - if ( getCurrentTreePanel() != null ) { - getCurrentTreePanel().updateOvSizes(); - } - } - else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi ) - || ( o == _convex_type_cbmi ) || ( o == _rounded_type_cbmi ) || ( o == _euro_type_cbmi ) - || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) { - typeChanged( o ); - } - else if ( o == _screen_antialias_cbmi ) { - updateOptions( getOptions() ); - setupScreenTextAntialias( getMainPanel().getTreePanels(), isScreenAntialias() ); - } - else if ( o == _background_gradient_cbmi ) { - updateOptions( getOptions() ); - } - else if ( o == _show_domain_labels ) { - updateOptions( getOptions() ); - } - else if ( o == _color_labels_same_as_parent_branch ) { - updateOptions( getOptions() ); - } - else if ( o == _show_default_node_shapes_internal_cbmi ) { - updateOptions( getOptions() ); - } - else if ( o == _show_default_node_shapes_external_cbmi ) { - updateOptions( getOptions() ); - } - else if ( o == _about_item ) { - getMainPanel().getMainFrame().about(); - } - else if ( o == _help_item ) { - try { - AptxUtil.openWebsite( AptxConstants.APTX_DOC_SITE, true, this ); - } - catch ( final IOException e1 ) { - ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() ); - } - } - else if ( o == _website_item ) { - try { - AptxUtil.openWebsite( AptxConstants.APTX_WEB_SITE, true, this ); - } - catch ( final IOException e1 ) { - ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() ); - } - } - else if ( o == _phyloxml_website_item ) { - try { - AptxUtil.openWebsite( AptxConstants.PHYLOXML_WEB_SITE, true, this ); - } - catch ( final IOException e1 ) { - ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() ); - } - } - else if ( o == _aptx_ref_item ) { - try { - AptxUtil.openWebsite( AptxConstants.APTX_REFERENCE_URL, true, this ); - } - catch ( final IOException e1 ) { - ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() ); - } - } - else if ( o == _phyloxml_ref_item ) { - try { - AptxUtil.openWebsite( AptxConstants.PHYLOXML_REFERENCE_URL, true, this ); - } - catch ( final IOException e1 ) { - ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() ); - } - } - else if ( o == _color_by_taxonomic_group_cbmi ) { - updateOptions( getOptions() ); - } - else if ( o == _line_up_renderable_data_cbmi ) { - if ( !_line_up_renderable_data_cbmi.isSelected() ) { - _right_line_up_domains_cbmi.setSelected( false ); - } - updateOptions( getOptions() ); - } - else if ( o == _right_line_up_domains_cbmi ) { - if ( _right_line_up_domains_cbmi.isSelected() ) { - _line_up_renderable_data_cbmi.setSelected( true ); - } - updateOptions( getOptions() ); - } - else if ( o == _write_to_pdf_item ) { - final File curr_dir = MainFrame.writeToPdf( _mainpanel.getCurrentPhylogeny(), - getMainPanel(), - _writetopdf_filechooser, - _current_dir, - getContentPane(), - this ); - if ( curr_dir != null ) { - setCurrentDir( curr_dir ); - } - } - else if ( o == _write_to_jpg_item ) { - final File curr_dir = MainFrame.writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), - GraphicsExportType.JPG, - _mainpanel, - _writetographics_filechooser, - this, - getContentPane(), - _current_dir ); - if ( curr_dir != null ) { - setCurrentDir( curr_dir ); - } - } - else if ( o == _write_to_gif_item ) { - final File curr_dir = MainFrame.writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), - GraphicsExportType.GIF, - _mainpanel, - _writetographics_filechooser, - this, - getContentPane(), - _current_dir ); - if ( curr_dir != null ) { - setCurrentDir( curr_dir ); - } - } - else if ( o == _write_to_tif_item ) { - final File curr_dir = MainFrame.writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), - GraphicsExportType.TIFF, - _mainpanel, - _writetographics_filechooser, - this, - getContentPane(), - _current_dir ); - if ( curr_dir != null ) { - setCurrentDir( curr_dir ); - } - } - else if ( o == _write_to_bmp_item ) { - final File curr_dir = MainFrame.writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), - GraphicsExportType.BMP, - _mainpanel, - _writetographics_filechooser, - this, - getContentPane(), - _current_dir ); - if ( curr_dir != null ) { - setCurrentDir( curr_dir ); - } - } - else if ( o == _write_to_png_item ) { - final File curr_dir = MainFrame.writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), - GraphicsExportType.PNG, - _mainpanel, - _writetographics_filechooser, - this, - getContentPane(), - _current_dir ); - if ( curr_dir != null ) { - setCurrentDir( curr_dir ); - } - } - else if ( o == _print_item ) { - MainFrame.print( getCurrentTreePanel(), getOptions(), this ); - } - else if ( o == _save_item ) { - final File new_dir = MainFrame.writeToFile( _mainpanel.getCurrentPhylogeny(), - getMainPanel(), - _save_filechooser, - _current_dir, - getContentPane(), - this ); - if ( new_dir != null ) { - setCurrentDir( new_dir ); - } - } - else if ( o == _graphics_export_visible_only_cbmi ) { - updateOptions( getOptions() ); - } - else if ( o == _antialias_print_cbmi ) { - updateOptions( getOptions() ); - } - else if ( o == _print_black_and_white_cbmi ) { - updateOptions( getOptions() ); - } - else if ( o == _choose_pdf_width_mi ) { - choosePdfWidth(); - } - repaint(); - } - - @Override - public void destroy() { - AptxUtil.printAppletMessage( NAME, "going to be destroyed " ); - removeAllTextFrames(); - if ( getMainPanel() != null ) { - getMainPanel().terminate(); - } - } - - /** - * This method returns the current external node data which - * has been selected by the user by clicking the "Return ..." - * menu item. This method is expected to be called from Javascript or - * something like it. - * - * @return current external node data as String - */ - public String getCurrentExternalNodesDataBuffer() { - return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString(); - } - - public int getCurrentExternalNodesDataBufferChangeCounter() { - return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter(); - } - - public int getCurrentExternalNodesDataBufferLength() { - return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length(); - } - - /** - * This method returns the current phylogeny as a string in the chosen format - * - * @param format must be NH, NHX, NEXUS or PHYLOXML - * @return the phylogeny string - * @author Herve Menager - */ - public String getCurrentPhylogeny( final String format ) { - removeAllTextFrames(); - if ( ( getMainPanel().getCurrentPhylogeny() == null ) || getMainPanel().getCurrentPhylogeny().isEmpty() - || ( getMainPanel().getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) { - return new String(); - } - switch ( ForesterConstants.PhylogeneticTreeFormats.valueOf( format ) ) { - case NH: - return getMainPanel().getCurrentPhylogeny().toNewHampshire(); - case NHX: - return getMainPanel().getCurrentPhylogeny().toNewHampshireX(); - case NEXUS: - return getMainPanel().getCurrentPhylogeny().toNexus(); - case PHYLOXML: - return getMainPanel().getCurrentPhylogeny().toPhyloXML( -1 ); - default: - break; - } - return new String(); - } - - /** - * This method returns a view of the current phylogeny in a chosen - * graphics format, base64-encoded in a string so that in can be used - * from javascript. - * - * @param format must be GraphicsExportType (gif, jpg, pdf, png, tif, bmp) - * @return the phylogeny string - * @author Herve Menager - */ - public String getCurrentPhylogenyGraphicsAsBase64EncodedString( final String format ) { - final ByteArrayOutputStream baos = new ByteArrayOutputStream(); - try { - AptxUtil.writePhylogenyToGraphicsByteArrayOutputStream( baos, - _mainpanel.getWidth(), - _mainpanel.getHeight(), - getCurrentTreePanel(), - getCurrentTreePanel().getControlPanel(), - GraphicsExportType.valueOf( format ), - getOptions() ); - } - catch ( final IOException ioe ) { - ForesterUtil.printErrorMessage( NAME, ioe.toString() ); - ioe.printStackTrace(); - JOptionPane.showMessageDialog( this, - NAME + ": Failed to generate graphics: " + "\nException: " + ioe, - "Failed to generate graphics", - JOptionPane.ERROR_MESSAGE ); - return null; - } - final byte[] bytes = baos.toByteArray(); - final String dataImg = Base64.encodeBase64String( bytes ); - return dataImg; - } - - public Options getOptions() { - return _options; - } - - @Override - public void init() { - _writetopdf_filechooser = new JFileChooser(); - _writetopdf_filechooser.setMultiSelectionEnabled( false ); - _writetopdf_filechooser.addChoosableFileFilter( MainFrame.pdffilter ); - _writetographics_filechooser = new JFileChooser(); - _writetographics_filechooser.setMultiSelectionEnabled( false ); - _writetographics_filechooser.addChoosableFileFilter( MainFrame.graphicsfilefilter ); - _save_filechooser = new JFileChooser(); - _save_filechooser.setMultiSelectionEnabled( false ); - _save_filechooser.setFileFilter( MainFrame.xmlfilter ); - _save_filechooser.addChoosableFileFilter( MainFrame.nhfilter ); - _save_filechooser.addChoosableFileFilter( MainFrame.nexusfilter ); - _save_filechooser.addChoosableFileFilter( _save_filechooser.getAcceptAllFileFilter() ); - try { - final String home_dir = System.getProperty( "user.home" ); - _save_filechooser.setCurrentDirectory( new File( home_dir ) ); - _writetopdf_filechooser.setCurrentDirectory( new File( home_dir ) ); - _writetographics_filechooser.setCurrentDirectory( new File( home_dir ) ); - } - catch ( final Exception e ) { - e.printStackTrace(); - // Do nothing. Not important. - } - final String config_filename = getParameter( AptxConstants.APPLET_PARAM_NAME_FOR_CONFIG_FILE_URL ); - AptxUtil.printAppletMessage( NAME, "URL for configuration file is: " + config_filename ); - final Configuration configuration = new Configuration( config_filename, true, true, true ); - setConfiguration( configuration ); - setOptions( Options.createInstance( configuration ) ); - setupUI(); - final String tree_url_str = getParameter( AptxConstants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD ); - if ( ForesterUtil.isEmpty( tree_url_str ) ) { - ForesterUtil.printErrorMessage( NAME, "could not get tree URL from " - + AptxConstants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD ); - JOptionPane.showMessageDialog( this, NAME + ": could not get tree URL from " - + AptxConstants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD, "Failed get URL", JOptionPane.ERROR_MESSAGE ); - return; - } - AptxUtil.printAppletMessage( NAME, "URL for phylogenies is " + tree_url_str ); - // Get URL to tree file - URL phys_url = null; - try { - phys_url = new URL( tree_url_str ); - } - catch ( final Exception e ) { - ForesterUtil.printErrorMessage( NAME, "error: " + e ); - e.printStackTrace(); - JOptionPane.showMessageDialog( this, NAME + ": Could not create URL from: \"" + tree_url_str - + "\"\nException: " + e, "Failed to create URL", JOptionPane.ERROR_MESSAGE ); - } - if ( phys_url == null ) { - ForesterUtil.printErrorMessage( NAME, "failed to get tree URL from " - + AptxConstants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD ); - JOptionPane.showMessageDialog( this, - NAME + ": Could not create URL from: \"" + tree_url_str, - "Failed to create URL", - JOptionPane.ERROR_MESSAGE ); - return; - } - // Load the tree from URL - Phylogeny[] phys = null; - try { - phys = AptxUtil.readPhylogeniesFromUrl( phys_url, - getConfiguration().isValidatePhyloXmlAgainstSchema(), - getConfiguration().isReplaceUnderscoresInNhParsing(), - getConfiguration().isInternalNumberAreConfidenceForNhParsing(), - getConfiguration().getTaxonomyExtraction(), - getConfiguration().isMidpointReroot() ); - } - catch ( final Exception e ) { - ForesterUtil.printErrorMessage( NAME, e.toString() ); - e.printStackTrace(); - JOptionPane.showMessageDialog( this, - NAME + ": Failed to read phylogenies: " + "\nException: " + e, - "Failed to read phylogenies", - JOptionPane.ERROR_MESSAGE ); - } - if ( phys == null ) { - ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + phys_url + "] are null" ); - JOptionPane.showMessageDialog( this, - NAME + ": phylogenies from [" + phys_url + "] are null", - "Failed to read phylogenies", - JOptionPane.ERROR_MESSAGE ); - return; - } - else if ( phys.length < 1 ) { - ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + phys_url + "] are empty" ); - JOptionPane.showMessageDialog( this, - NAME + ": phylogenies from [" + phys_url + "] are empty", - "Failed to read phylogenies", - JOptionPane.ERROR_MESSAGE ); - return; - } - else { - AptxUtil.printAppletMessage( NAME, "loaded " + phys.length + " phylogenies from: " + phys_url ); - } - // - final String species_tree_url_str = getParameter( AptxConstants.APPLET_PARAM_NAME_FOR_URL_OF_SPECIES_TREE_TO_LOAD ); - if ( !ForesterUtil.isEmpty( species_tree_url_str ) ) { - AptxUtil.printAppletMessage( NAME, "URL of species tree to load: \"" + species_tree_url_str + "\"" ); - Phylogeny[] species_trees = null; - try { - final URL species_tree_url = new URL( species_tree_url_str ); - species_trees = AptxUtil.readPhylogeniesFromUrl( species_tree_url, - configuration.isValidatePhyloXmlAgainstSchema(), - configuration.isReplaceUnderscoresInNhParsing(), - false, - TAXONOMY_EXTRACTION.NO, - false ); - } - catch ( final IOException e ) { - ForesterUtil.printErrorMessage( NAME, "could not read species tree from [" + species_tree_url_str - + "]" ); - JOptionPane.showMessageDialog( this, NAME + ": could not read species tree from [" - + species_tree_url_str + "]", "Failed to read species tree", JOptionPane.ERROR_MESSAGE ); - } - if ( ( species_trees != null ) && ( species_trees.length > 0 ) ) { - AptxUtil.printAppletMessage( NAME, "successfully read species tree" ); - if ( species_trees[ 0 ].isEmpty() ) { - ForesterUtil.printErrorMessage( NAME, "species tree is empty" ); - } - else if ( !species_trees[ 0 ].isRooted() ) { - ForesterUtil.printErrorMessage( NAME, "species tree is not rooted" ); - } - else { - setSpeciesTree( species_trees[ 0 ] ); - AptxUtil.printAppletMessage( NAME, "species tree OK" ); - } - } - } - try { - setVisible( false ); - setMainPanel( new MainPanelApplets( getConfiguration(), this ) ); - _jmenubar = new JMenuBar(); - if ( !getConfiguration().isHideControlPanelAndMenubar() ) { - buildFileMenu(); - if ( !getConfiguration().isUseNativeUI() ) { - _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() ); - } - if ( getSpeciesTree() != null ) { - buildAnalysisMenu(); - } - buildToolsMenu(); - buildViewMenu(); - buildFontSizeMenu(); - buildOptionsMenu(); - buildTypeMenu(); - buildHelpMenu(); - setJMenuBar( _jmenubar ); - } - final Container contentpane = getContentPane(); - contentpane.setLayout( new BorderLayout() ); - contentpane.add( getMainPanel(), BorderLayout.CENTER ); - addComponentListener( new ComponentAdapter() { - - @Override - public void componentResized( final ComponentEvent e ) { - if ( getMainPanel().getCurrentTreePanel() != null ) { - getMainPanel().getCurrentTreePanel().calcParametersForPainting( getMainPanel() - .getCurrentTreePanel() - .getWidth(), - getMainPanel() - .getCurrentTreePanel() - .getHeight() ); - } - } - } ); - if ( getConfiguration().isUseTabbedDisplay() ) { - try { - AptxUtil.printAppletMessage( NAME, "using tabbed display" ); - AptxUtil.addPhylogeniesToTabs( phys, - new File( phys_url.getFile() ).getName(), - phys_url.toString(), - getConfiguration(), - getMainPanel() ); - } - catch ( final Exception e ) { - ForesterUtil.printErrorMessage( NAME, e.toString() ); - e.printStackTrace(); - } - } - else { - AptxUtil.printAppletMessage( NAME, "not using tabbed display" ); - if ( getSpeciesTree() != null ) { - AptxUtil.printAppletMessage( NAME, - "Warning: gsdi (gene duplication inference) only available tabbed display" ); - } - AptxUtil.addPhylogenyToPanel( phys, getConfiguration(), getMainPanel() ); - } - validate(); - setName( NAME ); - getMainPanel().getControlPanel().showWholeAll(); - getMainPanel().getControlPanel().showWhole(); - /* GUILHEM_BEG */ - getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().removeAllItems(); - for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : getMainPanel().getCurrentPhylogeny() - .getRelevantSequenceRelationTypes() ) { - getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().addItem( type ); - } - final String default_relation = getParameter( AptxConstants.APPLET_PARAM_NAME_FOR_DEFAULT_SEQUENCE_RELATION_TYPE ); - if ( default_relation != null ) { - getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().setSelectedItem( default_relation ); - } - final String default_sequence = getParameter( AptxConstants.APPLET_PARAM_NAME_FOR_DEFAULT_QUERY_SEQUENCE ); - if ( default_sequence != null ) { - getCurrentTreePanel().getControlPanel().getSequenceRelationBox().setSelectedItem( default_sequence ); - } - /* GUILHEM_END */ - System.gc(); - AptxUtil.printAppletMessage( NAME, "successfully initialized" ); - setVisible( true ); - } - catch ( final Exception e ) { - ForesterUtil.printErrorMessage( NAME, e.toString() ); - e.printStackTrace(); - } - } - - public void showTextFrame( final String s, final String title ) { - checkTextFrames(); - _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) ); - } - - @Override - public void start() { - if ( getMainPanel() != null ) { - getMainPanel().validate(); - } - requestFocus(); - requestFocusInWindow(); - requestFocus(); - AptxUtil.printAppletMessage( NAME, "started" ); - } - - private void chooseFont() { - final FontChooser fc = new FontChooser(); - fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() ); - fc.showDialog( this, "Select the Base Font" ); - getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() ); - } - - private void chooseMinimalConfidence() { - final String s = ( String ) JOptionPane - .showInputDialog( this, - "Please the minimum for confidence values to be displayed.\n" + "[current value: " - + getOptions().getMinConfidenceValue() + "]\n", - "Minimal Confidence Value", - JOptionPane.QUESTION_MESSAGE, - null, - null, - getOptions().getMinConfidenceValue() ); - if ( !ForesterUtil.isEmpty( s ) ) { - boolean success = true; - double m = 0.0; - final String m_str = s.trim(); - if ( !ForesterUtil.isEmpty( m_str ) ) { - try { - m = Double.parseDouble( m_str ); - } - catch ( final Exception ex ) { - success = false; - } - } - else { - success = false; - } - if ( success && ( m >= 0.0 ) ) { - getOptions().setMinConfidenceValue( m ); - } - } - } - - private void choosePdfWidth() { - final String s = ( String ) JOptionPane.showInputDialog( this, - "Please enter the default line width for PDF export.\n" - + "[current value: " - + getOptions().getPrintLineWidth() + "]\n", - "Line Width for PDF Export", - JOptionPane.QUESTION_MESSAGE, - null, - null, - getOptions().getPrintLineWidth() ); - if ( !ForesterUtil.isEmpty( s ) ) { - boolean success = true; - float f = 0.0f; - final String m_str = s.trim(); - if ( !ForesterUtil.isEmpty( m_str ) ) { - try { - f = Float.parseFloat( m_str ); - } - catch ( final Exception ex ) { - success = false; - } - } - else { - success = false; - } - if ( success && ( f > 0.0 ) ) { - getOptions().setPrintLineWidth( f ); - } - } - } - - private void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) { - if ( item != null ) { - item.setFont( MainFrame.menu_font ); - if ( !getConfiguration().isUseNativeUI() ) { - item.setBackground( getConfiguration().getGuiMenuBackgroundColor() ); - item.setForeground( getConfiguration().getGuiMenuTextColor() ); - } - item.setSelected( is_selected ); - item.addActionListener( this ); - } - } - - private Phylogeny getSpeciesTree() { - return _species_tree; - } - - private boolean isScreenAntialias() { - return true; - } - - private void removeBranchColors() { - if ( getMainPanel().getCurrentPhylogeny() != null ) { - AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() ); - } - } - - private void removeVisualStyles() { - if ( getMainPanel().getCurrentPhylogeny() != null ) { - AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() ); - } - } - - private void setMainPanel( final MainPanelApplets main_panel ) { - _mainpanel = main_panel; - } - - private void setSpeciesTree( final Phylogeny species_tree ) { - _species_tree = species_tree; - } - - private void setupUI() { - try { - if ( getConfiguration().isUseNativeUI() ) { - UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() ); - } - else { - UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() ); - } - } - catch ( final UnsupportedLookAndFeelException e ) { - AptxUtil.dieWithSystemError( "UnsupportedLookAndFeelException: " + e.toString() ); - } - catch ( final ClassNotFoundException e ) { - AptxUtil.dieWithSystemError( "ClassNotFoundException: " + e.toString() ); - } - catch ( final InstantiationException e ) { - AptxUtil.dieWithSystemError( "InstantiationException: " + e.toString() ); - } - catch ( final IllegalAccessException e ) { - AptxUtil.dieWithSystemError( "IllegalAccessException: " + e.toString() ); - } - catch ( final Exception e ) { - AptxUtil.dieWithSystemError( e.toString() ); - } - } - - void buildAnalysisMenu() { - _analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() ); - _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) ); - _analysis_menu.add( _gsdir_item = new JMenuItem( "GSDIR (GSDI with re-rooting)" ) ); - customizeJMenuItem( _gsdi_item ); - customizeJMenuItem( _gsdir_item ); - _analysis_menu.addSeparator(); - _jmenubar.add( _analysis_menu ); - } - - void buildFileMenu() { - _file_jmenu = MainFrame.createMenu( "File", getConfiguration() ); - _file_jmenu.add( _save_item = new JMenuItem( "Save Tree As..." ) ); - _file_jmenu.addSeparator(); - _file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) ); - if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" ) || AptxUtil.canWriteFormat( "TIF" ) ) { - _file_jmenu.add( _write_to_tif_item = new JMenuItem( "Export to TIFF file..." ) ); - } - _file_jmenu.add( _write_to_png_item = new JMenuItem( "Export to PNG file..." ) ); - _file_jmenu.add( _write_to_jpg_item = new JMenuItem( "Export to JPG file..." ) ); - if ( AptxUtil.canWriteFormat( "gif" ) ) { - _file_jmenu.add( _write_to_gif_item = new JMenuItem( "Export to GIF file..." ) ); - } - if ( AptxUtil.canWriteFormat( "bmp" ) ) { - _file_jmenu.add( _write_to_bmp_item = new JMenuItem( "Export to BMP file..." ) ); - } - _file_jmenu.addSeparator(); - _file_jmenu.add( _print_item = new JMenuItem( "Print..." ) ); - customizeJMenuItem( _save_item ); - customizeJMenuItem( _write_to_pdf_item ); - customizeJMenuItem( _write_to_png_item ); - customizeJMenuItem( _write_to_jpg_item ); - customizeJMenuItem( _write_to_gif_item ); - customizeJMenuItem( _write_to_tif_item ); - customizeJMenuItem( _write_to_bmp_item ); - customizeJMenuItem( _print_item ); - _jmenubar.add( _file_jmenu ); - } - - void buildFontSizeMenu() { - _font_size_menu = MainFrame.createMenu( MainFrame.FONT_SIZE_MENU_LABEL, getConfiguration() ); - _font_size_menu.add( _super_tiny_fonts_mi = new JMenuItem( "Super tiny fonts" ) ); - _font_size_menu.add( _tiny_fonts_mi = new JMenuItem( "Tiny fonts" ) ); - _font_size_menu.add( _small_fonts_mi = new JMenuItem( "Small fonts" ) ); - _font_size_menu.add( _medium_fonts_mi = new JMenuItem( "Medium fonts" ) ); - _font_size_menu.add( _large_fonts_mi = new JMenuItem( "Large fonts" ) ); - customizeJMenuItem( _super_tiny_fonts_mi ); - customizeJMenuItem( _tiny_fonts_mi ); - customizeJMenuItem( _small_fonts_mi ); - customizeJMenuItem( _medium_fonts_mi ); - customizeJMenuItem( _large_fonts_mi ); - _jmenubar.add( _font_size_menu ); - } - - void buildHelpMenu() { - _help_jmenu = MainFrame.createMenu( "Help", getConfiguration() ); - _help_jmenu.add( _help_item = new JMenuItem( "Documentation" ) ); - _help_jmenu.addSeparator(); - _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) ); - _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" ); - _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) ); - _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) ); - _help_jmenu.addSeparator(); - _help_jmenu.add( _about_item = new JMenuItem( "About" ) ); - customizeJMenuItem( _help_item ); - customizeJMenuItem( _website_item ); - customizeJMenuItem( _phyloxml_website_item ); - customizeJMenuItem( _aptx_ref_item ); - customizeJMenuItem( _phyloxml_ref_item ); - customizeJMenuItem( _about_item ); - _phyloxml_ref_item.setToolTipText( MainFrame.PHYLOXML_REF_TOOL_TIP ); - _aptx_ref_item.setToolTipText( MainFrame.APTX_REF_TOOL_TIP ); - _jmenubar.add( _help_jmenu ); - } - - void buildOptionsMenu() { - _options_jmenu = MainFrame.createMenu( MainFrame.OPTIONS_HEADER, getConfiguration() ); - _options_jmenu.addChangeListener( new ChangeListener() { - - @Override - public void stateChanged( final ChangeEvent e ) { - MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() ); - MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() ); - MainFrame - .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() ); - MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame - .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) ); - setTextForPdfLineWidthChooserMenuItem( _choose_pdf_width_mi, getOptions() ); - MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() ); - MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() ); - MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() ); - try { - getMainPanel().getControlPanel().setVisibilityOfDomainStrucureCB(); - getMainPanel().getControlPanel().setVisibilityOfX(); - } - catch ( final Exception ignore ) { - // do nothing, not important. - } - } - } ); - _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.DISPLAY_SUBHEADER ), - getConfiguration() ) ); - _options_jmenu - .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) ); - _options_jmenu - .add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.NON_LINED_UP_CLADOGRAMS_LABEL ) ); - _radio_group_1 = new ButtonGroup(); - _radio_group_1.add( _ext_node_dependent_cladogram_rbmi ); - _radio_group_1.add( _non_lined_up_cladograms_rbmi ); - _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) ); - _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) ); - _options_jmenu - .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_INT ) ); - _options_jmenu - .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) ); - _options_jmenu - .add( _show_default_node_shapes_for_marked_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_MARKED ) ); - _options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) ); - if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) { - _options_jmenu.add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) ); - _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) ); - } - _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( MainFrame.SHOW_ANN_REF_SOURCE_LABEL ) ); - _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_CONF_STDDEV_LABEL ) ); - _options_jmenu - .add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( MainFrame.COLOR_BY_TAXONOMIC_GROUP ) ); - _options_jmenu - .add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) ); - _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP ); - _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( MainFrame.ABBREV_SN_LABEL ) ); - _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( MainFrame.LABEL_DIRECTION_LABEL ) ); - _label_direction_cbmi.setToolTipText( MainFrame.LABEL_DIRECTION_TIP ); - _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( MainFrame.SCREEN_ANTIALIAS_LABEL ) ); - _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( MainFrame.BG_GRAD_LABEL ) ); - _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) ); - _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) ); - _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) ); - _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) ); - _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) ); - _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) ); - _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) ); - _options_jmenu.addSeparator(); - _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.SEARCH_SUBHEADER ), - getConfiguration() ) ); - _options_jmenu - .add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_CASE_SENSITIVE_LABEL ) ); - _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_TERMS_ONLY_LABEL ) ); - _options_jmenu.add( _search_with_regex_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_REGEX_LABEL ) ); - _search_with_regex_cbmi.setToolTipText( MainFrame.SEARCH_WITH_REGEX_TIP ); - _options_jmenu - .add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( MainFrame.INVERSE_SEARCH_RESULT_LABEL ) ); - // - _options_jmenu.addSeparator(); - _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( "Graphics Export & Printing:" ), - getConfiguration() ) ); - _options_jmenu.add( _antialias_print_cbmi = new JCheckBoxMenuItem( "Antialias" ) ); - _options_jmenu.add( _print_black_and_white_cbmi = new JCheckBoxMenuItem( "Export in Black and White" ) ); - _options_jmenu - .add( _graphics_export_visible_only_cbmi = new JCheckBoxMenuItem( "Limit to Visible ('Screenshot') for PNG, JPG, and GIF export" ) ); - _options_jmenu.add( _choose_pdf_width_mi = new JMenuItem( "" ) ); - // - customizeCheckBoxMenuItem( _antialias_print_cbmi, getOptions().isAntialiasPrint() ); - customizeCheckBoxMenuItem( _print_black_and_white_cbmi, getOptions().isPrintBlackAndWhite() ); - customizeCheckBoxMenuItem( _graphics_export_visible_only_cbmi, getOptions().isGraphicsExportVisibleOnly() ); - customizeJMenuItem( _choose_pdf_width_mi ); - // - customizeJMenuItem( _choose_font_mi ); - customizeJMenuItem( _choose_minimal_confidence_mi ); - customizeJMenuItem( _switch_colors_mi ); - customizeJMenuItem( _overview_placment_mi ); - customizeCheckBoxMenuItem( _color_by_taxonomic_group_cbmi, getOptions().isColorByTaxonomicGroup() ); - customizeCheckBoxMenuItem( _label_direction_cbmi, - getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL ); - customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() ); - customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() ); - customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() ); - customizeCheckBoxMenuItem( _show_annotation_ref_source, getOptions().isShowAnnotationRefSource() ); - customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() ); - customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions() - .isShowDefaultNodeShapesExternal() ); - customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions() - .isShowDefaultNodeShapesInternal() ); - customizeCheckBoxMenuItem( _show_default_node_shapes_for_marked_cbmi, getOptions() - .isShowDefaultNodeShapesForMarkedNodes() ); - customizeJMenuItem( _cycle_node_shape_mi ); - customizeJMenuItem( _cycle_node_fill_mi ); - customizeJMenuItem( _choose_node_size_mi ); - customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() ); - customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() ); - customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() ); - customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi, - getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP ); - customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi, - getOptions().getCladogramType() == CLADOGRAM_TYPE.LINED_UP ); - customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() ); - customizeCheckBoxMenuItem( _search_with_regex_cbmi, getOptions().isSearchWithRegex() ); - customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() ); - customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() ); - customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() ); - customizeCheckBoxMenuItem( _line_up_renderable_data_cbmi, getOptions().isLineUpRendarableNodeData() ); - customizeCheckBoxMenuItem( _right_line_up_domains_cbmi, getOptions().isRightLineUpDomains() ); - _jmenubar.add( _options_jmenu ); - } - - void buildToolsMenu() { - _tools_menu = MainFrame.createMenu( "Tools", getConfiguration() ); - _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) ); - customizeJMenuItem( _confcolor_item ); - _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) ); - customizeJMenuItem( _taxcolor_item ); - _tools_menu.addSeparator(); - _tools_menu.add( _remove_visual_styles_item = new JMenuItem( "Delete All Visual Styles From Nodes" ) ); - _remove_visual_styles_item - .