public final static boolean __SYNTH_LF = false; // TODO remove me
public final static boolean ALLOW_DDBJ_BLAST = false;
public final static String PRG_NAME = "Archaeopteryx";
- final static String VERSION = "0.989 beta";
- final static String PRG_DATE = "140514";
+ final static String VERSION = "0.9891 beta";
+ final static String PRG_DATE = "140605";
final static String DEFAULT_CONFIGURATION_FILE_NAME = "_aptx_configuration_file";
final static String[] DEFAULT_FONT_CHOICES = { "Arial", "Helvetica",
"Verdana", "Tahoma", "Dialog", "Lucida Sans", "SansSerif", "Sans-serif", "Sans" };
-// $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.io.File;
-import java.io.IOException;
-import java.util.LinkedList;
-import java.util.List;
-import java.util.Locale;
-import java.util.NoSuchElementException;
-import java.util.Set;
-
-import javax.swing.Box;
-import javax.swing.JApplet;
-import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JFrame;
-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 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.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.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.NodeVisualData.NodeFill;
-import org.forester.phylogeny.data.NodeVisualData.NodeShape;
-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;
-
-public abstract class MainFrame extends JFrame implements ActionListener {
-
- static final String USE_MOUSEWHEEL_SHIFT_TO_ROTATE = "In this display type, use mousewheel + Shift to rotate [or A and S]";
- static final String PHYLOXML_REF_TOOL_TIP = Constants.PHYLOXML_REFERENCE; //TODO //FIXME
- static final String APTX_REF_TOOL_TIP = Constants.APTX_REFERENCE;
- private static final long serialVersionUID = 3655000897845508358L;
- 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 = "Match Complete Terms Only";
- static final String SEARCH_CASE_SENSITIVE_LABEL = "Case Sensitive";
- static final String INVERSE_SEARCH_RESULT_LABEL = "Negate Result";
- static final String DISPLAY_BRANCH_LENGTH_VALUES_LABEL = "Branch Length Values";
- 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 Cladograms";
- static final String UNIFORM_CLADOGRAMS_LABEL = "Total Node Sum Dependent Cladograms";
- static final String LABEL_DIRECTION_LABEL = "Radial Labels";
- static final String LABEL_DIRECTION_TIP = "To use radial node labels in radial and unrooted display types";
- static final String SCREEN_ANTIALIAS_LABEL = "Antialias";
- static final String COLOR_LABELS_LABEL = "Colorize Labels Same as Parent Branch";
- static final String BG_GRAD_LABEL = "Background Color Gradient";
- static final String DISPLAY_NODE_BOXES_LABEL_EXT = "External Node Shapes";
- static final String DISPLAY_NODE_BOXES_LABEL_INT = "Internal Node Shapes";
- static final String SHOW_OVERVIEW_LABEL = "Overview";
- static final String FONT_SIZE_MENU_LABEL = "Font Size";
- static final String NONUNIFORM_CLADOGRAMS_LABEL = "External Node Sum Dependent Cladograms";
- static final String SHOW_DOMAIN_LABELS_LABEL = "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";
- 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 _save_item;
- JMenuItem _save_all_item;
- JMenuItem _close_item;
- JMenuItem _exit_item;
- JMenuItem _new_item;
- // tools menu:
- JMenuItem _midpoint_root_item;
- JMenuItem _taxcolor_item;
- JMenuItem _confcolor_item;
- JMenuItem _color_rank_jmi;
- JMenuItem _collapse_species_specific_subtrees;
- JMenuItem _collapse_below_threshold; //TODO implememt me
- 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;
- // 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 _uniform_cladograms_rbmi;
- JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi;
- JCheckBoxMenuItem _show_branch_length_values_cbmi;
- 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;
- JMenuItem _cycle_node_shape_mi;
- JMenuItem _cycle_node_fill_mi;
- JMenuItem _choose_node_size_mi;
- JCheckBoxMenuItem _show_confidence_stddev_cbmi;
- // _ print
- JCheckBoxMenuItem _graphics_export_visible_only_cbmi;
- JCheckBoxMenuItem _antialias_print_cbmi;
- JCheckBoxMenuItem _print_black_and_white_cbmi;
- JCheckBoxMenuItem _print_using_actual_size_cbmi;
- JCheckBoxMenuItem _graphics_export_using_actual_size_cbmi;
- JMenuItem _print_size_mi;
- JMenuItem _choose_pdf_width_mi;
- // _ parsing
- JCheckBoxMenuItem _internal_number_are_confidence_for_nh_parsing_cbmi;
- 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;
- // _ search
- JCheckBoxMenuItem _search_case_senstive_cbmi;
- JCheckBoxMenuItem _search_whole_words_only_cbmi;
- JCheckBoxMenuItem _inverse_search_result_cbmi;
- // type menu:
- JMenu _type_menu;
- JCheckBoxMenuItem _rectangular_type_cbmi;
- JCheckBoxMenuItem _triangular_type_cbmi;
- JCheckBoxMenuItem _curved_type_cbmi;
- JCheckBoxMenuItem _convex_type_cbmi;
- JCheckBoxMenuItem _euro_type_cbmi;
- JCheckBoxMenuItem _rounded_type_cbmi;
- JCheckBoxMenuItem _unrooted_type_cbmi;
- JCheckBoxMenuItem _circular_type_cbmi;
- // view as text menu:
- JMenuItem _view_as_NH_item;
- JMenuItem _view_as_XML_item;
- JMenuItem _view_as_nexus_item;
- JMenuItem _display_basic_information_item;
- // help menu:
- JMenuItem _about_item;
- JMenuItem _help_item;
- JMenuItem _website_item;
- JMenuItem _phyloxml_website_item;
- JMenuItem _phyloxml_ref_item;
- JMenuItem _aptx_ref_item;
- // process menu:
- JMenu _process_menu;
- // Handy pointers to child components:
- MainPanel _mainpanel;
- Container _contentpane;
- final LinkedList<TextFrame> _textframes = new LinkedList<TextFrame>(); ;
- Configuration _configuration;
- Options _options;
- private Phylogeny _species_tree;
- InferenceManager _inference_manager;
- final ProcessPool _process_pool;
- private String _previous_node_annotation_ref;
-
- MainFrame() {
- _process_pool = ProcessPool.createInstance();
- }
-
- /**
- * Action performed.
- */
- @Override
- public void actionPerformed( final ActionEvent e ) {
- final Object o = e.getSource();
- boolean is_applet = false;
- JApplet applet = null;
- if ( getCurrentTreePanel() != null ) {
- is_applet = getCurrentTreePanel().isApplet();
- if ( is_applet ) {
- applet = getCurrentTreePanel().obtainApplet();
- }
- }
- if ( o == _exit_item ) {
- close();
- }
- 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 == _annotate_item ) {
- annotateSequences();
- }
- else if ( o == _switch_colors_mi ) {
- switchColors();
- }
- else if ( o == _display_basic_information_item ) {
- 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(), this );
- }
- else if ( o == _overview_placment_mi ) {
- MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );
- }
- else if ( o == _cycle_node_fill_mi ) {
- MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() );
- }
- else if ( o == _cycle_node_shape_mi ) {
- MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() );
- }
- else if ( o == _screen_antialias_cbmi ) {
- updateOptions( getOptions() );
- updateScreenTextAntialias( getMainPanel().getTreePanels() );
- }
- else if ( o == _background_gradient_cbmi ) {
- updateOptions( getOptions() );
- }
- else if ( o == _show_domain_labels ) {
- updateOptions( getOptions() );
- }
- else if ( o == _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 == _non_lined_up_cladograms_rbmi ) {
- updateOptions( getOptions() );
- showWhole();
- }
- else if ( o == _uniform_cladograms_rbmi ) {
- updateOptions( getOptions() );
- showWhole();
- }
- else if ( o == _ext_node_dependent_cladogram_rbmi ) {
- updateOptions( getOptions() );
- showWhole();
- }
- else if ( o == _search_case_senstive_cbmi ) {
- updateOptions( getOptions() );
- getMainPanel().getControlPanel().search0();
- getMainPanel().getControlPanel().search1();
- }
- else if ( o == _search_whole_words_only_cbmi ) {
- 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 == _show_scale_cbmi ) {
- updateOptions( getOptions() );
- }
- else if ( o == _show_branch_length_values_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 == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )
- || ( o == _convex_type_cbmi ) || ( o == _euro_type_cbmi ) || ( o == _rounded_type_cbmi )
- || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {
- typeChanged( o );
- }
- else if ( o == _about_item ) {
- about();
- }
- else if ( o == _help_item ) {
- help();
- }
- else if ( o == _website_item ) {
- try {
- AptxUtil.openWebsite( Constants.APTX_WEB_SITE, is_applet, applet );
- }
- catch ( final IOException e1 ) {
- ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
- }
- }
- else if ( o == _phyloxml_website_item ) {
- try {
- AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, is_applet, applet );
- }
- catch ( final IOException e1 ) {
- ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
- }
- }
- else if ( o == _aptx_ref_item ) {
- try {
- AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, is_applet, applet );
- }
- catch ( final IOException e1 ) {
- ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
- }
- }
- else if ( o == _phyloxml_ref_item ) {
- try {
- AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, is_applet, applet );
- }
- catch ( final IOException e1 ) {
- ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
- }
- }
- else {
- if ( _load_phylogeny_from_webservice_menu_items != null ) {
- for( int i = 0; i < _load_phylogeny_from_webservice_menu_items.length; ++i ) {
- if ( o == _load_phylogeny_from_webservice_menu_items[ i ] ) {
- readPhylogeniesFromWebservice( i );
- }
- }
- }
- }
- _contentpane.repaint();
- }
-
- 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();
- }
- } );
- }
-
- void activateSaveAllIfNeeded() {
- if ( ( getMainPanel().getTabbedPane() != null ) && ( getMainPanel().getTabbedPane().getTabCount() > 1 ) ) {
- _save_all_item.setEnabled( true );
- }
- else {
- _save_all_item.setEnabled( false );
- }
- }
-
- void buildFileMenu() {
- _file_jmenu = createMenu( "File", getConfiguration() );
- _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );
- customizeJMenuItem( _exit_item );
- _jmenubar.add( _file_jmenu );
- }
-
- void buildFontSizeMenu() {
- _font_size_menu = createMenu( FONT_SIZE_MENU_LABEL, getConfiguration() );
- _font_size_menu.add( _super_tiny_fonts_item = new JMenuItem( "Super Tiny Fonts" ) );
- _font_size_menu.add( _tiny_fonts_item = new JMenuItem( "Tiny Fonts" ) );
- _font_size_menu.add( _small_fonts_item = new JMenuItem( "Small Fonts" ) );
- _font_size_menu.add( _medium_fonts_item = new JMenuItem( "Medium Fonts" ) );
- _font_size_menu.add( _large_fonts_item = new JMenuItem( "Large Fonts" ) );
- customizeJMenuItem( _super_tiny_fonts_item );
- customizeJMenuItem( _tiny_fonts_item );
- customizeJMenuItem( _small_fonts_item );
- customizeJMenuItem( _medium_fonts_item );
- customizeJMenuItem( _large_fonts_item );
- _jmenubar.add( _font_size_menu );
- }
-
- void buildHelpMenu() {
- _help_jmenu = createMenu( "Help", getConfiguration() );
- _help_jmenu.add( _help_item = new JMenuItem( "Help" ) );
- _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );
- _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" );
- _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );
- _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );
- _help_jmenu.addSeparator();
- _help_jmenu.add( _about_item = new JMenuItem( "About" ) );
- customizeJMenuItem( _help_item );
- customizeJMenuItem( _website_item );
- customizeJMenuItem( _phyloxml_website_item );
- customizeJMenuItem( _aptx_ref_item );
- customizeJMenuItem( _phyloxml_ref_item );
- customizeJMenuItem( _about_item );
- _phyloxml_ref_item.setToolTipText( PHYLOXML_REF_TOOL_TIP );
- _aptx_ref_item.setToolTipText( APTX_REF_TOOL_TIP );
- _jmenubar.add( _help_jmenu );
- }
-
- void buildTypeMenu() {
- _type_menu = createMenu( TYPE_MENU_HEADER, getConfiguration() );
- _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );
- _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );
- _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );
- _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );
- _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );
- _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );
- _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );
- _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );
- customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );
- customizeCheckBoxMenuItem( _triangular_type_cbmi, false );
- customizeCheckBoxMenuItem( _euro_type_cbmi, false );
- customizeCheckBoxMenuItem( _rounded_type_cbmi, false );
- customizeCheckBoxMenuItem( _curved_type_cbmi, false );
- customizeCheckBoxMenuItem( _convex_type_cbmi, false );
- customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );
- customizeCheckBoxMenuItem( _circular_type_cbmi, false );
- _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
- _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
- initializeTypeMenu( getOptions() );
- _jmenubar.add( _type_menu );
- }
-
- void buildViewMenu() {
- _view_jmenu = createMenu( "View", 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 close() {
- removeAllTextFrames();
- if ( _mainpanel != null ) {
- _mainpanel.terminate();
- }
- if ( _contentpane != null ) {
- _contentpane.removeAll();
- }
- setVisible( false );
- dispose();
- }
-
- void colorRank() {
- if ( _mainpanel.getCurrentTreePanel() != null ) {
- final String[] ranks = AptxUtil.getAllPossibleRanks();
- final String rank = ( String ) JOptionPane
- .showInputDialog( this,
- "What rank should the colorization be based on",
- "Rank Selection",
- JOptionPane.QUESTION_MESSAGE,
- null,
- ranks,
- null );
- if ( !ForesterUtil.isEmpty( rank ) ) {
- _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( this,
- ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
- "Error during File|Open",
- JOptionPane.ERROR_MESSAGE );
- }
-
- void exceptionOccuredDuringSaveAs( final Exception e ) {
- try {
- _mainpanel.getCurrentTreePanel().setArrowCursor();
- }
- catch ( final Exception ex ) {
- // Do nothing.
- }
- JOptionPane.showMessageDialog( this, "Exception" + e, "Error during File|SaveAs", JOptionPane.ERROR_MESSAGE );
- }
-
- void executeGSDI() {
- if ( !isOKforSDI( false, true ) ) {
- return;
- }
- if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
- JOptionPane.showMessageDialog( this,
- "Gene tree is not rooted.",
- "Cannot execute GSDI",
- JOptionPane.ERROR_MESSAGE );
- return;
- }
- final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
- gene_tree.setAllNodesToNotCollapse();
- gene_tree.recalculateNumberOfExternalDescendants( false );
- GSDI gsdi = null;
- final Phylogeny species_tree = getSpeciesTree().copy();
- try {
- gsdi = new GSDI( gene_tree, species_tree, false, true, true, true );
- }
- catch ( final SDIException e ) {
- JOptionPane.showMessageDialog( this,
- e.getLocalizedMessage(),
- "Error during GSDI",
- JOptionPane.ERROR_MESSAGE );
- return;
- }
- catch ( final Exception e ) {
- AptxUtil.unexpectedException( e );
- return;
- }
- gene_tree.setRerootable( false );
- gene_tree.clearHashIdToNodeMap();
- gene_tree.recalculateNumberOfExternalDescendants( true );
- _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null );
- getMainPanel().getControlPanel().setShowEvents( true );
- showWhole();
- final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
- _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
- showWhole();
- _mainpanel.getTabbedPane().setSelectedIndex( selected );
- showWhole();
- _mainpanel.getCurrentTreePanel().setEdited( true );
- final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
- if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) {
- JOptionPane.showMessageDialog( this,
- "Duplications: " + gsdi.getDuplicationsSum() + "\n"
- + "Potential duplications: "
- + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
- + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
- + "Stripped gene tree nodes: "
- + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
- + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
- + "Number of polytomies in species tree used: " + poly + "\n",
- "GSDI successfully completed",
- JOptionPane.WARNING_MESSAGE );
- }
- else {
- JOptionPane.showMessageDialog( this,
- "Duplications: " + gsdi.getDuplicationsSum() + "\n"
- + "Potential duplications: "
- + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
- + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
- + "Stripped gene tree nodes: "
- + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
- + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
- + "Number of polytomies in species tree used: " + poly + "\n",
- "GSDI successfully completed",
- JOptionPane.INFORMATION_MESSAGE );
- }
- }
-
- void executeGSDIR() {
- if ( !isOKforSDI( false, false ) ) {
- return;
- }
- final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() );
- if ( ( p > 0 )
- && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) {
- JOptionPane.showMessageDialog( this,
- "Gene tree is not completely binary",
- "Cannot execute GSDI",
- JOptionPane.ERROR_MESSAGE );
- return;
- }
- final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
- gene_tree.setAllNodesToNotCollapse();
- gene_tree.recalculateNumberOfExternalDescendants( false );
- GSDIR gsdir = null;
- final Phylogeny species_tree = getSpeciesTree().copy();
- try {
- gsdir = new GSDIR( gene_tree, species_tree, true, true, true );
- }
- catch ( final SDIException e ) {
- JOptionPane.showMessageDialog( this,
- e.getLocalizedMessage(),
- "Error during GSDIR",
- JOptionPane.ERROR_MESSAGE );
- return;
- }
- catch ( final Exception e ) {
- AptxUtil.unexpectedException( e );
- return;
- }
- final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree();
- result_gene_tree.setRerootable( false );
- result_gene_tree.clearHashIdToNodeMap();
- result_gene_tree.recalculateNumberOfExternalDescendants( true );
- PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );
- _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );
- getMainPanel().getControlPanel().setShowEvents( true );
- showWhole();
- final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
- _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
- showWhole();
- _mainpanel.getTabbedPane().setSelectedIndex( selected );
- showWhole();
- _mainpanel.getCurrentTreePanel().setEdited( true );
- final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
- if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) {
- JOptionPane.showMessageDialog( this,
- "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
- + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
- + "Stripped gene tree nodes: "
- + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
- + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
- + "Number of polytomies in species tree used: " + poly + "\n",
- "GSDIR successfully completed",
- JOptionPane.WARNING_MESSAGE );
- }
- else {
- JOptionPane.showMessageDialog( this,
- "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
- + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
- + "Stripped gene tree nodes: "
- + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
- + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
- + "Number of polytomies in species tree used: " + poly + "\n",
- "GSDIR successfully completed",
- JOptionPane.INFORMATION_MESSAGE );
- }
- }
-
- boolean GAndSDoHaveMoreThanOneSpeciesInComman( final Phylogeny gene_tree ) {
- if ( ( gene_tree == null ) || gene_tree.isEmpty() ) {
- JOptionPane.showMessageDialog( this,
- "Gene tree and species tree have no species in common.",
- "Error during SDI",
- JOptionPane.ERROR_MESSAGE );
- return false;
- }
- else if ( gene_tree.getNumberOfExternalNodes() < 2 ) {
- JOptionPane.showMessageDialog( this,
- "Gene tree and species tree have only one species in common.",
- "Error during SDI",
- JOptionPane.ERROR_MESSAGE );
- return false;
- }
- else {
- return true;
- }
- }
-
- 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 help() {
- final StringBuilder sb = new StringBuilder();
- sb.append( "Display options\n" );
- sb.append( "-------------------\n" );
- sb.append( "Use the checkboxes to select types of information to display on the tree.\n\n" );
- sb.append( "Clickable tree nodes\n" );
- sb.append( "--------------------\n" );
- sb.append( "Tree nodes can be clicked, the action is determined by the 'click on node to' menu\n" );
- sb.append( "or by right clicking:\n" );
- sb.append( "o Display Node Data -- display information for a node\n" );
- sb.append( "o Collapse/Uncollapse -- collapse and uncollapse subtree from clicked node\n" );
- sb.append( "o Root/Reroot -- change tree root to clicked node\n" );
- sb.append( "o Sub/Super Tree -- toggle between subtree from clicked node and whole tree\n" );
- sb.append( "o Swap Descendants -- switch descendant on either side of clicked node\n" );
- sb.append( "o Colorize Subtree -- color a subtree\n" );
- sb.append( "o Open Sequence Web -- launch a web browser to display sequence information\n" );
- sb.append( "o Open Taxonomy Web -- launch a web browser to display taxonomy information\n" );
- sb.append( "- there may be additional choices depending on this particular setup\n\n" );
- sb.append( "Right clicking on a node always displays the information of a node.\n\n" );
- sb.append( "Zooming\n" );
- sb.append( "---------\n" );
- sb.append( "The mouse wheel and the plus and minus keys control zooming.\n" );
- sb.append( "Mouse wheel+Ctrl changes the text size.\n" );
- sb.append( "Mouse wheel+Shift controls zooming in vertical direction only.\n" );
- sb.append( "Use the buttons on the control panel to zoom the tree in and out, horizontally or vertically.\n" );
- sb.append( "The entire tree can be fitted into the window by clicking the \"F\" button, or by pressing F, Delete, or Home.\n" );
- sb.append( "The up, down, left, and right keys can be used to move the visible part (if zoomed in).\n" );
- sb.append( "Up, down, left, and right+Shift can be used to control zooming horizontally and vertically.\n" );
- sb.append( "Plus and minus keys+Ctrl change the text size; F+Ctrl, Delete+Ctrl, or Home+Ctrl resets it.\n\n" );
- sb.append( "Quick tree manipulation:\n" );
- sb.append( "------------------------\n" );
- sb.append( "Order Subtrees -- order the tree by branch length\n" );
- sb.append( "Uncollapse All -- uncollapse any and all collapsed branches\n\n" );
- sb.append( "Memory problems (Java heap space error)\n" );
- sb.append( "---------------------------------------\n" );
- sb.append( "Since the Java default memory allocation is quite small, it might by necessary (for trees\n" );
- sb.append( "with more than approximately 5000 external nodes) to increase the memory which Java can use, with\n" );
- sb.append( "the '-Xmx' Java command line option. For example:\n" );
- sb.append( "java -Xmx1024m -cp path\\to\\forester.jar org.forester.archaeopteryx.Archaeopteryx\n\n" );
- // + "General remarks\n"
- // + "---------------\n"
- // +
- // "o The application version permits copying to the clipboard \n"
- // +
- // " in the \"View\"|\"View as ...\" frame (either by control-c or button press).\n"
- // +
- // "o Changes made to a subtree affect this subtree and its subtrees,\n"
- // + " but not any of its parent tree(s).\n"
- // +
- // "o Archaeopteryx tries to detect whether the numerical values in a NH tree\n"
- // +
- // " are likely to be bootstrap values instead of branch length values.\n\n"
- // +
- // " Remarks regarding SDI (Speciation Duplication Inference):\n"
- // +
- // "o Each external node of the gene tree (in display) needs to be associated with\n"
- // +
- // " a species: either directly through the \"Species\" field, or the species\n"
- // +
- // " is part of the sequence name in the form \"XXXX_SPECIES\"\n"
- // +
- // " (e.g. \"ACON_DROME\" or \"ACON_DROME/123-4489\" which is also acceptable).\n"
- // +
- // "o A species tree for each species of the gene tree needs to be loaded with\n"
- // +
- // " \"SDI\"|\"Load species tree\" prior the SDI execution.\n"
- // +
- // "o !External nodes of the gene tree associated with species not present in\n"
- // +
- // " the species tree are REMOVED prior to SDI execution!\n"
- // +
- // "o Both the gene tree and the species tree must be completely binary.\n"
- // +
- // "o Duplications and speciations are a function of the position of the root.\n"
- // +
- // " Hence, after each manual \"Root/Reroot\"ing some duplications will be\n"
- // + " incorrect and need to be inferred again\n"
- // +
- // " with: \"SDI\"|\"SDI (Speciation Duplication Inference)\n\n"
- sb.append( "phyloXML\n" );
- sb.append( "-------------------\n" );
- sb.append( "Reference: " + Constants.PHYLOXML_REFERENCE + "\n" );
- sb.append( "Website: " + Constants.PHYLOXML_WEB_SITE + "\n" );
- sb.append( "Version: " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
- sb.append( "\n" );
- sb.append( "For more information: https://sites.google.com/site/cmzmasek/home/software/archaeopteryx\n" );
- sb.append( "Email: " + Constants.AUTHOR_EMAIL + "\n\n" );
- TextFrame.instantiate( sb.toString(), "Help", _textframes );
- }
-
- 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( this,
- "No species tree loaded",
- "Cannot execute GSDI",
- JOptionPane.ERROR_MESSAGE );
- return false;
- }
- else if ( species_tree_has_to_binary && !getSpeciesTree().isCompletelyBinary() ) {
- JOptionPane.showMessageDialog( this,
- "Species tree is not completely binary",
- "Cannot execute GSDI",
- JOptionPane.ERROR_MESSAGE );
- return false;
- }
- else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {
- JOptionPane.showMessageDialog( this,
- "Gene tree is not completely binary",
- "Cannot execute GSDI",
- JOptionPane.ERROR_MESSAGE );
- return false;
- }
- else {
- return true;
- }
- }
-
- boolean isSubtreeDisplayed() {
- if ( getCurrentTreePanel() != null ) {
- if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {
- JOptionPane
- .showMessageDialog( this,
- "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",
- "Operation can not be exectuted on a sub-tree",
- JOptionPane.WARNING_MESSAGE );
- return true;
- }
- }
- return false;
- }
-
- void 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 setConfiguration( final Configuration configuration ) {
- _configuration = configuration;
- }
-
- 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() );
- if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
- options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
- }
- else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {
- options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
- }
- else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {
- options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
- }
- options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )
- && _search_case_senstive_cbmi.isSelected() );
- if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {
- options.setShowScale( _show_scale_cbmi.isSelected() );
- }
- if ( _label_direction_cbmi != null ) {
- if ( _label_direction_cbmi.isSelected() ) {
- options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
- }
- else {
- options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
- }
- }
- options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
- options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )
- && _show_confidence_stddev_cbmi.isSelected() );
- if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) {
- options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() );
- }
- if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) {
- options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() );
- }
- options.setPrintUsingActualSize( ( _print_using_actual_size_cbmi != null )
- && ( _print_using_actual_size_cbmi.isSelected() ) );
- options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null )
- && ( _graphics_export_using_actual_size_cbmi.isSelected() ) );
- options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() );
- 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.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
- && _inverse_search_result_cbmi.isSelected() );
- if ( _graphics_export_visible_only_cbmi != null ) {
- options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_cbmi.isSelected() );
- if ( _graphics_export_visible_only_cbmi.isSelected() && ( _graphics_export_using_actual_size_cbmi != null ) ) {
- _graphics_export_using_actual_size_cbmi.setSelected( true );
- _graphics_export_using_actual_size_cbmi.setEnabled( false );
- }
- else {
- _graphics_export_using_actual_size_cbmi.setEnabled( true );
- }
- }
- if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {
- options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
- }
- else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {
- options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
- }
- else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {
- options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
- }
- else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {
- options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
- }
- else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {
- options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
- }
- else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {
- options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
- }
- else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {
- options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
- }
- else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {
- options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
- }
- }
-
- void updateTypeCheckboxes( final Options options, final Object o ) {
- setTypeMenuToAllUnselected();
- ( ( JCheckBoxMenuItem ) o ).setSelected( true );
- }
-
- void viewAsNexus() {
- 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 void annotateSequences() {
- if ( getCurrentTreePanel() != null ) {
- final Set<Long> nodes = getCurrentTreePanel().getFoundNodes0();
- if ( ( nodes == null ) || nodes.isEmpty() ) {
- JOptionPane
- .showMessageDialog( this,
- "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( this,
- "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 Long id : nodes ) {
- final PhylogenyNode n = phy.getNode( id );
- 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( this, "Select the Base Font" );
- getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );
- }
-
- private void chooseMinimalConfidence() {
- final String s = ( String ) JOptionPane
- .showInputDialog( this,
- "Please enter the minimum for confidence values to be displayed.\n"
- + "[current value: " + getOptions().getMinConfidenceValue() + "]\n",
- "Minimal Confidence Value",
- JOptionPane.QUESTION_MESSAGE,
- null,
- null,
- getOptions().getMinConfidenceValue() );
- if ( !ForesterUtil.isEmpty( s ) ) {
- boolean success = true;
- double m = 0.0;
- final String m_str = s.trim();
- if ( !ForesterUtil.isEmpty( m_str ) ) {
- try {
- m = Double.parseDouble( m_str );
- }
- catch ( final Exception ex ) {
- success = false;
- }
- }
- else {
- success = false;
- }
- if ( success && ( m >= 0.0 ) ) {
- getOptions().setMinConfidenceValue( m );
- }
- }
- }
-
- 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;
- }
-
- /**
- * Display the about box.
