// $Id: // FORESTER -- software libraries and applications // for evolutionary biology research and applications. // // Copyright (C) 2008-2010 Christian M. Zmasek // All rights reserved // // This library is free software; you can redistribute it and/or // modify it under the terms of the GNU Lesser General Public // License as published by the Free Software Foundation; either // version 2.1 of the License, or (at your option) any later version. // // This library is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU // Lesser General Public License for more details. // // You should have received a copy of the GNU Lesser General Public // License along with this library; if not, write to the Free Software // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com // WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.archaeopteryx; import java.awt.Color; import java.awt.Component; import java.awt.Container; import java.awt.Font; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.ComponentAdapter; import java.awt.event.ComponentListener; import java.io.File; import java.io.IOException; import java.util.ArrayList; import java.util.LinkedList; import java.util.List; import java.util.Locale; import java.util.Map; import java.util.NoSuchElementException; import javax.swing.Box; import javax.swing.JCheckBoxMenuItem; import javax.swing.JFileChooser; import javax.swing.JFrame; import javax.swing.JInternalFrame; import javax.swing.JLabel; import javax.swing.JMenu; import javax.swing.JMenuBar; import javax.swing.JMenuItem; import javax.swing.JOptionPane; import javax.swing.JPanel; import javax.swing.JRadioButtonMenuItem; import javax.swing.JTextField; import javax.swing.SwingUtilities; import javax.swing.filechooser.FileFilter; 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.archaeopteryx.tools.AncestralTaxonomyInferrer; import org.forester.archaeopteryx.tools.InferenceManager; import org.forester.archaeopteryx.tools.ProcessPool; import org.forester.archaeopteryx.tools.ProcessRunning; import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION; import org.forester.io.writers.PhylogenyWriter; import org.forester.phylogeny.Phylogeny; import org.forester.phylogeny.PhylogenyMethods; import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY; import org.forester.phylogeny.PhylogenyNode; import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE; import org.forester.phylogeny.data.Annotation; import org.forester.phylogeny.data.NodeDataField; import org.forester.phylogeny.data.NodeVisualData.NodeFill; import org.forester.phylogeny.data.NodeVisualData.NodeShape; import org.forester.phylogeny.iterators.PhylogenyNodeIterator; 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; public abstract class MainFrame implements ActionListener { public final static NHFilter nhfilter = new NHFilter(); public final static NHXFilter nhxfilter = new NHXFilter(); public final static XMLFilter xmlfilter = new XMLFilter(); public final static TolFilter tolfilter = new TolFilter(); public final static NexusFilter nexusfilter = new NexusFilter(); public final static PdfFilter pdffilter = new PdfFilter(); public final static GraphicsFileFilter graphicsfilefilter = new GraphicsFileFilter(); public final static MsaFileFilter msafilter = new MsaFileFilter(); public final static SequencesFileFilter seqsfilter = new SequencesFileFilter(); public final static DefaultFilter defaultfilter = new DefaultFilter(); static final String USE_MOUSEWHEEL_SHIFT_TO_ROTATE = "rotate with mousewheel + Shift (or A and S), D toggles between horizontal and radial labels"; static final String PHYLOXML_REF_TOOL_TIP = AptxConstants.PHYLOXML_REFERENCE; //TODO //FIXME static final String APTX_REF_TOOL_TIP = AptxConstants.APTX_REFERENCE; private static final long serialVersionUID = 3655000897845508358L; final static Font menu_font = new Font( Configuration.getDefaultFontFamilyName(), Font.PLAIN, 10 ); static final String TYPE_MENU_HEADER = "Type"; static final String RECTANGULAR_TYPE_CBMI_LABEL = "Rectangular"; static final String EURO_TYPE_CBMI_LABEL = "Euro Type"; static final String CURVED_TYPE_CBMI_LABEL = "Curved"; static final String TRIANGULAR_TYPE_CBMI_LABEL = "Triangular"; static final String CONVEX_TYPE_CBMI_LABEL = "Convex"; static final String ROUNDED_TYPE_CBMI_LABEL = "Rounded"; static final String UNROOTED_TYPE_CBMI_LABEL = "Unrooted (alpha)"; //TODO static final String CIRCULAR_TYPE_CBMI_LABEL = "Circular (alpha)"; //TODO static final String OPTIONS_HEADER = "Options"; static final String SEARCH_SUBHEADER = "Search:"; static final String DISPLAY_SUBHEADER = "Display:"; static final String SEARCH_TERMS_ONLY_LABEL = "Words"; static final String SEARCH_REGEX_LABEL = "Regex"; static final String SEARCH_CASE_SENSITIVE_LABEL = "Match Case"; static final String INVERSE_SEARCH_RESULT_LABEL = "Inverse"; static final String COLOR_BY_TAXONOMIC_GROUP = "Colorize by Taxonomic Group"; static final String DISPLAY_SCALE_LABEL = "Scale"; static final String NON_LINED_UP_CLADOGRAMS_LABEL = "Non-Lined Up Cladogram"; static final String LABEL_DIRECTION_LABEL = "Radial Labels"; static final String LABEL_DIRECTION_TIP = "To use radial node labels in radial and unrooted display types"; static final String SEARCH_WITH_REGEX_TIP = "To search using regular expressions (~Java/Perl syntax). For example, use \"^B.+\\d{2,}$\" to search for everything starting with a B and ending with at least two digits."; static final String SCREEN_ANTIALIAS_LABEL = "Antialias"; static final String COLOR_LABELS_LABEL = "Colorize Labels Same as Parent Branch"; static final String BG_GRAD_LABEL = "Background Color Gradient"; static final String DISPLAY_NODE_BOXES_LABEL_EXT = "Shapes for External Nodes"; static final String DISPLAY_NODE_BOXES_LABEL_INT = "Shapes for Internal Nodes"; static final String DISPLAY_NODE_BOXES_LABEL_MARKED = "Shapes for Nodes with Visual Data"; static final String SHOW_OVERVIEW_LABEL = "Overview"; static final String FONT_SIZE_MENU_LABEL = "Font Size"; static final String NONUNIFORM_CLADOGRAMS_LABEL = "Lined Up Cladogram"; static final String SHOW_DOMAIN_LABELS_LABEL = "Domain Labels"; static final String SHOW_ANN_REF_SOURCE_LABEL = "Seq Annotation Ref Sources"; static final String COLOR_LABELS_TIP = "To use parent branch colors for node labels as well, need to turn off taxonomy dependent colorization and turn on branch colorization for this to become apparent"; static final String ABBREV_SN_LABEL = "Abbreviate Scientific Taxonomic Names"; static final String TAXONOMY_COLORIZE_NODE_SHAPES_LABEL = "Colorize Node Shapes According to Taxonomy"; static final String CYCLE_NODE_SHAPE_LABEL = "Cycle Node Shapes"; static final String CYCLE_NODE_FILL_LABEL = "Cycle Node Fill Type"; static final String CHOOSE_NODE_SIZE_LABEL = "Choose Node Shape Size"; static final String SHOW_CONF_STDDEV_LABEL = "Confidence Standard Deviations"; static final String USE_BRACKETS_FOR_CONF_IN_NH_LABEL = "Use Brackets for Confidence Values"; static final String USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL = "Use Internal Node Names for Confidence Values"; static final String SHOW_BASIC_TREE_INFORMATION_LABEL = "Basic Tree Information"; static final String RIGHT_LINE_UP_DOMAINS = "Right-align Domain Architectures"; static final String LINE_UP_RENDERABLE_DATA = "Line Up Diagrams (such as Domain Architectures)"; static final String INFER_ANCESTOR_TAXONOMIES = "Infer Ancestor Taxonomies"; static final String OBTAIN_DETAILED_TAXONOMIC_INFORMATION = "Obtain Detailed Taxonomic Information"; final AptxFrame _frame; JMenuBar _jmenubar; JMenu _file_jmenu; JMenu _tools_menu; JMenu _view_jmenu; JMenu _options_jmenu; JMenu _font_size_menu; JMenu _help_jmenu; JMenuItem[] _load_phylogeny_from_webservice_menu_items; // Analysis menu JMenu _analysis_menu; JMenuItem _load_species_tree_item; JMenuItem _gsdi_item; JMenuItem _gsdir_item; JMenuItem _lineage_inference; // file menu: JMenuItem _open_item; JMenuItem _open_url_item; JMenuItem _save_item; JMenuItem _save_all_item; JMenuItem _close_item; JMenuItem _exit_item; JMenuItem _new_item; JMenuItem _print_item; JMenuItem _write_to_pdf_item; JMenuItem _write_to_jpg_item; JMenuItem _write_to_gif_item; JMenuItem _write_to_tif_item; JMenuItem _write_to_png_item; JMenuItem _write_to_bmp_item; // tools menu: JMenuItem _midpoint_root_item; JMenuItem _taxcolor_item; JMenuItem _confcolor_item; JMenuItem _color_rank_jmi; JMenuItem _collapse_species_specific_subtrees; JMenuItem _obtain_detailed_taxonomic_information_jmi; JMenuItem _obtain_detailed_taxonomic_information_deleting_jmi; JMenuItem _obtain_seq_information_jmi; JMenuItem _move_node_names_to_tax_sn_jmi; JMenuItem _move_node_names_to_seq_names_jmi; JMenuItem _extract_tax_code_from_node_names_jmi; JMenuItem _annotate_item; JMenuItem _remove_branch_color_item; JMenuItem _remove_visual_styles_item; JMenuItem _delete_selected_nodes_item; JMenuItem _delete_not_selected_nodes_item; // font size menu: JMenuItem _super_tiny_fonts_item; JMenuItem _tiny_fonts_item; JMenuItem _small_fonts_item; JMenuItem _medium_fonts_item; JMenuItem _large_fonts_item; // options menu: // _ screen and print JMenuItem _choose_font_mi; JMenuItem _switch_colors_mi; JCheckBoxMenuItem _label_direction_cbmi; // _ screen display JCheckBoxMenuItem _screen_antialias_cbmi; JCheckBoxMenuItem _background_gradient_cbmi; JRadioButtonMenuItem _non_lined_up_cladograms_rbmi; JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi; JCheckBoxMenuItem _color_by_taxonomic_group_cbmi; JCheckBoxMenuItem _show_scale_cbmi; //TODO