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny." ); - customizeJMenuItem( _remove_visual_styles_item ); - _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete All Colors From Branches" ) ); - _remove_branch_color_item.setToolTipText( "To remove all branch color values from the current phylogeny." ); - customizeJMenuItem( _remove_branch_color_item ); - _tools_menu.addSeparator(); - _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) ); - customizeJMenuItem( _midpoint_root_item ); - _tools_menu.addSeparator(); - _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) ); - customizeJMenuItem( _collapse_species_specific_subtrees ); - _jmenubar.add( _tools_menu ); - } - - void buildTypeMenu() { - _type_menu = MainFrame.createMenu( MainFrame.TYPE_MENU_HEADER, getConfiguration() ); - _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) ); - _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) ); - _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) ); - _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) ); - _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) ); - _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) ); - _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) ); - _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) ); - customizeCheckBoxMenuItem( _rectangular_type_cbmi, false ); - customizeCheckBoxMenuItem( _triangular_type_cbmi, false ); - customizeCheckBoxMenuItem( _euro_type_cbmi, false ); - customizeCheckBoxMenuItem( _rounded_type_cbmi, false ); - customizeCheckBoxMenuItem( _curved_type_cbmi, false ); - customizeCheckBoxMenuItem( _convex_type_cbmi, false ); - customizeCheckBoxMenuItem( _unrooted_type_cbmi, false ); - customizeCheckBoxMenuItem( _circular_type_cbmi, false ); - _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE ); - _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE ); - initializeTypeMenu( getOptions() ); - _jmenubar.add( _type_menu ); - } - - void buildViewMenu() { - _view_jmenu = MainFrame.createMenu( "View", getConfiguration() ); - _view_jmenu - .add( _display_basic_information_item = new JMenuItem( MainFrame.SHOW_BASIC_TREE_INFORMATION_LABEL ) ); - _view_jmenu.addSeparator(); - _view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) ); - _view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) ); - _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "as Nexus" ) ); - customizeJMenuItem( _display_basic_information_item ); - customizeJMenuItem( _view_as_NH_item ); - customizeJMenuItem( _view_as_XML_item ); - customizeJMenuItem( _view_as_nexus_item ); - _jmenubar.add( _view_jmenu ); - } - - void checkTextFrames() { - if ( _textframes.size() > 5 ) { - try { - if ( _textframes.getFirst() != null ) { - _textframes.getFirst().removeMe(); - } - else { - _textframes.removeFirst(); - } - } - catch ( final NoSuchElementException e ) { - // Ignore. - } - } - } - - void clearCurrentExternalNodesDataBuffer() { - getCurrentTreePanel().clearCurrentExternalNodesDataBuffer(); - } - - void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) { - if ( item != null ) { - item.setFont( MainFrame.menu_font ); - if ( !getConfiguration().isUseNativeUI() ) { - item.setBackground( getConfiguration().getGuiMenuBackgroundColor() ); - item.setForeground( getConfiguration().getGuiMenuTextColor() ); - } - item.setSelected( is_selected ); - item.addActionListener( this ); - } - } - - void customizeJMenuItem( final JMenuItem jmi ) { - if ( jmi != null ) { - jmi.setFont( MainFrame.menu_font ); - if ( !getConfiguration().isUseNativeUI() ) { - jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() ); - jmi.setForeground( getConfiguration().getGuiMenuTextColor() ); - } - jmi.addActionListener( this ); - } - } - - void displayBasicInformation() { - if ( ( getMainPanel() != null ) && ( getMainPanel().getCurrentPhylogeny() != null ) - && !getMainPanel().getCurrentPhylogeny().isEmpty() ) { - String title = "Basic Information"; - if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) { - title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\""; - } - showTextFrame( AptxUtil.createBasicInformation( getMainPanel().getCurrentPhylogeny(), null ), title ); - } - } - - void executeGSDI() { - if ( !isOKforSDI( false, true ) ) { - return; - } - if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) { - JOptionPane.showMessageDialog( this, - "Gene tree is not rooted.", - "Cannot execute GSDI", - JOptionPane.ERROR_MESSAGE ); - return; - } - final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy(); - gene_tree.setAllNodesToNotCollapse(); - gene_tree.recalculateNumberOfExternalDescendants( false ); - GSDI gsdi = null; - final Phylogeny species_tree = _species_tree.copy(); - try { - gsdi = new GSDI( gene_tree, species_tree, false, true, true, true ); - } - catch ( final SDIException e ) { - JOptionPane.showMessageDialog( this, - e.getLocalizedMessage(), - "Error during GSDI", - JOptionPane.ERROR_MESSAGE ); - return; - } - catch ( final Exception e ) { - AptxUtil.unexpectedException( e ); - return; - } - gene_tree.setRerootable( false ); - gene_tree.clearHashIdToNodeMap(); - gene_tree.recalculateNumberOfExternalDescendants( true ); - _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null ); - getMainPanel().getControlPanel().setShowEvents( true ); - showWhole(); - final int selected = _mainpanel.getTabbedPane().getSelectedIndex(); - _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null ); - showWhole(); - _mainpanel.getTabbedPane().setSelectedIndex( selected ); - showWhole(); - _mainpanel.getCurrentTreePanel().setEdited( true ); - final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree ); - if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) { - JOptionPane.showMessageDialog( this, - "Duplications: " + gsdi.getDuplicationsSum() + "\n" - + "Potential duplications: " - + gsdi.getSpeciationOrDuplicationEventsSum() + "\n" - + "Speciations: " + gsdi.getSpeciationsSum() + "\n" - + "Stripped gene tree nodes: " - + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n" - + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n" - + "Number of polytomies in species tree used: " + poly + "\n", - "GSDI successfully completed", - JOptionPane.WARNING_MESSAGE ); - } - else { - JOptionPane.showMessageDialog( this, - "Duplications: " + gsdi.getDuplicationsSum() + "\n" - + "Potential duplications: " - + gsdi.getSpeciationOrDuplicationEventsSum() + "\n" - + "Speciations: " + gsdi.getSpeciationsSum() + "\n" - + "Stripped gene tree nodes: " - + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n" - + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n" - + "Number of polytomies in species tree used: " + poly + "\n", - "GSDI successfully completed", - JOptionPane.INFORMATION_MESSAGE ); - } - } - - void executeGSDIR() { - if ( !isOKforSDI( false, false ) ) { - return; - } - final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() ); - if ( ( p > 0 ) - && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) { - JOptionPane.showMessageDialog( this, - "Gene tree is not completely binary", - "Cannot execute GSDI", - JOptionPane.ERROR_MESSAGE ); - return; - } - final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy(); - gene_tree.setAllNodesToNotCollapse(); - gene_tree.recalculateNumberOfExternalDescendants( false ); - GSDIR gsdir = null; - final Phylogeny species_tree = _species_tree.copy(); - try { - gsdir = new GSDIR( gene_tree, species_tree, true, true, true ); - } - catch ( final SDIException e ) { - JOptionPane.showMessageDialog( this, - e.getLocalizedMessage(), - "Error during GSDIR", - JOptionPane.ERROR_MESSAGE ); - return; - } - catch ( final Exception e ) { - AptxUtil.unexpectedException( e ); - return; - } - final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree(); - result_gene_tree.setRerootable( false ); - result_gene_tree.clearHashIdToNodeMap(); - result_gene_tree.recalculateNumberOfExternalDescendants( true ); - PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME ); - _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null ); - getMainPanel().getControlPanel().setShowEvents( true ); - showWhole(); - final int selected = _mainpanel.getTabbedPane().getSelectedIndex(); - _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null ); - showWhole(); - _mainpanel.getTabbedPane().setSelectedIndex( selected ); - showWhole(); - _mainpanel.getCurrentTreePanel().setEdited( true ); - final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree ); - if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) { - JOptionPane.showMessageDialog( this, - "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n" - + "Speciations: " + gsdir.getSpeciationsSum() + "\n" - + "Stripped gene tree nodes: " - + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n" - + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n" - + "Number of polytomies in species tree used: " + poly + "\n", - "GSDIR successfully completed", - JOptionPane.WARNING_MESSAGE ); - } - else { - JOptionPane.showMessageDialog( this, - "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n" - + "Speciations: " + gsdir.getSpeciationsSum() + "\n" - + "Stripped gene tree nodes: " - + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n" - + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n" - + "Number of polytomies in species tree used: " + poly + "\n", - "GSDIR successfully completed", - JOptionPane.INFORMATION_MESSAGE ); - } - } - - Configuration getConfiguration() { - return _configuration; - } - - File getCurrentDir() { - if ( ( _current_dir == null ) || !_current_dir.canRead() ) { - if ( ForesterUtil.isWindows() ) { - try { - _current_dir = new File( WindowsUtils.getCurrentUserDesktopPath() ); - } - catch ( final Exception e ) { - _current_dir = null; - } - } - } - if ( ( _current_dir == null ) || !_current_dir.canRead() ) { - if ( System.getProperty( "user.home" ) != null ) { - _current_dir = new File( System.getProperty( "user.home" ) ); - } - else if ( System.getProperty( "user.dir" ) != null ) { - _current_dir = new File( System.getProperty( "user.dir" ) ); - } - } - return _current_dir; - } - - TreePanel getCurrentTreePanel() { - return getMainPanel().getCurrentTreePanel(); - } - - JCheckBoxMenuItem getlabelDirectionCbmi() { - return _label_direction_cbmi; - } - - MainPanel getMainPanel() { - return _mainpanel; - } - - Options getOtions() { - return _options; - } - - void initializeTypeMenu( final Options options ) { - setTypeMenuToAllUnselected(); - try { - switch ( options.getPhylogenyGraphicsType() ) { - case CONVEX: - _convex_type_cbmi.setSelected( true ); - break; - case CURVED: - _curved_type_cbmi.setSelected( true ); - break; - case EURO_STYLE: - _euro_type_cbmi.setSelected( true ); - break; - case ROUNDED: - _rounded_type_cbmi.setSelected( true ); - break; - case TRIANGULAR: - _triangular_type_cbmi.setSelected( true ); - break; - case UNROOTED: - _unrooted_type_cbmi.setSelected( true ); - break; - case CIRCULAR: - _circular_type_cbmi.setSelected( true ); - break; - default: - _rectangular_type_cbmi.setSelected( true ); - break; - } - } - catch ( final NullPointerException np ) { - // In all likelihood, this is caused by menu-less display. - } - } - - boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) { - if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) { - return false; - } - else if ( ( _species_tree == null ) || _species_tree.isEmpty() ) { - JOptionPane.showMessageDialog( this, - "No species tree loaded", - "Cannot execute GSDI", - JOptionPane.ERROR_MESSAGE ); - return false; - } - else if ( species_tree_has_to_binary && !