- */
- static void about() {
- final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + Constants.VERSION + "\n" );
- about.append( "Copyright (C) 2013 Christian M. Zmasek\n" );
- about.append( "All Rights Reserved\n" );
- about.append( "License: GNU Lesser General Public License (LGPL)\n" );
- about.append( "Last modified: " + Constants.PRG_DATE + "\n" );
- about.append( "Based on: " + ForesterUtil.getForesterLibraryInformation() + "\n" );
- about.append( "phyloXML version : " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
- about.append( "phyloXML location: " + ForesterConstants.PHYLO_XML_LOCATION + "\n" );
- if ( !ForesterUtil.isEmpty( ForesterUtil.JAVA_VERSION ) && !ForesterUtil.isEmpty( ForesterUtil.JAVA_VENDOR ) ) {
- about.append( "[your Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]\n" );
- }
- if ( !ForesterUtil.isEmpty( ForesterUtil.OS_NAME ) && !ForesterUtil.isEmpty( ForesterUtil.OS_ARCH )
- && !ForesterUtil.isEmpty( ForesterUtil.OS_VERSION ) ) {
- about.append( "[your OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " "
- + ForesterUtil.OS_VERSION + "]\n" );
- }
- final Runtime rt = java.lang.Runtime.getRuntime();
- final long free_memory = rt.freeMemory() / 1000000;
- final long total_memory = rt.totalMemory() / 1000000;
- about.append( "[free memory: " + free_memory + "MB, total memory: " + total_memory + "MB]\n" );
- about.append( "[locale: " + Locale.getDefault() + "]\n" );
- about.append( "References:\n" );
- about.append( Constants.PHYLOXML_REFERENCE_SHORT + "\n" );
- about.append( "For more information & download:\n" );
- about.append( Constants.APTX_WEB_SITE + "\n" );
- about.append( "Comments: " + Constants.AUTHOR_EMAIL );
- JOptionPane.showMessageDialog( null, about, Constants.PRG_NAME, JOptionPane.PLAIN_MESSAGE );
- }
-
- static 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, final TreePanel tree_panel ) {
- 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, final TreePanel tree_panel ) {
- 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 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 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 updateOptionsMenuDependingOnPhylogenyType( final MainPanel main_panel,
- final JCheckBoxMenuItem scale,
- final JCheckBoxMenuItem branch_lengths,
- final JRadioButtonMenuItem non_lined_up,
- final JRadioButtonMenuItem uniform_clado,
- final JRadioButtonMenuItem nonuniform_clado,
- final JCheckBoxMenuItem label_direction_cbmi ) {
- final TreePanel tree_panel = main_panel.getCurrentTreePanel();
- final ControlPanel control = main_panel.getControlPanel();
- final Options options = main_panel.getOptions();
- scale.setSelected( options.isShowScale() );
- branch_lengths.setSelected( options.isShowBranchLengthValues() );
- // non_lined_up.setSelected( options.isNonLinedUpCladogram() );
- if ( ( tree_panel != null ) && ( !tree_panel.isPhyHasBranchLengths() ) ) {
- scale.setSelected( false );
- scale.setEnabled( false );
- branch_lengths.setSelected( false );
- branch_lengths.setEnabled( false );
- }
- else if ( ( tree_panel != null ) && !control.isDrawPhylogram() ) {
- scale.setSelected( false );
- scale.setEnabled( false );
- branch_lengths.setEnabled( true );
- }
- else {
- scale.setEnabled( true );
- branch_lengths.setEnabled( true );
- }
- if ( ( tree_panel != null )
- && ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.ROUNDED )
- && ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) && ( tree_panel
- .getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) ) ) {
- branch_lengths.setSelected( false );
- branch_lengths.setEnabled( false );
- }
- if ( tree_panel != null ) {
- if ( ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR )
- || ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) {
- non_lined_up.setEnabled( false );
- uniform_clado.setEnabled( false );
- nonuniform_clado.setEnabled( false );
- }
- else {
- non_lined_up.setEnabled( true );
- uniform_clado.setEnabled( true );
- nonuniform_clado.setEnabled( true );
- }
- }
- else {
- if ( ( tree_panel != null )
- && ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) && ( tree_panel
- .getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) ) ) {
- branch_lengths.setSelected( false );
- branch_lengths.setEnabled( false );
- }
- if ( ( tree_panel != null )
- && ( ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) || ( tree_panel
- .getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) ) {
- non_lined_up.setEnabled( false );
- }
- else {
- // non_lined_up.setSelected( options.isNonLinedUpCladogram() );
- non_lined_up.setEnabled( true );
- }
- }
- label_direction_cbmi.setEnabled( true );
- if ( tree_panel != null ) {
- if ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
- && ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
- label_direction_cbmi.setEnabled( false );
- }
- if ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
- scale.setSelected( false );
- scale.setEnabled( false );
- }
- }
- }
-
- static void updateScreenTextAntialias( final List<TreePanel> treepanels ) {
- for( final TreePanel tree_panel : treepanels ) {
- tree_panel.setTextAntialias();
- }
- }
-}
+// $Id:\r
+// FORESTER -- software libraries and applications\r
+// for evolutionary biology research and applications.\r
+//\r
+// Copyright (C) 2008-2010 Christian M. Zmasek\r
+// All rights reserved\r
+//\r
+// This library is free software; you can redistribute it and/or\r
+// modify it under the terms of the GNU Lesser General Public\r
+// License as published by the Free Software Foundation; either\r
+// version 2.1 of the License, or (at your option) any later version.\r
+//\r
+// This library is distributed in the hope that it will be useful,\r
+// but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU\r
+// Lesser General Public License for more details.\r
+//\r
+// You should have received a copy of the GNU Lesser General Public\r
+// License along with this library; if not, write to the Free Software\r
+// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+//\r
+// Contact: phylosoft @ gmail . com\r
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester\r
+\r
+package org.forester.archaeopteryx;\r
+\r
+import java.awt.Color;\r
+import java.awt.Component;\r
+import java.awt.Container;\r
+import java.awt.Font;\r
+import java.awt.event.ActionEvent;\r
+import java.awt.event.ActionListener;\r
+import java.io.File;\r
+import java.io.IOException;\r
+import java.util.LinkedList;\r
+import java.util.List;\r
+import java.util.Locale;\r
+import java.util.NoSuchElementException;\r
+import java.util.Set;\r
+\r
+import javax.swing.Box;\r
+import javax.swing.JApplet;\r
+import javax.swing.JCheckBoxMenuItem;\r
+import javax.swing.JFrame;\r
+import javax.swing.JLabel;\r
+import javax.swing.JMenu;\r
+import javax.swing.JMenuBar;\r
+import javax.swing.JMenuItem;\r
+import javax.swing.JOptionPane;\r
+import javax.swing.JPanel;\r
+import javax.swing.JRadioButtonMenuItem;\r
+import javax.swing.JTextField;\r
+import javax.swing.SwingUtilities;\r
+\r
+import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;\r
+import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;\r
+import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;\r
+import org.forester.archaeopteryx.tools.InferenceManager;\r
+import org.forester.archaeopteryx.tools.ProcessPool;\r
+import org.forester.archaeopteryx.tools.ProcessRunning;\r
+import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;\r
+import org.forester.phylogeny.Phylogeny;\r
+import org.forester.phylogeny.PhylogenyMethods;\r
+import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;\r
+import org.forester.phylogeny.PhylogenyNode;\r
+import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;\r
+import org.forester.phylogeny.data.Annotation;\r
+import org.forester.phylogeny.data.NodeVisualData.NodeFill;\r
+import org.forester.phylogeny.data.NodeVisualData.NodeShape;\r
+import org.forester.sdi.GSDI;\r
+import org.forester.sdi.GSDIR;\r
+import org.forester.sdi.SDIException;\r
+import org.forester.util.ForesterConstants;\r
+import org.forester.util.ForesterUtil;\r
+\r
+public abstract class MainFrame extends JFrame implements ActionListener {\r
+\r
+ static final String USE_MOUSEWHEEL_SHIFT_TO_ROTATE = "In this display type, use mousewheel + Shift to rotate [or A and S]";\r
+ static final String PHYLOXML_REF_TOOL_TIP = Constants.PHYLOXML_REFERENCE; //TODO //FIXME\r
+ static final String APTX_REF_TOOL_TIP = Constants.APTX_REFERENCE;\r
+ private static final long serialVersionUID = 3655000897845508358L;\r
+ final static Font menu_font = new Font( Configuration.getDefaultFontFamilyName(),\r
+ Font.PLAIN,\r
+ 10 );\r
+ static final String TYPE_MENU_HEADER = "Type";\r
+ static final String RECTANGULAR_TYPE_CBMI_LABEL = "Rectangular";\r
+ static final String EURO_TYPE_CBMI_LABEL = "Euro Type";\r
+ static final String CURVED_TYPE_CBMI_LABEL = "Curved";\r
+ static final String TRIANGULAR_TYPE_CBMI_LABEL = "Triangular";\r
+ static final String CONVEX_TYPE_CBMI_LABEL = "Convex";\r
+ static final String ROUNDED_TYPE_CBMI_LABEL = "Rounded";\r
+ static final String UNROOTED_TYPE_CBMI_LABEL = "Unrooted (alpha)"; //TODO\r
+ static final String CIRCULAR_TYPE_CBMI_LABEL = "Circular (alpha)"; //TODO\r
+ static final String OPTIONS_HEADER = "Options";\r
+ static final String SEARCH_SUBHEADER = "Search:";\r
+ static final String DISPLAY_SUBHEADER = "Display:";\r
+ static final String SEARCH_TERMS_ONLY_LABEL = "Match Complete Terms Only";\r
+ static final String SEARCH_CASE_SENSITIVE_LABEL = "Case Sensitive";\r
+ static final String INVERSE_SEARCH_RESULT_LABEL = "Negate Result";\r
+ static final String DISPLAY_BRANCH_LENGTH_VALUES_LABEL = "Branch Length Values";\r
+ static final String COLOR_BY_TAXONOMIC_GROUP = "Colorize by Taxonomic Group";\r
+ static final String DISPLAY_SCALE_LABEL = "Scale";\r
+ static final String NON_LINED_UP_CLADOGRAMS_LABEL = "Non-Lined Up Cladograms";\r
+ static final String UNIFORM_CLADOGRAMS_LABEL = "Total Node Sum Dependent Cladograms";\r
+ static final String LABEL_DIRECTION_LABEL = "Radial Labels";\r
+ static final String LABEL_DIRECTION_TIP = "To use radial node labels in radial and unrooted display types";\r
+ static final String SCREEN_ANTIALIAS_LABEL = "Antialias";\r
+ static final String COLOR_LABELS_LABEL = "Colorize Labels Same as Parent Branch";\r
+ static final String BG_GRAD_LABEL = "Background Color Gradient";\r
+ static final String DISPLAY_NODE_BOXES_LABEL_EXT = "External Node Shapes";\r
+ static final String DISPLAY_NODE_BOXES_LABEL_INT = "Internal Node Shapes";\r
+ static final String SHOW_OVERVIEW_LABEL = "Overview";\r
+ static final String FONT_SIZE_MENU_LABEL = "Font Size";\r
+ static final String NONUNIFORM_CLADOGRAMS_LABEL = "External Node Sum Dependent Cladograms";\r
+ static final String SHOW_DOMAIN_LABELS_LABEL = "Domain Labels";\r
+ static final String SHOW_ANN_REF_SOURCE_LABEL = "Seq Annotation Ref Sources";\r
+ 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";\r
+ static final String ABBREV_SN_LABEL = "Abbreviate Scientific Taxonomic Names";\r
+ static final String TAXONOMY_COLORIZE_NODE_SHAPES_LABEL = "Colorize Node Shapes According to Taxonomy";\r
+ static final String CYCLE_NODE_SHAPE_LABEL = "Cycle Node Shapes";\r
+ static final String CYCLE_NODE_FILL_LABEL = "Cycle Node Fill Type";\r
+ static final String CHOOSE_NODE_SIZE_LABEL = "Choose Node Shape Size";\r
+ static final String SHOW_CONF_STDDEV_LABEL = "Confidence Standard Deviations";\r
+ static final String USE_BRACKETS_FOR_CONF_IN_NH_LABEL = "Use Brackets for Confidence Values";\r
+ static final String USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL = "Use Internal Node Names for Confidence Values";\r
+ static final String SHOW_BASIC_TREE_INFORMATION_LABEL = "Basic Tree Information";\r
+ JMenuBar _jmenubar;\r
+ JMenu _file_jmenu;\r
+ JMenu _tools_menu;\r
+ JMenu _view_jmenu;\r
+ JMenu _options_jmenu;\r
+ JMenu _font_size_menu;\r
+ JMenu _help_jmenu;\r
+ JMenuItem[] _load_phylogeny_from_webservice_menu_items;\r
+ // Analysis menu\r
+ JMenu _analysis_menu;\r
+ JMenuItem _load_species_tree_item;\r
+ JMenuItem _gsdi_item;\r
+ JMenuItem _gsdir_item;\r
+ JMenuItem _lineage_inference;\r
+ // file menu:\r
+ JMenuItem _open_item;\r
+ JMenuItem _open_url_item;\r
+ JMenuItem _save_item;\r
+ JMenuItem _save_all_item;\r
+ JMenuItem _close_item;\r
+ JMenuItem _exit_item;\r
+ JMenuItem _new_item;\r
+ // tools menu:\r
+ JMenuItem _midpoint_root_item;\r
+ JMenuItem _taxcolor_item;\r
+ JMenuItem _confcolor_item;\r
+ JMenuItem _color_rank_jmi;\r
+ JMenuItem _collapse_species_specific_subtrees;\r
+ JMenuItem _collapse_below_threshold; //TODO implememt me\r
+ JMenuItem _obtain_detailed_taxonomic_information_jmi;\r
+ JMenuItem _obtain_detailed_taxonomic_information_deleting_jmi;\r
+ JMenuItem _obtain_seq_information_jmi;\r
+ JMenuItem _move_node_names_to_tax_sn_jmi;\r
+ JMenuItem _move_node_names_to_seq_names_jmi;\r
+ JMenuItem _extract_tax_code_from_node_names_jmi;\r
+ JMenuItem _annotate_item;\r
+ JMenuItem _remove_branch_color_item;\r
+ JMenuItem _remove_visual_styles_item;\r
+ // font size menu:\r
+ JMenuItem _super_tiny_fonts_item;\r
+ JMenuItem _tiny_fonts_item;\r
+ JMenuItem _small_fonts_item;\r
+ JMenuItem _medium_fonts_item;\r
+ JMenuItem _large_fonts_item;\r
+ // options menu:\r
+ // _ screen and print\r
+ JMenuItem _choose_font_mi;\r
+ JMenuItem _switch_colors_mi;\r
+ JCheckBoxMenuItem _label_direction_cbmi;\r
+ // _ screen display\r
+ JCheckBoxMenuItem _screen_antialias_cbmi;\r
+ JCheckBoxMenuItem _background_gradient_cbmi;\r
+ JRadioButtonMenuItem _non_lined_up_cladograms_rbmi;\r
+ JRadioButtonMenuItem _uniform_cladograms_rbmi;\r
+ JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi;\r
+ JCheckBoxMenuItem _show_branch_length_values_cbmi;\r
+ JCheckBoxMenuItem _color_by_taxonomic_group_cbmi;\r
+ JCheckBoxMenuItem _show_scale_cbmi; //TODO fix me\r
+ JCheckBoxMenuItem _show_overview_cbmi;\r
+ JCheckBoxMenuItem _show_domain_labels;\r
+ JCheckBoxMenuItem _show_annotation_ref_source;\r
+ JCheckBoxMenuItem _abbreviate_scientific_names;\r
+ JCheckBoxMenuItem _color_labels_same_as_parent_branch;\r
+ JMenuItem _overview_placment_mi;\r
+ JMenuItem _choose_minimal_confidence_mi;\r
+ JCheckBoxMenuItem _show_default_node_shapes_internal_cbmi;\r
+ JCheckBoxMenuItem _show_default_node_shapes_external_cbmi;\r
+ JMenuItem _cycle_node_shape_mi;\r
+ JMenuItem _cycle_node_fill_mi;\r
+ JMenuItem _choose_node_size_mi;\r
+ JCheckBoxMenuItem _show_confidence_stddev_cbmi;\r
+ // _ print\r
+ JCheckBoxMenuItem _graphics_export_visible_only_cbmi;\r
+ JCheckBoxMenuItem _antialias_print_cbmi;\r
+ JCheckBoxMenuItem _print_black_and_white_cbmi;\r
+ JCheckBoxMenuItem _print_using_actual_size_cbmi;\r
+ JCheckBoxMenuItem _graphics_export_using_actual_size_cbmi;\r
+ JMenuItem _print_size_mi;\r
+ JMenuItem _choose_pdf_width_mi;\r
+ // _ parsing\r
+ JCheckBoxMenuItem _internal_number_are_confidence_for_nh_parsing_cbmi;\r
+ JRadioButtonMenuItem _extract_taxonomy_no_rbmi;\r
+ JRadioButtonMenuItem _extract_taxonomy_agressive_rbmi;\r
+ JRadioButtonMenuItem _extract_taxonomy_pfam_strict_rbmi;\r
+ JRadioButtonMenuItem _extract_taxonomy_pfam_relaxed_rbmi;\r
+ JCheckBoxMenuItem _replace_underscores_cbmi;\r
+ JCheckBoxMenuItem _allow_errors_in_distance_to_parent_cbmi;\r
+ JCheckBoxMenuItem _use_brackets_for_conf_in_nh_export_cbmi;\r
+ JCheckBoxMenuItem _use_internal_names_for_conf_in_nh_export_cbmi;\r
+ // _ search\r
+ JCheckBoxMenuItem _search_case_senstive_cbmi;\r
+ JCheckBoxMenuItem _search_whole_words_only_cbmi;\r
+ JCheckBoxMenuItem _inverse_search_result_cbmi;\r
+ // type menu:\r
+ JMenu _type_menu;\r
+ JCheckBoxMenuItem _rectangular_type_cbmi;\r
+ JCheckBoxMenuItem _triangular_type_cbmi;\r
+ JCheckBoxMenuItem _curved_type_cbmi;\r
+ JCheckBoxMenuItem _convex_type_cbmi;\r
+ JCheckBoxMenuItem _euro_type_cbmi;\r
+ JCheckBoxMenuItem _rounded_type_cbmi;\r
+ JCheckBoxMenuItem _unrooted_type_cbmi;\r
+ JCheckBoxMenuItem _circular_type_cbmi;\r
+ // view as text menu:\r
+ JMenuItem _view_as_NH_item;\r
+ JMenuItem _view_as_XML_item;\r
+ JMenuItem _view_as_nexus_item;\r
+ JMenuItem _display_basic_information_item;\r
+ // help menu:\r
+ JMenuItem _about_item;\r
+ JMenuItem _help_item;\r
+ JMenuItem _website_item;\r
+ JMenuItem _phyloxml_website_item;\r
+ JMenuItem _phyloxml_ref_item;\r
+ JMenuItem _aptx_ref_item;\r
+ // process menu:\r
+ JMenu _process_menu;\r
+ // Handy pointers to child components:\r
+ MainPanel _mainpanel;\r
+ Container _contentpane;\r
+ final LinkedList<TextFrame> _textframes = new LinkedList<TextFrame>(); ;\r
+ Configuration _configuration;\r
+ Options _options;\r
+ private Phylogeny _species_tree;\r
+ InferenceManager _inference_manager;\r
+ final ProcessPool _process_pool;\r
+ private String _previous_node_annotation_ref;\r
+\r
+ MainFrame() {\r
+ _process_pool = ProcessPool.createInstance();\r
+ }\r
+\r
+ /**\r
+ * Action performed.\r
+ */\r
+ @Override\r
+ public void actionPerformed( final ActionEvent e ) {\r
+ final Object o = e.getSource();\r
+ boolean is_applet = false;\r
+ JApplet applet = null;\r
+ if ( getCurrentTreePanel() != null ) {\r
+ is_applet = getCurrentTreePanel().isApplet();\r
+ if ( is_applet ) {\r
+ applet = getCurrentTreePanel().obtainApplet();\r
+ }\r
+ }\r
+ if ( o == _exit_item ) {\r
+ close();\r
+ }\r
+ else if ( o == _gsdi_item ) {\r
+ if ( isSubtreeDisplayed() ) {\r
+ return;\r
+ }\r
+ executeGSDI();\r
+ }\r
+ else if ( o == _gsdir_item ) {\r
+ if ( isSubtreeDisplayed() ) {\r
+ return;\r
+ }\r
+ executeGSDIR();\r
+ }\r
+ else if ( o == _taxcolor_item ) {\r
+ taxColor();\r
+ }\r
+ else if ( o == _confcolor_item ) {\r
+ confColor();\r
+ }\r
+ else if ( o == _color_rank_jmi ) {\r
+ colorRank();\r
+ }\r
+ else if ( o == _collapse_species_specific_subtrees ) {\r
+ if ( isSubtreeDisplayed() ) {\r
+ return;\r
+ }\r
+ if ( getCurrentTreePanel() != null ) {\r
+ getCurrentTreePanel().collapseSpeciesSpecificSubtrees();\r
+ }\r
+ }\r
+ else if ( o == _remove_branch_color_item ) {\r
+ if ( isSubtreeDisplayed() ) {\r
+ return;\r
+ }\r
+ removeBranchColors();\r
+ }\r
+ else if ( o == _remove_visual_styles_item ) {\r
+ if ( isSubtreeDisplayed() ) {\r
+ return;\r
+ }\r
+ removeVisualStyles();\r
+ }\r
+ else if ( o == _midpoint_root_item ) {\r
+ if ( isSubtreeDisplayed() ) {\r
+ return;\r
+ }\r
+ midpointRoot();\r
+ }\r
+ else if ( o == _annotate_item ) {\r
+ annotateSequences();\r
+ }\r
+ else if ( o == _switch_colors_mi ) {\r
+ switchColors();\r
+ }\r
+ else if ( o == _display_basic_information_item ) {\r
+ displayBasicInformation( getCurrentTreePanel().getTreeFile() );\r
+ }\r
+ else if ( o == _view_as_NH_item ) {\r
+ viewAsNH();\r
+ }\r
+ else if ( o == _view_as_XML_item ) {\r
+ viewAsXML();\r
+ }\r
+ else if ( o == _view_as_nexus_item ) {\r
+ viewAsNexus();\r
+ }\r
+ else if ( o == _super_tiny_fonts_item ) {\r
+ if ( getCurrentTreePanel() != null ) {\r
+ getCurrentTreePanel().setSuperTinyFonts();\r
+ getCurrentTreePanel().repaint();\r
+ }\r
+ }\r
+ else if ( o == _tiny_fonts_item ) {\r
+ if ( getCurrentTreePanel() != null ) {\r
+ getCurrentTreePanel().setTinyFonts();\r
+ getCurrentTreePanel().repaint();\r
+ }\r
+ }\r
+ else if ( o == _small_fonts_item ) {\r
+ if ( getCurrentTreePanel() != null ) {\r
+ getCurrentTreePanel().setSmallFonts();\r
+ getCurrentTreePanel().repaint();\r
+ }\r
+ }\r
+ else if ( o == _medium_fonts_item ) {\r
+ if ( getCurrentTreePanel() != null ) {\r
+ getCurrentTreePanel().setMediumFonts();\r
+ getCurrentTreePanel().repaint();\r
+ }\r
+ }\r
+ else if ( o == _large_fonts_item ) {\r
+ if ( getCurrentTreePanel() != null ) {\r
+ getCurrentTreePanel().setLargeFonts();\r
+ getCurrentTreePanel().repaint();\r
+ }\r
+ }\r
+ else if ( o == _choose_font_mi ) {\r
+ chooseFont();\r
+ }\r
+ else if ( o == _choose_minimal_confidence_mi ) {\r
+ chooseMinimalConfidence();\r
+ }\r
+ else if ( o == _choose_node_size_mi ) {\r
+ chooseNodeSize( getOptions(), this );\r
+ }\r
+ else if ( o == _overview_placment_mi ) {\r
+ MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );\r
+ }\r
+ else if ( o == _cycle_node_fill_mi ) {\r
+ MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() );\r
+ }\r
+ else if ( o == _cycle_node_shape_mi ) {\r
+ MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() );\r
+ }\r
+ else if ( o == _screen_antialias_cbmi ) {\r
+ updateOptions( getOptions() );\r
+ updateScreenTextAntialias( getMainPanel().getTreePanels() );\r
+ }\r
+ else if ( o == _background_gradient_cbmi ) {\r
+ updateOptions( getOptions() );\r
+ }\r
+ else if ( o == _show_domain_labels ) {\r
+ updateOptions( getOptions() );\r
+ }\r
+ else if ( o == _show_annotation_ref_source ) {\r
+ updateOptions( getOptions() );\r
+ }\r
+ else if ( o == _abbreviate_scientific_names ) {\r
+ updateOptions( getOptions() );\r
+ }\r
+ else if ( o == _color_labels_same_as_parent_branch ) {\r
+ updateOptions( getOptions() );\r
+ }\r
+ else if ( o == _show_default_node_shapes_internal_cbmi ) {\r
+ updateOptions( getOptions() );\r
+ }\r
+ else if ( o == _show_default_node_shapes_external_cbmi ) {\r
+ updateOptions( getOptions() );\r
+ }\r
+ else if ( o == _non_lined_up_cladograms_rbmi ) {\r
+ updateOptions( getOptions() );\r
+ showWhole();\r
+ }\r
+ else if ( o == _uniform_cladograms_rbmi ) {\r
+ updateOptions( getOptions() );\r
+ showWhole();\r
+ }\r
+ else if ( o == _ext_node_dependent_cladogram_rbmi ) {\r
+ updateOptions( getOptions() );\r
+ showWhole();\r
+ }\r
+ else if ( o == _search_case_senstive_cbmi ) {\r
+ updateOptions( getOptions() );\r
+ getMainPanel().getControlPanel().search0();\r
+ getMainPanel().getControlPanel().search1();\r
+ }\r
+ else if ( o == _search_whole_words_only_cbmi ) {\r
+ updateOptions( getOptions() );\r
+ getMainPanel().getControlPanel().search0();\r
+ getMainPanel().getControlPanel().search1();\r
+ }\r
+ else if ( o == _inverse_search_result_cbmi ) {\r
+ updateOptions( getOptions() );\r
+ getMainPanel().getControlPanel().search0();\r
+ getMainPanel().getControlPanel().search1();\r
+ }\r
+ else if ( o == _show_scale_cbmi ) {\r
+ updateOptions( getOptions() );\r
+ }\r
+ else if ( o == _show_branch_length_values_cbmi ) {\r
+ updateOptions( getOptions() );\r
+ }\r
+ else if ( o == _color_by_taxonomic_group_cbmi ) {\r
+ updateOptions( getOptions() );\r
+ }\r
+ else if ( o == _show_confidence_stddev_cbmi ) {\r
+ updateOptions( getOptions() );\r
+ }\r
+ else if ( o == _use_brackets_for_conf_in_nh_export_cbmi ) {\r
+ if ( _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {\r
+ _use_internal_names_for_conf_in_nh_export_cbmi.setSelected( false );\r
+ }\r
+ updateOptions( getOptions() );\r
+ }\r
+ else if ( o == _use_internal_names_for_conf_in_nh_export_cbmi ) {\r
+ if ( _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {\r