fix me JCheckBoxMenuItem _show_overview_cbmi; JCheckBoxMenuItem _show_domain_labels; JCheckBoxMenuItem _show_annotation_ref_source; JCheckBoxMenuItem _abbreviate_scientific_names; JCheckBoxMenuItem _color_labels_same_as_parent_branch; JMenuItem _overview_placment_mi; JMenuItem _choose_minimal_confidence_mi; JCheckBoxMenuItem _show_default_node_shapes_internal_cbmi; JCheckBoxMenuItem _show_default_node_shapes_external_cbmi; JCheckBoxMenuItem _show_default_node_shapes_for_marked_cbmi; JMenuItem _cycle_node_shape_mi; JMenuItem _cycle_node_fill_mi; JMenuItem _choose_node_size_mi; JMenuItem _cycle_data_return; JCheckBoxMenuItem _show_confidence_stddev_cbmi; JCheckBoxMenuItem _right_line_up_domains_cbmi; JCheckBoxMenuItem _line_up_renderable_data_cbmi; JCheckBoxMenuItem _collapsed_with_average_height_cbmi; JCheckBoxMenuItem _show_abbreviated_labels_for_collapsed_nodes_cbmi; // _ print JCheckBoxMenuItem _graphics_export_visible_only_cbmi; JCheckBoxMenuItem _antialias_print_cbmi; JCheckBoxMenuItem _print_black_and_white_cbmi; //JMenuItem _print_size_mi; JMenuItem _choose_pdf_width_mi; // _ parsing JCheckBoxMenuItem _internal_number_are_confidence_for_nh_parsing_cbmi; JRadioButtonMenuItem _extract_taxonomy_no_rbmi; JRadioButtonMenuItem _extract_taxonomy_agressive_rbmi; JRadioButtonMenuItem _extract_taxonomy_pfam_strict_rbmi; JRadioButtonMenuItem _extract_taxonomy_pfam_relaxed_rbmi; JCheckBoxMenuItem _replace_underscores_cbmi; JCheckBoxMenuItem _allow_errors_in_distance_to_parent_cbmi; JCheckBoxMenuItem _use_brackets_for_conf_in_nh_export_cbmi; JCheckBoxMenuItem _use_internal_names_for_conf_in_nh_export_cbmi; JCheckBoxMenuItem _parse_beast_style_extended_nexus_tags_cbmi; // _ search JCheckBoxMenuItem _search_case_senstive_cbmi; JCheckBoxMenuItem _search_whole_words_only_cbmi; JCheckBoxMenuItem _inverse_search_result_cbmi; JCheckBoxMenuItem _search_with_regex_cbmi; JCheckBoxMenuItem _color_all_found_nodes_when_coloring_subtree_cbmi; // type menu: JMenu _type_menu; JCheckBoxMenuItem _rectangular_type_cbmi; JCheckBoxMenuItem _triangular_type_cbmi; JCheckBoxMenuItem _curved_type_cbmi; JCheckBoxMenuItem _convex_type_cbmi; JCheckBoxMenuItem _euro_type_cbmi; JCheckBoxMenuItem _rounded_type_cbmi; JCheckBoxMenuItem _unrooted_type_cbmi; JCheckBoxMenuItem _circular_type_cbmi; // view as text menu: JMenuItem _view_as_NH_item; JMenuItem _view_as_XML_item; JMenuItem _view_as_nexus_item; JMenuItem _display_basic_information_item; // help menu: JMenuItem _about_item; JMenuItem _help_item; JMenuItem _website_item; JMenuItem _aptxjs_website_item; JMenuItem _mailing_list_item; JMenuItem _phyloxml_website_item; JMenuItem _phyloxml_ref_item; JMenuItem _aptx_ref_item; // File _current_dir; JFileChooser _writetopdf_filechooser; JFileChooser _save_filechooser; JFileChooser _writetographics_filechooser; // process menu: JMenu _process_menu; MainPanel _mainpanel; Container _contentpane; final LinkedList _textframes = new LinkedList(); ; Configuration _configuration; Options _options; private Phylogeny _species_tree; InferenceManager _inference_manager; final ProcessPool _process_pool; private String _previous_node_annotation_ref; MainFrame() { this(false); } MainFrame(boolean embedded){ if (embedded) { _frame = new EmbeddedFrame(); } else { _frame = new StandaloneFrame(); } _process_pool = ProcessPool.createInstance(); _writetopdf_filechooser = new JFileChooser(); _writetopdf_filechooser.setMultiSelectionEnabled( false ); _writetopdf_filechooser.addChoosableFileFilter( pdffilter ); _writetographics_filechooser = new JFileChooser(); _writetographics_filechooser.setMultiSelectionEnabled( false ); _writetographics_filechooser.addChoosableFileFilter( graphicsfilefilter ); _save_filechooser = new JFileChooser(); _save_filechooser.setMultiSelectionEnabled( false ); _save_filechooser.setFileFilter( xmlfilter ); _save_filechooser.addChoosableFileFilter( nhfilter ); _save_filechooser.addChoosableFileFilter( 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. } } public void addComponentListener( ComponentListener componentListener ) { _frame.addComponentListener( componentListener ); } public void dispose() { _frame.dispose(); } public Container getContentPane() { return _frame.getContentPane(); } public void repaint() { _frame.repaint(); } public void addFrameListener(FrameListener frameListener) { _frame.addFrameListener(frameListener); } public void setSize(int x, int y) { _frame.setSize(x,y); } public Container getJMenuBar() { return _frame.getJMenuBar(); } public void setDefaultCloseOperation( int doNothingOnClose ) { _frame.setDefaultCloseOperation(doNothingOnClose); } public Container getParent() { return _frame.getParent(); } public void setVisible(boolean visible) { _frame.setVisible(visible); } public void requestFocusInWindow() { _frame.requestFocusInWindow(); } public void setJMenuBar( JMenuBar jmenubar ) { _frame.setJMenuBar(jmenubar); } public void setLocationRelativeTo( Component component ) { _frame.setLocationRelativeTo(component); } public void setTitle(String title) { _frame.setTitle(title); } public Container getThisFrame() { return _frame.getThisFrame(); } public void validate() { _frame.validate(); } /** * Action performed. */ @Override public void actionPerformed( final ActionEvent e ) { final Object o = e.getSource(); if ( o == _exit_item ) { close(); } else if ( o == _gsdi_item ) { if ( isSubtreeDisplayed() ) { return; } executeGSDI(); } else if ( o == _gsdir_item ) { if ( isSubtreeDisplayed() ) { return; } executeGSDIR(); } else if ( o == _taxcolor_item ) { taxColor(); } else if ( o == _confcolor_item ) { confColor(); } else if ( o == _color_rank_jmi ) { colorRank(); } else if ( o == _collapse_species_specific_subtrees ) { if ( isSubtreeDisplayed() ) { return; } if ( getCurrentTreePanel() != null ) { getCurrentTreePanel().collapseSpeciesSpecificSubtrees(); } } else if ( o == _remove_branch_color_item ) { if ( isSubtreeDisplayed() ) { return; } removeBranchColors(); } else if ( o == _remove_visual_styles_item ) { if ( isSubtreeDisplayed() ) { return; } removeVisualStyles(); } else if ( o == _midpoint_root_item ) { if ( isSubtreeDisplayed() ) { return; } midpointRoot(); } else if ( o == _delete_selected_nodes_item ) { if ( isSubtreeDisplayed() ) { return; } deleteSelectedNodes( true ); } else if ( o == _delete_not_selected_nodes_item ) { if ( isSubtreeDisplayed() ) { return; } deleteSelectedNodes( false ); } else if ( o == _annotate_item ) { annotateSequences(); } else if ( o == _switch_colors_mi ) { switchColors(); } else if ( o == _display_basic_information_item ) { if ( getCurrentTreePanel() != null ) { displayBasicInformation( getCurrentTreePanel().getTreeFile() ); } } 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_item ) { if ( getCurrentTreePanel() != null ) { getCurrentTreePanel().setSuperTinyFonts(); getCurrentTreePanel().repaint(); } } else if ( o == _tiny_fonts_item ) { if ( getCurrentTreePanel() != null ) { getCurrentTreePanel().setTinyFonts(); getCurrentTreePanel().repaint(); } } else if ( o == _small_fonts_item ) { if ( getCurrentTreePanel() != null ) { getCurrentTreePanel().setSmallFonts(); getCurrentTreePanel().repaint(); } } else if ( o == _medium_fonts_item ) { if ( getCurrentTreePanel() != null ) { getCurrentTreePanel().setMediumFonts(); getCurrentTreePanel().repaint(); } } else if ( o == _large_fonts_item ) { if ( getCurrentTreePanel() != null ) { getCurrentTreePanel().setLargeFonts(); getCurrentTreePanel().repaint(); } } else if ( o == _choose_font_mi ) { chooseFont(); } else if ( o == _choose_minimal_confidence_mi ) { chooseMinimalConfidence(); } else if ( o == _choose_node_size_mi ) { chooseNodeSize( getOptions(), _frame.getThisFrame() ); } 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 == _cycle_data_return ) { MainFrame.cycleNodeDataReturn( getOptions(), getConfiguration() ); } else if ( o == _screen_antialias_cbmi ) { updateOptions( getOptions() ); updateScreenTextAntialias( getMainPanel().getTreePanels() ); } else if ( o == _background_gradient_cbmi ) { updateOptions( getOptions() ); } else if ( o == _show_domain_labels ) { updateOptions( getOptions() ); } else if ( o == _show_annotation_ref_source ) { updateOptions( getOptions() ); } else if ( o == _abbreviate_scientific_names ) { 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 == _show_default_node_shapes_for_marked_cbmi ) { updateOptions( getOptions() ); } else if ( o == _non_lined_up_cladograms_rbmi ) { updateOptions( getOptions() ); showWhole(); } else if ( o == _ext_node_dependent_cladogram_rbmi ) { updateOptions( getOptions() ); showWhole(); } else if ( o == _search_case_senstive_cbmi ) { if ( ( _search_with_regex_cbmi != null ) && _search_case_senstive_cbmi.isSelected() ) { _search_with_regex_cbmi.setSelected( false ); } 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( false ); } updateOptions( getOptions() ); getMainPanel().getControlPanel().search0(); getMainPanel().getControlPanel().search1(); } else if ( o == _color_all_found_nodes_when_coloring_subtree_cbmi ) { updateOptions( getOptions() ); } else if ( o == _parse_beast_style_extended_nexus_tags_cbmi ) { updateOptions( getOptions() ); } else if ( o == _show_scale_cbmi ) { updateOptions( getOptions() ); } else if ( o == _color_by_taxonomic_group_cbmi ) { updateOptions( getOptions() ); } else if ( o == _show_confidence_stddev_cbmi ) { updateOptions( getOptions() ); } else if ( o == _use_brackets_for_conf_in_nh_export_cbmi ) { if ( _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) { _use_internal_names_for_conf_in_nh_export_cbmi.setSelected( false ); } updateOptions( getOptions() ); } else if ( o == _use_internal_names_for_conf_in_nh_export_cbmi ) { if ( _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) { _use_brackets_for_conf_in_nh_export_cbmi.setSelected( false ); } updateOptions( getOptions() ); } else if ( o == _label_direction_cbmi ) { updateOptions( getOptions() ); } else if ( o == _show_overview_cbmi ) { updateOptions( getOptions() ); if ( getCurrentTreePanel() != null ) { getCurrentTreePanel().updateOvSizes(); } } 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 == _collapsed_with_average_height_cbmi ) { if ( _collapsed_with_average_height_cbmi.isSelected() ) { _collapsed_with_average_height_cbmi.setSelected( true ); } updateOptions( getOptions() ); } else if ( o == _show_abbreviated_labels_for_collapsed_nodes_cbmi ) { if ( _show_abbreviated_labels_for_collapsed_nodes_cbmi.isSelected() ) { _show_abbreviated_labels_for_collapsed_nodes_cbmi.setSelected( true ); } 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 == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi ) || ( o == _convex_type_cbmi ) || ( o == _euro_type_cbmi ) || ( o == _rounded_type_cbmi ) || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) { typeChanged( o ); } else if ( o == _about_item ) { about(); } else if ( o == _help_item ) { try { AptxUtil.openWebsite( AptxConstants.APTX_DOC_SITE ); } catch ( final IOException e1 ) { ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() ); } } else if ( o == _website_item ) { try { AptxUtil.openWebsite( AptxConstants.APTX_WEB_SITE); } catch ( final IOException e1 ) { ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() ); } } else if ( o == _aptxjs_website_item ) { try { AptxUtil.openWebsite( AptxConstants.APTX_JS_WEB_SITE);; } catch ( final IOException e1 ) { ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() ); } } else if ( o == _mailing_list_item ) { try { AptxUtil.openWebsite( AptxConstants.APTX_MAILING_LIST ); } catch ( final IOException e1 ) { ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() ); } } else if ( o == _phyloxml_website_item ) { try { AptxUtil.openWebsite( AptxConstants.PHYLOXML_WEB_SITE ); } catch ( final IOException e1 ) { ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() ); } } else if ( o == _aptx_ref_item ) { try { AptxUtil.openWebsite( AptxConstants.APTX_REFERENCE_URL ); } catch ( final IOException e1 ) { ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() ); } } else if ( o == _phyloxml_ref_item ) { try { AptxUtil.openWebsite( AptxConstants.PHYLOXML_REFERENCE_URL ); } catch ( final IOException e1 ) { ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() ); } } else if ( o == _write_to_pdf_item ) { final File curr_dir = writeToPdf( _mainpanel.getCurrentPhylogeny(), getMainPanel(), _writetopdf_filechooser, _current_dir, getContentPane(), getThisFrame() ); if ( curr_dir != null ) { setCurrentDir( curr_dir ); } } else if ( o == _save_all_item ) { writeAllToFile(); } else if ( o == _write_to_jpg_item ) { final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.JPG, _mainpanel, _writetographics_filechooser, getThisFrame(), getContentPane(), _current_dir ); if ( new_dir != null ) { setCurrentDir( new_dir ); } } else if ( o == _write_to_gif_item ) { final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.GIF, _mainpanel, _writetographics_filechooser, getThisFrame(), getContentPane(), _current_dir ); if ( new_dir != null ) { setCurrentDir( new_dir ); } } else if ( o == _write_to_tif_item ) { final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.TIFF, _mainpanel, _writetographics_filechooser, getThisFrame(), getContentPane(), _current_dir ); if ( new_dir != null ) { setCurrentDir( new_dir ); } } else if ( o == _write_to_bmp_item ) { final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.BMP, _mainpanel, _writetographics_filechooser, getThisFrame(), getContentPane(), _current_dir ); if ( new_dir != null ) { setCurrentDir( new_dir ); } } else if ( o == _write_to_png_item ) { final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.PNG, _mainpanel, _writetographics_filechooser, getThisFrame(), getContentPane(), _current_dir ); if ( new_dir != null ) { setCurrentDir( new_dir ); } } else if ( o == _print_item ) { print( getCurrentTreePanel(), getOptions(), _frame.getThisFrame() ); } else if ( o == _save_item ) { final File new_dir = writeToFile( _mainpanel.getCurrentPhylogeny(), getMainPanel(), _save_filechooser, _current_dir, getContentPane(), _frame.getThisFrame() ); 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(); } else if ( o == _lineage_inference ) { if ( isSubtreeDisplayed() ) { JOptionPane.showMessageDialog( getThisFrame(), "Subtree is shown.", "Cannot infer ancestral taxonomies", JOptionPane.ERROR_MESSAGE ); return; } executeLineageInference(); } else { if ( _load_phylogeny_from_webservice_menu_items != null ) { for( int i = 0; i < _load_phylogeny_from_webservice_menu_items.length; ++i ) { if ( o == _load_phylogeny_from_webservice_menu_items[ i ] ) { readPhylogeniesFromWebservice( i ); } } } } _contentpane.repaint(); } public Configuration getConfiguration() { return _configuration; } /** * 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(); } public InferenceManager getInferenceManager() { return _inference_manager; } public MainPanel getMainPanel() { return _mainpanel; } public Options getOptions() { return _options; } public ProcessPool getProcessPool() { return _process_pool; } public void showTextFrame( final String s, final String title ) { checkTextFrames(); _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) ); } public void showWhole() { _mainpanel.getControlPanel().showWhole(); } public void updateProcessMenu() { // In general Swing is not thread safe. // See "Swing's Threading Policy". SwingUtilities.invokeLater( new Runnable() { @Override public void run() { doUpdateProcessMenu(); } } ); } private void annotateSequences() { if ( getCurrentTreePanel() != null ) { List nodes = null; if ( ( getCurrentTreePanel().getFoundNodes0() != null ) || ( getCurrentTreePanel().getFoundNodes1() != null ) ) { nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes(); } if ( ( nodes == null ) || nodes.isEmpty() ) { JOptionPane .showMessageDialog( getThisFrame(), "Need to select nodes, either via direct selection or via the \"Search\" function", "No nodes selected for annotation", JOptionPane.ERROR_MESSAGE ); return; } final Phylogeny phy = getMainPanel().getCurrentPhylogeny(); if ( ( phy != null ) && !phy.isEmpty() ) { final JTextField ref_field = new JTextField( 10 ); final JTextField desc_filed = new JTextField( 20 ); ref_field.setText( ForesterUtil.isEmpty( getPreviousNodeAnnotationReference() ) ? "" : getPreviousNodeAnnotationReference() ); final JPanel my_panel = new JPanel(); my_panel.add( new JLabel( "Reference " ) ); my_panel.add( ref_field ); my_panel.add( Box.createHorizontalStrut( 15 ) ); my_panel.add( new JLabel( "Description " ) ); my_panel.add( desc_filed ); final int result = JOptionPane.showConfirmDialog( null, my_panel, "Enter the sequence annotation(s) for the " + nodes.size() + " selected nodes", JOptionPane.OK_CANCEL_OPTION ); if ( result == JOptionPane.OK_OPTION ) { String ref = ref_field.getText(); String desc = desc_filed.getText(); if ( !ForesterUtil.isEmpty( ref ) ) { ref = ref.trim(); ref = ref.replaceAll( "\\s+", " " ); if ( ( ref.indexOf( ':' ) < 1 ) || ( ref.indexOf( ':' ) > ( ref.length() - 2 ) ) || ( ref.length() < 3 ) ) { JOptionPane.showMessageDialog( getThisFrame(), "Reference needs to be in the form of \"GO:1234567\"", "Illegal Format for Annotation Reference", JOptionPane.ERROR_MESSAGE ); return; } } if ( ref != null ) { setPreviousNodeAnnotationReference( ref ); } if ( desc != null ) { desc = desc.trim(); desc = desc.replaceAll( "\\s+", " " ); } if ( !ForesterUtil.isEmpty( ref ) || !ForesterUtil.isEmpty( desc ) ) { for( final PhylogenyNode n : nodes ) { ForesterUtil.ensurePresenceOfSequence( n ); final Annotation ann = ForesterUtil.isEmpty( ref ) ? new Annotation() : new Annotation( ref ); if ( !ForesterUtil.isEmpty( desc ) ) { ann.setDesc( desc ); } n.getNodeData().getSequence().addAnnotation( ann ); } } getMainPanel().getControlPanel().showAnnotations(); } } } } private void chooseFont() { final FontChooser fc = new FontChooser(); fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() ); fc.showDialog( getThisFrame(), "Select the Base Font" ); getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() ); getControlPanel().displayedPhylogenyMightHaveChanged( true ); if ( getMainPanel().getCurrentTreePanel() != null ) { getMainPanel().getCurrentTreePanel().resetPreferredSize(); getMainPanel().getCurrentTreePanel().updateOvSizes(); } repaint(); } private void chooseMinimalConfidence() { final String s = ( String ) JOptionPane .showInputDialog( getThisFrame(), "Please enter the minimum for confidence values to be displayed.