_species_tree.isCompletelyBinary() ) { - JOptionPane.showMessageDialog( this, - "Species tree is not completely binary", - "Cannot execute GSDI", - JOptionPane.ERROR_MESSAGE ); - return false; - } - else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) { - JOptionPane.showMessageDialog( this, - "Gene tree is not completely binary", - "Cannot execute GSDI", - JOptionPane.ERROR_MESSAGE ); - return false; - } - else { - return true; - } - } - - boolean isSubtreeDisplayed() { - if ( getCurrentTreePanel() != null ) { - if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) { - JOptionPane - .showMessageDialog( this, - "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.", - "Operation can not be exectuted on a sub-tree", - JOptionPane.WARNING_MESSAGE ); - return true; - } - } - return false; - } - - void removeAllTextFrames() { - for( final TextFrame tf : _textframes ) { - if ( tf != null ) { - tf.close(); - } - } - _textframes.clear(); - } - - void setConfiguration( final Configuration configuration ) { - _configuration = configuration; - } - - void setCurrentDir( final File current_dir ) { - _current_dir = current_dir; - } - - void setOptions( final Options options ) { - _options = options; - } - - void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) { - setTypeMenuToAllUnselected(); - try { - switch ( type ) { - case CIRCULAR: - _circular_type_cbmi.setSelected( true ); - break; - case CONVEX: - _convex_type_cbmi.setSelected( true ); - break; - case CURVED: - _curved_type_cbmi.setSelected( true ); - break; - case EURO_STYLE: - _euro_type_cbmi.setSelected( true ); - break; - case ROUNDED: - _rounded_type_cbmi.setSelected( true ); - break; - case RECTANGULAR: - _rectangular_type_cbmi.setSelected( true ); - break; - case TRIANGULAR: - _triangular_type_cbmi.setSelected( true ); - break; - case UNROOTED: - _unrooted_type_cbmi.setSelected( true ); - break; - default: - throw new IllegalArgumentException( "unknown type: " + type ); - } - } - catch ( final NullPointerException np ) { - // In all likelihood, this is caused by menu-less display. - } - } - - void setTypeMenuToAllUnselected() { - if ( _convex_type_cbmi != null ) { - _convex_type_cbmi.setSelected( false ); - } - if ( _curved_type_cbmi != null ) { - _curved_type_cbmi.setSelected( false ); - } - if ( _euro_type_cbmi != null ) { - _euro_type_cbmi.setSelected( false ); - } - if ( _rounded_type_cbmi != null ) { - _rounded_type_cbmi.setSelected( false ); - } - if ( _triangular_type_cbmi != null ) { - _triangular_type_cbmi.setSelected( false ); - } - if ( _rectangular_type_cbmi != null ) { - _rectangular_type_cbmi.setSelected( false ); - } - if ( _unrooted_type_cbmi != null ) { - _unrooted_type_cbmi.setSelected( false ); - } - if ( _circular_type_cbmi != null ) { - _circular_type_cbmi.setSelected( false ); - } - } - - void showWhole() { - _mainpanel.getControlPanel().showWhole(); - } - - void switchColors() { - final TreeColorSet colorset = getMainPanel().getCurrentTreePanel().getTreeColorSet(); - final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset ); - csc.setVisible( true ); - getMainPanel().setTreeColorSet( colorset ); - } - - void typeChanged( final Object o ) { - updateTypeCheckboxes( getOptions(), o ); - updateOptions( getOptions() ); - if ( getCurrentTreePanel() != null ) { - final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType(); - final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType(); - if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) - || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) - || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) - || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) { - getCurrentTreePanel().getControlPanel().showWhole(); - } - if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) { - getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true ); - } - else { - getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false ); - } - getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() ); - MainFrame.updateScreenTextAntialias( getMainPanel().getTreePanels() ); - } - } - - void updateOptions( final Options options ) { - options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() ); - options.setBackgroundColorGradient( ( _background_gradient_cbmi != null ) - && _background_gradient_cbmi.isSelected() ); - options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() ); - options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null ) - && _show_annotation_ref_source.isSelected() ); - options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null ) - && _abbreviate_scientific_names.isSelected() ); - options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null ) - && _color_labels_same_as_parent_branch.isSelected() ); - options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null ) - && _show_default_node_shapes_internal_cbmi.isSelected() ); - options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null ) - && _show_default_node_shapes_external_cbmi.isSelected() ); - options.setShowDefaultNodeShapesForMarkedNodes( ( _show_default_node_shapes_for_marked_cbmi != null ) - && _show_default_node_shapes_for_marked_cbmi.isSelected() ); - if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) { - options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP ); - } - - else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) { - options.setCladogramType( CLADOGRAM_TYPE.LINED_UP ); - } - options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null ) - && _search_case_senstive_cbmi.isSelected() ); - if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) { - options.setShowScale( _show_scale_cbmi.isSelected() ); - } - if ( _label_direction_cbmi != null ) { - if ( _label_direction_cbmi.isSelected() ) { - options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL ); - } - else { - options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL ); - } - } - options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() ); - options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null ) - && _show_confidence_stddev_cbmi.isSelected() ); - options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null ) - && _search_whole_words_only_cbmi.isSelected() ); - options.setSearchWithRegex( ( _search_with_regex_cbmi != null ) && _search_with_regex_cbmi.isSelected() ); - options.setInverseSearchResult( ( _inverse_search_result_cbmi != null ) - && _inverse_search_result_cbmi.isSelected() ); - options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() ); - options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null ) - && _print_black_and_white_cbmi.isSelected() ); - if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) { - options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ); - } - else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) { - options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR ); - } - else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) { - options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED ); - } - else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) { - options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX ); - } - else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) { - options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ); - } - else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) { - options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED ); - } - else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) { - options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED ); - } - else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) { - options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ); - } - if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) { - options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() ); - } - if ( ( _right_line_up_domains_cbmi != null ) && _right_line_up_domains_cbmi.isEnabled() ) { - options.setRightLineUpDomains( _right_line_up_domains_cbmi.isSelected() ); - } - if ( ( _line_up_renderable_data_cbmi != null ) && _line_up_renderable_data_cbmi.isEnabled() ) { - options.setLineUpRendarableNodeData( _line_up_renderable_data_cbmi.isSelected() ); - } - if ( _graphics_export_visible_only_cbmi != null ) { - options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_cbmi.isSelected() ); - } - } - - void updateTypeCheckboxes( final Options options, final Object o ) { - setTypeMenuToAllUnselected(); - ( ( JCheckBoxMenuItem ) o ).setSelected( true ); - } - - void viewAsNexus() { - if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) { - String title = "Nexus"; - if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) { - title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title; - } - showTextFrame( getMainPanel().getCurrentPhylogeny().toNexus( getOptions() - .getNhConversionSupportValueStyle() ), - title ); - } - } - - void viewAsNH() { - if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) { - String title = "New Hampshire"; - if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) { - title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title; - } - showTextFrame( getMainPanel().getCurrentPhylogeny().toNewHampshire( getOptions() - .getNhConversionSupportValueStyle() ), - title ); - } - } - - void viewAsXML() { - if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) { - String title = "phyloXML"; - if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) { - title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title; - } - showTextFrame( getMainPanel().getCurrentPhylogeny().toPhyloXML( 0 ), title ); - } - } - - static void setTextForPdfLineWidthChooserMenuItem( final JMenuItem mi, final Options o ) { - mi.setText( "Enter Default Line Width for PDF Export... (current: " + o.getPrintLineWidth() + ")" ); - } - - static void setupScreenTextAntialias( final List treepanels, final boolean antialias ) { - for( final TreePanel tree_panel : treepanels ) { - tree_panel.setTextAntialias(); - } - } -} \ No newline at end of file diff --git a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java index 4e5e29b..3183972 100644 --- a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java +++ b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java @@ -60,7 +60,6 @@ import javax.swing.JScrollBar; import javax.swing.JTextField; import