+ _use_brackets_for_conf_in_nh_export_cbmi.setSelected( false );\r
+ }\r
+ updateOptions( getOptions() );\r
+ }\r
+ else if ( o == _label_direction_cbmi ) {\r
+ updateOptions( getOptions() );\r
+ }\r
+ else if ( o == _show_overview_cbmi ) {\r
+ updateOptions( getOptions() );\r
+ if ( getCurrentTreePanel() != null ) {\r
+ getCurrentTreePanel().updateOvSizes();\r
+ }\r
+ }\r
+ else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )\r
+ || ( o == _convex_type_cbmi ) || ( o == _euro_type_cbmi ) || ( o == _rounded_type_cbmi )\r
+ || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {\r
+ typeChanged( o );\r
+ }\r
+ else if ( o == _about_item ) {\r
+ about();\r
+ }\r
+ else if ( o == _help_item ) {\r
+ help();\r
+ }\r
+ else if ( o == _website_item ) {\r
+ try {\r
+ AptxUtil.openWebsite( Constants.APTX_WEB_SITE, is_applet, applet );\r
+ }\r
+ catch ( final IOException e1 ) {\r
+ ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
+ }\r
+ }\r
+ else if ( o == _phyloxml_website_item ) {\r
+ try {\r
+ AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, is_applet, applet );\r
+ }\r
+ catch ( final IOException e1 ) {\r
+ ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
+ }\r
+ }\r
+ else if ( o == _aptx_ref_item ) {\r
+ try {\r
+ AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, is_applet, applet );\r
+ }\r
+ catch ( final IOException e1 ) {\r
+ ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
+ }\r
+ }\r
+ else if ( o == _phyloxml_ref_item ) {\r
+ try {\r
+ AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, is_applet, applet );\r
+ }\r
+ catch ( final IOException e1 ) {\r
+ ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
+ }\r
+ }\r
+ else {\r
+ if ( _load_phylogeny_from_webservice_menu_items != null ) {\r
+ for( int i = 0; i < _load_phylogeny_from_webservice_menu_items.length; ++i ) {\r
+ if ( o == _load_phylogeny_from_webservice_menu_items[ i ] ) {\r
+ readPhylogeniesFromWebservice( i );\r
+ }\r
+ }\r
+ }\r
+ }\r
+ _contentpane.repaint();\r
+ }\r
+\r
+ public Configuration getConfiguration() {\r
+ return _configuration;\r
+ }\r
+\r
+ /**\r
+ * This method returns the current external node data which\r
+ * has been selected by the user by clicking the "Return ..."\r
+ * menu item. This method is expected to be called from Javascript or\r
+ * something like it.\r
+ * \r
+ * @return current external node data as String\r
+ */\r
+ public String getCurrentExternalNodesDataBuffer() {\r
+ return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();\r
+ }\r
+\r
+ public int getCurrentExternalNodesDataBufferChangeCounter() {\r
+ return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();\r
+ }\r
+\r
+ public int getCurrentExternalNodesDataBufferLength() {\r
+ return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();\r
+ }\r
+\r
+ public InferenceManager getInferenceManager() {\r
+ return _inference_manager;\r
+ }\r
+\r
+ public MainPanel getMainPanel() {\r
+ return _mainpanel;\r
+ }\r
+\r
+ public Options getOptions() {\r
+ return _options;\r
+ }\r
+\r
+ public ProcessPool getProcessPool() {\r
+ return _process_pool;\r
+ }\r
+\r
+ public void showTextFrame( final String s, final String title ) {\r
+ checkTextFrames();\r
+ _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );\r
+ }\r
+\r
+ public void showWhole() {\r
+ _mainpanel.getControlPanel().showWhole();\r
+ }\r
+\r
+ public void updateProcessMenu() {\r
+ // In general Swing is not thread safe.\r
+ // See "Swing's Threading Policy".\r
+ SwingUtilities.invokeLater( new Runnable() {\r
+\r
+ @Override\r
+ public void run() {\r
+ doUpdateProcessMenu();\r
+ }\r
+ } );\r
+ }\r
+\r
+ void activateSaveAllIfNeeded() {\r
+ if ( ( getMainPanel().getTabbedPane() != null ) && ( getMainPanel().getTabbedPane().getTabCount() > 1 ) ) {\r
+ _save_all_item.setEnabled( true );\r
+ }\r
+ else {\r
+ _save_all_item.setEnabled( false );\r
+ }\r
+ }\r
+\r
+ void buildFileMenu() {\r
+ _file_jmenu = createMenu( "File", getConfiguration() );\r
+ _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );\r
+ customizeJMenuItem( _exit_item );\r
+ _jmenubar.add( _file_jmenu );\r
+ }\r
+\r
+ void buildFontSizeMenu() {\r
+ _font_size_menu = createMenu( FONT_SIZE_MENU_LABEL, getConfiguration() );\r
+ _font_size_menu.add( _super_tiny_fonts_item = new JMenuItem( "Super Tiny Fonts" ) );\r
+ _font_size_menu.add( _tiny_fonts_item = new JMenuItem( "Tiny Fonts" ) );\r
+ _font_size_menu.add( _small_fonts_item = new JMenuItem( "Small Fonts" ) );\r
+ _font_size_menu.add( _medium_fonts_item = new JMenuItem( "Medium Fonts" ) );\r
+ _font_size_menu.add( _large_fonts_item = new JMenuItem( "Large Fonts" ) );\r
+ customizeJMenuItem( _super_tiny_fonts_item );\r
+ customizeJMenuItem( _tiny_fonts_item );\r
+ customizeJMenuItem( _small_fonts_item );\r
+ customizeJMenuItem( _medium_fonts_item );\r
+ customizeJMenuItem( _large_fonts_item );\r
+ _jmenubar.add( _font_size_menu );\r
+ }\r
+\r
+ void buildHelpMenu() {\r
+ _help_jmenu = createMenu( "Help", getConfiguration() );\r
+ _help_jmenu.add( _help_item = new JMenuItem( "Help" ) );\r
+ _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );\r
+ _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" );\r
+ _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );\r
+ _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );\r
+ _help_jmenu.addSeparator();\r
+ _help_jmenu.add( _about_item = new JMenuItem( "About" ) );\r
+ customizeJMenuItem( _help_item );\r
+ customizeJMenuItem( _website_item );\r
+ customizeJMenuItem( _phyloxml_website_item );\r
+ customizeJMenuItem( _aptx_ref_item );\r
+ customizeJMenuItem( _phyloxml_ref_item );\r
+ customizeJMenuItem( _about_item );\r
+ _phyloxml_ref_item.setToolTipText( PHYLOXML_REF_TOOL_TIP );\r
+ _aptx_ref_item.setToolTipText( APTX_REF_TOOL_TIP );\r
+ _jmenubar.add( _help_jmenu );\r
+ }\r
+\r
+ void buildTypeMenu() {\r
+ _type_menu = createMenu( TYPE_MENU_HEADER, getConfiguration() );\r
+ _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );\r
+ _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );\r
+ _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );\r
+ _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );\r
+ _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );\r
+ _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );\r
+ _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );\r
+ _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );\r
+ customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );\r
+ customizeCheckBoxMenuItem( _triangular_type_cbmi, false );\r
+ customizeCheckBoxMenuItem( _euro_type_cbmi, false );\r
+ customizeCheckBoxMenuItem( _rounded_type_cbmi, false );\r
+ customizeCheckBoxMenuItem( _curved_type_cbmi, false );\r
+ customizeCheckBoxMenuItem( _convex_type_cbmi, false );\r
+ customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );\r
+ customizeCheckBoxMenuItem( _circular_type_cbmi, false );\r
+ _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );\r
+ _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );\r
+ initializeTypeMenu( getOptions() );\r
+ _jmenubar.add( _type_menu );\r
+ }\r
+\r
+ void buildViewMenu() {\r
+ _view_jmenu = createMenu( "View", getConfiguration() );\r
+ _view_jmenu.add( _display_basic_information_item = new JMenuItem( SHOW_BASIC_TREE_INFORMATION_LABEL ) );\r
+ _view_jmenu.addSeparator();\r
+ _view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) );\r
+ _view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) );\r
+ _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "as Nexus" ) );\r
+ customizeJMenuItem( _display_basic_information_item );\r
+ customizeJMenuItem( _view_as_NH_item );\r
+ customizeJMenuItem( _view_as_XML_item );\r
+ customizeJMenuItem( _view_as_nexus_item );\r
+ _jmenubar.add( _view_jmenu );\r
+ }\r
+\r
+ void checkTextFrames() {\r
+ if ( _textframes.size() > 5 ) {\r
+ try {\r
+ if ( _textframes.getFirst() != null ) {\r
+ _textframes.getFirst().removeMe();\r
+ }\r
+ else {\r
+ _textframes.removeFirst();\r
+ }\r
+ }\r
+ catch ( final NoSuchElementException e ) {\r
+ // Ignore.\r
+ }\r
+ }\r
+ }\r
+\r
+ void close() {\r
+ removeAllTextFrames();\r
+ if ( _mainpanel != null ) {\r
+ _mainpanel.terminate();\r
+ }\r
+ if ( _contentpane != null ) {\r
+ _contentpane.removeAll();\r
+ }\r
+ setVisible( false );\r
+ dispose();\r
+ }\r
+\r
+ void colorRank() {\r
+ if ( _mainpanel.getCurrentTreePanel() != null ) {\r
+ final String[] ranks = AptxUtil.getAllPossibleRanks();\r
+ final String rank = ( String ) JOptionPane\r
+ .showInputDialog( this,\r
+ "What rank should the colorization be based on",\r
+ "Rank Selection",\r
+ JOptionPane.QUESTION_MESSAGE,\r
+ null,\r
+ ranks,\r
+ null );\r
+ if ( !ForesterUtil.isEmpty( rank ) ) {\r
+ _mainpanel.getCurrentTreePanel().colorRank( rank );\r
+ }\r
+ }\r
+ }\r
+\r
+ void confColor() {\r
+ if ( _mainpanel.getCurrentTreePanel() != null ) {\r
+ _mainpanel.getCurrentTreePanel().confColor();\r
+ }\r
+ }\r
+\r
+ void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {\r
+ if ( item != null ) {\r
+ item.setFont( MainFrame.menu_font );\r
+ if ( !getConfiguration().isUseNativeUI() ) {\r
+ item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
+ item.setForeground( getConfiguration().getGuiMenuTextColor() );\r
+ }\r
+ item.setSelected( is_selected );\r
+ item.addActionListener( this );\r
+ }\r
+ }\r
+\r
+ JMenuItem customizeJMenuItem( final JMenuItem jmi ) {\r
+ if ( jmi != null ) {\r
+ jmi.setFont( MainFrame.menu_font );\r
+ if ( !getConfiguration().isUseNativeUI() ) {\r
+ jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
+ jmi.setForeground( getConfiguration().getGuiMenuTextColor() );\r
+ }\r
+ jmi.addActionListener( this );\r
+ }\r
+ return jmi;\r
+ }\r
+\r
+ void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {\r
+ if ( item != null ) {\r
+ item.setFont( MainFrame.menu_font );\r
+ if ( !getConfiguration().isUseNativeUI() ) {\r
+ item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
+ item.setForeground( getConfiguration().getGuiMenuTextColor() );\r
+ }\r
+ item.setSelected( is_selected );\r
+ item.addActionListener( this );\r
+ }\r
+ }\r
+\r
+ void displayBasicInformation( final File treefile ) {\r
+ if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
+ String title = "Basic Information";\r
+ if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
+ title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\"";\r
+ }\r
+ showTextFrame( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny(), treefile ), title );\r
+ }\r
+ }\r
+\r
+ void exceptionOccuredDuringOpenFile( final Exception e ) {\r
+ try {\r
+ _mainpanel.getCurrentTreePanel().setArrowCursor();\r
+ }\r
+ catch ( final Exception ex ) {\r
+ // Do nothing.\r
+ }\r
+ JOptionPane.showMessageDialog( this,\r
+ ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),\r
+ "Error during File|Open",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ }\r
+\r
+ void exceptionOccuredDuringSaveAs( final Exception e ) {\r
+ try {\r
+ _mainpanel.getCurrentTreePanel().setArrowCursor();\r
+ }\r
+ catch ( final Exception ex ) {\r
+ // Do nothing.\r
+ }\r
+ JOptionPane.showMessageDialog( this, "Exception" + e, "Error during File|SaveAs", JOptionPane.ERROR_MESSAGE );\r
+ }\r
+\r
+ void executeGSDI() {\r
+ if ( !isOKforSDI( false, true ) ) {\r
+ return;\r
+ }\r
+ if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Gene tree is not rooted.",\r
+ "Cannot execute GSDI",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();\r
+ gene_tree.setAllNodesToNotCollapse();\r
+ gene_tree.recalculateNumberOfExternalDescendants( false );\r
+ GSDI gsdi = null;\r
+ final Phylogeny species_tree = getSpeciesTree().copy();\r
+ try {\r
+ gsdi = new GSDI( gene_tree, species_tree, false, true, true, true );\r
+ }\r
+ catch ( final SDIException e ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ e.getLocalizedMessage(),\r
+ "Error during GSDI",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ catch ( final Exception e ) {\r
+ AptxUtil.unexpectedException( e );\r
+ return;\r
+ }\r
+ gene_tree.setRerootable( false );\r
+ gene_tree.clearHashIdToNodeMap();\r
+ gene_tree.recalculateNumberOfExternalDescendants( true );\r
+ _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null );\r
+ getMainPanel().getControlPanel().setShowEvents( true );\r
+ showWhole();\r
+ final int selected = _mainpanel.getTabbedPane().getSelectedIndex();\r
+ _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );\r
+ showWhole();\r
+ _mainpanel.getTabbedPane().setSelectedIndex( selected );\r
+ showWhole();\r
+ _mainpanel.getCurrentTreePanel().setEdited( true );\r
+ final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );\r
+ if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Duplications: " + gsdi.getDuplicationsSum() + "\n"\r
+ + "Potential duplications: "\r
+ + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"\r
+ + "Speciations: " + gsdi.getSpeciationsSum() + "\n"\r
+ + "Stripped gene tree nodes: "\r
+ + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"\r
+ + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"\r
+ + "Number of polytomies in species tree used: " + poly + "\n",\r
+ "GSDI successfully completed",\r
+ JOptionPane.WARNING_MESSAGE );\r
+ }\r
+ else {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Duplications: " + gsdi.getDuplicationsSum() + "\n"\r
+ + "Potential duplications: "\r
+ + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"\r
+ + "Speciations: " + gsdi.getSpeciationsSum() + "\n"\r
+ + "Stripped gene tree nodes: "\r
+ + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"\r
+ + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"\r
+ + "Number of polytomies in species tree used: " + poly + "\n",\r
+ "GSDI successfully completed",\r
+ JOptionPane.INFORMATION_MESSAGE );\r
+ }\r
+ }\r
+\r
+ void executeGSDIR() {\r
+ if ( !isOKforSDI( false, false ) ) {\r
+ return;\r
+ }\r
+ final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() );\r
+ if ( ( p > 0 )\r
+ && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Gene tree is not completely binary",\r
+ "Cannot execute GSDI",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();\r
+ gene_tree.setAllNodesToNotCollapse();\r
+ gene_tree.recalculateNumberOfExternalDescendants( false );\r
+ GSDIR gsdir = null;\r
+ final Phylogeny species_tree = getSpeciesTree().copy();\r
+ try {\r
+ gsdir = new GSDIR( gene_tree, species_tree, true, true, true );\r
+ }\r
+ catch ( final SDIException e ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ e.getLocalizedMessage(),\r
+ "Error during GSDIR",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ catch ( final Exception e ) {\r
+ AptxUtil.unexpectedException( e );\r
+ return;\r
+ }\r
+ final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree();\r
+ result_gene_tree.setRerootable( false );\r
+ result_gene_tree.clearHashIdToNodeMap();\r
+ result_gene_tree.recalculateNumberOfExternalDescendants( true );\r
+ PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );\r
+ _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );\r
+ getMainPanel().getControlPanel().setShowEvents( true );\r
+ showWhole();\r
+ final int selected = _mainpanel.getTabbedPane().getSelectedIndex();\r
+ _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );\r
+ showWhole();\r
+ _mainpanel.getTabbedPane().setSelectedIndex( selected );\r
+ showWhole();\r
+ _mainpanel.getCurrentTreePanel().setEdited( true );\r
+ final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );\r
+ if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"\r
+ + "Speciations: " + gsdir.getSpeciationsSum() + "\n"\r
+ + "Stripped gene tree nodes: "\r
+ + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"\r
+ + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"\r
+ + "Number of polytomies in species tree used: " + poly + "\n",\r
+ "GSDIR successfully completed",\r
+ JOptionPane.WARNING_MESSAGE );\r
+ }\r
+ else {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"\r
+ + "Speciations: " + gsdir.getSpeciationsSum() + "\n"\r
+ + "Stripped gene tree nodes: "\r
+ + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"\r
+ + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"\r
+ + "Number of polytomies in species tree used: " + poly + "\n",\r
+ "GSDIR successfully completed",\r
+ JOptionPane.INFORMATION_MESSAGE );\r
+ }\r
+ }\r
+\r
+ boolean GAndSDoHaveMoreThanOneSpeciesInComman( final Phylogeny gene_tree ) {\r
+ if ( ( gene_tree == null ) || gene_tree.isEmpty() ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Gene tree and species tree have no species in common.",\r
+ "Error during SDI",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return false;\r
+ }\r
+ else if ( gene_tree.getNumberOfExternalNodes() < 2 ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Gene tree and species tree have only one species in common.",\r
+ "Error during SDI",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return false;\r
+ }\r
+ else {\r
+ return true;\r
+ }\r
+ }\r
+\r
+ TreePanel getCurrentTreePanel() {\r
+ return getMainPanel().getCurrentTreePanel();\r
+ }\r
+\r
+ JMenu getHelpMenu() {\r
+ return _help_jmenu;\r
+ }\r
+\r
+ JCheckBoxMenuItem getlabelDirectionCbmi() {\r
+ return _label_direction_cbmi;\r
+ }\r
+\r
+ JMenuBar getMenuBarOfMainFrame() {\r
+ return _jmenubar;\r
+ }\r
+\r
+ final Phylogeny getSpeciesTree() {\r
+ return _species_tree;\r
+ }\r
+\r
+ void help() {\r
+ final StringBuilder sb = new StringBuilder();\r
+ sb.append( "Display options\n" );\r
+ sb.append( "-------------------\n" );\r
+ sb.append( "Use the checkboxes to select types of information to display on the tree.\n\n" );\r
+ sb.append( "Clickable tree nodes\n" );\r
+ sb.append( "--------------------\n" );\r
+ sb.append( "Tree nodes can be clicked, the action is determined by the 'click on node to' menu\n" );\r
+ sb.append( "or by right clicking:\n" );\r
+ sb.append( "o Display Node Data -- display information for a node\n" );\r
+ sb.append( "o Collapse/Uncollapse -- collapse and uncollapse subtree from clicked node\n" );\r
+ sb.append( "o Root/Reroot -- change tree root to clicked node\n" );\r
+ sb.append( "o Sub/Super Tree -- toggle between subtree from clicked node and whole tree\n" );\r
+ sb.append( "o Swap Descendants -- switch descendant on either side of clicked node\n" );\r
+ sb.append( "o Colorize Subtree -- color a subtree\n" );\r
+ sb.append( "o Open Sequence Web -- launch a web browser to display sequence information\n" );\r
+ sb.append( "o Open Taxonomy Web -- launch a web browser to display taxonomy information\n" );\r
+ sb.append( "- there may be additional choices depending on this particular setup\n\n" );\r
+ sb.append( "Right clicking on a node always displays the information of a node.\n\n" );\r
+ sb.append( "Zooming\n" );\r
+ sb.append( "---------\n" );\r
+ sb.append( "The mouse wheel and the plus and minus keys control zooming.\n" );\r
+ sb.append( "Mouse wheel+Ctrl changes the text size.\n" );\r
+ sb.append( "Mouse wheel+Shift controls zooming in vertical direction only.\n" );\r
+ sb.append( "Use the buttons on the control panel to zoom the tree in and out, horizontally or vertically.\n" );\r
+ sb.append( "The entire tree can be fitted into the window by clicking the \"F\" button, or by pressing F, Delete, or Home.\n" );\r
+ sb.append( "The up, down, left, and right keys can be used to move the visible part (if zoomed in).\n" );\r
+ sb.append( "Up, down, left, and right+Shift can be used to control zooming horizontally and vertically.\n" );\r
+ sb.append( "Plus and minus keys+Ctrl change the text size; F+Ctrl, Delete+Ctrl, or Home+Ctrl resets it.\n\n" );\r
+ sb.append( "Quick tree manipulation:\n" );\r
+ sb.append( "------------------------\n" );\r
+ sb.append( "Order Subtrees -- order the tree by branch length\n" );\r
+ sb.append( "Uncollapse All -- uncollapse any and all collapsed branches\n\n" );\r
+ sb.append( "Memory problems (Java heap space error)\n" );\r
+ sb.append( "---------------------------------------\n" );\r
+ sb.append( "Since the Java default memory allocation is quite small, it might by necessary (for trees\n" );\r
+ sb.append( "with more than approximately 5000 external nodes) to increase the memory which Java can use, with\n" );\r
+ sb.append( "the '-Xmx' Java command line option. For example:\n" );\r
+ sb.append( "java -Xmx1024m -cp path\\to\\forester.jar org.forester.archaeopteryx.Archaeopteryx\n\n" );\r
+ // + "General remarks\n"\r
+ // + "---------------\n"\r
+ // +\r
+ // "o The application version permits copying to the clipboard \n"\r
+ // +\r
+ // " in the \"View\"|\"View as ...\" frame (either by control-c or button press).\n"\r
+ // +\r
+ // "o Changes made to a subtree affect this subtree and its subtrees,\n"\r
+ // + " but not any of its parent tree(s).\n"\r
+ // +\r
+ // "o Archaeopteryx tries to detect whether the numerical values in a NH tree\n"\r
+ // +\r
+ // " are likely to be bootstrap values instead of branch length values.\n\n"\r
+ // +\r
+ // " Remarks regarding SDI (Speciation Duplication Inference):\n"\r
+ // +\r
+ // "o Each external node of the gene tree (in display) needs to be associated with\n"\r
+ // +\r
+ // " a species: either directly through the \"Species\" field, or the species\n"\r
+ // +\r
+ // " is part of the sequence name in the form \"XXXX_SPECIES\"\n"\r
+ // +\r
+ // " (e.g. \"ACON_DROME\" or \"ACON_DROME/123-4489\" which is also acceptable).\n"\r
+ // +\r
+ // "o A species tree for each species of the gene tree needs to be loaded with\n"\r
+ // +\r
+ // " \"SDI\"|\"Load species tree\" prior the SDI execution.\n"\r
+ // +\r
+ // "o !External nodes of the gene tree associated with species not present in\n"\r
+ // +\r
+ // " the species tree are REMOVED prior to SDI execution!\n"\r
+ // +\r
+ // "o Both the gene tree and the species tree must be completely binary.\n"\r
+ // +\r
+ // "o Duplications and speciations are a function of the position of the root.\n"\r
+ // +\r
+ // " Hence, after each manual \"Root/Reroot\"ing some duplications will be\n"\r
+ // + " incorrect and need to be inferred again\n"\r
+ // +\r
+ // " with: \"SDI\"|\"SDI (Speciation Duplication Inference)\n\n"\r
+ sb.append( "phyloXML\n" );\r
+ sb.append( "-------------------\n" );\r
+ sb.append( "Reference: " + Constants.PHYLOXML_REFERENCE + "\n" );\r
+ sb.append( "Website: " + Constants.PHYLOXML_WEB_SITE + "\n" );\r
+ sb.append( "Version: " + ForesterConstants.PHYLO_XML_VERSION + "\n" );\r
+ sb.append( "\n" );\r
+ sb.append( "For more information: https://sites.google.com/site/cmzmasek/home/software/archaeopteryx\n" );\r
+ sb.append( "Email: " + Constants.AUTHOR_EMAIL + "\n\n" );\r
+ TextFrame.instantiate( sb.toString(), "Help", _textframes );\r
+ }\r
+\r
+ void initializeTypeMenu( final Options options ) {\r
+ setTypeMenuToAllUnselected();\r