\n" + "[current value: " + getOptions().getMinConfidenceValue() + "]\n", "Minimal Confidence Value", JOptionPane.QUESTION_MESSAGE, null, null, getOptions().getMinConfidenceValue() ); if ( !ForesterUtil.isEmpty( s ) ) { boolean success = true; double m = 0.0; final String m_str = s.trim(); if ( !ForesterUtil.isEmpty( m_str ) ) { try { m = Double.parseDouble( m_str ); } catch ( final Exception ex ) { success = false; } } else { success = false; } if ( success && ( m >= 0.0 ) ) { getOptions().setMinConfidenceValue( m ); } } } private void deleteSelectedNodes( final boolean delete ) { final Phylogeny phy = getMainPanel().getCurrentPhylogeny(); if ( ( phy == null ) || ( phy.getNumberOfExternalNodes() < 2 ) ) { return; } final List nodes = new ArrayList(); if ( ( getCurrentTreePanel().getFoundNodes0() != null ) || ( getCurrentTreePanel().getFoundNodes1() != null ) ) { final List all_selected_nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes(); for( final PhylogenyNode n : all_selected_nodes ) { if ( n.isExternal() ) { nodes.add( n ); } } } String function = "Retain"; if ( delete ) { function = "Delete"; } if ( ( nodes == null ) || nodes.isEmpty() ) { JOptionPane .showMessageDialog( getThisFrame(), "Need to select external nodes, either via direct selection or via the \"Search\" function", "No external nodes selected to " + function.toLowerCase(), JOptionPane.ERROR_MESSAGE ); return; } final int todo = nodes.size(); final int ext = phy.getNumberOfExternalNodes(); int res = todo; if ( delete ) { res = ext - todo; } if ( res < 1 ) { JOptionPane.showMessageDialog( getThisFrame(), "Cannot delete all nodes", "Attempt to delete all nodes ", JOptionPane.ERROR_MESSAGE ); return; } final int result = JOptionPane.showConfirmDialog( null, function + " " + todo + " external node(s), from a total of " + ext + " external nodes," + "\nresulting in tree with " + res + " nodes?", function + " external nodes", JOptionPane.OK_CANCEL_OPTION ); if ( result == JOptionPane.OK_OPTION ) { if ( !delete ) { final List to_delete = new ArrayList(); for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) { final PhylogenyNode n = it.next(); if ( !nodes.contains( n ) ) { to_delete.add( n ); } } for( final PhylogenyNode n : to_delete ) { phy.deleteSubtree( n, true ); } } else { for( final PhylogenyNode n : nodes ) { phy.deleteSubtree( n, true ); } } resetSearch(); getCurrentTreePanel().setNodeInPreorderToNull(); phy.externalNodesHaveChanged(); phy.clearHashIdToNodeMap(); phy.recalculateNumberOfExternalDescendants( true ); getCurrentTreePanel().resetNodeIdToDistToLeafMap(); getCurrentTreePanel().setEdited( true ); repaint(); } } private void doUpdateProcessMenu() { if ( _process_pool.size() > 0 ) { if ( _process_menu == null ) { _process_menu = createMenu( "", getConfiguration() ); _process_menu.setForeground( Color.RED ); } _process_menu.removeAll(); final String text = "Processes Running: " + _process_pool.size(); _process_menu.setText( text ); _jmenubar.add( _process_menu ); for( int i = 0; i < _process_pool.size(); ++i ) { final ProcessRunning p = _process_pool.getProcessByIndex( i ); _process_menu.add( customizeJMenuItem( new JMenuItem( p.getName() + " [" + p.getStart() + "]" ) ) ); } } else { if ( _process_menu != null ) { _process_menu.removeAll(); _jmenubar.remove( _process_menu ); } } _jmenubar.validate(); _jmenubar.repaint(); repaint(); } private String getPreviousNodeAnnotationReference() { return _previous_node_annotation_ref; } private void removeBranchColors() { if ( getMainPanel().getCurrentPhylogeny() != null ) { AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() ); } } private void removeVisualStyles() { if ( getMainPanel().getCurrentPhylogeny() != null ) { AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() ); } } private void setPreviousNodeAnnotationReference( final String previous_node_annotation_ref ) { _previous_node_annotation_ref = previous_node_annotation_ref; } private void writeAllToFile() { if ( ( getMainPanel().getTabbedPane() == null ) || ( getMainPanel().getTabbedPane().getTabCount() < 1 ) ) { return; } final File my_dir = getCurrentDir(); if ( my_dir != null ) { _save_filechooser.setCurrentDirectory( my_dir ); } _save_filechooser.setSelectedFile( new File( "" ) ); final int result = _save_filechooser.showSaveDialog( _contentpane ); final File file = _save_filechooser.getSelectedFile(); setCurrentDir( _save_filechooser.getCurrentDirectory() ); if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) { if ( file.exists() ) { final int i = JOptionPane.showConfirmDialog( getThisFrame(), file + " already exists. Overwrite?", "Warning", JOptionPane.OK_CANCEL_OPTION, JOptionPane.WARNING_MESSAGE ); if ( i != JOptionPane.OK_OPTION ) { return; } else { try { file.delete(); } catch ( final Exception e ) { JOptionPane.showMessageDialog( getThisFrame(), "Failed to delete: " + file, "Error", JOptionPane.WARNING_MESSAGE ); } } } final int count = getMainPanel().getTabbedPane().getTabCount(); final List trees = new ArrayList(); for( int i = 0; i < count; ++i ) { final Phylogeny phy = getMainPanel().getPhylogeny( i ); if ( ForesterUtil.isEmpty( phy.getName() ) && !ForesterUtil.isEmpty( getMainPanel().getTabbedPane().getTitleAt( i ) ) ) { phy.setName( getMainPanel().getTabbedPane().getTitleAt( i ) ); } trees.add( phy ); getMainPanel().getTreePanels().get( i ).setEdited( false ); } final PhylogenyWriter writer = new PhylogenyWriter(); try { writer.toPhyloXML( file, trees, 0, ForesterUtil.LINE_SEPARATOR ); } catch ( final IOException e ) { JOptionPane.showMessageDialog( getThisFrame(), "Failed to write to: " + file, "Error", JOptionPane.WARNING_MESSAGE ); } } } public void activateSaveAllIfNeeded() { if ( ( getMainPanel().getTabbedPane() != null ) && ( getMainPanel().getTabbedPane().getTabCount() > 1 ) ) { _save_all_item.setEnabled( true ); } else { _save_all_item.setEnabled( false ); } } void buildFileMenu() { _file_jmenu = 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..." ) ); _file_jmenu.addSeparator(); _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) ); 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 ); customizeJMenuItem( _exit_item ); _jmenubar.add( _file_jmenu ); } void buildFontSizeMenu() { _font_size_menu = createMenu( FONT_SIZE_MENU_LABEL, getConfiguration() ); _font_size_menu.add( _super_tiny_fonts_item = new JMenuItem( "Super Tiny Fonts" ) ); _font_size_menu.add( _tiny_fonts_item = new JMenuItem( "Tiny Fonts" ) ); _font_size_menu.add( _small_fonts_item = new JMenuItem( "Small Fonts" ) ); _font_size_menu.add( _medium_fonts_item = new JMenuItem( "Medium Fonts" ) ); _font_size_menu.add( _large_fonts_item = new JMenuItem( "Large Fonts" ) ); customizeJMenuItem( _super_tiny_fonts_item ); customizeJMenuItem( _tiny_fonts_item ); customizeJMenuItem( _small_fonts_item ); customizeJMenuItem( _medium_fonts_item ); customizeJMenuItem( _large_fonts_item ); _jmenubar.add( _font_size_menu ); } void buildHelpMenu() { _help_jmenu = createMenu( "Help", getConfiguration() ); _help_jmenu.add( _help_item = new JMenuItem( "Documentation" ) ); _help_jmenu.addSeparator(); _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) ); _help_jmenu.add( _aptxjs_website_item = new JMenuItem( "NEW! Archaeopteryx online version: Archaeopteryx.js" ) ); _help_jmenu.add( _mailing_list_item = new JMenuItem( "Mailing List" ) ); _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" ); //TODO need to add this... _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( _aptxjs_website_item ); customizeJMenuItem( _mailing_list_item ); customizeJMenuItem( _phyloxml_website_item ); customizeJMenuItem( _aptx_ref_item ); customizeJMenuItem( _phyloxml_ref_item ); customizeJMenuItem( _about_item ); _phyloxml_ref_item.setToolTipText( PHYLOXML_REF_TOOL_TIP ); _aptx_ref_item.setToolTipText( APTX_REF_TOOL_TIP ); _jmenubar.add( _help_jmenu ); } void buildTypeMenu() { _type_menu = createMenu( TYPE_MENU_HEADER, getConfiguration() ); _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) ); _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) ); _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) ); _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) ); _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) ); _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) ); _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) ); _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) ); customizeCheckBoxMenuItem( _rectangular_type_cbmi, false ); customizeCheckBoxMenuItem( _triangular_type_cbmi, false ); customizeCheckBoxMenuItem( _euro_type_cbmi, false ); customizeCheckBoxMenuItem( _rounded_type_cbmi, false ); customizeCheckBoxMenuItem( _curved_type_cbmi, false ); customizeCheckBoxMenuItem( _convex_type_cbmi, false ); customizeCheckBoxMenuItem( _unrooted_type_cbmi, false ); customizeCheckBoxMenuItem( _circular_type_cbmi, false ); _triangular_type_cbmi.setToolTipText( "not suitable for phylograms" ); _curved_type_cbmi.setToolTipText( "not suitable for phylograms" ); _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE ); _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE ); initializeTypeMenu( getOptions() ); _jmenubar.add( _type_menu ); } void buildViewMenu() { _view_jmenu = createMenu( "View", getConfiguration() ); _view_jmenu.add( _display_basic_information_item = new JMenuItem( 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 choosePdfWidth() { final String s = ( String ) JOptionPane.showInputDialog( getThisFrame(), "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 ); } } } void close() { removeAllTextFrames(); if ( _mainpanel != null ) { _mainpanel.terminate(); } if ( _contentpane != null ) { _contentpane.removeAll(); } setVisible( false ); dispose(); } void colorRank() { if ( _mainpanel.getCurrentTreePanel() != null ) { final Map present_ranks = AptxUtil.getRankCounts( _mainpanel.getCurrentTreePanel().getPhylogeny()); final String[] ranks = AptxUtil.getAllPossibleRanks(present_ranks); String rank = ( String ) JOptionPane .showInputDialog( getThisFrame(), "What rank should the colorization be based on", "Rank Selection", JOptionPane.QUESTION_MESSAGE, null, ranks, null ); if ( !ForesterUtil.isEmpty( rank ) ) { if ( rank.indexOf( '(' ) > 