javax.swing.ListCellRenderer; -import org.forester.archaeopteryx.ControlPanel.TreeDisplayType; import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE; import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE; import org.forester.archaeopteryx.util.TypomaticJButton; @@ -644,19 +643,8 @@ final class ControlPanel extends JPanel implements ActionListener { return _tree_display_types; } - // This takes care of ArchaeopteryxE-issue. - // Can, and will, return null prior to ArchaeopteryxE initialization completion. - final private MainFrame getMainFrame() { - MainFrame mf = getMainPanel().getMainFrame(); - if ( mf == null ) { - // Must be "E" applet version. - final ArchaeopteryxE e = ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet(); - if ( e.getMainPanel() == null ) { - return null; - } - mf = e.getMainPanel().getMainFrame(); - } - return mf; + final private MainFrame getMainFrame() { + return getMainPanel().getMainFrame(); } private void init() { @@ -2611,15 +2599,10 @@ final class ControlPanel extends JPanel implements ActionListener { setDrawPhylogramEnabled( false ); setTreeDisplayType( TreeDisplayType.CLADOGRAM ); } - if ( getMainPanel().getMainFrame() == null ) { - // Must be "E" applet version. - final ArchaeopteryxE e = ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet(); - e.setSelectedTypeInTypeMenu( e.getCurrentTreePanel().getPhylogenyGraphicsType() ); - } - else { + getMainPanel().getMainFrame() .setSelectedTypeInTypeMenu( getMainPanel().getCurrentTreePanel().getPhylogenyGraphicsType() ); - } + getMainPanel().getCurrentTreePanel().updateSubSuperTreeButton(); getMainPanel().getCurrentTreePanel().updateButtonToUncollapseAll(); getMainPanel().getControlPanel().search0(); diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrame.java b/forester/java/src/org/forester/archaeopteryx/MainFrame.java index 74a8fff..d0a8d90 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrame.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrame.java @@ -40,7 +40,6 @@ import java.util.Map; import java.util.NoSuchElementException; import javax.swing.Box; -import javax.swing.JApplet; import javax.swing.JCheckBoxMenuItem; import javax.swing.JFileChooser; import javax.swing.JFrame; @@ -327,14 +326,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { @Override 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 == _exit_item ) { close(); } @@ -607,7 +599,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { } else if ( o == _help_item ) { try { - AptxUtil.openWebsite( AptxConstants.APTX_DOC_SITE, is_applet, applet ); + AptxUtil.openWebsite( AptxConstants.APTX_DOC_SITE ); } catch ( final IOException e1 ) { ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() ); @@ -615,7 +607,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { } else if ( o == _website_item ) { try { - AptxUtil.openWebsite( AptxConstants.APTX_WEB_SITE, is_applet, applet ); + AptxUtil.openWebsite( AptxConstants.APTX_WEB_SITE); } catch ( final IOException e1 ) { ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() ); @@ -623,7 +615,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { } else if ( o == _mailing_list_item ) { try { - AptxUtil.openWebsite( AptxConstants.APTX_MAILING_LIST, is_applet, applet ); + AptxUtil.openWebsite( AptxConstants.APTX_MAILING_LIST ); } catch ( final IOException e1 ) { ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() ); @@ -631,7 +623,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { } else if ( o == _phyloxml_website_item ) { try { - AptxUtil.openWebsite( AptxConstants.PHYLOXML_WEB_SITE, is_applet, applet ); + AptxUtil.openWebsite( AptxConstants.PHYLOXML_WEB_SITE ); } catch ( final IOException e1 ) { ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() ); @@ -639,7 +631,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { } else if ( o == _aptx_ref_item ) { try { - AptxUtil.openWebsite( AptxConstants.APTX_REFERENCE_URL, is_applet, applet ); + AptxUtil.openWebsite( AptxConstants.APTX_REFERENCE_URL ); } catch ( final IOException e1 ) { ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() ); @@ -647,7 +639,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { } else if ( o == _phyloxml_ref_item ) { try { - AptxUtil.openWebsite( AptxConstants.PHYLOXML_REFERENCE_URL, is_applet, applet ); + AptxUtil.openWebsite( AptxConstants.PHYLOXML_REFERENCE_URL ); } catch ( final IOException e1 ) { ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() ); diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java deleted file mode 100644 index c44a75c..0000000 --- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java +++ /dev/null @@ -1,330 +0,0 @@ -// $Id: -// FORESTER -- software libraries and applications -// for evolutionary biology research and applications. -// -// Copyright (C) 2008-2009 Christian M. Zmasek -// Copyright (C) 2008-2009 Burnham Institute for Medical Research -// Copyright (C) 2000-2001 Washington University School of Medicine -// and Howard Hughes Medical Institute -// Copyright (C) 2003-2007 Ethalinda K.S. Cannon -// All rights reserved -// -// This library is free software; you can redistribute it and/or -// modify it under the terms of the GNU Lesser General Public -// License as published by the Free Software Foundation; either -// version 2.1 of the License, or (at your option) any later version. -// -// This library is distributed in the hope that it will be useful, -// but WITHOUT ANY WARRANTY; without even the implied warranty of -// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU -// Lesser General Public License for more details. -// -// You should have received a copy of the GNU Lesser General Public -// License along with this library; if not, write to the Free Software -// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA -// -// Contact: phylosoft @ gmail . com -// WWW: https://sites.google.com/site/cmzmasek/home/software/forester - -package org.forester.archaeopteryx; - -import java.awt.BorderLayout; -import java.awt.event.ComponentAdapter; -import java.awt.event.ComponentEvent; -import java.awt.event.WindowAdapter; -import java.awt.event.WindowEvent; -import java.io.FileNotFoundException; -import java.io.IOException; -import java.net.MalformedURLException; -import java.net.URL; - -import javax.swing.ButtonGroup; -import javax.swing.JApplet; -import javax.swing.JCheckBoxMenuItem; -import javax.swing.JMenuBar; -import javax.swing.JMenuItem; -import javax.swing.JRadioButtonMenuItem; -import javax.swing.event.ChangeEvent; -import javax.swing.event.ChangeListener; - -import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE; -import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION; -import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION; -import org.forester.phylogeny.Phylogeny; -import org.forester.util.ForesterUtil; - -public final class MainFrameApplet extends MainFrame { - - private static final long serialVersionUID = 1941019292746717053L; - private final static int DEFAULT_FRAME_X_SIZE = 640; - private final static int DEFAULT_FRAME_Y_SIZE = 580; - private final ArchaeopteryxA _applet; - private ButtonGroup _radio_group_1; - - MainFrameApplet( final ArchaeopteryxA parent_applet, - final Configuration configuration, - final String species_tree_url_str ) { - setTitle( ArchaeopteryxA.NAME ); - _applet = parent_applet; - setConfiguration( configuration ); - setOptions( Options.createInstance( configuration ) ); - _mainpanel = new MainPanelApplets( _configuration, this ); - if ( !ForesterUtil.isEmpty( species_tree_url_str ) ) { - try { - readSpeciesTree( configuration, species_tree_url_str ); - } - catch ( final Exception e ) { - ForesterUtil.printErrorMessage( ArchaeopteryxA.NAME, "failed to read species tree from " - + species_tree_url_str ); - ForesterUtil.printErrorMessage( ArchaeopteryxA.NAME, e.toString() ); - } - } - // build the menu bar - _jmenubar = new JMenuBar(); - buildFileMenu(); - if ( !_configuration.isUseNativeUI() ) { - _jmenubar.setBackground( _configuration.getGuiMenuBackgroundColor() ); - } - buildAnalysisMenu(); - buildToolsMenu(); - buildViewMenu(); - buildFontSizeMenu(); - buildOptionsMenu(); - buildTypeMenu(); - buildHelpMenu(); - setJMenuBar( _jmenubar ); - _contentpane = getContentPane(); - _contentpane.setLayout( new BorderLayout() ); - _contentpane.add( _mainpanel, BorderLayout.CENTER ); - setSize( getConfiguration().getFrameXSize() > 40 ? getConfiguration().getFrameXSize() : DEFAULT_FRAME_X_SIZE, - getConfiguration().getFrameYSize() > 40 ? getConfiguration().getFrameYSize() : DEFAULT_FRAME_Y_SIZE ); - addWindowListener( new WindowAdapter() { - - @Override - public void windowClosing( final WindowEvent e ) { - close(); - } - } ); - addComponentListener( new ComponentAdapter() { - - @Override - public void componentResized( final ComponentEvent e ) { - if ( _mainpanel.getCurrentTreePanel() != null ) { - _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel() - .getWidth(), - _mainpanel.getCurrentTreePanel() - .getHeight() ); - } - } - } ); - setFocusable( true ); - requestFocus(); - requestFocusInWindow(); - setVisible( true ); - System.gc(); - } - - @Override - public MainPanel getMainPanel() { - return _mainpanel; - } - - private void readSpeciesTree( final Configuration configuration, final String species_tree_url_str ) - throws MalformedURLException, FileNotFoundException, IOException { - final URL species_tree_url = new URL( species_tree_url_str ); - final Phylogeny[] species_trees = AptxUtil.readPhylogeniesFromUrl( species_tree_url, - configuration - .isValidatePhyloXmlAgainstSchema(), - configuration - .isReplaceUnderscoresInNhParsing(), - false, - TAXONOMY_EXTRACTION.NO, - false ); - if ( ( species_trees != null ) && ( species_trees.length > 0 ) ) { - AptxUtil.printAppletMessage( ArchaeopteryxA.NAME, "successfully read species tree" ); - if ( species_trees[ 0 ].isEmpty() ) { - ForesterUtil.printErrorMessage( ArchaeopteryxA.NAME, "species tree is empty" ); - } - else if ( !species_trees[ 0 ].isRooted() ) { - ForesterUtil.printErrorMessage( ArchaeopteryxA.NAME, "species tree is not rooted" ); - } - else { - setSpeciesTree( species_trees[ 0 ] ); - AptxUtil.printAppletMessage( ArchaeopteryxA.NAME, "species tree OK" ); - } - } - else { - ForesterUtil.printErrorMessage( ArchaeopteryxA.NAME, "failed to read species tree from " - + species_tree_url_str ); - } - } - - void buildAnalysisMenu() { - _analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() ); - if ( getSpeciesTree() != null ) { - _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) ); - _analysis_menu.add( _gsdir_item = new JMenuItem( "GSDIR (GSDI with re-rooting)" ) ); - customizeJMenuItem( _gsdi_item ); - customizeJMenuItem( _gsdir_item ); - _analysis_menu.addSeparator(); - } - _analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) ); - customizeJMenuItem( _lineage_inference ); - _lineage_inference.setToolTipText( "Inference of ancestor taxonomies/lineages" ); - _jmenubar.add( _analysis_menu ); - } - - void buildOptionsMenu() { - _options_jmenu = MainFrame.createMenu( MainFrame.OPTIONS_HEADER, getConfiguration() ); - _options_jmenu.addChangeListener( new ChangeListener() { - - @Override - public void stateChanged( final ChangeEvent e ) { - MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() ); - MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() ); - MainFrame - .