+ switch ( options.getPhylogenyGraphicsType() ) {\r
+ case CONVEX:\r
+ _convex_type_cbmi.setSelected( true );\r
+ break;\r
+ case CURVED:\r
+ _curved_type_cbmi.setSelected( true );\r
+ break;\r
+ case EURO_STYLE:\r
+ _euro_type_cbmi.setSelected( true );\r
+ break;\r
+ case ROUNDED:\r
+ _rounded_type_cbmi.setSelected( true );\r
+ break;\r
+ case TRIANGULAR:\r
+ _triangular_type_cbmi.setSelected( true );\r
+ break;\r
+ case UNROOTED:\r
+ _unrooted_type_cbmi.setSelected( true );\r
+ break;\r
+ case CIRCULAR:\r
+ _circular_type_cbmi.setSelected( true );\r
+ break;\r
+ default:\r
+ _rectangular_type_cbmi.setSelected( true );\r
+ break;\r
+ }\r
+ }\r
+\r
+ boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {\r
+ if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
+ return false;\r
+ }\r
+ else if ( ( getSpeciesTree() == null ) || getSpeciesTree().isEmpty() ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "No species tree loaded",\r
+ "Cannot execute GSDI",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return false;\r
+ }\r
+ else if ( species_tree_has_to_binary && !getSpeciesTree().isCompletelyBinary() ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Species tree is not completely binary",\r
+ "Cannot execute GSDI",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return false;\r
+ }\r
+ else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Gene tree is not completely binary",\r
+ "Cannot execute GSDI",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return false;\r
+ }\r
+ else {\r
+ return true;\r
+ }\r
+ }\r
+\r
+ boolean isSubtreeDisplayed() {\r
+ if ( getCurrentTreePanel() != null ) {\r
+ if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {\r
+ JOptionPane\r
+ .showMessageDialog( this,\r
+ "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",\r
+ "Operation can not be exectuted on a sub-tree",\r
+ JOptionPane.WARNING_MESSAGE );\r
+ return true;\r
+ }\r
+ }\r
+ return false;\r
+ }\r
+\r
+ void midpointRoot() {\r
+ if ( _mainpanel.getCurrentTreePanel() != null ) {\r
+ _mainpanel.getCurrentTreePanel().midpointRoot();\r
+ }\r
+ }\r
+\r
+ void readPhylogeniesFromWebservice( final int i ) {\r
+ final UrlTreeReader reader = new UrlTreeReader( this, i );\r
+ new Thread( reader ).start();\r
+ }\r
+\r
+ void removeAllTextFrames() {\r
+ for( final TextFrame tf : _textframes ) {\r
+ if ( tf != null ) {\r
+ tf.close();\r
+ }\r
+ }\r
+ _textframes.clear();\r
+ }\r
+\r
+ void setConfiguration( final Configuration configuration ) {\r
+ _configuration = configuration;\r
+ }\r
+\r
+ void setInferenceManager( final InferenceManager i ) {\r
+ _inference_manager = i;\r
+ }\r
+\r
+ void setOptions( final Options options ) {\r
+ _options = options;\r
+ }\r
+\r
+ void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {\r
+ setTypeMenuToAllUnselected();\r
+ switch ( type ) {\r
+ case CIRCULAR:\r
+ _circular_type_cbmi.setSelected( true );\r
+ break;\r
+ case CONVEX:\r
+ _convex_type_cbmi.setSelected( true );\r
+ break;\r
+ case CURVED:\r
+ _curved_type_cbmi.setSelected( true );\r
+ break;\r
+ case EURO_STYLE:\r
+ _euro_type_cbmi.setSelected( true );\r
+ break;\r
+ case ROUNDED:\r
+ _rounded_type_cbmi.setSelected( true );\r
+ break;\r
+ case RECTANGULAR:\r
+ _rectangular_type_cbmi.setSelected( true );\r
+ break;\r
+ case TRIANGULAR:\r
+ _triangular_type_cbmi.setSelected( true );\r
+ break;\r
+ case UNROOTED:\r
+ _unrooted_type_cbmi.setSelected( true );\r
+ break;\r
+ default:\r
+ throw new IllegalArgumentException( "unknown type: " + type );\r
+ }\r
+ }\r
+\r
+ final void setSpeciesTree( final Phylogeny species_tree ) {\r
+ _species_tree = species_tree;\r
+ }\r
+\r
+ void setTypeMenuToAllUnselected() {\r
+ _convex_type_cbmi.setSelected( false );\r
+ _curved_type_cbmi.setSelected( false );\r
+ _euro_type_cbmi.setSelected( false );\r
+ _rounded_type_cbmi.setSelected( false );\r
+ _triangular_type_cbmi.setSelected( false );\r
+ _rectangular_type_cbmi.setSelected( false );\r
+ _unrooted_type_cbmi.setSelected( false );\r
+ _circular_type_cbmi.setSelected( false );\r
+ }\r
+\r
+ void switchColors() {\r
+ final TreeColorSet colorset = _mainpanel.getTreeColorSet();\r
+ final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );\r
+ csc.setVisible( true );\r
+ }\r
+\r
+ void taxColor() {\r
+ if ( _mainpanel.getCurrentTreePanel() != null ) {\r
+ _mainpanel.getCurrentTreePanel().taxColor();\r
+ }\r
+ }\r
+\r
+ void typeChanged( final Object o ) {\r
+ updateTypeCheckboxes( getOptions(), o );\r
+ updateOptions( getOptions() );\r
+ if ( getCurrentTreePanel() != null ) {\r
+ final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();\r
+ final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();\r
+ if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )\r
+ || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )\r
+ || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )\r
+ || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {\r
+ getCurrentTreePanel().getControlPanel().showWhole();\r
+ }\r
+ if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {\r
+ getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );\r
+ }\r
+ else {\r
+ getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );\r
+ }\r
+ getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );\r
+ updateScreenTextAntialias( getMainPanel().getTreePanels() );\r
+ if ( getCurrentTreePanel().getControlPanel().getDynamicallyHideData() != null ) {\r
+ if ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {\r
+ getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( false );\r
+ }\r
+ else {\r
+ getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( true );\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ void updateOptions( final Options options ) {\r
+ options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );\r
+ options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )\r
+ && _background_gradient_cbmi.isSelected() );\r
+ options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );\r
+ options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null )\r
+ && _show_annotation_ref_source.isSelected() );\r
+ options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )\r
+ && _abbreviate_scientific_names.isSelected() );\r
+ options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )\r
+ && _color_labels_same_as_parent_branch.isSelected() );\r
+ options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )\r
+ && _show_default_node_shapes_internal_cbmi.isSelected() );\r
+ options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )\r
+ && _show_default_node_shapes_external_cbmi.isSelected() );\r
+ if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {\r
+ options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );\r
+ }\r
+ else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {\r
+ options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );\r
+ }\r
+ else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {\r
+ options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );\r
+ }\r
+ options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )\r
+ && _search_case_senstive_cbmi.isSelected() );\r
+ if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {\r
+ options.setShowScale( _show_scale_cbmi.isSelected() );\r
+ }\r
+ if ( _label_direction_cbmi != null ) {\r
+ if ( _label_direction_cbmi.isSelected() ) {\r
+ options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );\r
+ }\r
+ else {\r
+ options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );\r
+ }\r
+ }\r
+ options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );\r
+ options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )\r
+ && _show_confidence_stddev_cbmi.isSelected() );\r
+ if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) {\r
+ options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() );\r
+ }\r
+ if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) {\r
+ options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() );\r
+ }\r
+ options.setPrintUsingActualSize( ( _print_using_actual_size_cbmi != null )\r
+ && ( _print_using_actual_size_cbmi.isSelected() ) );\r
+ options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null )\r
+ && ( _graphics_export_using_actual_size_cbmi.isSelected() ) );\r
+ options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() );\r
+ if ( ( _use_brackets_for_conf_in_nh_export_cbmi != null )\r
+ && _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {\r
+ options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );\r
+ }\r
+ else if ( ( _use_internal_names_for_conf_in_nh_export_cbmi != null )\r
+ && _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {\r
+ options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );\r
+ }\r
+ else {\r
+ options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );\r
+ }\r
+ options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null )\r
+ && _print_black_and_white_cbmi.isSelected() );\r
+ options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null )\r
+ && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );\r
+ if ( ( _extract_taxonomy_pfam_strict_rbmi != null ) && _extract_taxonomy_pfam_strict_rbmi.isSelected() ) {\r
+ options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );\r
+ }\r
+ else if ( ( _extract_taxonomy_pfam_relaxed_rbmi != null ) && _extract_taxonomy_pfam_relaxed_rbmi.isSelected() ) {\r
+ options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );\r
+ }\r
+ else if ( ( _extract_taxonomy_agressive_rbmi != null ) && _extract_taxonomy_agressive_rbmi.isSelected() ) {\r
+ options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );\r
+ }\r
+ else if ( ( _extract_taxonomy_no_rbmi != null ) && _extract_taxonomy_no_rbmi.isSelected() ) {\r
+ options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );\r
+ }\r
+ options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )\r
+ && _replace_underscores_cbmi.isSelected() );\r
+ options.setAllowErrorsInDistanceToParent( ( _allow_errors_in_distance_to_parent_cbmi != null )\r
+ && _allow_errors_in_distance_to_parent_cbmi.isSelected() );\r
+ options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )\r
+ && _search_whole_words_only_cbmi.isSelected() );\r
+ options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )\r
+ && _inverse_search_result_cbmi.isSelected() );\r
+ if ( _graphics_export_visible_only_cbmi != null ) {\r
+ options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_cbmi.isSelected() );\r
+ if ( _graphics_export_visible_only_cbmi.isSelected() && ( _graphics_export_using_actual_size_cbmi != null ) ) {\r
+ _graphics_export_using_actual_size_cbmi.setSelected( true );\r
+ _graphics_export_using_actual_size_cbmi.setEnabled( false );\r
+ }\r
+ else {\r
+ _graphics_export_using_actual_size_cbmi.setEnabled( true );\r
+ }\r
+ }\r
+ if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {\r
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );\r
+ }\r
+ else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {\r
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );\r
+ }\r
+ else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {\r
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );\r
+ }\r
+ else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {\r
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );\r
+ }\r
+ else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {\r
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );\r
+ }\r
+ else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {\r
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );\r
+ }\r
+ else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {\r
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );\r
+ }\r
+ else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {\r
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );\r
+ }\r
+ }\r
+\r
+ void updateTypeCheckboxes( final Options options, final Object o ) {\r
+ setTypeMenuToAllUnselected();\r
+ ( ( JCheckBoxMenuItem ) o ).setSelected( true );\r
+ }\r
+\r
+ void viewAsNexus() {\r
+ if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
+ String title = "Nexus";\r
+ if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
+ title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
+ }\r
+ showTextFrame( _mainpanel.getCurrentPhylogeny().toNexus( getOptions().getNhConversionSupportValueStyle() ),\r
+ title );\r
+ }\r
+ }\r
+\r
+ void viewAsNH() {\r
+ if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
+ String title = "New Hampshire";\r
+ if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
+ title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
+ }\r
+ showTextFrame( _mainpanel.getCurrentPhylogeny().toNewHampshire( getOptions()\r
+ .getNhConversionSupportValueStyle() ),\r
+ title );\r
+ }\r
+ }\r
+\r
+ void viewAsXML() {\r
+ if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
+ String title = "phyloXML";\r
+ if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
+ title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
+ }\r
+ showTextFrame( _mainpanel.getCurrentPhylogeny().toPhyloXML( 0 ), title );\r
+ }\r
+ }\r
+\r
+ private void annotateSequences() {\r
+ if ( getCurrentTreePanel() != null ) {\r
+ final Set<Long> nodes = getCurrentTreePanel().getFoundNodes0();\r
+ if ( ( nodes == null ) || nodes.isEmpty() ) {\r
+ JOptionPane\r
+ .showMessageDialog( this,\r
+ "Need to select nodes, either via direct selection or via the \"Search\" function",\r
+ "No nodes selected for annotation",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ final Phylogeny phy = getMainPanel().getCurrentPhylogeny();\r
+ if ( ( phy != null ) && !phy.isEmpty() ) {\r
+ final JTextField ref_field = new JTextField( 10 );\r
+ final JTextField desc_filed = new JTextField( 20 );\r
+ ref_field.setText( ForesterUtil.isEmpty( getPreviousNodeAnnotationReference() ) ? ""\r
+ : getPreviousNodeAnnotationReference() );\r
+ final JPanel my_panel = new JPanel();\r
+ my_panel.add( new JLabel( "Reference " ) );\r
+ my_panel.add( ref_field );\r
+ my_panel.add( Box.createHorizontalStrut( 15 ) );\r
+ my_panel.add( new JLabel( "Description " ) );\r
+ my_panel.add( desc_filed );\r
+ final int result = JOptionPane.showConfirmDialog( null,\r
+ my_panel,\r
+ "Enter the sequence annotation(s) for the "\r
+ + nodes.size() + " selected nodes",\r
+ JOptionPane.OK_CANCEL_OPTION );\r
+ if ( result == JOptionPane.OK_OPTION ) {\r
+ String ref = ref_field.getText();\r
+ String desc = desc_filed.getText();\r
+ if ( !ForesterUtil.isEmpty( ref ) ) {\r
+ ref = ref.trim();\r
+ ref = ref.replaceAll( "\\s+", " " );\r
+ if ( ( ref.indexOf( ':' ) < 1 ) || ( ref.indexOf( ':' ) > ( ref.length() - 2 ) )\r
+ || ( ref.length() < 3 ) ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Reference needs to be in the form of \"GO:1234567\"",\r
+ "Illegal Format for Annotation Reference",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ }\r
+ if ( ref != null ) {\r
+ setPreviousNodeAnnotationReference( ref );\r
+ }\r
+ if ( desc != null ) {\r
+ desc = desc.trim();\r
+ desc = desc.replaceAll( "\\s+", " " );\r
+ }\r
+ if ( !ForesterUtil.isEmpty( ref ) || !ForesterUtil.isEmpty( desc ) ) {\r
+ for( final Long id : nodes ) {\r
+ final PhylogenyNode n = phy.getNode( id );\r
+ ForesterUtil.ensurePresenceOfSequence( n );\r
+ final Annotation ann = ForesterUtil.isEmpty( ref ) ? new Annotation()\r
+ : new Annotation( ref );\r
+ if ( !ForesterUtil.isEmpty( desc ) ) {\r
+ ann.setDesc( desc );\r
+ }\r
+ n.getNodeData().getSequence().addAnnotation( ann );\r
+ }\r
+ }\r
+ getMainPanel().getControlPanel().showAnnotations();\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ private void chooseFont() {\r
+ final FontChooser fc = new FontChooser();\r
+ fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );\r
+ fc.showDialog( this, "Select the Base Font" );\r
+ getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );\r
+ }\r
+\r
+ private void chooseMinimalConfidence() {\r
+ final String s = ( String ) JOptionPane\r
+ .showInputDialog( this,\r
+ "Please enter the minimum for confidence values to be displayed.\n"\r
+ + "[current value: " + getOptions().getMinConfidenceValue() + "]\n",\r
+ "Minimal Confidence Value",\r
+ JOptionPane.QUESTION_MESSAGE,\r
+ null,\r
+ null,\r
+ getOptions().getMinConfidenceValue() );\r
+ if ( !ForesterUtil.isEmpty( s ) ) {\r
+ boolean success = true;\r
+ double m = 0.0;\r
+ final String m_str = s.trim();\r
+ if ( !ForesterUtil.isEmpty( m_str ) ) {\r
+ try {\r
+ m = Double.parseDouble( m_str );\r
+ }\r
+ catch ( final Exception ex ) {\r
+ success = false;\r
+ }\r
+ }\r
+ else {\r
+ success = false;\r
+ }\r
+ if ( success && ( m >= 0.0 ) ) {\r
+ getOptions().setMinConfidenceValue( m );\r
+ }\r
+ }\r
+ }\r
+\r
+ private void doUpdateProcessMenu() {\r
+ if ( _process_pool.size() > 0 ) {\r
+ if ( _process_menu == null ) {\r
+ _process_menu = createMenu( "", getConfiguration() );\r
+ _process_menu.setForeground( Color.RED );\r
+ }\r
+ _process_menu.removeAll();\r
+ final String text = "processes running: " + _process_pool.size();\r
+ _process_menu.setText( text );\r
+ _jmenubar.add( _process_menu );\r
+ for( int i = 0; i < _process_pool.size(); ++i ) {\r
+ final ProcessRunning p = _process_pool.getProcessByIndex( i );\r
+ _process_menu.add( customizeJMenuItem( new JMenuItem( p.getName() + " [" + p.getStart() + "]" ) ) );\r
+ }\r
+ }\r
+ else {\r
+ if ( _process_menu != null ) {\r
+ _process_menu.removeAll();\r
+ _jmenubar.remove( _process_menu );\r
+ }\r
+ }\r
+ _jmenubar.validate();\r
+ _jmenubar.repaint();\r
+ repaint();\r
+ }\r
+\r
+ private String getPreviousNodeAnnotationReference() {\r
+ return _previous_node_annotation_ref;\r
+ }\r
+\r
+ private void removeBranchColors() {\r
+ if ( getMainPanel().getCurrentPhylogeny() != null ) {\r
+ AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );\r
+ }\r
+ }\r
+\r
+ private void removeVisualStyles() {\r
+ if ( getMainPanel().getCurrentPhylogeny() != null ) {\r
+ AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() );\r
+ }\r
+ }\r
+\r
+ private void setPreviousNodeAnnotationReference( final String previous_node_annotation_ref ) {\r
+ _previous_node_annotation_ref = previous_node_annotation_ref;\r
+ }\r
+\r
+ /**\r
+ * Display the about box.\r
+ */\r
+ static void about() {\r
+ final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + Constants.VERSION + "\n" );\r
+ about.append( "Copyright (C) 2013 Christian M. Zmasek\n" );\r
+ about.append( "All Rights Reserved\n" );\r
+ about.append( "License: GNU Lesser General Public License (LGPL)\n" );\r
+ about.append( "Last modified: " + Constants.PRG_DATE + "\n" );\r
+ about.append( "Based on: " + ForesterUtil.getForesterLibraryInformation() + "\n" );\r
+ about.append( "phyloXML version : " + ForesterConstants.PHYLO_XML_VERSION + "\n" );\r
+ about.append( "phyloXML location: " + ForesterConstants.PHYLO_XML_LOCATION + "\n" );\r
+ if ( !ForesterUtil.isEmpty( ForesterUtil.JAVA_VERSION ) && !ForesterUtil.isEmpty( ForesterUtil.JAVA_VENDOR ) ) {\r
+ about.append( "[your Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]\n" );\r
+ }\r
+ if ( !ForesterUtil.isEmpty( ForesterUtil.OS_NAME ) && !ForesterUtil.isEmpty( ForesterUtil.OS_ARCH )\r
+ && !ForesterUtil.isEmpty( ForesterUtil.OS_VERSION ) ) {\r
+ about.append( "[your OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " "\r
+ + ForesterUtil.OS_VERSION + "]\n" );\r
+ }\r
+ final Runtime rt = java.lang.Runtime.getRuntime();\r
+ final long free_memory = rt.freeMemory() / 1000000;\r
+ final long total_memory = rt.totalMemory() / 1000000;\r
+ about.append( "[free memory: " + free_memory + "MB, total memory: " + total_memory + "MB]\n" );\r
+ about.append( "[locale: " + Locale.getDefault() + "]\n" );\r
+ about.append( "References:\n" );\r
+ about.append( Constants.PHYLOXML_REFERENCE_SHORT + "\n" );\r
+ about.append( "For more information & download:\n" );\r
+ about.append( Constants.APTX_WEB_SITE + "\n" );\r
+ about.append( "Comments: " + Constants.AUTHOR_EMAIL );\r
+ JOptionPane.showMessageDialog( null, about, Constants.PRG_NAME, JOptionPane.PLAIN_MESSAGE );\r
+ }\r
+\r
+ static void chooseNodeSize( final Options options, final Component parent ) {\r
+ final String s = ( String ) JOptionPane.showInputDialog( parent,\r
+ "Please enter the default size for node shapes.\n"\r
+ + "[current value: "\r
+ + options.getDefaultNodeShapeSize() + "]\n",\r
+ "Node Shape Size",\r
+ JOptionPane.QUESTION_MESSAGE,\r
+ null,\r
+ null,\r
+ options.getDefaultNodeShapeSize() );\r
+ if ( !ForesterUtil.isEmpty( s ) ) {\r
+ boolean success = true;\r
+ double m = 0.0;\r
+ final String m_str = s.trim();\r
+ if ( !ForesterUtil.isEmpty( m_str ) ) {\r
+ try {\r
+ m = Double.parseDouble( m_str );\r
+ }\r
+ catch ( final Exception ex ) {\r
+ success = false;\r
+ }\r
+ }\r
+ else {\r
+ success = false;\r
+ }\r
+ if ( success && ( m >= 0.0 ) ) {\r
+ final short size = ForesterUtil.roundToShort( m );\r
+ if ( size >= 0.0 ) {\r
+ options.setDefaultNodeShapeSize( size );\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ static String createCurrentFontDesc( final TreeFontSet tree_font_set ) {\r
+ return tree_font_set.getLargeFont().getFamily() + " " + tree_font_set.getLargeFont().getSize();\r
+ }\r
+\r
+ static JMenu createMenu( final String title, final Configuration conf ) {\r
+ final JMenu jmenu = new JMenu( title );\r
+ if ( !conf.isUseNativeUI() ) {\r
+ jmenu.setFont( MainFrame.menu_font );\r
+ jmenu.setBackground( conf.getGuiMenuBackgroundColor() );\r
+ jmenu.setForeground( conf.getGuiMenuTextColor() );\r
+ }\r
+ return jmenu;\r
+ }\r
+\r
+ static JMenuItem customizeMenuItemAsLabel( final JMenuItem label, final Configuration configuration ) {\r
+ label.setFont( MainFrame.menu_font.deriveFont( Font.BOLD ) );\r
+ if ( !configuration.isUseNativeUI() ) {\r
+ label.setBackground( configuration.getGuiMenuBackgroundColor() );\r
+ label.setForeground( configuration.getGuiMenuTextColor() );\r
+ label.setOpaque( true );\r
+ }\r
+ label.setSelected( false );\r
+ label.setEnabled( false );\r
+ return label;\r
+ }\r
+\r
+ static void cycleNodeFill( final Options op, final TreePanel tree_panel ) {\r
+ switch ( op.getDefaultNodeFill() ) {\r
+ case GRADIENT:\r
+ op.setDefaultNodeFill( NodeFill.SOLID );\r
+ break;\r
+ case NONE:\r
+ op.setDefaultNodeFill( NodeFill.GRADIENT );\r
+ break;\r
+ case SOLID:\r
+ op.setDefaultNodeFill( NodeFill.NONE );\r
+ break;\r
+ default:\r
+ throw new RuntimeException( "unknown fill: " + op.getDefaultNodeFill() );\r
+ }\r
+ }\r
+\r
+ static void cycleNodeShape( final Options op, final TreePanel tree_panel ) {\r
+ switch ( op.getDefaultNodeShape() ) {\r
+ case CIRCLE:\r
+ op.setDefaultNodeShape( NodeShape.RECTANGLE );\r
+ break;\r
+ case RECTANGLE:\r
+ op.setDefaultNodeShape( NodeShape.CIRCLE );\r
+ break;\r
+ default:\r