0 ) { rank = rank.substring( 0, rank.indexOf( '(' ) ).trim(); } _mainpanel.getCurrentTreePanel().colorRank( rank ); } } } void confColor() { if ( _mainpanel.getCurrentTreePanel() != null ) { _mainpanel.getCurrentTreePanel().confColor(); } } void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) { if ( item != null ) { item.setFont( MainFrame.menu_font ); if ( !getConfiguration().isUseNativeUI() ) { item.setBackground( getConfiguration().getGuiMenuBackgroundColor() ); item.setForeground( getConfiguration().getGuiMenuTextColor() ); } item.setSelected( is_selected ); item.addActionListener( this ); } } JMenuItem 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 ); } return jmi; } void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) { if ( item != null ) { item.setFont( MainFrame.menu_font ); if ( !getConfiguration().isUseNativeUI() ) { item.setBackground( getConfiguration().getGuiMenuBackgroundColor() ); item.setForeground( getConfiguration().getGuiMenuTextColor() ); } item.setSelected( is_selected ); item.addActionListener( this ); } } void displayBasicInformation( final File treefile ) { if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) { String title = "Basic Information"; if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) { title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\""; } showTextFrame( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny(), treefile ), title ); } } void exceptionOccuredDuringOpenFile( final Exception e ) { try { _mainpanel.getCurrentTreePanel().setArrowCursor(); } catch ( final Exception ex ) { // Do nothing. } JOptionPane.showMessageDialog( getThisFrame(), ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ), "Error during File|Open", JOptionPane.ERROR_MESSAGE ); } void executeGSDI() { if ( !isOKforSDI( false, true ) ) { return; } if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) { JOptionPane.showMessageDialog( getThisFrame(), "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 = getSpeciesTree().copy(); try { gsdi = new GSDI( gene_tree, species_tree, false, true, true, true ); } catch ( final SDIException e ) { JOptionPane.showMessageDialog( getThisFrame(), 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( getThisFrame(), "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( getThisFrame(), "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( getThisFrame(), "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 = getSpeciesTree().copy(); try { gsdir = new GSDIR( gene_tree, species_tree, true, true, true ); } catch ( final SDIException e ) { JOptionPane.showMessageDialog( getThisFrame(), 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( getThisFrame(), "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( getThisFrame(), "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 ); } } void executeLineageInference() { if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) { return; } if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) { JOptionPane.showMessageDialog( getThisFrame(), "Phylogeny is not rooted.", "Cannot infer ancestral taxonomies", JOptionPane.ERROR_MESSAGE ); return; } final AncestralTaxonomyInferrer inferrer = new AncestralTaxonomyInferrer( this, _mainpanel.getCurrentTreePanel(), _mainpanel.getCurrentPhylogeny() .copy() ); new Thread( inferrer ).start(); } boolean GAndSDoHaveMoreThanOneSpeciesInComman( final Phylogeny gene_tree ) { if ( ( gene_tree == null ) || gene_tree.isEmpty() ) { JOptionPane.showMessageDialog( getThisFrame(), "Gene tree and species tree have no species in common.", "Error during SDI", JOptionPane.ERROR_MESSAGE ); return false; } else if ( gene_tree.getNumberOfExternalNodes() < 2 ) { JOptionPane.showMessageDialog( getThisFrame(), "Gene tree and species tree have only one species in common.", "Error during SDI", JOptionPane.ERROR_MESSAGE ); return false; } else { return true; } } ControlPanel getControlPanel() { return getMainPanel().getControlPanel(); } 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(); } JMenu getHelpMenu() { return _help_jmenu; } JCheckBoxMenuItem getlabelDirectionCbmi() { return _label_direction_cbmi; } JMenuBar getMenuBarOfMainFrame() { return _jmenubar; } final Phylogeny getSpeciesTree() { return _species_tree; } void initializeTypeMenu( final Options options ) { setTypeMenuToAllUnselected(); switch ( options.getPhylogenyGraphicsType() ) { case CONVEX: _convex_type_cbmi.setSelected( true ); break; case CURVED: _curved_type_cbmi.setSelected( true ); break; case EURO_STYLE: _euro_type_cbmi.setSelected( true ); break; case ROUNDED: _rounded_type_cbmi.setSelected( true ); break; case TRIANGULAR: _triangular_type_cbmi.setSelected( true ); break; case UNROOTED: _unrooted_type_cbmi.setSelected( true ); break; case CIRCULAR: _circular_type_cbmi.setSelected( true ); break; default: _rectangular_type_cbmi.setSelected( true ); break; } } 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 ( ( getSpeciesTree() == null ) || getSpeciesTree().isEmpty() ) { JOptionPane.showMessageDialog( getThisFrame(), "No species tree loaded", "Cannot execute GSDI", JOptionPane.ERROR_MESSAGE ); return false; } else if ( species_tree_has_to_binary && !getSpeciesTree().isCompletelyBinary() ) { JOptionPane.showMessageDialog( getThisFrame(), "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( getThisFrame(), "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( getThisFrame(), "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 midpointRoot() { if ( _mainpanel.getCurrentTreePanel() != null ) { _mainpanel.getCurrentTreePanel().midpointRoot(); } } void readPhylogeniesFromWebservice( final int i ) { final UrlTreeReader reader = new UrlTreeReader( this, i ); new Thread( reader ).start(); } void removeAllTextFrames() { for( final TextFrame tf : _textframes ) { if ( tf != null ) { tf.close(); } } _textframes.clear(); } void resetSearch() { getMainPanel().getCurrentTreePanel().setFoundNodes0( null ); getMainPanel().getCurrentTreePanel().setFoundNodes1( null ); getMainPanel().getControlPanel().setSearchFoundCountsOnLabel0( 0 ); getMainPanel().getControlPanel().getSearchFoundCountsLabel0().setVisible( false ); getMainPanel().getControlPanel().getSearchTextField0().setText( "" ); getMainPanel().getControlPanel().getSearchResetButton0().setEnabled( false ); getMainPanel().getControlPanel().getSearchResetButton0().setVisible( false ); getMainPanel().getControlPanel().setSearchFoundCountsOnLabel1( 0 ); getMainPanel().getControlPanel().getSearchFoundCountsLabel1().setVisible( false ); getMainPanel().getControlPanel().getSearchTextField1().setText( "" ); getMainPanel().getControlPanel().getSearchResetButton1().setEnabled( false ); getMainPanel().getControlPanel().getSearchResetButton1().setVisible( false ); } void setConfiguration( final Configuration configuration ) { _configuration = configuration; } void setCurrentDir( final File current_dir ) { _current_dir = current_dir; } void setInferenceManager( final InferenceManager i ) { _inference_manager = i; } void setOptions( final Options options ) { _options = options; } void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) { setTypeMenuToAllUnselected(); switch ( type ) { case CIRCULAR: _circular_type_cbmi.setSelected( true ); break; case CONVEX: _convex_type_cbmi.setSelected( true ); break; case CURVED: _curved_type_cbmi.setSelected( true ); break; case EURO_STYLE: _euro_type_cbmi.setSelected( true ); break; case ROUNDED: _rounded_type_cbmi.setSelected( true ); break; case RECTANGULAR: _rectangular_type_cbmi.setSelected( true ); break; case TRIANGULAR: _triangular_type_cbmi.setSelected( true ); break; case UNROOTED: _unrooted_type_cbmi.setSelected( true ); break; default: throw new IllegalArgumentException( "unknown type: " + type ); } } final void setSpeciesTree( final Phylogeny species_tree ) { _species_tree = species_tree; } void setTypeMenuToAllUnselected() { _convex_type_cbmi.setSelected( false ); _curved_type_cbmi.setSelected( false ); _euro_type_cbmi.setSelected( false ); _rounded_type_cbmi.setSelected( false ); _triangular_type_cbmi.setSelected( false ); _rectangular_type_cbmi.setSelected( false ); _unrooted_type_cbmi.setSelected( false ); _circular_type_cbmi.setSelected( false ); } void switchColors() { final TreeColorSet colorset = _mainpanel.getTreeColorSet(); final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset ); csc.setVisible( true ); } void taxColor() { if ( _mainpanel.getCurrentTreePanel() != null ) { _mainpanel.getCurrentTreePanel().taxColor(); } } void typeChanged( final Object o ) { updateTypeCheckboxes( getOptions(), o ); updateOptions( getOptions() ); if ( getCurrentTreePanel() != null ) { final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType(); final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType(); if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) { getCurrentTreePanel().getControlPanel().showWhole(); } if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) { getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true ); } else { getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false ); } getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() ); updateScreenTextAntialias( getMainPanel().getTreePanels() ); if ( getCurrentTreePanel().getControlPanel().getDynamicallyHideData() != null ) { if ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) { getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( false ); } else { getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( true ); } } } } void updateOptions( final Options options ) { options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() ); options.setBackgroundColorGradient( ( _background_gradient_cbmi != null ) && _background_gradient_cbmi.isSelected() ); options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() ); options.