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() ); - MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, createCurrentFontDesc( getMainPanel() - .getTreeFontSet() ) ); - // setTextForGraphicsSizeChooserMenuItem( _print_size_mi, getOptions() ); - setTextForPdfLineWidthChooserMenuItem( _choose_pdf_width_mi, getOptions() ); - MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() ); - MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() ); - MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() ); - try { - getMainPanel().getControlPanel().setVisibilityOfDomainStrucureCB(); - getMainPanel().getControlPanel().setVisibilityOfX(); - } - catch ( final Exception ignore ) { - // do nothing, not important. - } - } - } ); - _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.DISPLAY_SUBHEADER ), - getConfiguration() ) ); - _options_jmenu - .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) ); - _options_jmenu.add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( NON_LINED_UP_CLADOGRAMS_LABEL ) ); - _radio_group_1 = new ButtonGroup(); - _radio_group_1.add( _ext_node_dependent_cladogram_rbmi ); - _radio_group_1.add( _non_lined_up_cladograms_rbmi ); - _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) ); - _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) ); - _options_jmenu - .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_INT ) ); - _options_jmenu - .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) ); - _options_jmenu - .add( _show_default_node_shapes_for_marked_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_MARKED ) ); - _options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) ); - if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) { - _options_jmenu.add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) ); - _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) ); - } - _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( MainFrame.SHOW_ANN_REF_SOURCE_LABEL ) ); - _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_CONF_STDDEV_LABEL ) ); - _options_jmenu - .add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( MainFrame.COLOR_BY_TAXONOMIC_GROUP ) ); - _options_jmenu - .add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) ); - _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP ); - _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( MainFrame.ABBREV_SN_LABEL ) ); - _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( MainFrame.LABEL_DIRECTION_LABEL ) ); - _label_direction_cbmi.setToolTipText( MainFrame.LABEL_DIRECTION_TIP ); - _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( MainFrame.SCREEN_ANTIALIAS_LABEL ) ); - _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( MainFrame.BG_GRAD_LABEL ) ); - _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) ); - _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) ); - _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) ); - _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) ); - _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) ); - _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) ); - _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) ); - _options_jmenu.addSeparator(); - _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.SEARCH_SUBHEADER ), - getConfiguration() ) ); - _options_jmenu - .add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_CASE_SENSITIVE_LABEL ) ); - _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_TERMS_ONLY_LABEL ) ); - _options_jmenu.add( _search_with_regex_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_REGEX_LABEL ) ); - _search_with_regex_cbmi.setToolTipText( MainFrame.SEARCH_WITH_REGEX_TIP ); - _options_jmenu.add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( INVERSE_SEARCH_RESULT_LABEL ) ); - - _options_jmenu.addSeparator(); - _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Graphics Export & Printing:" ), - getConfiguration() ) ); - _options_jmenu.add( _antialias_print_cbmi = new JCheckBoxMenuItem( "Antialias" ) ); - _options_jmenu.add( _print_black_and_white_cbmi = new JCheckBoxMenuItem( "Export in Black and White" ) ); - _options_jmenu - .add( _graphics_export_visible_only_cbmi = new JCheckBoxMenuItem( "Limit to Visible ('Screenshot') for PNG, JPG, and GIF export" ) ); - _options_jmenu.add( _choose_pdf_width_mi = new JMenuItem( "" ) ); - - customizeCheckBoxMenuItem( _antialias_print_cbmi, getOptions().isAntialiasPrint() ); - customizeCheckBoxMenuItem( _print_black_and_white_cbmi, getOptions().isPrintBlackAndWhite() ); - customizeJMenuItem( _choose_pdf_width_mi ); - - customizeJMenuItem( _choose_font_mi ); - customizeJMenuItem( _switch_colors_mi ); - customizeJMenuItem( _choose_minimal_confidence_mi ); - customizeJMenuItem( _overview_placment_mi ); - customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions() - .isShowDefaultNodeShapesInternal() ); - customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions() - .isShowDefaultNodeShapesExternal() ); - customizeCheckBoxMenuItem( _show_default_node_shapes_for_marked_cbmi, getOptions() - .isShowDefaultNodeShapesForMarkedNodes() ); - customizeJMenuItem( _cycle_node_shape_mi ); - customizeJMenuItem( _cycle_node_fill_mi ); - customizeJMenuItem( _choose_node_size_mi ); - customizeCheckBoxMenuItem( _color_by_taxonomic_group_cbmi, getOptions().isColorByTaxonomicGroup() ); - customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() ); - customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() ); - customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() ); - customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() ); - customizeCheckBoxMenuItem( _show_annotation_ref_source, getOptions().isShowAnnotationRefSource() ); - customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() ); - customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() ); - customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() ); - customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi, - getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP ); - customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi, - getOptions().getCladogramType() == CLADOGRAM_TYPE.LINED_UP ); - customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() ); - customizeCheckBoxMenuItem( _label_direction_cbmi, - getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL ); - customizeCheckBoxMenuItem( _search_with_regex_cbmi, getOptions().isSearchWithRegex() ); - customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() ); - customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() ); - customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() ); - customizeCheckBoxMenuItem( _line_up_renderable_data_cbmi, getOptions().isLineUpRendarableNodeData() ); - customizeCheckBoxMenuItem( _right_line_up_domains_cbmi, getOptions().isRightLineUpDomains() ); - _jmenubar.add( _options_jmenu ); - } - - void buildToolsMenu() { - _tools_menu = MainFrame.createMenu( "Tools", getConfiguration() ); - _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) ); - customizeJMenuItem( _confcolor_item ); - _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) ); - customizeJMenuItem( _taxcolor_item ); - _tools_menu.addSeparator(); - _tools_menu.add( _remove_visual_styles_item = new JMenuItem( "Delete All Visual Styles From Nodes" ) ); - _remove_visual_styles_item - .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny." ); - customizeJMenuItem( _remove_visual_styles_item ); - _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete All Colors From Branches" ) ); - _remove_branch_color_item.setToolTipText( "To remove all branch color values from the current phylogeny." ); - customizeJMenuItem( _remove_branch_color_item ); - _tools_menu.addSeparator(); - _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) ); - customizeJMenuItem( _midpoint_root_item ); - _tools_menu.addSeparator(); - _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) ); - customizeJMenuItem( _collapse_species_specific_subtrees ); - _jmenubar.add( _tools_menu ); - } - - JApplet getApplet() { - return _applet; - } -} diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java index f5b88fb..3c939e4 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java @@ -1353,14 +1353,9 @@ public final class MainFrameApplication extends MainFrame { _mainpanel.getControlPanel().showWhole(); _mainpanel.getCurrentTreePanel().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ); _mainpanel.getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ); - if ( getMainPanel().getMainFrame() == null ) { - // Must be "E" applet version. - ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() ) - .setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ); - } - else { - getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ); - } + + getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ); + activateSaveAllIfNeeded(); System.gc(); } diff --git a/forester/java/src/org/forester/archaeopteryx/MainPanelApplets.java b/forester/java/src/org/forester/archaeopteryx/MainPanelApplets.java deleted file mode 100644 index cfd54d7..0000000 --- a/forester/java/src/org/forester/archaeopteryx/MainPanelApplets.java +++ /dev/null @@ -1,90 +0,0 @@ -// $Id: -// FORESTER -- software libraries and applications -// for evolutionary biology research and applications. -// -// Copyright (C) 2008-2009 Christian M. Zmasek -// Copyright (C) 2008-2009 Burnham Institute for Medical Research -// Copyright (C) 2000-2001 Washington University School of Medicine -// and Howard Hughes Medical Institute -// Copyright (C) 2003-2007 Ethalinda K.S. Cannon -// All rights reserved -// -// This library is free software; you can redistribute it and/or -// modify it under the terms of the GNU Lesser General Public -// License as published by the Free Software Foundation; either -// version 2.1 of the License, or (at your option) any later version. -// -// This library is distributed in the hope that it will be useful, -// but WITHOUT ANY WARRANTY; without even the implied warranty of -// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU -// Lesser General Public License for more details. -// -// You should have received a copy of the GNU Lesser General Public -// License along with this library; if not, write to the Free