+ throw new RuntimeException( "unknown shape: " + op.getDefaultNodeShape() );\r
+ }\r
+ }\r
+\r
+ static void cycleOverview( final Options op, final TreePanel tree_panel ) {\r
+ switch ( op.getOvPlacement() ) {\r
+ case LOWER_LEFT:\r
+ op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );\r
+ break;\r
+ case LOWER_RIGHT:\r
+ op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );\r
+ break;\r
+ case UPPER_LEFT:\r
+ op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );\r
+ break;\r
+ case UPPER_RIGHT:\r
+ op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );\r
+ break;\r
+ default:\r
+ throw new RuntimeException( "unknown placement: " + op.getOvPlacement() );\r
+ }\r
+ if ( tree_panel != null ) {\r
+ tree_panel.updateOvSettings();\r
+ }\r
+ }\r
+\r
+ static void setCycleNodeFillMenuItem( final JMenuItem mi, final Options options ) {\r
+ if ( ( options != null ) && ( options.getDefaultNodeFill() != null ) ) {\r
+ mi.setText( "Cycle Node Shape Fill Type... (current: "\r
+ + options.getDefaultNodeFill().toString().toLowerCase() + ")" );\r
+ }\r
+ else {\r
+ mi.setText( "Cycle Node Shape Fill Type..." );\r
+ }\r
+ }\r
+\r
+ static void setCycleNodeShapeMenuItem( final JMenuItem mi, final Options options ) {\r
+ if ( ( options != null ) && ( options.getDefaultNodeShape() != null ) ) {\r
+ mi.setText( "Cycle Node Shape Fill Type... (current: "\r
+ + options.getDefaultNodeShape().toString().toLowerCase() + ")" );\r
+ }\r
+ else {\r
+ mi.setText( "Cycle Node Shape Fill Type..." );\r
+ }\r
+ }\r
+\r
+ static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) {\r
+ if ( ( options != null ) && ( options.getOvPlacement() != null ) ) {\r
+ mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" );\r
+ }\r
+ else {\r
+ mi.setText( "Cycle Overview Placement..." );\r
+ }\r
+ }\r
+\r
+ static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) {\r
+ if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) {\r
+ mi.setText( "Select Color Scheme... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName()\r
+ + ")" );\r
+ }\r
+ else {\r
+ mi.setText( "Select Color Scheme..." );\r
+ }\r
+ }\r
+\r
+ static void setTextForFontChooserMenuItem( final JMenuItem mi, final String font_desc ) {\r
+ mi.setText( "Select Default Font... (current: " + font_desc + ")" );\r
+ }\r
+\r
+ static void setTextMinSupportMenuItem( final JMenuItem mi, final Options options, final TreePanel current_tree_panel ) {\r
+ if ( ( current_tree_panel == null ) || ( current_tree_panel.getPhylogeny() == null ) ) {\r
+ mi.setEnabled( true );\r
+ }\r
+ else if ( AptxUtil.isHasAtLeastOneBranchWithSupportValues( current_tree_panel.getPhylogeny() ) ) {\r
+ mi.setEnabled( true );\r
+ }\r
+ else {\r
+ mi.setEnabled( false );\r
+ }\r
+ mi.setText( "Enter Min Confidence Value... (current: " + options.getMinConfidenceValue() + ")" );\r
+ }\r
+\r
+ static void setTextNodeSizeMenuItem( final JMenuItem mi, final Options options ) {\r
+ mi.setText( "Enter Default Node Shape Size... (current: " + options.getDefaultNodeShapeSize() + ")" );\r
+ }\r
+\r
+ static void updateOptionsMenuDependingOnPhylogenyType( final MainPanel main_panel,\r
+ final JCheckBoxMenuItem scale,\r
+ final JCheckBoxMenuItem branch_lengths,\r
+ final JRadioButtonMenuItem non_lined_up,\r
+ final JRadioButtonMenuItem uniform_clado,\r
+ final JRadioButtonMenuItem nonuniform_clado,\r
+ final JCheckBoxMenuItem label_direction_cbmi ) {\r
+ final TreePanel tree_panel = main_panel.getCurrentTreePanel();\r
+ final ControlPanel control = main_panel.getControlPanel();\r
+ final Options options = main_panel.getOptions();\r
+ scale.setSelected( options.isShowScale() );\r
+ branch_lengths.setSelected( options.isShowBranchLengthValues() );\r
+ // non_lined_up.setSelected( options.isNonLinedUpCladogram() );\r
+ if ( ( tree_panel != null ) && ( !tree_panel.isPhyHasBranchLengths() ) ) {\r
+ scale.setSelected( false );\r
+ scale.setEnabled( false );\r
+ branch_lengths.setSelected( false );\r
+ branch_lengths.setEnabled( false );\r
+ }\r
+ else if ( ( tree_panel != null ) && !control.isDrawPhylogram() ) {\r
+ scale.setSelected( false );\r
+ scale.setEnabled( false );\r
+ branch_lengths.setEnabled( true );\r
+ }\r
+ else {\r
+ scale.setEnabled( true );\r
+ branch_lengths.setEnabled( true );\r
+ }\r
+ if ( ( tree_panel != null )\r
+ && ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.ROUNDED )\r
+ && ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) && ( tree_panel\r
+ .getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) ) ) {\r
+ branch_lengths.setSelected( false );\r
+ branch_lengths.setEnabled( false );\r
+ }\r
+ if ( tree_panel != null ) {\r
+ if ( ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR )\r
+ || ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) {\r
+ non_lined_up.setEnabled( false );\r
+ uniform_clado.setEnabled( false );\r
+ nonuniform_clado.setEnabled( false );\r
+ }\r
+ else {\r
+ non_lined_up.setEnabled( true );\r
+ uniform_clado.setEnabled( true );\r
+ nonuniform_clado.setEnabled( true );\r
+ }\r
+ }\r
+ else {\r
+ if ( ( tree_panel != null )\r
+ && ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) && ( tree_panel\r
+ .getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) ) ) {\r
+ branch_lengths.setSelected( false );\r
+ branch_lengths.setEnabled( false );\r
+ }\r
+ if ( ( tree_panel != null )\r
+ && ( ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) || ( tree_panel\r
+ .getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) ) {\r
+ non_lined_up.setEnabled( false );\r
+ }\r
+ else {\r
+ // non_lined_up.setSelected( options.isNonLinedUpCladogram() );\r
+ non_lined_up.setEnabled( true );\r
+ }\r
+ }\r
+ label_direction_cbmi.setEnabled( true );\r
+ if ( tree_panel != null ) {\r
+ if ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED )\r
+ && ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {\r
+ label_direction_cbmi.setEnabled( false );\r
+ }\r
+ if ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {\r
+ scale.setSelected( false );\r
+ scale.setEnabled( false );\r
+ }\r
+ }\r
+ }\r
+\r
+ static void updateScreenTextAntialias( final List<TreePanel> treepanels ) {\r
+ for( final TreePanel tree_panel : treepanels ) {\r
+ tree_panel.setTextAntialias();\r
+ }\r
+ }\r
+}\r
-// $Id:
-// FORESTER -- software libraries and applications
-// for evolutionary biology research and applications.
-//
-// Copyright (C) 2008-2009 Christian M. Zmasek
-// Copyright (C) 2008-2009 Burnham Institute for Medical Research
-// Copyright (C) 2003-2007 Ethalinda K.S. Cannon
-// All rights reserved
-//
-// This library is free software; you can redistribute it and/or
-// modify it under the terms of the GNU Lesser General Public
-// License as published by the Free Software Foundation; either
-// version 2.1 of the License, or (at your option) any later version.
-//
-// This library is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
-// Lesser General Public License for more details.
-//
-// You should have received a copy of the GNU Lesser General Public
-// License along with this library; if not, write to the Free Software
-// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-//
-// Contact: phylosoft @ gmail . com
-// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
-
-package org.forester.archaeopteryx;
-
-import java.awt.BorderLayout;
-import java.awt.Font;
-import java.awt.event.ActionEvent;
-import java.awt.event.ComponentAdapter;
-import java.awt.event.ComponentEvent;
-import java.awt.event.WindowAdapter;
-import java.awt.event.WindowEvent;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.util.ArrayList;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import javax.swing.ButtonGroup;
-import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JFileChooser;
-import javax.swing.JMenu;
-import javax.swing.JMenuBar;
-import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
-import javax.swing.JRadioButtonMenuItem;
-import javax.swing.UIManager;
-import javax.swing.UnsupportedLookAndFeelException;
-import javax.swing.WindowConstants;
-import javax.swing.event.ChangeEvent;
-import javax.swing.event.ChangeListener;
-import javax.swing.filechooser.FileFilter;
-import javax.swing.plaf.synth.SynthLookAndFeel;
-
-import org.forester.analysis.TaxonomyDataManager;
-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.PhyloInferenceDialog;
-import org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions;
-import org.forester.archaeopteryx.tools.PhylogeneticInferrer;
-import org.forester.archaeopteryx.tools.SequenceDataRetriver;
-import org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient;
-import org.forester.archaeopteryx.webservices.WebservicesManager;
-import org.forester.io.parsers.FastaParser;
-import org.forester.io.parsers.GeneralMsaParser;
-import org.forester.io.parsers.PhylogenyParser;
-import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
-import org.forester.io.parsers.nhx.NHXParser;
-import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
-import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
-import org.forester.io.parsers.phyloxml.PhyloXmlParser;
-import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
-import org.forester.io.parsers.tol.TolParser;
-import org.forester.io.parsers.util.ParserUtils;
-import org.forester.io.writers.PhylogenyWriter;
-import org.forester.io.writers.SequenceWriter;
-import org.forester.msa.Msa;
-import org.forester.msa.MsaFormatException;
-import org.forester.phylogeny.Phylogeny;
-import org.forester.phylogeny.PhylogenyMethods;
-import org.forester.phylogeny.PhylogenyNode;
-import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
-import org.forester.phylogeny.data.Confidence;
-import org.forester.phylogeny.data.Taxonomy;
-import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
-import org.forester.sequence.Sequence;
-import org.forester.util.BasicDescriptiveStatistics;
-import org.forester.util.BasicTable;
-import org.forester.util.BasicTableParser;
-import org.forester.util.DescriptiveStatistics;
-import org.forester.util.ForesterUtil;
-import org.forester.util.WindowsUtils;
-
-public final class MainFrameApplication extends MainFrame {
-
- static final String INFER_ANCESTOR_TAXONOMIES = "Infer Ancestor Taxonomies";
- static final String OBTAIN_DETAILED_TAXONOMIC_INFORMATION = "Obtain Detailed Taxonomic Information";
- private final static int FRAME_X_SIZE = 800;
- private final static int FRAME_Y_SIZE = 800;
- // Filters for the file-open dialog (classes defined in this file)
- private final static NHFilter nhfilter = new NHFilter();
- private final static NHXFilter nhxfilter = new NHXFilter();
- private final static XMLFilter xmlfilter = new XMLFilter();
- private final static TolFilter tolfilter = new TolFilter();
- private final static NexusFilter nexusfilter = new NexusFilter();
- private final static PdfFilter pdffilter = new PdfFilter();
- private final static GraphicsFileFilter graphicsfilefilter = new GraphicsFileFilter();
- private final static MsaFileFilter msafilter = new MsaFileFilter();
- private final static SequencesFileFilter seqsfilter = new SequencesFileFilter();
- private final static DefaultFilter defaultfilter = new DefaultFilter();
- private static final long serialVersionUID = -799735726778865234L;
- private final JFileChooser _values_filechooser;
- private final JFileChooser _sequences_filechooser;
- private final JFileChooser _open_filechooser;
- private final JFileChooser _msa_filechooser;
- private final JFileChooser _seqs_pi_filechooser;
- private final JFileChooser _open_filechooser_for_species_tree;
- private final JFileChooser _save_filechooser;
- private final JFileChooser _writetopdf_filechooser;
- private final JFileChooser _writetographics_filechooser;
- // Application-only print menu items
- private JMenuItem _print_item;
- private JMenuItem _write_to_pdf_item;
- private JMenuItem _write_to_jpg_item;
- private JMenuItem _write_to_gif_item;
- private JMenuItem _write_to_tif_item;
- private JMenuItem _write_to_png_item;
- private JMenuItem _write_to_bmp_item;
- private File _current_dir;
- private ButtonGroup _radio_group_1;
- private ButtonGroup _radio_group_2;
- // Others:
- double _min_not_collapse = Constants.MIN_NOT_COLLAPSE_DEFAULT;
- // Phylogeny Inference menu
- private JMenu _inference_menu;
- private JMenuItem _inference_from_msa_item;
- private JMenuItem _inference_from_seqs_item;
- // Phylogeny Inference
- private PhylogeneticInferenceOptions _phylogenetic_inference_options = null;
- private Msa _msa = null;
- private File _msa_file = null;
- private List<Sequence> _seqs = null;
- private File _seqs_file = null;
- JMenuItem _read_values_jmi;
- JMenuItem _read_seqs_jmi;
-
- private MainFrameApplication( final Phylogeny[] phys, final Configuration config ) {
- _configuration = config;
- if ( _configuration == null ) {
- throw new IllegalArgumentException( "configuration is null" );
- }
- setVisible( false );
- setOptions( Options.createInstance( _configuration ) );
- _mainpanel = new MainPanel( _configuration, this );
- _open_filechooser = null;
- _open_filechooser_for_species_tree = null;
- _save_filechooser = null;
- _writetopdf_filechooser = null;
- _writetographics_filechooser = null;
- _msa_filechooser = null;
- _seqs_pi_filechooser = null;
- _values_filechooser = null;
- _sequences_filechooser = null;
- _jmenubar = new JMenuBar();
- buildFileMenu();
- buildTypeMenu();
- _contentpane = getContentPane();
- _contentpane.setLayout( new BorderLayout() );
- _contentpane.add( _mainpanel, BorderLayout.CENTER );
- // App is this big
- setSize( MainFrameApplication.FRAME_X_SIZE, MainFrameApplication.FRAME_Y_SIZE );
- // The window listener
- setDefaultCloseOperation( WindowConstants.DO_NOTHING_ON_CLOSE );
- addWindowListener( new WindowAdapter() {
-
- @Override
- public void windowClosing( final WindowEvent e ) {
- exit();
- }
- } );
- // setVisible( true );
- if ( ( phys != null ) && ( phys.length > 0 ) ) {
- AptxUtil.addPhylogeniesToTabs( phys, "", null, _configuration, _mainpanel );
- validate();
- getMainPanel().getControlPanel().showWholeAll();
- getMainPanel().getControlPanel().showWhole();
- }
- //activateSaveAllIfNeeded();
- // ...and its children
- _contentpane.repaint();
- }
-
- private MainFrameApplication( final Phylogeny[] phys, final Configuration config, final String title ) {
- this( phys, config, title, null );
- }
-
- private MainFrameApplication( final Phylogeny[] phys,
- final Configuration config,
- final String title,
- final File current_dir ) {
- super();
- _configuration = config;
- if ( _configuration == null ) {
- throw new IllegalArgumentException( "configuration is null" );
- }
- try {
- boolean synth_exception = false;
- if ( Constants.__SYNTH_LF ) {
- try {
- final SynthLookAndFeel synth = new SynthLookAndFeel();
- synth.load( MainFrameApplication.class.getResourceAsStream( "/resources/synth_look_and_feel_1.xml" ),
- MainFrameApplication.class );
- UIManager.setLookAndFeel( synth );
- }
- catch ( final Exception ex ) {
- synth_exception = true;
- ForesterUtil.printWarningMessage( Constants.PRG_NAME,
- "could not create synth look and feel: "
- + ex.getLocalizedMessage() );
- }
- }
- if ( !Constants.__SYNTH_LF || synth_exception ) {
- if ( _configuration.isUseNativeUI() ) {
- UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
- }
- else {
- UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );
- }
- }
- //UIManager.setLookAndFeel( "com.sun.java.swing.plaf.nimbus.NimbusLookAndFeel" );
- }
- catch ( final UnsupportedLookAndFeelException e ) {
- AptxUtil.dieWithSystemError( "unsupported look and feel: " + e.toString() );
- }
- catch ( final ClassNotFoundException e ) {
- AptxUtil.dieWithSystemError( "class not found exception: " + e.toString() );
- }
- catch ( final InstantiationException e ) {
- AptxUtil.dieWithSystemError( "instantiation exception: " + e.toString() );
- }
- catch ( final IllegalAccessException e ) {
- AptxUtil.dieWithSystemError( "illegal access exception: " + e.toString() );
- }
- if ( ( current_dir != null ) && current_dir.canRead() && current_dir.isDirectory() ) {
- setCurrentDir( current_dir );
- }
- // hide until everything is ready
- setVisible( false );
- setOptions( Options.createInstance( _configuration ) );
- setInferenceManager( InferenceManager.createInstance( _configuration ) );
- setPhylogeneticInferenceOptions( PhylogeneticInferenceOptions.createInstance( _configuration ) );
- // _textframe = null; #~~~~
- // set title
- setTitle( Constants.PRG_NAME + " " + Constants.VERSION + " (" + Constants.PRG_DATE + ")" );
- _mainpanel = new MainPanel( _configuration, this );
- // The file dialogs
- _open_filechooser = new JFileChooser();
- _open_filechooser.setCurrentDirectory( new File( "." ) );
- _open_filechooser.setMultiSelectionEnabled( false );
- _open_filechooser.addChoosableFileFilter( MainFrameApplication.xmlfilter );
- _open_filechooser.addChoosableFileFilter( MainFrameApplication.nhxfilter );
- _open_filechooser.addChoosableFileFilter( MainFrameApplication.nhfilter );
- _open_filechooser.addChoosableFileFilter( MainFrameApplication.nexusfilter );
- _open_filechooser.addChoosableFileFilter( MainFrameApplication.tolfilter );
- _open_filechooser.addChoosableFileFilter( _open_filechooser.getAcceptAllFileFilter() );
- _open_filechooser.setFileFilter( MainFrameApplication.defaultfilter );
- _open_filechooser_for_species_tree = new JFileChooser();
- _open_filechooser_for_species_tree.setCurrentDirectory( new File( "." ) );
- _open_filechooser_for_species_tree.setMultiSelectionEnabled( false );
- _open_filechooser_for_species_tree.addChoosableFileFilter( MainFrameApplication.xmlfilter );
- _open_filechooser_for_species_tree.addChoosableFileFilter( MainFrameApplication.tolfilter );
- _open_filechooser_for_species_tree.setFileFilter( MainFrameApplication.xmlfilter );
- _save_filechooser = new JFileChooser();
- _save_filechooser.setCurrentDirectory( new File( "." ) );
- _save_filechooser.setMultiSelectionEnabled( false );
- _save_filechooser.setFileFilter( MainFrameApplication.xmlfilter );
- _save_filechooser.addChoosableFileFilter( MainFrameApplication.nhfilter );
- _save_filechooser.addChoosableFileFilter( MainFrameApplication.nexusfilter );
- _save_filechooser.addChoosableFileFilter( _save_filechooser.getAcceptAllFileFilter() );
- _writetopdf_filechooser = new JFileChooser();
- _writetopdf_filechooser.addChoosableFileFilter( MainFrameApplication.pdffilter );
- _writetographics_filechooser = new JFileChooser();
- _writetographics_filechooser.addChoosableFileFilter( MainFrameApplication.graphicsfilefilter );
- // Msa:
- _msa_filechooser = new JFileChooser();
- _msa_filechooser.setName( "Read Multiple Sequence Alignment File" );
- _msa_filechooser.setCurrentDirectory( new File( "." ) );
- _msa_filechooser.setMultiSelectionEnabled( false );
- _msa_filechooser.addChoosableFileFilter( _msa_filechooser.getAcceptAllFileFilter() );
- _msa_filechooser.addChoosableFileFilter( MainFrameApplication.msafilter );
- // Seqs:
- _seqs_pi_filechooser = new JFileChooser();
- _seqs_pi_filechooser.setName( "Read Sequences File" );
- _seqs_pi_filechooser.setCurrentDirectory( new File( "." ) );
- _seqs_pi_filechooser.setMultiSelectionEnabled( false );
- _seqs_pi_filechooser.addChoosableFileFilter( _seqs_pi_filechooser.getAcceptAllFileFilter() );
- _seqs_pi_filechooser.addChoosableFileFilter( MainFrameApplication.seqsfilter );
- // Expression
- _values_filechooser = new JFileChooser();
- _values_filechooser.setCurrentDirectory( new File( "." ) );
- _values_filechooser.setMultiSelectionEnabled( false );
- // Sequences
- _sequences_filechooser = new JFileChooser();
- _sequences_filechooser.setCurrentDirectory( new File( "." ) );
- _sequences_filechooser.setMultiSelectionEnabled( false );
- // build the menu bar
- _jmenubar = new JMenuBar();
- if ( !_configuration.isUseNativeUI() ) {
- _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
- }
- buildFileMenu();
- if ( Constants.__ALLOW_PHYLOGENETIC_INFERENCE ) {
- buildPhylogeneticInferenceMenu();
- }
- buildAnalysisMenu();
- buildToolsMenu();
- buildViewMenu();
- buildFontSizeMenu();
- buildOptionsMenu();
- buildTypeMenu();
- buildHelpMenu();
- setJMenuBar( _jmenubar );
- _jmenubar.add( _help_jmenu );
- _contentpane = getContentPane();
- _contentpane.setLayout( new BorderLayout() );
- _contentpane.add( _mainpanel, BorderLayout.CENTER );
- // App is this big
- setSize( MainFrameApplication.FRAME_X_SIZE, MainFrameApplication.FRAME_Y_SIZE );
- // addWindowFocusListener( new WindowAdapter() {
- //
- // @Override
- // public void windowGainedFocus( WindowEvent e ) {
- // requestFocusInWindow();
- // }
- // } );
- // The window listener
- setDefaultCloseOperation( WindowConstants.DO_NOTHING_ON_CLOSE );
- addWindowListener( new WindowAdapter() {
-
- @Override
- public void windowClosing( final WindowEvent e ) {
- if ( isUnsavedDataPresent() ) {
- final int r = JOptionPane.showConfirmDialog( null,
- "Exit despite potentially unsaved changes?",
- "Exit?",
- JOptionPane.YES_NO_OPTION );
- if ( r != JOptionPane.YES_OPTION ) {
- return;
- }
- }
- else {
- final int r = JOptionPane.showConfirmDialog( null,
- "Exit Archaeopteryx?",
- "Exit?",
- JOptionPane.YES_NO_OPTION );
- if ( r != JOptionPane.YES_OPTION ) {
- return;
- }
- }
- exit();
- }
- } );
- // The component listener
- addComponentListener( new ComponentAdapter() {
-
- @Override
- public void componentResized( final ComponentEvent e ) {
- if ( _mainpanel.getCurrentTreePanel() != null ) {
- _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel()
- .getWidth(),
- _mainpanel.getCurrentTreePanel()
- .getHeight(),
- getOptions().isAllowFontSizeChange() );
- }
- }
- } );
- requestFocusInWindow();
- // addKeyListener( this );
- setVisible( true );
- if ( ( phys != null ) && ( phys.length > 0 ) ) {
- AptxUtil.addPhylogeniesToTabs( phys, title, null, _configuration, _mainpanel );
- validate();
- getMainPanel().getControlPanel().showWholeAll();
- getMainPanel().getControlPanel().showWhole();
- }
- activateSaveAllIfNeeded();
- // ...and its children
- _contentpane.repaint();
- System.gc();
- }
-
- private MainFrameApplication( final Phylogeny[] phys, final String config_file, final String title ) {
- // Reads the config file (false, false => not url, not applet):
- this( phys, new Configuration( config_file, false, false, true ), title );
- }
-
- @Override
- public void actionPerformed( final ActionEvent e ) {
- try {
- super.actionPerformed( e );
- final Object o = e.getSource();
- // Handle app-specific actions here:
- if ( o == _open_item ) {
- readPhylogeniesFromFile();
- }
- else if ( o == _save_item ) {
- writeToFile( _mainpanel.getCurrentPhylogeny() );
- // If subtree currently displayed, save it, instead of complete
- // tree.