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() ); if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) { options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() ); } options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() ); if ( ( _use_brackets_for_conf_in_nh_export_cbmi != null ) && _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) { options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS ); } else if ( ( _use_internal_names_for_conf_in_nh_export_cbmi != null ) && _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) { options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES ); } else { options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE ); } options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null ) && _print_black_and_white_cbmi.isSelected() ); options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null ) && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() ); if ( ( _extract_taxonomy_pfam_strict_rbmi != null ) && _extract_taxonomy_pfam_strict_rbmi.isSelected() ) { options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); } else if ( ( _extract_taxonomy_pfam_relaxed_rbmi != null ) && _extract_taxonomy_pfam_relaxed_rbmi.isSelected() ) { options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); } else if ( ( _extract_taxonomy_agressive_rbmi != null ) && _extract_taxonomy_agressive_rbmi.isSelected() ) { options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE ); } else if ( ( _extract_taxonomy_no_rbmi != null ) && _extract_taxonomy_no_rbmi.isSelected() ) { options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO ); } options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null ) && _replace_underscores_cbmi.isSelected() ); options.setAllowErrorsInDistanceToParent( ( _allow_errors_in_distance_to_parent_cbmi != null ) && _allow_errors_in_distance_to_parent_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() ); if ( _graphics_export_visible_only_cbmi != null ) { options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_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 ( ( _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 ( ( _color_all_found_nodes_when_coloring_subtree_cbmi != null ) && _color_all_found_nodes_when_coloring_subtree_cbmi.isEnabled() ) { options.setColorAllFoundNodesWhenColoringSubtree( _color_all_found_nodes_when_coloring_subtree_cbmi.isSelected() ); } if ( ( _parse_beast_style_extended_nexus_tags_cbmi != null ) && _parse_beast_style_extended_nexus_tags_cbmi.isEnabled() ) { options.setParseBeastStyleExtendedNexusTags(_parse_beast_style_extended_nexus_tags_cbmi.isSelected() ); } if ( ( _collapsed_with_average_height_cbmi != null ) && _collapsed_with_average_height_cbmi.isEnabled() ) { options.setCollapsedWithAverageHeigh(_collapsed_with_average_height_cbmi.isSelected() ); } if ( ( _show_abbreviated_labels_for_collapsed_nodes_cbmi != null ) && _show_abbreviated_labels_for_collapsed_nodes_cbmi.isEnabled() ) { options.setShowAbbreviatedLabelsForCollapsedNodes(_show_abbreviated_labels_for_collapsed_nodes_cbmi.isSelected() ); } } void updateTypeCheckboxes( final Options options, final Object o ) { setTypeMenuToAllUnselected(); ( ( JCheckBoxMenuItem ) o ).setSelected( true ); } void viewAsNexus() { if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) { String title = "Nexus"; if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) { title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title; } showTextFrame( _mainpanel.getCurrentPhylogeny().toNexus( getOptions().getNhConversionSupportValueStyle() ), title ); } } void viewAsNH() { if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) { String title = "New Hampshire"; if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) { title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title; } showTextFrame( _mainpanel.getCurrentPhylogeny().toNewHampshire( getOptions() .getNhConversionSupportValueStyle() ), title ); } } void viewAsXML() { if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) { String title = "phyloXML"; if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) { title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title; } showTextFrame( _mainpanel.getCurrentPhylogeny().toPhyloXML( 0 ), title ); } } private static void cycleNodeDataReturn( final Options op, final Configuration conf ) { switch ( op.getExtDescNodeDataToReturn() ) { case UNKNOWN: op.setExtDescNodeDataToReturn( NodeDataField.DOMAINS_ALL ); break; case DOMAINS_ALL: op.setExtDescNodeDataToReturn( NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN ); break; case DOMAINS_COLLAPSED_PER_PROTEIN: op.setExtDescNodeDataToReturn( NodeDataField.SEQ_ANNOTATIONS ); break; case SEQ_ANNOTATIONS: op.setExtDescNodeDataToReturn( NodeDataField.GO_TERM_IDS ); break; case GO_TERM_IDS: op.setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_MOL_SEQ_FASTA ); break; case SEQUENCE_MOL_SEQ_FASTA: if ( ( conf != null ) && ( conf.getExtDescNodeDataToReturn() != null ) && ( conf.getExtDescNodeDataToReturn() != NodeDataField.DOMAINS_ALL ) && ( conf.getExtDescNodeDataToReturn() != NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN ) && ( conf.getExtDescNodeDataToReturn() != NodeDataField.SEQ_ANNOTATIONS ) && ( conf.getExtDescNodeDataToReturn() != NodeDataField.GO_TERM_IDS ) && ( conf.getExtDescNodeDataToReturn() != NodeDataField.SEQUENCE_MOL_SEQ_FASTA ) ) { op.setExtDescNodeDataToReturn( conf.getExtDescNodeDataToReturn() ); } else { op.setExtDescNodeDataToReturn( NodeDataField.UNKNOWN ); } break; default: op.setExtDescNodeDataToReturn( NodeDataField.UNKNOWN ); } } /** * Display the about box. */ void about() { final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + AptxConstants.VERSION + "\n" ); about.append( "Copyright (C) 2016 Christian M Zmasek\n" ); about.append( "All Rights Reserved\n" ); about.append( "License: GNU Lesser General Public License (LGPL)\n" ); about.append( "Last modified: " + AptxConstants.PRG_DATE + "\n" ); about.append( "Based on: " + ForesterUtil.getForesterLibraryInformation() + "\n" ); if ( _configuration.isCouldReadConfigFile() ) { about.append( "Using configuration file: " + _configuration.config_filename + "\n" ); } else { about.append( "Not using a configuration file\n" ); } about.append( "phyloXML version : " + ForesterConstants.PHYLO_XML_VERSION + "\n" ); about.append( "phyloXML location: " + ForesterConstants.PHYLO_XML_LOCATION + "\n" ); if ( !ForesterUtil.isEmpty( ForesterUtil.JAVA_VERSION ) && !ForesterUtil.isEmpty( ForesterUtil.JAVA_VENDOR ) ) { about.append( "[your Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]\n" ); } if ( !ForesterUtil.isEmpty( ForesterUtil.OS_NAME ) && !ForesterUtil.isEmpty( ForesterUtil.OS_ARCH ) && !ForesterUtil.isEmpty( ForesterUtil.OS_VERSION ) ) { about.append( "[your OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " " + ForesterUtil.OS_VERSION + "]\n" ); } final Runtime rt = java.lang.Runtime.getRuntime(); final long free_memory = rt.freeMemory() / 1000000; final long total_memory = rt.totalMemory() / 1000000; about.append( "[free memory: " + free_memory + "MB, total memory: " + total_memory + "MB]\n" ); about.append( "[locale: " + Locale.getDefault() + "]\n" ); about.append( "References:\n" ); about.append( AptxConstants.PHYLOXML_REFERENCE_SHORT + "\n" ); about.append( "For more information & download:\n" ); about.append( AptxConstants.APTX_WEB_SITE + "\n" ); about.append( "Documentation:\n" ); about.append( AptxConstants.APTX_DOC_SITE + "\n" ); about.append( "Comments: " + AptxConstants.AUTHOR_EMAIL ); JOptionPane.showMessageDialog( null, about, AptxConstants.PRG_NAME, JOptionPane.PLAIN_MESSAGE ); } static void chooseNodeSize( final Options options, final Component parent ) { final String s = ( String ) JOptionPane.showInputDialog( parent, "Please enter the default size for node shapes.\n" + "[current value: " + options.getDefaultNodeShapeSize() + "]\n", "Node Shape Size", JOptionPane.QUESTION_MESSAGE, null, null, options.getDefaultNodeShapeSize() ); 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 ) ) { final short size = ForesterUtil.roundToShort( m ); if ( size >= 0.0 ) { options.setDefaultNodeShapeSize( size ); } } } } static String createCurrentFontDesc( final TreeFontSet tree_font_set ) { return tree_font_set.getLargeFont().getFamily() + " " + tree_font_set.getLargeFont().getSize(); } static JMenu createMenu( final String title, final Configuration conf ) { final JMenu jmenu = new JMenu( title ); if ( !conf.isUseNativeUI() ) { jmenu.setFont( MainFrame.menu_font ); jmenu.setBackground( conf.getGuiMenuBackgroundColor() ); jmenu.setForeground( conf.getGuiMenuTextColor() ); } return jmenu; } static JMenuItem customizeMenuItemAsLabel( final JMenuItem label, final Configuration configuration ) { label.setFont( MainFrame.menu_font.deriveFont( Font.BOLD ) ); if ( !configuration.isUseNativeUI() ) { label.setBackground( configuration.getGuiMenuBackgroundColor() ); label.setForeground( configuration.getGuiMenuTextColor() ); label.setOpaque( true ); } label.setSelected( false ); label.setEnabled( false ); return label; } static void cycleNodeFill( final Options op ) { switch ( op.getDefaultNodeFill() ) { case GRADIENT: op.setDefaultNodeFill( NodeFill.SOLID ); break; case NONE: op.setDefaultNodeFill( NodeFill.GRADIENT ); break; case SOLID: op.setDefaultNodeFill( NodeFill.NONE ); break; default: throw new RuntimeException( "unknown fill: " + op.getDefaultNodeFill() ); } } static void cycleNodeShape( final Options op ) { switch ( op.getDefaultNodeShape() ) { case CIRCLE: op.setDefaultNodeShape( NodeShape.RECTANGLE ); break; case RECTANGLE: op.setDefaultNodeShape( NodeShape.CIRCLE ); break; default: throw new RuntimeException( "unknown shape: " + op.getDefaultNodeShape() ); } } static void cycleOverview( final Options op, final TreePanel tree_panel ) { switch ( op.getOvPlacement() ) { case LOWER_LEFT: op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT ); break; case LOWER_RIGHT: op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT ); break; case UPPER_LEFT: op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT ); break; case UPPER_RIGHT: op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT ); break; default: throw new RuntimeException( "unknown placement: " + op.getOvPlacement() ); } if ( tree_panel != null ) { tree_panel.updateOvSettings(); } } static void exceptionOccuredDuringSaveAs( final Exception e, final TreePanel tp, final Component comp ) { try { tp.setArrowCursor(); } catch ( final Exception ex ) { // Do nothing. } JOptionPane.showMessageDialog( comp, "Exception" + e, "Error during File|SaveAs", JOptionPane.ERROR_MESSAGE ); } static void print( final TreePanel tp, final Options op, final Component c ) { if ( ( tp == null ) || ( tp.getPhylogeny() == null ) || tp.getPhylogeny().isEmpty() ) { return; } final String job_name = AptxConstants.PRG_NAME; boolean error = false; String printer_name = null; try { printer_name = Printer.print( tp, job_name ); } catch ( final Exception e ) { error = true; JOptionPane.showMessageDialog( c, e.getMessage(), "Printing Error", JOptionPane.ERROR_MESSAGE ); } if ( !error && ( printer_name != null ) ) { String msg = "Printing data sent to printer"; if ( printer_name.length() > 1 ) { msg += " [" + printer_name + "]"; } JOptionPane.showMessageDialog( c, msg, "Printing...", JOptionPane.INFORMATION_MESSAGE ); } if ( !op.isPrintUsingActualSize() ) { tp.getControlPanel().showWhole(); } } static void printPhylogenyToPdf( final String file_name, final Options opts, final TreePanel tp, final Component comp ) { String pdf_written_to = ""; boolean error = false; try { if ( opts.isPrintUsingActualSize() ) { pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name, tp, tp.getWidth() , tp.getHeight() ); } else { // Never false. } } catch ( final IOException e ) { error = true; JOptionPane.showMessageDialog( comp, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE ); } if ( !error ) { if ( !ForesterUtil.isEmpty( pdf_written_to ) ) { JOptionPane.showMessageDialog( comp, "Wrote PDF to: " + pdf_written_to, "Information", JOptionPane.INFORMATION_MESSAGE ); } else { JOptionPane.showMessageDialog( comp, "There was an unknown problem when attempting to write to PDF file: \"" + file_name + "\"", "Error", JOptionPane.ERROR_MESSAGE ); } } if ( !opts.isPrintUsingActualSize() ) { tp.getControlPanel().showWhole(); } } static void setCycleDataReturnMenuItem( final JMenuItem mi, final Options options ) { if ( ( options != null ) && ( options.getExtDescNodeDataToReturn() != null ) ) { mi.setText( "Cycle Node Return Data... (current: " + options.getExtDescNodeDataToReturn().toString() + ")" ); } else { mi.setText( "Cycle Node Return Data..." ); } } static void setCycleNodeFillMenuItem( final JMenuItem mi, final Options options ) { if ( ( options != null ) && ( options.getDefaultNodeFill() != null ) ) { mi.setText( "Cycle Node Shape Fill Type... (current: " + options.getDefaultNodeFill().toString().toLowerCase() + ")" ); } else { mi.setText( "Cycle Node Shape Fill Type..." ); } } static void setCycleNodeShapeMenuItem( final JMenuItem mi, final Options options ) { if ( ( options != null ) && ( options.getDefaultNodeShape() != null ) ) { mi.setText( "Cycle Node Shape Fill Type... (current: " + options.getDefaultNodeShape().toString().toLowerCase() + ")" ); } else { mi.setText( "Cycle Node Shape Fill Type..." ); } } static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) { if ( ( options != null ) && ( options.getOvPlacement() != null ) ) { mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" ); } else { mi.setText( "Cycle Overview Placement..." ); } } static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) { if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) { mi.setText( "Select Color Scheme... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName() + ")" ); } else { mi.setText( "Select Color Scheme..." ); } } static void setTextForFontChooserMenuItem( final JMenuItem mi, final String font_desc ) { mi.setText( "Select Default Font... (current: " + font_desc + ")" ); } static void setTextForPdfLineWidthChooserMenuItem( final JMenuItem mi, final Options o ) { mi.setText( "Enter Default Line Width for PDF Export... (current: " + o.getPrintLineWidth() + ")" ); } static void setTextMinSupportMenuItem( final JMenuItem mi, final Options options, final TreePanel current_tree_panel ) { if ( ( current_tree_panel == null ) || ( current_tree_panel.getPhylogeny() == null ) ) { mi.setEnabled( true ); } else if ( AptxUtil.isHasAtLeastOneBranchWithSupportValues( current_tree_panel.getPhylogeny() ) ) { mi.setEnabled( true ); } else { mi.setEnabled( false ); } mi.setText( "Enter Min Confidence Value... (current: " + options.getMinConfidenceValue() + ")" ); } static void setTextNodeSizeMenuItem( final JMenuItem mi, final Options options ) { mi.setText( "Enter Default Node Shape Size... (current: " + options.getDefaultNodeShapeSize() + ")" ); } static void updateScreenTextAntialias( final List treepanels ) { for( final TreePanel tree_panel : treepanels ) { tree_panel.setTextAntialias(); } } static boolean writeAsNewHampshire( final TreePanel tp, final Options op, boolean exception, final File file ) { try { final PhylogenyWriter writer = new PhylogenyWriter(); writer.toNewHampshire( tp.getPhylogeny(), true, op.getNhConversionSupportValueStyle(), file ); } catch ( final Exception e ) { exception = true; exceptionOccuredDuringSaveAs( e, tp, tp ); } return exception; } static boolean writeAsNexus( final TreePanel tp, final Options op, boolean exception, final File file ) { try { final PhylogenyWriter writer = new PhylogenyWriter(); writer.toNexus( file, tp.getPhylogeny(), op.getNhConversionSupportValueStyle() ); } catch ( final Exception e ) { exception = true; exceptionOccuredDuringSaveAs( e, tp, tp ); } return exception; } static boolean writeAsPhyloXml( final TreePanel tp, final Options op, boolean exception, final File file ) { try { final PhylogenyWriter writer = new PhylogenyWriter(); writer.toPhyloXML( file, tp.getPhylogeny(), 0 ); } catch ( final Exception e ) { exception = true; exceptionOccuredDuringSaveAs( e, tp, tp ); } return exception; } static void writePhylogenyToGraphicsFile( final String file_name, final GraphicsExportType type, final MainPanel mp, final Component comp, final Container contentpane ) { mp.getCurrentTreePanel().calcParametersForPainting( mp.getCurrentTreePanel().getWidth(), mp.getCurrentTreePanel().getHeight() ); String file_written_to = ""; boolean error = false; try { file_written_to = AptxUtil.writePhylogenyToGraphicsFile( file_name, mp.getCurrentTreePanel().getWidth(), mp.getCurrentTreePanel().getHeight(), mp.getCurrentTreePanel(), mp.getControlPanel(), type, mp.getOptions() ); } catch ( final IOException e ) { error = true; JOptionPane.showMessageDialog( comp, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE ); } if ( !error ) { if ( ( file_written_to != null ) && ( file_written_to.length() > 0 ) ) { JOptionPane.showMessageDialog( comp, "Wrote image to: " + file_written_to, "Graphics Export", JOptionPane.INFORMATION_MESSAGE ); } else { JOptionPane.showMessageDialog( comp, "There was an unknown problem when attempting to write to an image file: \"" + file_name + "\"", "Error", JOptionPane.ERROR_MESSAGE ); } } contentpane.repaint(); } static File writeToFile( final Phylogeny t, final MainPanel mp, final JFileChooser save_filechooser, final File current_dir, final Container contentpane, final Component comp ) { File new_file = null; if ( t == null ) { return null; } String initial_filename = null; if ( mp.getCurrentTreePanel().getTreeFile() != null ) { try { initial_filename = mp.getCurrentTreePanel().getTreeFile().getCanonicalPath(); } catch ( final IOException e ) { initial_filename = null; } } if ( !ForesterUtil.isEmpty( initial_filename ) ) { save_filechooser.setSelectedFile( new File( initial_filename ) ); } else { save_filechooser.setSelectedFile( new File( "" ) ); } final File my_dir = current_dir; if ( my_dir != null ) { save_filechooser.setCurrentDirectory( my_dir ); } final int result = save_filechooser.showSaveDialog( contentpane ); final File file = save_filechooser.getSelectedFile(); new_file = save_filechooser.getCurrentDirectory(); boolean exception = false; if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) { if ( file.exists() ) { final int i = JOptionPane.showConfirmDialog( comp, file + " already exists.