Software -// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA -// -// Contact: phylosoft @ gmail . com -// WWW: https://sites.google.com/site/cmzmasek/home/software/forester - -package org.forester.archaeopteryx; - -import java.awt.BorderLayout; -import java.util.ArrayList; - -import javax.swing.JApplet; - -final class MainPanelApplets extends MainPanel { - - private static final long serialVersionUID = -7142615479464963140L; - private final JApplet _applet; - - public MainPanelApplets( final Configuration configuration, final ArchaeopteryxE em_applet ) { - if ( configuration == null ) { - throw new IllegalArgumentException( "configuration is null" ); - } - addComponentListener( this ); - _configuration = configuration; - _mainframe = null; - _treepanels = new ArrayList(); - _applet = em_applet; - initialize(); - _control_panel = new ControlPanel( this, configuration ); - if ( !configuration.isHideControlPanelAndMenubar() ) { - add( _control_panel, BorderLayout.WEST ); - } - setupTreeGraphic( configuration, getControlPanel() ); - } - - public MainPanelApplets( final Configuration configuration, final MainFrameApplet aaf ) { - if ( configuration == null ) { - throw new IllegalArgumentException( "configuration is null" ); - } - addComponentListener( this ); - _configuration = configuration; - _mainframe = aaf; - _treepanels = new ArrayList(); - _applet = aaf.getApplet(); - initialize(); - _control_panel = new ControlPanel( this, configuration ); - add( _control_panel, BorderLayout.WEST ); - setupTreeGraphic( configuration, getControlPanel() ); - } - - @Override - public Options getOptions() { - if ( _mainframe != null ) { - return _mainframe.getOptions(); - } - else { - return ( ( ArchaeopteryxE ) _applet ).getOptions(); - } - } - - JApplet getApplet() { - return _applet; - } - - MainFrameApplet getAppletFrame() { - return ( MainFrameApplet ) _mainframe; - } -} \ No newline at end of file diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java index 6d0c4ae..ccd3652 100644 --- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java +++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java @@ -84,7 +84,6 @@ import java.util.Set; import java.util.SortedSet; import javax.swing.BorderFactory; -import javax.swing.JApplet; import javax.swing.JColorChooser; import javax.swing.JDialog; import javax.swing.JMenuItem; @@ -741,12 +740,10 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee type = 'n'; } } - JApplet applet = null; - if ( isApplet() ) { - applet = obtainApplet(); - } + + try { - Blast.openNcbiBlastWeb( query, type == 'n', applet, this ); + Blast.openNcbiBlastWeb( query, type == 'n', this ); } catch ( final Exception e ) { e.printStackTrace(); @@ -2005,8 +2002,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee for( final String uri_str : uri_strs ) { try { AptxUtil.launchWebBrowser( new URI( uri_str ), - isApplet(), - isApplet() ? obtainApplet() : null, "_aptx_seq" ); } catch ( final IOException e ) { @@ -2033,8 +2028,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee if ( !ForesterUtil.isEmpty( uri_str ) ) { try { AptxUtil.launchWebBrowser( new URI( uri_str ), - isApplet(), - isApplet() ? obtainApplet() : null, + "_aptx_seq" ); } catch ( final IOException e ) { @@ -2115,8 +2109,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee if ( !ForesterUtil.isEmpty( uri_str ) ) { try { AptxUtil.launchWebBrowser( new URI( uri_str ), - isApplet(), - isApplet() ? obtainApplet() : null, "_aptx_tax" ); } catch ( final IOException e ) { @@ -4268,14 +4260,9 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee + ", unique entries: " + size; } final String s = sb.toString().trim(); - if ( getMainPanel().getMainFrame() == null ) { - // Must be "E" applet version. - final ArchaeopteryxE ae = ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet(); - ae.showTextFrame( s, title ); - } - else { + getMainPanel().getMainFrame().showTextFrame( s, title ); - } + } } } @@ -4587,14 +4574,9 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee else { getControlPanel().setDrawPhylogramEnabled( false ); } - if ( getMainPanel().getMainFrame() == null ) { - // Must be "E" applet version. - ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() ) - .setSelectedTypeInTypeMenu( getPhylogenyGraphicsType() ); - } - else { + getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( getPhylogenyGraphicsType() ); - } + } final void calcMaxDepth() { @@ -5301,9 +5283,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee && ( e.getY() <= ( getOvRectangle().getY() + getOvRectangle().getHeight() + 1 ) ) ); } - final boolean isApplet() { - return getMainPanel() instanceof MainPanelApplets; - } + final boolean isCanCollapse() { return ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ); @@ -5606,9 +5586,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee _urt_factor *= f; } - final JApplet obtainApplet() { - return ( ( MainPanelApplets ) getMainPanel() ).getApplet(); - } + final void paintBranchCircular( final PhylogenyNode p, final PhylogenyNode c, diff --git a/forester/java/src/org/forester/archaeopteryx/phylogeny/data/RenderableDomainArchitecture.java b/forester/java/src/org/forester/archaeopteryx/phylogeny/data/RenderableDomainArchitecture.java index bbc804e..32038e0 100644 --- a/forester/java/src/org/forester/archaeopteryx/phylogeny/data/RenderableDomainArchitecture.java +++ b/forester/java/src/org/forester/archaeopteryx/phylogeny/data/RenderableDomainArchitecture.java @@ -38,8 +38,8 @@ import java.math.BigDecimal; import java.util.Map; import java.util.SortedMap; -import org.forester.archaeopteryx.AptxUtil; import org.forester.archaeopteryx.AptxConstants; +import org.forester.archaeopteryx.AptxUtil; import org.forester.archaeopteryx.TreePanel; import org.forester.phylogeny.data.DomainArchitecture; import org.forester.phylogeny.data.PhylogenyData; diff --git a/forester/java/src/org/forester/archaeopteryx/tools/AncestralTaxonomyInferrer.java b/forester/java/src/org/forester/archaeopteryx/tools/AncestralTaxonomyInferrer.java index fa159b4..19ab6d5 100644 --- a/forester/java/src/org/forester/archaeopteryx/tools/AncestralTaxonomyInferrer.java +++ b/forester/java/src/org/forester/archaeopteryx/tools/AncestralTaxonomyInferrer.java @@ -32,7 +32,6 @@ import javax.swing.JOptionPane; import org.forester.analysis.AncestralTaxonomyInference; import org.forester.analysis.AncestralTaxonomyInferenceException; import org.forester.archaeopteryx.MainFrame; -import org.forester.archaeopteryx.MainFrameApplication; import org.forester.archaeopteryx.TreePanel; import org.forester.phylogeny.Phylogeny; import org.forester.ws.seqdb.SequenceDbWsTools; diff --git a/forester/java/src/org/forester/archaeopteryx/tools/Blast.java b/forester/java/src/org/forester/archaeopteryx/tools/Blast.java index c9f0e83..0d99d1b 100644 --- a/forester/java/src/org/forester/archaeopteryx/tools/Blast.java +++ b/forester/java/src/org/forester/archaeopteryx/tools/Blast.java @@ -28,12 +28,6 @@ package org.forester.archaeopteryx.tools; import java.io.IOException; import java.net.URI; import java.net.URISyntaxException; -import java.util.Arrays; -import java.util.Enumeration; -import java.util.Hashtable; -import java.util.Vector; - -import javax.swing.JApplet; import org.forester.archaeopteryx.AptxUtil; import org.forester.archaeopteryx.TreePanel; @@ -46,7 +40,7 @@ public final class Blast { final public static void openNcbiBlastWeb( final String query, final boolean is_nucleic_acids, - final JApplet applet, + final TreePanel p ) { //http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&PAGE=Proteins&DATABASE=swissprot&QUERY=gi|163848401 final StringBuilder uri_str = new StringBuilder(); @@ -60,7 +54,7 @@ public final class Blast { uri_str.append( "&QUERY=" ); uri_str.append( query ); try { - AptxUtil.launchWebBrowser( new URI( uri_str.toString() ), applet != null, applet, "_aptx_blast" ); + AptxUtil.launchWebBrowser( new URI( uri_str.toString() ), "_aptx_blast" ); } catch ( final IOException e ) { AptxUtil.showErrorMessage( p, e.toString() ); diff --git a/forester/java/src/org/forester/archaeopteryx/tools/ImageLoader.java b/forester/java/src/org/forester/archaeopteryx/tools/ImageLoader.java index afe47f0..899d8ce 100644 --- a/forester/java/src/org/forester/archaeopteryx/tools/ImageLoader.java +++ b/forester/java/src/org/forester/archaeopteryx/tools/ImageLoader.java @@ -35,8 +35,8 @@ import java.util.List; import javax.imageio.ImageIO; -import org.forester.archaeopteryx.AptxUtil; import org.forester.archaeopteryx.AptxConstants; +import org.forester.archaeopteryx.AptxUtil; import org.forester.archaeopteryx.TreePanel; import org.forester.phylogeny.PhylogenyNode; import org.forester.phylogeny.data.Taxonomy; diff --git a/forester/java/src/org/forester/phylogeny/Phylogeny.java b/forester/java/src/org/forester/phylogeny/Phylogeny.java index 876510c..4aefb5c 100644 --- a/forester/java/src/org/forester/phylogeny/Phylogeny.java +++ b/forester/java/src/org/forester/phylogeny/Phylogeny.java @@ -56,7 +56,6 @@ import org.forester.phylogeny.iterators.PhylogenyNodeIterator; import org.forester.phylogeny.iterators.PostorderTreeIterator; import org.forester.phylogeny.iterators.PreorderTreeIterator; import org.forester.util.FailedConditionCheckException; -import org.forester.util.ForesterUtil; public class Phylogeny { diff --git a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java index 1532e41..f31c657 100644 --- a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java +++ b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java @@ -42,7 +42,6 @@ import java.util.regex.Matcher; import java.util.regex.Pattern; import java.util.regex.PatternSyntaxException; -import org.forester.archaeopteryx.TreePanelUtil; import org.forester.io.parsers.FastaParser; import org.forester.io.parsers.PhylogenyParser; import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException; @@ -66,7 +65,6 @@ import org.forester.phylogeny.iterators.PhylogenyNodeIterator; import org.forester.phylogeny.iterators.PreorderTreeIterator; import org.forester.util.BasicDescriptiveStatistics; import org.forester.util.DescriptiveStatistics; -import org.forester.util.FailedConditionCheckException; import org.forester.util.ForesterUtil; import org.forester.util.TaxonomyUtil; diff --git a/forester/java/src/org/forester/test/Test.java b/forester/java/src/org/forester/test/Test.java index de8ec6e..75000a9 100644 --- a/forester/java/src/org/forester/test/Test.java +++ b/forester/java/src/org/forester/test/Test.java @@ -40,9 +40,6 @@ import java.util.Locale; import java.util.Set; import java.util.SortedSet; -import javax.net.ssl.HttpsURLConnection; -import javax.net.ssl.SSLContext; - import org.forester.application.support_transfer; import org.forester.archaeopteryx.AptxUtil; import org.forester.archaeopteryx.TreePanelUtil;