- }
- else if ( o == _new_item ) {
- newTree();
- }
- else if ( o == _save_all_item ) {
- writeAllToFile();
- }
- else if ( o == _close_item ) {
- closeCurrentPane();
- }
- else if ( o == _write_to_pdf_item ) {
- writeToPdf( _mainpanel.getCurrentPhylogeny() );
- }
- else if ( o == _write_to_jpg_item ) {
- writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.JPG );
- }
- else if ( o == _write_to_png_item ) {
- writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.PNG );
- }
- else if ( o == _write_to_gif_item ) {
- writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.GIF );
- }
- else if ( o == _write_to_tif_item ) {
- writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.TIFF );
- }
- else if ( o == _write_to_bmp_item ) {
- writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.BMP );
- }
- else if ( o == _print_item ) {
- print();
- }
- else if ( o == _load_species_tree_item ) {
- readSpeciesTreeFromFile();
- }
- else if ( o == _lineage_inference ) {
- if ( isSubtreeDisplayed() ) {
- JOptionPane.showMessageDialog( this,
- "Subtree is shown.",
- "Cannot infer ancestral taxonomies",
- JOptionPane.ERROR_MESSAGE );
- return;
- }
- executeLineageInference();
- }
- else if ( o == _obtain_detailed_taxonomic_information_jmi ) {
- if ( isSubtreeDisplayed() ) {
- return;
- }
- obtainDetailedTaxonomicInformation();
- }
- else if ( o == _obtain_detailed_taxonomic_information_deleting_jmi ) {
- if ( isSubtreeDisplayed() ) {
- return;
- }
- obtainDetailedTaxonomicInformationDelete();
- }
- else if ( o == _obtain_seq_information_jmi ) {
- obtainSequenceInformation();
- }
- else if ( o == _read_values_jmi ) {
- if ( isSubtreeDisplayed() ) {
- return;
- }
- addExpressionValuesFromFile();
- }
- else if ( o == _read_seqs_jmi ) {
- if ( isSubtreeDisplayed() ) {
- return;
- }
- addSequencesFromFile();
- }
- else if ( o == _move_node_names_to_tax_sn_jmi ) {
- moveNodeNamesToTaxSn();
- }
- else if ( o == _move_node_names_to_seq_names_jmi ) {
- moveNodeNamesToSeqNames();
- }
- else if ( o == _extract_tax_code_from_node_names_jmi ) {
- extractTaxDataFromNodeNames();
- }
- else if ( o == _graphics_export_visible_only_cbmi ) {
- updateOptions( getOptions() );
- }
- else if ( o == _antialias_print_cbmi ) {
- updateOptions( getOptions() );
- }
- else if ( o == _print_black_and_white_cbmi ) {
- updateOptions( getOptions() );
- }
- else if ( o == _print_using_actual_size_cbmi ) {
- updateOptions( getOptions() );
- }
- else if ( o == _graphics_export_using_actual_size_cbmi ) {
- updateOptions( getOptions() );
- }
- else if ( o == _print_size_mi ) {
- choosePrintSize();
- }
- else if ( o == _choose_pdf_width_mi ) {
- choosePdfWidth();
- }
- else if ( o == _internal_number_are_confidence_for_nh_parsing_cbmi ) {
- updateOptions( getOptions() );
- }
- else if ( o == _replace_underscores_cbmi ) {
- if ( ( _extract_taxonomy_no_rbmi != null ) && !_extract_taxonomy_no_rbmi.isSelected() ) {
- _extract_taxonomy_no_rbmi.setSelected( true );
- }
- updateOptions( getOptions() );
- }
- else if ( o == _allow_errors_in_distance_to_parent_cbmi ) {
- updateOptions( getOptions() );
- }
- else if ( o == _collapse_below_threshold ) {
- if ( isSubtreeDisplayed() ) {
- return;
- }
- collapseBelowThreshold();
- }
- else if ( ( o == _extract_taxonomy_pfam_strict_rbmi ) || ( o == _extract_taxonomy_pfam_relaxed_rbmi )
- || ( o == _extract_taxonomy_agressive_rbmi ) ) {
- if ( _replace_underscores_cbmi != null ) {
- _replace_underscores_cbmi.setSelected( false );
- }
- updateOptions( getOptions() );
- }
- else if ( o == _extract_taxonomy_no_rbmi ) {
- updateOptions( getOptions() );
- }
- else if ( o == _inference_from_msa_item ) {
- executePhyleneticInference( false );
- }
- else if ( o == _inference_from_seqs_item ) {
- executePhyleneticInference( true );
- }
- _contentpane.repaint();
- }
- catch ( final Exception ex ) {
- AptxUtil.unexpectedException( ex );
- }
- catch ( final Error err ) {
- AptxUtil.unexpectedError( err );
- }
- }
-
- public void end() {
- _mainpanel.terminate();
- _contentpane.removeAll();
- setVisible( false );
- dispose();
- }
-
- @Override
- public MainPanel getMainPanel() {
- return _mainpanel;
- }
-
- public Msa getMsa() {
- return _msa;
- }
-
- public File getMsaFile() {
- return _msa_file;
- }
-
- public List<Sequence> getSeqs() {
- return _seqs;
- }
-
- public File getSeqsFile() {
- return _seqs_file;
- }
-
- public void readMsaFromFile() {
- // Set an initial directory if none set yet
- final File my_dir = getCurrentDir();
- _msa_filechooser.setMultiSelectionEnabled( false );
- // Open file-open dialog and set current directory
- if ( my_dir != null ) {
- _msa_filechooser.setCurrentDirectory( my_dir );
- }
- final int result = _msa_filechooser.showOpenDialog( _contentpane );
- // All done: get the msa
- final File file = _msa_filechooser.getSelectedFile();
- setCurrentDir( _msa_filechooser.getCurrentDirectory() );
- if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {
- setMsaFile( null );
- setMsa( null );
- Msa msa = null;
- try {
- final InputStream is = new FileInputStream( file );
- if ( FastaParser.isLikelyFasta( file ) ) {
- msa = FastaParser.parseMsa( is );
- }
- else {
- msa = GeneralMsaParser.parse( is );
- }
- }
- catch ( final MsaFormatException e ) {
- setArrowCursor();
- JOptionPane.showMessageDialog( this,
- e.getLocalizedMessage(),
- "Multiple sequence alignment format error",
- JOptionPane.ERROR_MESSAGE );
- return;
- }
- catch ( final IOException e ) {
- setArrowCursor();
- JOptionPane.showMessageDialog( this,
- e.getLocalizedMessage(),
- "Failed to read multiple sequence alignment",
- JOptionPane.ERROR_MESSAGE );
- return;
- }
- catch ( final IllegalArgumentException e ) {
- setArrowCursor();
- JOptionPane.showMessageDialog( this,
- e.getLocalizedMessage(),
- "Unexpected error during reading of multiple sequence alignment",
- JOptionPane.ERROR_MESSAGE );
- return;
- }
- catch ( final Exception e ) {
- setArrowCursor();
- e.printStackTrace();
- JOptionPane.showMessageDialog( this,
- e.getLocalizedMessage(),
- "Unexpected error during reading of multiple sequence alignment",
- JOptionPane.ERROR_MESSAGE );
- return;
- }
- if ( ( msa == null ) || ( msa.getNumberOfSequences() < 1 ) ) {
- JOptionPane.showMessageDialog( this,
- "Multiple sequence alignment is empty",
- "Illegal Multiple Sequence Alignment",
- JOptionPane.ERROR_MESSAGE );
- return;
- }
- if ( msa.getNumberOfSequences() < 4 ) {
- JOptionPane.showMessageDialog( this,
- "Multiple sequence alignment needs to contain at least 3 sequences",
- "Illegal multiple sequence alignment",
- JOptionPane.ERROR_MESSAGE );
- return;
- }
- if ( msa.getLength() < 2 ) {
- JOptionPane.showMessageDialog( this,
- "Multiple sequence alignment needs to contain at least 2 residues",
- "Illegal multiple sequence alignment",
- JOptionPane.ERROR_MESSAGE );
- return;
- }
- System.gc();
- setMsaFile( _msa_filechooser.getSelectedFile() );
- setMsa( msa );
- }
- }
-
- public void readSeqsFromFileforPI() {
- // Set an initial directory if none set yet
- final File my_dir = getCurrentDir();
- _seqs_pi_filechooser.setMultiSelectionEnabled( false );
- // Open file-open dialog and set current directory
- if ( my_dir != null ) {
- _seqs_pi_filechooser.setCurrentDirectory( my_dir );
- }
- final int result = _seqs_pi_filechooser.showOpenDialog( _contentpane );
- // All done: get the seqs
- final File file = _seqs_pi_filechooser.getSelectedFile();
- setCurrentDir( _seqs_pi_filechooser.getCurrentDirectory() );
- if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {
- setSeqsFile( null );
- setSeqs( null );
- List<Sequence> seqs = null;
- try {
- if ( FastaParser.isLikelyFasta( new FileInputStream( file ) ) ) {
- seqs = FastaParser.parse( new FileInputStream( file ) );
- for( final Sequence seq : seqs ) {
- System.out.println( SequenceWriter.toFasta( seq, 60 ) );
- }
- }
- else {
- //TODO error
- }
- }
- catch ( final MsaFormatException e ) {
- setArrowCursor();
- JOptionPane.showMessageDialog( this,
- e.getLocalizedMessage(),
- "Multiple sequence file format error",
- JOptionPane.ERROR_MESSAGE );
- return;
- }
- catch ( final IOException e ) {
- setArrowCursor();
- JOptionPane.showMessageDialog( this,
- e.getLocalizedMessage(),
- "Failed to read multiple sequence file",
- JOptionPane.ERROR_MESSAGE );
- return;
- }
- catch ( final IllegalArgumentException e ) {
- setArrowCursor();
- JOptionPane.showMessageDialog( this,
- e.getLocalizedMessage(),
- "Unexpected error during reading of multiple sequence file",
- JOptionPane.ERROR_MESSAGE );
- return;
- }
- catch ( final Exception e ) {
- setArrowCursor();
- e.printStackTrace();
- JOptionPane.showMessageDialog( this,
- e.getLocalizedMessage(),
- "Unexpected error during reading of multiple sequence file",
- JOptionPane.ERROR_MESSAGE );
- return;
- }
- if ( ( seqs == null ) || ( seqs.size() < 1 ) ) {
- JOptionPane.showMessageDialog( this,
- "Multiple sequence file is empty",
- "Illegal multiple sequence file",
- JOptionPane.ERROR_MESSAGE );
- return;
- }
- if ( seqs.size() < 4 ) {
- JOptionPane.showMessageDialog( this,
- "Multiple sequence file needs to contain at least 3 sequences",
- "Illegal multiple sequence file",
- JOptionPane.ERROR_MESSAGE );
- return;
- }
- // if ( msa.getLength() < 2 ) {
- // JOptionPane.showMessageDialog( this,
- // "Multiple sequence alignment needs to contain at least 2 residues",
- // "Illegal multiple sequence file",
- // JOptionPane.ERROR_MESSAGE );
- // return;
- // }
- System.gc();
- setSeqsFile( _seqs_pi_filechooser.getSelectedFile() );
- setSeqs( seqs );
- }
- }
-
- void buildAnalysisMenu() {
- _analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );
- _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );
- _analysis_menu.add( _gsdir_item = new JMenuItem( "GSDIR (GSDI with re-rooting)" ) );
- _analysis_menu.add( _load_species_tree_item = new JMenuItem( "Load Species Tree..." ) );
- customizeJMenuItem( _gsdi_item );
- customizeJMenuItem( _gsdir_item );
- customizeJMenuItem( _load_species_tree_item );
- _analysis_menu.addSeparator();
- _analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) );
- customizeJMenuItem( _lineage_inference );
- _lineage_inference.setToolTipText( "Inference of ancestor taxonomies/lineages" );
- _jmenubar.add( _analysis_menu );
- }
-
- @Override
- void buildFileMenu() {
- _file_jmenu = MainFrame.createMenu( "File", getConfiguration() );
- _file_jmenu.add( _open_item = new JMenuItem( "Read Tree from File..." ) );
- _file_jmenu.addSeparator();
- final WebservicesManager webservices_manager = WebservicesManager.getInstance();
- _load_phylogeny_from_webservice_menu_items = new JMenuItem[ webservices_manager
- .getAvailablePhylogeniesWebserviceClients().size() ];
- for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {
- final PhylogeniesWebserviceClient client = webservices_manager.getAvailablePhylogeniesWebserviceClient( i );
- _load_phylogeny_from_webservice_menu_items[ i ] = new JMenuItem( client.getMenuName() );
- _file_jmenu.add( _load_phylogeny_from_webservice_menu_items[ i ] );
- }
- if ( getConfiguration().isEditable() ) {
- _file_jmenu.addSeparator();
- _file_jmenu.add( _new_item = new JMenuItem( "New" ) );
- _new_item.setToolTipText( "to create a new tree with one node, as source for manual tree construction" );
- }
- _file_jmenu.addSeparator();
- _file_jmenu.add( _save_item = new JMenuItem( "Save Tree As..." ) );
- _file_jmenu.add( _save_all_item = new JMenuItem( "Save All Trees As..." ) );
- _save_all_item.setToolTipText( "Write all phylogenies to one file." );
- _save_all_item.setEnabled( false );
- _file_jmenu.addSeparator();
- _file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) );
- if ( 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( _close_item = new JMenuItem( "Close Tab" ) );
- _close_item.setToolTipText( "To close the current pane." );
- _close_item.setEnabled( true );
- _file_jmenu.addSeparator();
- _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );
- // For print in color option item
- customizeJMenuItem( _open_item );
- _open_item
- .setFont( new Font( _open_item.getFont().getFontName(), Font.BOLD, _open_item.getFont().getSize() + 4 ) );
- for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {
- customizeJMenuItem( _load_phylogeny_from_webservice_menu_items[ i ] );
- }
- customizeJMenuItem( _save_item );
- if ( getConfiguration().isEditable() ) {
- customizeJMenuItem( _new_item );
- }
- customizeJMenuItem( _close_item );
- customizeJMenuItem( _save_all_item );
- customizeJMenuItem( _write_to_pdf_item );
- customizeJMenuItem( _write_to_png_item );
- customizeJMenuItem( _write_to_jpg_item );
- customizeJMenuItem( _write_to_gif_item );
- customizeJMenuItem( _write_to_tif_item );
- customizeJMenuItem( _write_to_bmp_item );
- customizeJMenuItem( _print_item );
- customizeJMenuItem( _exit_item );
- _jmenubar.add( _file_jmenu );
- }
-
- void buildOptionsMenu() {
- _options_jmenu = MainFrame.createMenu( OPTIONS_HEADER, getConfiguration() );
- _options_jmenu.addChangeListener( new ChangeListener() {
-
- @Override
- public void stateChanged( final ChangeEvent e ) {
- MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
- MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
- MainFrame
- .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
- MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame
- .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );
- setTextForGraphicsSizeChooserMenuItem( _print_size_mi, getOptions() );
- setTextForPdfLineWidthChooserMenuItem( _choose_pdf_width_mi, getOptions() );
- MainFrame.updateOptionsMenuDependingOnPhylogenyType( getMainPanel(),
- _show_scale_cbmi,
- _show_branch_length_values_cbmi,
- _non_lined_up_cladograms_rbmi,
- _uniform_cladograms_rbmi,
- _ext_node_dependent_cladogram_rbmi,
- _label_direction_cbmi );
- MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
- MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
- MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
- }
- } );
- _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( DISPLAY_SUBHEADER ), getConfiguration() ) );
- _options_jmenu
- .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
- _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );
- _options_jmenu.add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( NON_LINED_UP_CLADOGRAMS_LABEL ) );
- _radio_group_1 = new ButtonGroup();
- _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
- _radio_group_1.add( _uniform_cladograms_rbmi );
- _radio_group_1.add( _non_lined_up_cladograms_rbmi );
- ///////
- _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( SHOW_OVERVIEW_LABEL ) );
- _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( DISPLAY_SCALE_LABEL ) );
- _options_jmenu
- .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );
- _options_jmenu
- .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_INT ) );
- _options_jmenu
- .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_EXT ) );
- if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
- _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( SHOW_DOMAIN_LABELS_LABEL ) );
- }
- _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( SHOW_ANN_REF_SOURCE_LABEL ) );
- _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( SHOW_CONF_STDDEV_LABEL ) );
- _options_jmenu.add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( COLOR_BY_TAXONOMIC_GROUP ) );
- _options_jmenu.add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( COLOR_LABELS_LABEL ) );
- _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
- _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( ABBREV_SN_LABEL ) );
- _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( LABEL_DIRECTION_LABEL ) );
- _label_direction_cbmi.setToolTipText( LABEL_DIRECTION_TIP );
- _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( SCREEN_ANTIALIAS_LABEL ) );
- _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( BG_GRAD_LABEL ) );
- _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
- _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
- _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
- _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
- _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
- _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
- _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
- ///////
- _options_jmenu.addSeparator();
- _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( SEARCH_SUBHEADER ), getConfiguration() ) );
- _options_jmenu.add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( SEARCH_CASE_SENSITIVE_LABEL ) );
- _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( SEARCH_TERMS_ONLY_LABEL ) );
- _options_jmenu.add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( INVERSE_SEARCH_RESULT_LABEL ) );
- _options_jmenu.addSeparator();
- _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Graphics Export & Printing:" ),
- getConfiguration() ) );
- _options_jmenu.add( _antialias_print_cbmi = new JCheckBoxMenuItem( "Antialias" ) );
- _options_jmenu.add( _print_black_and_white_cbmi = new JCheckBoxMenuItem( "Export in Black and White" ) );
- _options_jmenu
- .add( _print_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PDF export and Printing" ) );
- _options_jmenu
- .add( _graphics_export_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PNG, JPG, and GIF export" ) );
- _options_jmenu
- .add( _graphics_export_visible_only_cbmi = new JCheckBoxMenuItem( "Limit to Visible ('Screenshot') for PNG, JPG, and GIF export" ) );
- _options_jmenu.add( _print_size_mi = new JMenuItem( "" ) );
- _options_jmenu.add( _choose_pdf_width_mi = new JMenuItem( "" ) );
- _options_jmenu.addSeparator();
- _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/NHX/Nexus Input:" ), getConfiguration() ) );
- _options_jmenu
- .add( _internal_number_are_confidence_for_nh_parsing_cbmi = new JCheckBoxMenuItem( "Internal Node Names are Confidence Values" ) );
- _options_jmenu.add( _replace_underscores_cbmi = new JCheckBoxMenuItem( "Replace Underscores with Spaces" ) );
- _options_jmenu
- .add( _allow_errors_in_distance_to_parent_cbmi = new JCheckBoxMenuItem( "Ignore Distance Values Format Errors" ) );
- //
- _options_jmenu.add( _extract_taxonomy_no_rbmi = new JRadioButtonMenuItem( "No Taxonomy Extraction" ) );
- _options_jmenu
- .add( _extract_taxonomy_pfam_strict_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style Node Names" ) );
- _options_jmenu
- .add( _extract_taxonomy_pfam_relaxed_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style like Node Names" ) );
- _options_jmenu
- .add( _extract_taxonomy_agressive_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids/Scientific Names from Node Names" ) );
- _extract_taxonomy_pfam_strict_rbmi
- .setToolTipText( "To extract taxonomy codes/ids from node names in the form of e.g. \"BCL2_MOUSE/123-304\" or \"BCL2_10090/123-304\"" );
- _extract_taxonomy_pfam_relaxed_rbmi
- .setToolTipText( "To extract taxonomy codes/ids from node names in the form of e.g. \"bax_MOUSE\" or \"bax_10090\"" );
- _extract_taxonomy_agressive_rbmi
- .setToolTipText( "To extract taxonomy codes/ids or scientific names from node names in the form of e.g. \"MOUSE\" or \"10090\" or \"xyz_Nematostella_vectensis\"" );
- _radio_group_2 = new ButtonGroup();
- _radio_group_2.add( _extract_taxonomy_no_rbmi );
- _radio_group_2.add( _extract_taxonomy_pfam_strict_rbmi );
- _radio_group_2.add( _extract_taxonomy_pfam_relaxed_rbmi );
- _radio_group_2.add( _extract_taxonomy_agressive_rbmi );
- //
- _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/Nexus Output:" ), getConfiguration() ) );
- _options_jmenu
- .add( _use_brackets_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_BRACKETS_FOR_CONF_IN_NH_LABEL ) );
- _use_brackets_for_conf_in_nh_export_cbmi
- .setToolTipText( "e.g. \"0.1[90]\" for a branch with support 90 and a length of 0.1" );
- _options_jmenu
- .add( _use_internal_names_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL ) );
- customizeJMenuItem( _choose_font_mi );
- customizeJMenuItem( _choose_minimal_confidence_mi );
- customizeJMenuItem( _switch_colors_mi );
- customizeJMenuItem( _print_size_mi );
- customizeJMenuItem( _choose_pdf_width_mi );
- customizeJMenuItem( _overview_placment_mi );
- customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions()
- .isShowDefaultNodeShapesExternal() );
- customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()
- .isShowDefaultNodeShapesInternal() );
- customizeJMenuItem( _cycle_node_shape_mi );
- customizeJMenuItem( _cycle_node_fill_mi );
- customizeJMenuItem( _choose_node_size_mi );
- customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
- customizeCheckBoxMenuItem( _color_by_taxonomic_group_cbmi, getOptions().isColorByTaxonomicGroup() );
- customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
- customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
- customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );
- customizeCheckBoxMenuItem( _show_annotation_ref_source, getOptions().isShowAnnotationRefSource() );
- customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
- customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );
- customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );
- customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,
- getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );
- customizeRadioButtonMenuItem( _uniform_cladograms_rbmi,
- getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
- customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
- getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
- customizeCheckBoxMenuItem( _show_branch_length_values_cbmi, getOptions().isShowBranchLengthValues() );
- customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
- customizeCheckBoxMenuItem( _label_direction_cbmi,
- getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
- customizeCheckBoxMenuItem( _antialias_print_cbmi, getOptions().isAntialiasPrint() );
- customizeCheckBoxMenuItem( _print_black_and_white_cbmi, getOptions().isPrintBlackAndWhite() );
- customizeCheckBoxMenuItem( _internal_number_are_confidence_for_nh_parsing_cbmi, getOptions()
- .isInternalNumberAreConfidenceForNhParsing() );
- customizeRadioButtonMenuItem( _extract_taxonomy_no_rbmi,
- getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.NO );
- customizeRadioButtonMenuItem( _extract_taxonomy_pfam_strict_rbmi,
- getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
- customizeRadioButtonMenuItem( _extract_taxonomy_pfam_relaxed_rbmi,
- getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
- customizeRadioButtonMenuItem( _extract_taxonomy_agressive_rbmi,
- getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.AGGRESSIVE );
- customizeCheckBoxMenuItem( _replace_underscores_cbmi, getOptions().isReplaceUnderscoresInNhParsing() );
- customizeCheckBoxMenuItem( _allow_errors_in_distance_to_parent_cbmi, getOptions()
- .isReplaceUnderscoresInNhParsing() );
- customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
- customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
- customizeCheckBoxMenuItem( _graphics_export_visible_only_cbmi, getOptions().isGraphicsExportVisibleOnly() );
- customizeCheckBoxMenuItem( _print_using_actual_size_cbmi, getOptions().isPrintUsingActualSize() );
- customizeCheckBoxMenuItem( _graphics_export_using_actual_size_cbmi, getOptions()
- .isGraphicsExportUsingActualSize() );
- customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
- customizeCheckBoxMenuItem( _use_brackets_for_conf_in_nh_export_cbmi, getOptions()
- .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );
- customizeCheckBoxMenuItem( _use_internal_names_for_conf_in_nh_export_cbmi, getOptions()
- .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );
- _jmenubar.add( _options_jmenu );
- }
-
- void buildPhylogeneticInferenceMenu() {
- final InferenceManager im = getInferenceManager();
- _inference_menu = MainFrame.createMenu( "Inference", getConfiguration() );
- _inference_menu.add( _inference_from_msa_item = new JMenuItem( "From Multiple Sequence Alignment..." ) );
- customizeJMenuItem( _inference_from_msa_item );
- _inference_from_msa_item.setToolTipText( "Basic phylogenetic inference from MSA" );
- if ( im.canDoMsa() ) {
- _inference_menu.add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences..." ) );
- customizeJMenuItem( _inference_from_seqs_item );
- _inference_from_seqs_item
- .setToolTipText( "Basic phylogenetic inference including multiple sequence alignment" );
- }
- else {
- _inference_menu
- .add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences (no program found)" ) );
- customizeJMenuItem( _inference_from_seqs_item );
- _inference_from_seqs_item.setEnabled( false );
- }
- _jmenubar.add( _inference_menu );
- }
-
- void buildToolsMenu() {
- _tools_menu = createMenu( "Tools", getConfiguration() );
- _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );
- customizeJMenuItem( _confcolor_item );
- _tools_menu.add( _color_rank_jmi = new JMenuItem( "Colorize Subtrees via Taxonomic Rank" ) );
- customizeJMenuItem( _color_rank_jmi );
- _color_rank_jmi.setToolTipText( "for example, at \"Class\" level, colorize mammal specific subtree red" );
- _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );
- customizeJMenuItem( _taxcolor_item );
- _tools_menu.addSeparator();