\nOverwrite?", "Overwrite?", JOptionPane.OK_CANCEL_OPTION, JOptionPane.QUESTION_MESSAGE ); if ( i != JOptionPane.OK_OPTION ) { return null; } else { final File to = new File( file.getAbsoluteFile().toString() + AptxConstants.BACKUP_FILE_SUFFIX ); try { ForesterUtil.copyFile( file, to ); } catch ( final Exception e ) { JOptionPane.showMessageDialog( comp, "Failed to create backup copy " + to, "Failed to Create Backup Copy", JOptionPane.WARNING_MESSAGE ); } try { file.delete(); } catch ( final Exception e ) { JOptionPane.showMessageDialog( comp, "Failed to delete: " + file, "Failed to Delete", JOptionPane.WARNING_MESSAGE ); } } } if ( save_filechooser.getFileFilter() == MainFrame.nhfilter ) { exception = writeAsNewHampshire( mp.getCurrentTreePanel(), mp.getOptions(), exception, file ); } else if ( save_filechooser.getFileFilter() == MainFrame.xmlfilter ) { exception = writeAsPhyloXml( mp.getCurrentTreePanel(), mp.getOptions(), exception, file ); } else if ( save_filechooser.getFileFilter() == MainFrame.nexusfilter ) { exception = writeAsNexus( mp.getCurrentTreePanel(), mp.getOptions(), exception, file ); } // "*.*": else { final String file_name = file.getName().trim().toLowerCase(); if ( file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" ) || file_name.endsWith( ".tree" ) ) { exception = writeAsNewHampshire( mp.getCurrentTreePanel(), mp.getOptions(), exception, file ); } else if ( file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) ) { exception = writeAsNexus( mp.getCurrentTreePanel(), mp.getOptions(), exception, file ); } // XML is default: else { exception = writeAsPhyloXml( mp.getCurrentTreePanel(), mp.getOptions(), exception, file ); } } if ( !exception ) { mp.setTitleOfSelectedTab( file.getName() ); mp.getCurrentTreePanel().setTreeFile( file ); mp.getCurrentTreePanel().setEdited( false ); } } return new_file; } static File writeToGraphicsFile( final Phylogeny t, final GraphicsExportType type, final MainPanel mp, final JFileChooser writetographics_filechooser, final Component component, final Container contentpane, final File current_dir ) { File new_dir = null; if ( ( t == null ) || t.isEmpty() ) { return null; } String initial_filename = ""; if ( mp.getCurrentTreePanel().getTreeFile() != null ) { initial_filename = mp.getCurrentTreePanel().getTreeFile().toString(); } if ( initial_filename.indexOf( '.' ) > 0 ) { initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) ); } initial_filename = initial_filename + "." + type; writetographics_filechooser.setSelectedFile( new File( initial_filename ) ); final File my_dir = current_dir; if ( my_dir != null ) { writetographics_filechooser.setCurrentDirectory( my_dir ); } final int result = writetographics_filechooser.showSaveDialog( contentpane ); File file = writetographics_filechooser.getSelectedFile(); //setCurrentDir( writetographics_filechooser.getCurrentDirectory() ); new_dir = writetographics_filechooser.getCurrentDirectory(); if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) { if ( !file.toString().toLowerCase().endsWith( type.toString() ) ) { file = new File( file.toString() + "." + type ); } if ( file.exists() ) { final int i = JOptionPane.showConfirmDialog( component, file + " already exists. Overwrite?", "Warning", JOptionPane.OK_CANCEL_OPTION, JOptionPane.WARNING_MESSAGE ); if ( i != JOptionPane.OK_OPTION ) { return null; } else { try { file.delete(); } catch ( final Exception e ) { JOptionPane.showMessageDialog( component, "Failed to delete: " + file, "Error", JOptionPane.WARNING_MESSAGE ); } } } writePhylogenyToGraphicsFile( file.toString(), type, mp, component, contentpane ); } return new_dir; } static File writeToPdf( final Phylogeny t, final MainPanel mp, final JFileChooser writetopdf_filechooser, final File curr_dir, final Container contentpane, final Component component ) { if ( ( t == null ) || t.isEmpty() ) { return null; } String initial_filename = ""; if ( mp.getCurrentTreePanel().getTreeFile() != null ) { initial_filename = mp.getCurrentTreePanel().getTreeFile().toString(); } if ( initial_filename.indexOf( '.' ) > 0 ) { initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) ); } initial_filename = initial_filename + ".pdf"; writetopdf_filechooser.setSelectedFile( new File( initial_filename ) ); final File my_dir = curr_dir; if ( my_dir != null ) { writetopdf_filechooser.setCurrentDirectory( my_dir ); } final int result = writetopdf_filechooser.showSaveDialog( contentpane ); File file = writetopdf_filechooser.getSelectedFile(); // setCurrentDir( writetopdf_filechooser.getCurrentDirectory() ); final File new_current_dir = writetopdf_filechooser.getCurrentDirectory(); if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) { if ( !file.toString().toLowerCase().endsWith( ".pdf" ) ) { file = new File( file.toString() + ".pdf" ); } if ( file.exists() ) { final int i = JOptionPane.showConfirmDialog( component, file + " already exists. Overwrite?", "WARNING", JOptionPane.OK_CANCEL_OPTION, JOptionPane.WARNING_MESSAGE ); if ( i != JOptionPane.OK_OPTION ) { return null; } } printPhylogenyToPdf( file.toString(), mp.getOptions(), mp.getCurrentTreePanel(), component ); } return new_current_dir; } } class DefaultFilter extends FileFilter { @Override public boolean accept( final File f ) { final String file_name = f.getName().trim().toLowerCase(); return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" ) || file_name.endsWith( ".nwk" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".ph" ) || file_name.endsWith( ".tr" ) || file_name.endsWith( ".dnd" ) || file_name.endsWith( ".tree" ) || file_name.endsWith( ".nhx" ) || file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" ) || file_name.endsWith( "phylo.xml" ) || file_name.endsWith( ".pxml" ) || file_name.endsWith( ".nexus" ) || file_name.endsWith( ".nx" ) || file_name.endsWith( ".nex" ) || file_name.endsWith( ".tre" ) || file_name.endsWith( ".zip" ) || file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" ) || file_name.endsWith( ".con" ) || f.isDirectory(); } @Override public String getDescription() { return "All supported files (*.xml, *.phyloxml, *phylo.xml, *.nhx, *.nh, *.newick, *.nex, *.nexus, *.phy, *.tre, *.tree, *.tol, ...)"; } } class GraphicsFileFilter extends FileFilter { @Override public boolean accept( final File f ) { final String file_name = f.getName().trim().toLowerCase(); return file_name.endsWith( ".jpg" ) || file_name.endsWith( ".jpeg" ) || file_name.endsWith( ".png" ) || file_name.endsWith( ".gif" ) || file_name.endsWith( ".bmp" ) || f.isDirectory(); } @Override public String getDescription() { return "Image files (*.jpg, *.jpeg, *.png, *.gif, *.bmp)"; } } class MsaFileFilter extends FileFilter { @Override public boolean accept( final File f ) { final String file_name = f.getName().trim().toLowerCase(); return file_name.endsWith( ".msa" ) || file_name.endsWith( ".aln" ) || file_name.endsWith( ".fasta" ) || file_name.endsWith( ".fas" ) || file_name.endsWith( ".fa" ) || f.isDirectory(); } @Override public String getDescription() { return "Multiple sequence alignment files (*.msa, *.aln, *.fasta, *.fa, *.fas)"; } } class NexusFilter extends FileFilter { @Override public boolean accept( final File f ) { final String file_name = f.getName().trim().toLowerCase(); return file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) || file_name.endsWith( ".nx" ) || file_name.endsWith( ".tre" ) || f.isDirectory(); } @Override public String getDescription() { return "Nexus files (*.nex, *.nexus, *.nx, *.tre)"; } } // NexusFilter class NHFilter extends FileFilter { @Override public boolean accept( final File f ) { final String file_name = f.getName().trim().toLowerCase(); return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" ) || file_name.endsWith( ".tr" ) || file_name.endsWith( ".tree" ) || file_name.endsWith( ".dnd" ) || file_name.endsWith( ".ph" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".nwk" ) || f.isDirectory(); } @Override public String getDescription() { return "New Hampshire - Newick files (*.nh, *.newick, *.phy, *.tree, *.dnd, *.tr, *.ph, *.phb, *.nwk)"; } } // NHFilter class NHXFilter extends FileFilter { @Override public boolean accept( final File f ) { final String file_name = f.getName().trim().toLowerCase(); return file_name.endsWith( ".nhx" ) || f.isDirectory(); } @Override public String getDescription() { return "NHX files (*.nhx) [deprecated]"; } } class PdfFilter extends FileFilter { @Override public boolean accept( final File f ) { return f.getName().trim().toLowerCase().endsWith( ".pdf" ) || f.isDirectory(); } @Override public String getDescription() { return "PDF files (*.pdf)"; } } // PdfFilter class SequencesFileFilter extends FileFilter { @Override public boolean accept( final File f ) { final String file_name = f.getName().trim().toLowerCase(); return file_name.endsWith( ".fasta" ) || file_name.endsWith( ".fa" ) || file_name.endsWith( ".fas" ) || file_name.endsWith( ".seqs" ) || f.isDirectory(); } @Override public String getDescription() { return "Sequences files (*.fasta, *.fa, *.fas, *.seqs )"; } } class TolFilter extends FileFilter { @Override public boolean accept( final File f ) { final String file_name = f.getName().trim().toLowerCase(); return ( file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" ) || file_name.endsWith( ".zip" ) || f .isDirectory() ) && ( !file_name.endsWith( ".xml.zip" ) ); } @Override public String getDescription() { return "Tree of Life files (*.tol, *.tolxml)"; } } // TolFilter class XMLFilter extends FileFilter { @Override public boolean accept( final File f ) { final String file_name = f.getName().trim().toLowerCase(); return file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" ) || file_name.endsWith( "phylo.xml" ) || file_name.endsWith( ".pxml" ) || file_name.endsWith( ".zip" ) || f.isDirectory(); } @Override public String getDescription() { return "phyloXML files (*.xml, *.phyloxml, *phylo.xml, *.pxml, *.zip)"; } } // XMLFilter