- _tools_menu.add( _remove_visual_styles_item = new JMenuItem( "Delete All Visual Styles From Nodes" ) );
- _remove_visual_styles_item
- .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny." );
- customizeJMenuItem( _remove_visual_styles_item );
- _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete All Colors From Branches" ) );
- _remove_branch_color_item.setToolTipText( "To remove all branch color values from the current phylogeny." );
- customizeJMenuItem( _remove_branch_color_item );
- _tools_menu.addSeparator();
- _tools_menu.add( _annotate_item = new JMenuItem( "Annotate Sequences of Selected Nodes" ) );
- customizeJMenuItem( _annotate_item );
- _tools_menu.addSeparator();
- _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );
- customizeJMenuItem( _midpoint_root_item );
- _tools_menu.addSeparator();
- _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );
- customizeJMenuItem( _collapse_species_specific_subtrees );
- _tools_menu
- .add( _collapse_below_threshold = new JMenuItem( "Collapse Branches with Confidence Below Threshold into Multifurcations" ) );
- customizeJMenuItem( _collapse_below_threshold );
- _collapse_below_threshold
- .setToolTipText( "To collapse branches with confidence values below a threshold into multifurcations (in the case of multiple confidences per branch: without at least one confidence value above a threshold)" );
- _tools_menu.addSeparator();
- _tools_menu
- .add( _extract_tax_code_from_node_names_jmi = new JMenuItem( "Extract Taxonomic Data from Node Names" ) );
- customizeJMenuItem( _extract_tax_code_from_node_names_jmi );
- _extract_tax_code_from_node_names_jmi
- .setToolTipText( "To extract SwissProt/Uniprot taxonomic codes (mnemonics) from nodes names in the form of 'xyz_CAEEL', Uniprot/NCBI identifiers form of 'xyz_6239', or scientific names form of 'xyz_Caenorhabditis_elegans'" );
- _tools_menu
- .add( _move_node_names_to_tax_sn_jmi = new JMenuItem( "Transfer Node Names to Taxonomic Scientific Names" ) );
- customizeJMenuItem( _move_node_names_to_tax_sn_jmi );
- _move_node_names_to_tax_sn_jmi.setToolTipText( "To interpret node names as taxonomic scientific names" );
- _tools_menu.add( _move_node_names_to_seq_names_jmi = new JMenuItem( "Transfer Node Names to Sequence Names" ) );
- customizeJMenuItem( _move_node_names_to_seq_names_jmi );
- _move_node_names_to_seq_names_jmi.setToolTipText( "To interpret node names as sequence (protein, gene) names" );
- _tools_menu.addSeparator();
- _tools_menu.add( _obtain_seq_information_jmi = new JMenuItem( "Obtain Sequence Information" ) );
- customizeJMenuItem( _obtain_seq_information_jmi );
- _obtain_seq_information_jmi.setToolTipText( "To add additional sequence information" );
- _tools_menu
- .add( _obtain_detailed_taxonomic_information_jmi = new JMenuItem( OBTAIN_DETAILED_TAXONOMIC_INFORMATION ) );
- customizeJMenuItem( _obtain_detailed_taxonomic_information_jmi );
- _obtain_detailed_taxonomic_information_jmi
- .setToolTipText( "To add additional taxonomic information (from UniProt Taxonomy)" );
- _tools_menu
- .add( _obtain_detailed_taxonomic_information_deleting_jmi = new JMenuItem( "Obtain Detailed Taxonomic Information (deletes nodes!)" ) );
- customizeJMenuItem( _obtain_detailed_taxonomic_information_deleting_jmi );
- _obtain_detailed_taxonomic_information_deleting_jmi
- .setToolTipText( "To add additional taxonomic information, deletes nodes for which taxonomy cannot found (from UniProt Taxonomy)" );
- _tools_menu.addSeparator();
- _tools_menu.add( _read_values_jmi = new JMenuItem( "Attach Vector/Expression Values" ) );
- customizeJMenuItem( _read_values_jmi );
- _read_values_jmi.setToolTipText( "To attach vector (e.g. gene expression) values to tree nodes (beta)" );
- _jmenubar.add( _tools_menu );
- _tools_menu.add( _read_seqs_jmi = new JMenuItem( "Attach Molecular Sequences" ) );
- customizeJMenuItem( _read_seqs_jmi );
- _read_seqs_jmi
- .setToolTipText( "To attach molecular sequences to tree nodes (from Fasta-formatted file) (beta)" );
- _jmenubar.add( _tools_menu );
- }
-
- @Override
- void close() {
- if ( isUnsavedDataPresent() ) {
- final int r = JOptionPane.showConfirmDialog( this,
- "Exit despite potentially unsaved changes?",
- "Exit?",
- JOptionPane.YES_NO_OPTION );
- if ( r != JOptionPane.YES_OPTION ) {
- return;
- }
- }
- exit();
- }
-
- void executeLineageInference() {
- if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) {
- return;
- }
- if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
- JOptionPane.showMessageDialog( this,
- "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();
- }
-
- void exit() {
- removeAllTextFrames();
- _mainpanel.terminate();
- _contentpane.removeAll();
- setVisible( false );
- dispose();
- System.exit( 0 );
- }
-
- void setMsa( final Msa msa ) {
- _msa = msa;
- }
-
- void setMsaFile( final File msa_file ) {
- _msa_file = msa_file;
- }
-
- void setSeqs( final List<Sequence> seqs ) {
- _seqs = seqs;
- }
-
- void setSeqsFile( final File seqs_file ) {
- _seqs_file = seqs_file;
- }
-
- void writePhylogenyToGraphicsFile( final String file_name, final GraphicsExportType type ) {
- _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel().getWidth(),
- _mainpanel.getCurrentTreePanel().getHeight(),
- true );
- String file_written_to = "";
- boolean error = false;
- try {
- file_written_to = AptxUtil.writePhylogenyToGraphicsFile( file_name,
- _mainpanel.getCurrentTreePanel().getWidth(),
- _mainpanel.getCurrentTreePanel().getHeight(),
- _mainpanel.getCurrentTreePanel(),
- _mainpanel.getControlPanel(),
- type,
- getOptions() );
- }
- catch ( final IOException e ) {
- error = true;
- JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );
- }
- if ( !error ) {
- if ( ( file_written_to != null ) && ( file_written_to.length() > 0 ) ) {
- JOptionPane.showMessageDialog( this,
- "Wrote image to: " + file_written_to,
- "Graphics Export",
- JOptionPane.INFORMATION_MESSAGE );
- }
- else {
- JOptionPane.showMessageDialog( this,
- "There was an unknown problem when attempting to write to an image file: \""
- + file_name + "\"",
- "Error",
- JOptionPane.ERROR_MESSAGE );
- }
- }
- _contentpane.repaint();
- }
-
- private void addExpressionValuesFromFile() {
- if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) {
- JOptionPane.showMessageDialog( this,
- "Need to load evolutionary tree first",
- "Can Not Read Expression Values",
- JOptionPane.WARNING_MESSAGE );
- return;
- }
- final File my_dir = getCurrentDir();
- if ( my_dir != null ) {
- _values_filechooser.setCurrentDirectory( my_dir );
- }
- final int result = _values_filechooser.showOpenDialog( _contentpane );
- final File file = _values_filechooser.getSelectedFile();
- if ( ( file != null ) && ( file.length() > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
- BasicTable<String> t = null;
- try {
- t = BasicTableParser.parse( file, '\t' );
- if ( t.getNumberOfColumns() < 2 ) {
- t = BasicTableParser.parse( file, ',' );
- }
- if ( t.getNumberOfColumns() < 2 ) {
- t = BasicTableParser.parse( file, ' ' );
- }
- }
- catch ( final IOException e ) {
- JOptionPane.showMessageDialog( this,
- e.getMessage(),
- "Could Not Read Expression Value Table",
- JOptionPane.ERROR_MESSAGE );
- return;
- }
- if ( t.getNumberOfColumns() < 2 ) {
- JOptionPane.showMessageDialog( this,
- "Table contains " + t.getNumberOfColumns() + " column(s)",
- "Problem with Expression Value Table",
- JOptionPane.ERROR_MESSAGE );
- return;
- }
- if ( t.getNumberOfRows() < 1 ) {
- JOptionPane.showMessageDialog( this,
- "Table contains zero rows",
- "Problem with Expression Value Table",
- JOptionPane.ERROR_MESSAGE );
- return;
- }
- final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
- if ( t.getNumberOfRows() != phy.getNumberOfExternalNodes() ) {
- JOptionPane.showMessageDialog( this,
- "Table contains " + t.getNumberOfRows() + " rows, but tree contains "
- + phy.getNumberOfExternalNodes() + " external nodes",
- "Warning",
- JOptionPane.WARNING_MESSAGE );
- }
- final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
- int not_found = 0;
- for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
- final PhylogenyNode node = iter.next();
- final String node_name = node.getName();
- if ( !ForesterUtil.isEmpty( node_name ) ) {
- int row = -1;
- try {
- row = t.findRow( node_name );
- }
- catch ( final IllegalArgumentException e ) {
- JOptionPane
- .showMessageDialog( this,
- e.getMessage(),
- "Error Mapping Node Identifiers to Expression Value Identifiers",
- JOptionPane.ERROR_MESSAGE );
- return;
- }
- if ( row < 0 ) {
- if ( node.isExternal() ) {
- not_found++;
- }
- continue;
- }
- final List<Double> l = new ArrayList<Double>();
- for( int col = 1; col < t.getNumberOfColumns(); ++col ) {
- double d = -100;
- try {
- d = Double.parseDouble( t.getValueAsString( col, row ) );
- }
- catch ( final NumberFormatException e ) {
- JOptionPane.showMessageDialog( this,
- "Could not parse \"" + t.getValueAsString( col, row )
- + "\" into a decimal value",
- "Issue with Expression Value Table",
- JOptionPane.ERROR_MESSAGE );
- return;
- }
- stats.addValue( d );
- l.add( d );
- }
- if ( !l.isEmpty() ) {
- if ( node.getNodeData().getProperties() != null ) {
- node.getNodeData().getProperties()
- .removePropertiesWithGivenReferencePrefix( PhyloXmlUtil.VECTOR_PROPERTY_REF );
- }
- node.getNodeData().setVector( l );
- }
- }
- }
- if ( not_found > 0 ) {
- JOptionPane.showMessageDialog( this, "Could not fine expression values for " + not_found
- + " external node(s)", "Warning", JOptionPane.WARNING_MESSAGE );
- }
- getCurrentTreePanel().setStatisticsForExpressionValues( stats );
- }
- }
-
- private void addSequencesFromFile() {
- if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) {
- JOptionPane.showMessageDialog( this,
- "Need to load evolutionary tree first",
- "Can Not Read Sequences",
- JOptionPane.WARNING_MESSAGE );
- return;
- }
- final File my_dir = getCurrentDir();
- if ( my_dir != null ) {
- _sequences_filechooser.setCurrentDirectory( my_dir );
- }
- final int result = _sequences_filechooser.showOpenDialog( _contentpane );
- final File file = _sequences_filechooser.getSelectedFile();
- List<Sequence> seqs = null;
- if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {
- try {
- if ( FastaParser.isLikelyFasta( new FileInputStream( file ) ) ) {
- seqs = FastaParser.parse( new FileInputStream( file ) );
- }
- else {
- JOptionPane.showMessageDialog( this,
- "Format does not appear to be Fasta",
- "Multiple sequence file format error",
- JOptionPane.ERROR_MESSAGE );
- return;
- }
- }
- catch ( final MsaFormatException e ) {
- setArrowCursor();
- JOptionPane.showMessageDialog( this,
- e.getLocalizedMessage(),
- "Multiple sequence file format error",
- JOptionPane.ERROR_MESSAGE );
- return;
- }
- catch ( final IOException e ) {
- setArrowCursor();
- JOptionPane.showMessageDialog( this,
- e.getLocalizedMessage(),
- "Failed to read multiple sequence file",
- JOptionPane.ERROR_MESSAGE );
- return;
- }
- catch ( final Exception e ) {
- setArrowCursor();
- e.printStackTrace();
- JOptionPane.showMessageDialog( this,
- e.getLocalizedMessage(),
- "Unexpected error during reading of multiple sequence file",
- JOptionPane.ERROR_MESSAGE );
- return;
- }
- if ( ( seqs == null ) || ( seqs.size() < 1 ) ) {
- JOptionPane.showMessageDialog( this,
- "Multiple sequence file is empty",
- "Empty multiple sequence file",
- JOptionPane.ERROR_MESSAGE );
- setArrowCursor();
- return;
- }
- }
- if ( seqs != null ) {
- for( final Sequence seq : seqs ) {
- System.out.println( seq.getIdentifier() );
- }
- final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
- int total_counter = 0;
- int attached_counter = 0;
- for( final Sequence seq : seqs ) {
- ++total_counter;
- final String seq_name = seq.getIdentifier();
- if ( !ForesterUtil.isEmpty( seq_name ) ) {
- List<PhylogenyNode> nodes = phy.getNodesViaSequenceName( seq_name );
- if ( nodes.isEmpty() ) {
- nodes = phy.getNodesViaSequenceSymbol( seq_name );
- }
- if ( nodes.isEmpty() ) {
- nodes = phy.getNodesViaGeneName( seq_name );
- }
- if ( nodes.isEmpty() ) {
- nodes = phy.getNodes( seq_name );
- }
- if ( nodes.size() > 1 ) {
- JOptionPane.showMessageDialog( this,
- "Sequence name \"" + seq_name + "\" is not unique",
- "Sequence name not unique",
- JOptionPane.ERROR_MESSAGE );
- setArrowCursor();
- return;
- }
- final String[] a = seq_name.split( "\\s" );
- if ( nodes.isEmpty() && ( a.length > 1 ) ) {
- final String seq_name_split = a[ 0 ];
- nodes = phy.getNodesViaSequenceName( seq_name_split );
- if ( nodes.isEmpty() ) {
- nodes = phy.getNodesViaSequenceSymbol( seq_name_split );
- }
- if ( nodes.isEmpty() ) {
- nodes = phy.getNodes( seq_name_split );
- }
- if ( nodes.size() > 1 ) {
- JOptionPane.showMessageDialog( this, "Split sequence name \"" + seq_name_split
- + "\" is not unique", "Sequence name not unique", JOptionPane.ERROR_MESSAGE );
- setArrowCursor();
- return;
- }
- }
- if ( nodes.size() == 1 ) {
- ++attached_counter;
- final PhylogenyNode n = nodes.get( 0 );
- if ( !n.getNodeData().isHasSequence() ) {
- n.getNodeData().addSequence( new org.forester.phylogeny.data.Sequence() );
- }
- n.getNodeData().getSequence().setMolecularSequence( seq.getMolecularSequenceAsString() );
- if ( ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) {
- n.getNodeData().getSequence().setName( seq_name );
- }
- }
- }
- }
- if ( attached_counter > 0 ) {
- int ext_nodes = 0;
- int ext_nodes_with_seq = 0;
- for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
- ++ext_nodes;
- final PhylogenyNode n = iter.next();
- if ( n.getNodeData().isHasSequence()
- && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getMolecularSequence() ) ) {
- ++ext_nodes_with_seq;
- }
- }
- final String s;
- if ( ext_nodes == ext_nodes_with_seq ) {
- s = "All " + ext_nodes_with_seq + " external nodes now have a molecular sequence attached to them.";
- }
- else {
- s = ext_nodes_with_seq + " out of " + ext_nodes
- + " external nodes now have a molecular sequence attached to them.";
- }
- if ( ( attached_counter == total_counter ) && ( ext_nodes == ext_nodes_with_seq ) ) {
- JOptionPane.showMessageDialog( this,
- "Attached all " + total_counter + " sequences to tree nodes.\n" + s,
- "All sequences attached",
- JOptionPane.INFORMATION_MESSAGE );
- }
- else {
- JOptionPane.showMessageDialog( this, "Attached " + attached_counter
- + " sequences out of a total of " + total_counter + " sequences.\n" + s, attached_counter
- + " sequences attached", JOptionPane.WARNING_MESSAGE );
- }
- }
- else {
- JOptionPane.showMessageDialog( this, "No maching tree node for any of the " + total_counter
- + " sequences", "Could not attach any sequences", JOptionPane.ERROR_MESSAGE );
- }
- }
- }
-
- private void choosePdfWidth() {
- final String s = ( String ) JOptionPane.showInputDialog( this,
- "Please enter the default line width for PDF export.\n"
- + "[current value: "
- + getOptions().getPrintLineWidth() + "]\n",
- "Line Width for PDF Export",
- JOptionPane.QUESTION_MESSAGE,
- null,
- null,
- getOptions().getPrintLineWidth() );
- if ( !ForesterUtil.isEmpty( s ) ) {
- boolean success = true;
- float f = 0.0f;
- final String m_str = s.trim();
- if ( !ForesterUtil.isEmpty( m_str ) ) {
- try {
- f = Float.parseFloat( m_str );
- }
- catch ( final Exception ex ) {
- success = false;
- }
- }
- else {
- success = false;
- }
- if ( success && ( f > 0.0 ) ) {
- getOptions().setPrintLineWidth( f );
- }
- }
- }
-
- private void choosePrintSize() {
- final String s = ( String ) JOptionPane.showInputDialog( this,
- "Please enter values for width and height,\nseparated by a comma.\n"
- + "[current values: "
- + getOptions().getPrintSizeX() + ", "
- + getOptions().getPrintSizeY() + "]\n"
- + "[A4: " + Constants.A4_SIZE_X + ", "
- + Constants.A4_SIZE_Y + "]\n" + "[US Letter: "
- + Constants.US_LETTER_SIZE_X + ", "
- + Constants.US_LETTER_SIZE_Y + "]",
- "Default Size for Graphics Export",
- JOptionPane.QUESTION_MESSAGE,
- null,
- null,
- getOptions().getPrintSizeX() + ", "
- + getOptions().getPrintSizeY() );
- if ( !ForesterUtil.isEmpty( s ) && ( s.indexOf( ',' ) > 0 ) ) {
- boolean success = true;
- int x = 0;
- int y = 0;
- final String[] str_ary = s.split( "," );
- if ( str_ary.length == 2 ) {
- final String x_str = str_ary[ 0 ].trim();
- final String y_str = str_ary[ 1 ].trim();
- if ( !ForesterUtil.isEmpty( x_str ) && !ForesterUtil.isEmpty( y_str ) ) {
- try {
- x = Integer.parseInt( x_str );
- y = Integer.parseInt( y_str );
- }
- catch ( final Exception ex ) {
- success = false;
- }
- }
- else {
- success = false;
- }
- }
- else {
- success = false;
- }
- if ( success && ( x > 1 ) && ( y > 1 ) ) {
- getOptions().setPrintSizeX( x );
- getOptions().setPrintSizeY( y );
- }
- }
- }
-
- private void closeCurrentPane() {
- if ( getMainPanel().getCurrentTreePanel() != null ) {
- if ( getMainPanel().getCurrentTreePanel().isEdited() ) {
- final int r = JOptionPane.showConfirmDialog( this,
- "Close tab despite potentially unsaved changes?",
- "Close Tab?",
- JOptionPane.YES_NO_OPTION );
- if ( r != JOptionPane.YES_OPTION ) {
- return;
- }
- }
- getMainPanel().closeCurrentPane();
- activateSaveAllIfNeeded();
- }
- }
-
- private void collapse( final Phylogeny phy, final double m ) {
- final PhylogenyNodeIterator it = phy.iteratorPostorder();
- final List<PhylogenyNode> to_be_removed = new ArrayList<PhylogenyNode>();
- double min_support = Double.MAX_VALUE;
- boolean conf_present = false;
- while ( it.hasNext() ) {
- final PhylogenyNode n = it.next();
- if ( !n.isExternal() && !n.isRoot() ) {
- final List<Confidence> c = n.getBranchData().getConfidences();
- if ( ( c != null ) && ( c.size() > 0 ) ) {
- conf_present = true;
- double max = 0;
- for( final Confidence confidence : c ) {
- if ( confidence.getValue() > max ) {
- max = confidence.getValue();
- }
- }
- if ( max < getMinNotCollapseConfidenceValue() ) {
- to_be_removed.add( n );
- }
- if ( max < min_support ) {
- min_support = max;
- }
- }
- }
- }
- if ( conf_present ) {
- for( final PhylogenyNode node : to_be_removed ) {
- PhylogenyMethods.removeNode( node, phy );
- }
- if ( to_be_removed.size() > 0 ) {
- phy.externalNodesHaveChanged();
- phy.clearHashIdToNodeMap();
- phy.recalculateNumberOfExternalDescendants( true );
- getCurrentTreePanel().resetNodeIdToDistToLeafMap();
- getCurrentTreePanel().updateSetOfCollapsedExternalNodes();
- getCurrentTreePanel().calculateLongestExtNodeInfo();
- getCurrentTreePanel().setNodeInPreorderToNull();
- getCurrentTreePanel().recalculateMaxDistanceToRoot();
- getCurrentTreePanel().resetPreferredSize();
- getCurrentTreePanel().setEdited( true );
- getCurrentTreePanel().repaint();
- repaint();
- }
- if ( to_be_removed.size() > 0 ) {
- JOptionPane.showMessageDialog( this, "Collapsed " + to_be_removed.size()
- + " branches with\nconfidence values below " + getMinNotCollapseConfidenceValue(), "Collapsed "
- + to_be_removed.size() + " branches", JOptionPane.INFORMATION_MESSAGE );
- }
- else {
- JOptionPane.showMessageDialog( this, "No branch collapsed,\nminimum confidence value per branch is "
- + min_support, "No branch collapsed", JOptionPane.INFORMATION_MESSAGE );
- }
- }
- else {
- JOptionPane.showMessageDialog( this,
- "No branch collapsed because no confidence values present",
- "No confidence values present",
- JOptionPane.INFORMATION_MESSAGE );
- }
- }
-
- private void collapseBelowThreshold() {
- if ( getCurrentTreePanel() != null ) {
- final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
- if ( ( phy != null ) && !phy.isEmpty() ) {
- final String s = ( String ) JOptionPane.showInputDialog( this,
- "Please enter the minimum confidence value\n",
- "Minimal Confidence Value",
- JOptionPane.QUESTION_MESSAGE,
- null,
- null,
- getMinNotCollapseConfidenceValue() );
- 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 ) ) {
- setMinNotCollapseConfidenceValue( m );
- collapse( phy, m );
- }
- }
- }
- }
- }
-
- private PhyloXmlParser createPhyloXmlParser() {
- PhyloXmlParser xml_parser = null;
- if ( getConfiguration().isValidatePhyloXmlAgainstSchema() ) {
- try {
- xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
- }
- catch ( final Exception e ) {
- JOptionPane.showMessageDialog( this,
- e.getLocalizedMessage(),
- "failed to create validating XML parser",
- JOptionPane.WARNING_MESSAGE );
- }
- }
- if ( xml_parser == null ) {
- xml_parser = PhyloXmlParser.createPhyloXmlParser();
- }
- return xml_parser;
- }
-
- private void executePhyleneticInference( final boolean from_unaligned_seqs ) {
- final PhyloInferenceDialog dialog = new PhyloInferenceDialog( this,
- getPhylogeneticInferenceOptions(),
- from_unaligned_seqs );
- dialog.activate();
- if ( dialog.getValue() == JOptionPane.OK_OPTION ) {
- if ( !from_unaligned_seqs ) {
- if ( getMsa() != null ) {
- final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getMsa(),
- getPhylogeneticInferenceOptions()
- .copy(), this );
- new Thread( inferrer ).start();
- }
- else {
- JOptionPane.showMessageDialog( this,
- "No multiple sequence alignment selected",
- "Phylogenetic Inference Not Launched",
- JOptionPane.WARNING_MESSAGE );
- }
- }
- else {
- if ( getSeqs() != null ) {
- final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getSeqs(),
- getPhylogeneticInferenceOptions()
- .copy(), this );
- new Thread( inferrer ).start();
- }
- else {
- JOptionPane.showMessageDialog( this,
- "No input sequences selected",
- "Phylogenetic Inference Not Launched",
- JOptionPane.WARNING_MESSAGE );
- }
- }
- }
- }
-
- private void extractTaxDataFromNodeNames() throws PhyloXmlDataFormatException {
- final StringBuilder sb = new StringBuilder();
- final StringBuilder sb_failed = new StringBuilder();
- int counter = 0;
- int counter_failed = 0;
- if ( getCurrentTreePanel() != null ) {
- final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
- if ( ( phy != null ) && !phy.isEmpty() ) {
- final PhylogenyNodeIterator it = phy.iteratorExternalForward();
- while ( it.hasNext() ) {
- final PhylogenyNode n = it.next();
- final String name = n.getName().trim();
- if ( !ForesterUtil.isEmpty( name ) ) {
- final String nt = ParserUtils.extractTaxonomyDataFromNodeName( n,
- TAXONOMY_EXTRACTION.AGGRESSIVE );
- if ( !ForesterUtil.isEmpty( nt ) ) {
- if ( counter < 15 ) {
- sb.append( name + ": " + nt + "\n" );
- }
- else if ( counter == 15 ) {
- sb.append( "...\n" );
- }
- counter++;
- }
- else {
- if ( counter_failed < 15 ) {
- sb_failed.append( name + "\n" );
- }
- else if ( counter_failed == 15 ) {
- sb_failed.append( "...\n" );
- }
- counter_failed++;
- }
- }
- }
- if ( counter > 0 ) {
- String failed = "";
- String all = "all ";
- if ( counter_failed > 0 ) {
- all = "";
- failed = "\nCould not extract taxonomic data for " + counter_failed
- + " named external nodes:\n" + sb_failed;
- }
- JOptionPane.showMessageDialog( this,
- "Extracted taxonomic data from " + all + counter
- + " named external nodes:\n" + sb.toString() + failed,
- "Taxonomic Data Extraction Completed",
- counter_failed > 0 ? JOptionPane.WARNING_MESSAGE
- : JOptionPane.INFORMATION_MESSAGE );
- }
- else {
- JOptionPane
- .showMessageDialog( this,
- "Could not extract any taxonomic data.\nMaybe node names are empty\n"
- + "or not in the forms \"XYZ_CAEEL\", \"XYZ_6239\", or \"XYZ_Caenorhabditis_elegans\"\n"
- + "or nodes already have taxonomic data?\n",
- "No Taxonomic Data Extracted",
- JOptionPane.ERROR_MESSAGE );
- }
- }
- }
- }
-
- private ControlPanel getControlPanel() {
- return getMainPanel().getControlPanel();
- }
-
- private 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;
- }
-
- private double getMinNotCollapseConfidenceValue() {
- return _min_not_collapse;
- }
-
- private PhylogeneticInferenceOptions getPhylogeneticInferenceOptions() {
- if ( _phylogenetic_inference_options == null ) {
- _phylogenetic_inference_options = new PhylogeneticInferenceOptions();
- }
- return _phylogenetic_inference_options;
- }
-
- private boolean isUnsavedDataPresent() {
- final List<TreePanel> tps = getMainPanel().getTreePanels();
- for( final TreePanel tp : tps ) {
- if ( tp.isEdited() ) {
- return true;
- }
- }
- return false;
- }
-
- private void moveNodeNamesToSeqNames() throws PhyloXmlDataFormatException {
- if ( getCurrentTreePanel() != null ) {
- final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
- if ( ( phy != null ) && !phy.isEmpty() ) {
- PhylogenyMethods
- .transferNodeNameToField( phy, PhylogenyMethods.PhylogenyNodeField.SEQUENCE_NAME, false );
- }
- }
- }
-
- private void moveNodeNamesToTaxSn() throws PhyloXmlDataFormatException {
- if ( getCurrentTreePanel() != null ) {
- final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
- if ( ( phy != null ) && !phy.isEmpty() ) {
- PhylogenyMethods.transferNodeNameToField( phy,
- PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME,
- false );
- }
- }
- }
-
- private void newTree() {
- final Phylogeny[] phys = new Phylogeny[ 1 ];
- final Phylogeny phy = new Phylogeny();
- final PhylogenyNode node = new PhylogenyNode();
- phy.setRoot( node );
- phy.setRooted( true );
- phys[ 0 ] = phy;
- AptxUtil.addPhylogeniesToTabs( phys, "", "", getConfiguration(), getMainPanel() );
- _mainpanel.getControlPanel().showWhole();
- _mainpanel.getCurrentTreePanel().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
- _mainpanel.getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
- if ( getMainPanel().getMainFrame() == null ) {
- // Must be "E" applet version.
- ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() )
- .setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
- }
- else {
- getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
- }
- activateSaveAllIfNeeded();
- System.gc();
- }
-
- private void obtainDetailedTaxonomicInformation() {
- if ( getCurrentTreePanel() != null ) {
- final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
- if ( ( phy != null ) && !phy.isEmpty() ) {
- final TaxonomyDataManager t = new TaxonomyDataManager( this,
- _mainpanel.getCurrentTreePanel(),
- phy.copy(),
- false,
- true );
- new Thread( t ).start();
- }
- }
- }
-
- private void obtainDetailedTaxonomicInformationDelete() {
- if ( getCurrentTreePanel() != null ) {
- final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
- if ( ( phy != null ) && !phy.isEmpty() ) {
- final TaxonomyDataManager t = new TaxonomyDataManager( this,
- _mainpanel.getCurrentTreePanel(),
- phy.copy(),
- true,
- true );
- new Thread( t ).start();
- }
- }
- }
-
- private void obtainSequenceInformation() {
- if ( getCurrentTreePanel() != null ) {
- final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
- if ( ( phy != null ) && !phy.isEmpty() ) {
- final SequenceDataRetriver u = new SequenceDataRetriver( this,
- _mainpanel.getCurrentTreePanel(),
- phy.copy() );
- new Thread( u ).start();
- }
- }
- }
-
- private void print() {
- if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null )
- || getCurrentTreePanel().getPhylogeny().isEmpty() ) {
- return;
- }
- if ( !getOptions().isPrintUsingActualSize() ) {
- getCurrentTreePanel().calcParametersForPainting( getOptions().getPrintSizeX() - 80,
- getOptions().getPrintSizeY() - 140,
- true );
- getCurrentTreePanel().resetPreferredSize();
- getCurrentTreePanel().repaint();
- }
- final String job_name = Constants.PRG_NAME;
- boolean error = false;
- String printer_name = null;
- try {
- printer_name = Printer.print( getCurrentTreePanel(), job_name );
- }
- catch ( final Exception e ) {
- error = true;
- JOptionPane.showMessageDialog( this, e.getMessage(), "Printing Error", JOptionPane.ERROR_MESSAGE );
- }
- if ( !error && ( printer_name != null ) ) {
- String msg = "Printing data sent to printer";
- if ( printer_name.length() > 1 ) {
- msg += " [" + printer_name + "]";
- }
- JOptionPane.showMessageDialog( this, msg, "Printing...", JOptionPane.INFORMATION_MESSAGE );
- }
- if ( !getOptions().isPrintUsingActualSize() ) {
- getControlPanel().showWhole();
- }
- }
-
- private void printPhylogenyToPdf( final String file_name ) {
- if ( !getOptions().isPrintUsingActualSize() ) {
- getCurrentTreePanel().calcParametersForPainting( getOptions().getPrintSizeX(),
- getOptions().getPrintSizeY(),
- true );
- getCurrentTreePanel().resetPreferredSize();
- getCurrentTreePanel().repaint();
- }
- String pdf_written_to = "";
- boolean error = false;
- try {
- if ( getOptions().isPrintUsingActualSize() ) {
- pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name,
- getCurrentTreePanel(),
- getCurrentTreePanel().getWidth(),
- getCurrentTreePanel().getHeight() );
- }
- else {
- pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name, getCurrentTreePanel(), getOptions()
- .getPrintSizeX(), getOptions().getPrintSizeY() );
- }
- }
- catch ( final IOException e ) {
- error = true;
- JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );
- }
- if ( !error ) {
- if ( !ForesterUtil.isEmpty( pdf_written_to ) ) {
- JOptionPane.showMessageDialog( this,
- "Wrote PDF to: " + pdf_written_to,
- "Information",
- JOptionPane.INFORMATION_MESSAGE );
- }
- else {
- JOptionPane.showMessageDialog( this,
- "There was an unknown problem when attempting to write to PDF file: \""
- + file_name + "\"",
- "Error",
- JOptionPane.ERROR_MESSAGE );
- }
- }
- if ( !getOptions().isPrintUsingActualSize() ) {
- getControlPanel().showWhole();
- }
- }
-
- private void readPhylogeniesFromFile() {
- boolean exception = false;
- Phylogeny[] phys = null;
- // Set an initial directory if none set yet
- final File my_dir = getCurrentDir();
- _open_filechooser.setMultiSelectionEnabled( true );
- // Open file-open dialog and set current directory
- if ( my_dir != null ) {
- _open_filechooser.setCurrentDirectory( my_dir );
- }
- final int result = _open_filechooser.showOpenDialog( _contentpane );
- // All done: get the file
- final File[] files = _open_filechooser.getSelectedFiles();
- setCurrentDir( _open_filechooser.getCurrentDirectory() );
- boolean nhx_or_nexus = false;
- if ( ( files != null ) && ( files.length > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
- for( final File file : files ) {
- if ( ( file != null ) && !file.isDirectory() ) {
- if ( _mainpanel.getCurrentTreePanel() != null ) {
- _mainpanel.getCurrentTreePanel().setWaitCursor();
- }
- else {
- _mainpanel.setWaitCursor();
- }
- if ( ( _open_filechooser.getFileFilter() == MainFrameApplication.nhfilter )
- || ( _open_filechooser.getFileFilter() == MainFrameApplication.nhxfilter ) ) {
- try {
- final NHXParser nhx = new NHXParser();
- setSpecialOptionsForNhxParser( nhx );
- phys = PhylogenyMethods.readPhylogenies( nhx, file );
- nhx_or_nexus = true;
- }
- catch ( final Exception e ) {
- exception = true;
- exceptionOccuredDuringOpenFile( e );
- }
- }
- else if ( _open_filechooser.getFileFilter() == MainFrameApplication.xmlfilter ) {
- warnIfNotPhyloXmlValidation( getConfiguration() );
- try {
- final PhyloXmlParser xml_parser = createPhyloXmlParser();
- phys = PhylogenyMethods.readPhylogenies( xml_parser, file );
- }
- catch ( final Exception e ) {
- exception = true;
- exceptionOccuredDuringOpenFile( e );
- }
- }
- else if ( _open_filechooser.getFileFilter() == MainFrameApplication.tolfilter ) {
- try {
- phys = PhylogenyMethods.readPhylogenies( new TolParser(), file );
- }
- catch ( final Exception e ) {
- exception = true;
- exceptionOccuredDuringOpenFile( e );
- }
- }
- else if ( _open_filechooser.getFileFilter() == MainFrameApplication.nexusfilter ) {
- try {
- final NexusPhylogeniesParser nex = new NexusPhylogeniesParser();
- setSpecialOptionsForNexParser( nex );
- phys = PhylogenyMethods.readPhylogenies( nex, file );
- nhx_or_nexus = true;
- }
- catch ( final Exception e ) {
- exception = true;
- exceptionOccuredDuringOpenFile( e );
- }
- }
- // "*.*":
- else {
- try {
- final PhylogenyParser parser = ParserUtils
- .createParserDependingOnFileType( file, getConfiguration()
- .isValidatePhyloXmlAgainstSchema() );
- if ( parser instanceof NexusPhylogeniesParser ) {
- final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) parser;
- setSpecialOptionsForNexParser( nex );
- nhx_or_nexus = true;
- }
- else if ( parser instanceof NHXParser ) {
- final NHXParser nhx = ( NHXParser ) parser;
- setSpecialOptionsForNhxParser( nhx );
- nhx_or_nexus = true;
- }
- else if ( parser instanceof PhyloXmlParser ) {
- warnIfNotPhyloXmlValidation( getConfiguration() );
- }
- phys = PhylogenyMethods.readPhylogenies( parser, file );
- }
- catch ( final Exception e ) {
- exception = true;
- exceptionOccuredDuringOpenFile( e );
- }
- }
- if ( _mainpanel.getCurrentTreePanel() != null ) {
- _mainpanel.getCurrentTreePanel().setArrowCursor();
- }
- else {
- _mainpanel.setArrowCursor();
- }
- if ( !exception && ( phys != null ) && ( phys.length > 0 ) ) {
- boolean one_desc = false;
- if ( nhx_or_nexus ) {
- for( final Phylogeny phy : phys ) {
- if ( getOptions().isInternalNumberAreConfidenceForNhParsing() ) {
- PhylogenyMethods.transferInternalNodeNamesToConfidence( phy, "" );
- }
- if ( PhylogenyMethods.getMinimumDescendentsPerInternalNodes( phy ) == 1 ) {
- one_desc = true;
- break;
- }
- }
- }
- AptxUtil.addPhylogeniesToTabs( phys,
- file.getName(),
- file.getAbsolutePath(),
- getConfiguration(),
- getMainPanel() );
- _mainpanel.getControlPanel().showWhole();
- if ( nhx_or_nexus && one_desc ) {
- JOptionPane
- .showMessageDialog( this,
- "One or more trees contain (a) node(s) with one descendant, "
- + ForesterUtil.LINE_SEPARATOR
- + "possibly indicating illegal parentheses within node names.",
- "Warning: Possible Error in New Hampshire Formatted Data",
- JOptionPane.WARNING_MESSAGE );
- }
- }
- }
- }
- }
- activateSaveAllIfNeeded();
- System.gc();
- }
-
- private void readSpeciesTreeFromFile() {
- Phylogeny t = null;
- boolean exception = false;
- final File my_dir = getCurrentDir();
- _open_filechooser_for_species_tree.setSelectedFile( new File( "" ) );
- if ( my_dir != null ) {
- _open_filechooser_for_species_tree.setCurrentDirectory( my_dir );
- }
- final int result = _open_filechooser_for_species_tree.showOpenDialog( _contentpane );
- final File file = _open_filechooser_for_species_tree.getSelectedFile();
- if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
- if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrameApplication.xmlfilter ) {
- try {
- final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( PhyloXmlParser
- .createPhyloXmlParserXsdValidating(), file );
- t = trees[ 0 ];
- }
- catch ( final Exception e ) {
- exception = true;
- exceptionOccuredDuringOpenFile( e );
- }
- }
- else if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrameApplication.tolfilter ) {
- try {
- final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new TolParser(), file );
- t = trees[ 0 ];
- }
- catch ( final Exception e ) {
- exception = true;
- exceptionOccuredDuringOpenFile( e );
- }
- }
- // "*.*":
- else {
- try {
- final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( PhyloXmlParser
- .createPhyloXmlParserXsdValidating(), file );
- t = trees[ 0 ];
- }
- catch ( final Exception e ) {
- exception = true;
- exceptionOccuredDuringOpenFile( e );
- }
- }
- if ( !exception && ( t != null ) && !t.isRooted() ) {
- exception = true;
- t = null;
- JOptionPane.showMessageDialog( this,
- "Species tree is not rooted",
- "Species tree not loaded",
- JOptionPane.ERROR_MESSAGE );
- }
- if ( !exception && ( t != null ) ) {
- final Set<Taxonomy> tax_set = new HashSet<Taxonomy>();
- for( final PhylogenyNodeIterator it = t.iteratorExternalForward(); it.hasNext(); ) {
- final PhylogenyNode node = it.next();
- if ( !node.getNodeData().isHasTaxonomy() ) {
- exception = true;
- t = null;
- JOptionPane
- .showMessageDialog( this,
- "Species tree contains external node(s) without taxonomy information",
- "Species tree not loaded",
- JOptionPane.ERROR_MESSAGE );
- break;
- }
- else {
- if ( tax_set.contains( node.getNodeData().getTaxonomy() ) ) {
- exception = true;
- t = null;
- JOptionPane.showMessageDialog( this,
- "Taxonomy ["
- + node.getNodeData().getTaxonomy().asSimpleText()
- + "] is not unique in species tree",
- "Species tree not loaded",
- JOptionPane.ERROR_MESSAGE );
- break;
- }
- else {
- tax_set.add( node.getNodeData().getTaxonomy() );
- }
- }
- }
- }
- if ( !exception && ( t != null ) ) {
- setSpeciesTree( t );
- JOptionPane.showMessageDialog( this,
- "Species tree successfully loaded",
- "Species tree loaded",
- JOptionPane.INFORMATION_MESSAGE );
- }
- _contentpane.repaint();
- System.gc();
- }
- }
-
- private void setArrowCursor() {
- try {
- _mainpanel.getCurrentTreePanel().setArrowCursor();
- }
- catch ( final Exception ex ) {
- // Do nothing.
- }
- }
-
- private void setCurrentDir( final File current_dir ) {
- _current_dir = current_dir;
- }
-
- private void setMinNotCollapseConfidenceValue( final double min_not_collapse ) {
- _min_not_collapse = min_not_collapse;
- }
-
- private void setPhylogeneticInferenceOptions( final PhylogeneticInferenceOptions phylogenetic_inference_options ) {
- _phylogenetic_inference_options = phylogenetic_inference_options;
- }
-
- private void setSpecialOptionsForNexParser( final NexusPhylogeniesParser nex ) {
- nex.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );
- nex.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() );
- }
-
- private void setSpecialOptionsForNhxParser( final NHXParser nhx ) {
- nhx.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );
- nhx.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() );
- nhx.setAllowErrorsInDistanceToParent( getOptions().isAllowErrorsInDistanceToParent() );
- }
-
- private void writeAllToFile() {
- if ( ( getMainPanel().getTabbedPane() == null ) || ( getMainPanel().getTabbedPane().getTabCount() < 1 ) ) {
- return;
- }
- final File my_dir = getCurrentDir();
- if ( my_dir != null ) {
- _save_filechooser.setCurrentDirectory( my_dir );
- }
- _save_filechooser.setSelectedFile( new File( "" ) );
- final int result = _save_filechooser.showSaveDialog( _contentpane );
- final File file = _save_filechooser.getSelectedFile();
- setCurrentDir( _save_filechooser.getCurrentDirectory() );
- if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
- if ( file.exists() ) {
- final int i = JOptionPane.showConfirmDialog( this,
- file + " already exists. Overwrite?",
- "Warning",
- JOptionPane.OK_CANCEL_OPTION,
- JOptionPane.WARNING_MESSAGE );
- if ( i != JOptionPane.OK_OPTION ) {
- return;
- }
- else {
- try {
- file.delete();
- }
- catch ( final Exception e ) {
- JOptionPane.showMessageDialog( this,
- "Failed to delete: " + file,
- "Error",
- JOptionPane.WARNING_MESSAGE );
- }
- }
- }
- final int count = getMainPanel().getTabbedPane().getTabCount();
- final List<Phylogeny> trees = new ArrayList<Phylogeny>();
- for( int i = 0; i < count; ++i ) {
- 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( this,
- "Failed to write to: " + file,
- "Error",
- JOptionPane.WARNING_MESSAGE );
- }
- }
- }
-
- private boolean writeAsNewHampshire( final Phylogeny t, boolean exception, final File file ) {
- try {
- final PhylogenyWriter writer = new PhylogenyWriter();
- writer.toNewHampshire( t, true, getOptions().getNhConversionSupportValueStyle(), file );
- }
- catch ( final Exception e ) {
- exception = true;
- exceptionOccuredDuringSaveAs( e );
- }
- return exception;
- }
-
- private boolean writeAsNexus( final Phylogeny t, boolean exception, final File file ) {
- try {
- final PhylogenyWriter writer = new PhylogenyWriter();
- writer.toNexus( file, t, getOptions().getNhConversionSupportValueStyle() );
- }
- catch ( final Exception e ) {
- exception = true;
- exceptionOccuredDuringSaveAs( e );
- }
- return exception;
- }
-
- private boolean writeAsPhyloXml( final Phylogeny t, boolean exception, final File file ) {
- try {
- final PhylogenyWriter writer = new PhylogenyWriter();
- writer.toPhyloXML( file, t, 0 );
- }
- catch ( final Exception e ) {
- exception = true;
- exceptionOccuredDuringSaveAs( e );
- }
- return exception;
- }
-
- private void writeToFile( final Phylogeny t ) {
- if ( t == null ) {
- return;
- }
- String initial_filename = null;
- if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {
- try {
- initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().getCanonicalPath();
- }
- catch ( final IOException e ) {
- initial_filename = null;
- }
- }
- if ( !ForesterUtil.isEmpty( initial_filename ) ) {
- _save_filechooser.setSelectedFile( new File( initial_filename ) );
- }
- else {
- _save_filechooser.setSelectedFile( new File( "" ) );
- }
- final File my_dir = getCurrentDir();
- if ( my_dir != null ) {
- _save_filechooser.setCurrentDirectory( my_dir );
- }
- final int result = _save_filechooser.showSaveDialog( _contentpane );
- final File file = _save_filechooser.getSelectedFile();
- setCurrentDir( _save_filechooser.getCurrentDirectory() );
- boolean exception = false;
- if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
- if ( file.exists() ) {
- final int i = JOptionPane.showConfirmDialog( this,
- file + " already exists.\nOverwrite?",
- "Overwrite?",
- JOptionPane.OK_CANCEL_OPTION,
- JOptionPane.QUESTION_MESSAGE );
- if ( i != JOptionPane.OK_OPTION ) {
- return;
- }
- else {
- final File to = new File( file.getAbsoluteFile().toString() + Constants.BACKUP_FILE_SUFFIX );
- try {
- ForesterUtil.copyFile( file, to );
- }
- catch ( final Exception e ) {
- JOptionPane.showMessageDialog( this,
- "Failed to create backup copy " + to,
- "Failed to Create Backup Copy",
- JOptionPane.WARNING_MESSAGE );
- }
- try {
- file.delete();
- }
- catch ( final Exception e ) {
- JOptionPane.showMessageDialog( this,
- "Failed to delete: " + file,
- "Failed to Delete",
- JOptionPane.WARNING_MESSAGE );
- }
- }
- }
- if ( _save_filechooser.getFileFilter() == MainFrameApplication.nhfilter ) {
- exception = writeAsNewHampshire( t, exception, file );
- }
- else if ( _save_filechooser.getFileFilter() == MainFrameApplication.xmlfilter ) {
- exception = writeAsPhyloXml( t, exception, file );
- }
- else if ( _save_filechooser.getFileFilter() == MainFrameApplication.nexusfilter ) {
- exception = writeAsNexus( t, exception, file );
- }
- // "*.*":
- else {
- final String file_name = file.getName().trim().toLowerCase();
- if ( file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )
- || file_name.endsWith( ".tree" ) ) {
- exception = writeAsNewHampshire( t, exception, file );
- }
- else if ( file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) ) {
- exception = writeAsNexus( t, exception, file );
- }
- // XML is default:
- else {
- exception = writeAsPhyloXml( t, exception, file );
- }
- }
- if ( !exception ) {
- getMainPanel().setTitleOfSelectedTab( file.getName() );
- getMainPanel().getCurrentTreePanel().setTreeFile( file );
- getMainPanel().getCurrentTreePanel().setEdited( false );
- }
- }
- }
-
- private void writeToGraphicsFile( final Phylogeny t, final GraphicsExportType type ) {
- if ( ( t == null ) || t.isEmpty() ) {
- return;
- }
- String initial_filename = "";
- if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {
- initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().toString();
- }
- if ( initial_filename.indexOf( '.' ) > 0 ) {
- initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );
- }
- initial_filename = initial_filename + "." + type;
- _writetographics_filechooser.setSelectedFile( new File( initial_filename ) );
- final File my_dir = getCurrentDir();
- if ( my_dir != null ) {
- _writetographics_filechooser.setCurrentDirectory( my_dir );
- }
- final int result = _writetographics_filechooser.showSaveDialog( _contentpane );
- File file = _writetographics_filechooser.getSelectedFile();
- setCurrentDir( _writetographics_filechooser.getCurrentDirectory() );
- if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
- if ( !file.toString().toLowerCase().endsWith( type.toString() ) ) {
- file = new File( file.toString() + "." + type );
- }
- if ( file.exists() ) {
- final int i = JOptionPane.showConfirmDialog( this,
- file + " already exists. Overwrite?",
- "Warning",
- JOptionPane.OK_CANCEL_OPTION,
- JOptionPane.WARNING_MESSAGE );
- if ( i != JOptionPane.OK_OPTION ) {
- return;
- }
- else {
- try {
- file.delete();
- }
- catch ( final Exception e ) {
- JOptionPane.showMessageDialog( this,
- "Failed to delete: " + file,
- "Error",
- JOptionPane.WARNING_MESSAGE );
- }
- }
- }
- writePhylogenyToGraphicsFile( file.toString(), type );
- }
- }
-
- private void writeToPdf( final Phylogeny t ) {
- if ( ( t == null ) || t.isEmpty() ) {
- return;
- }
- String initial_filename = "";
- if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {
- initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().toString();
- }
- if ( initial_filename.indexOf( '.' ) > 0 ) {
- initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );
- }
- initial_filename = initial_filename + ".pdf";
- _writetopdf_filechooser.setSelectedFile( new File( initial_filename ) );
- final File my_dir = getCurrentDir();
- if ( my_dir != null ) {
- _writetopdf_filechooser.setCurrentDirectory( my_dir );
- }
- final int result = _writetopdf_filechooser.showSaveDialog( _contentpane );
- File file = _writetopdf_filechooser.getSelectedFile();
- setCurrentDir( _writetopdf_filechooser.getCurrentDirectory() );
- if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
- if ( !file.toString().toLowerCase().endsWith( ".pdf" ) ) {
- file = new File( file.toString() + ".pdf" );
- }
- if ( file.exists() ) {
- final int i = JOptionPane.showConfirmDialog( this,
- file + " already exists. Overwrite?",
- "WARNING",
- JOptionPane.OK_CANCEL_OPTION,
- JOptionPane.WARNING_MESSAGE );
- if ( i != JOptionPane.OK_OPTION ) {
- return;
- }
- }
- printPhylogenyToPdf( file.toString() );
- }
- }
-
- public static MainFrameApplication createInstance( final Phylogeny[] phys, final Configuration config ) {
- return new MainFrameApplication( phys, config );
- }
-
- public static MainFrame createInstance( final Phylogeny[] phys,
- final Configuration config,
- final String title,
- final File current_dir ) {
- return new MainFrameApplication( phys, config, title, current_dir );
- }
-
- static MainFrame createInstance( final Phylogeny[] phys, final Configuration config, final String title ) {
- return new MainFrameApplication( phys, config, title );
- }
-
- static MainFrame createInstance( final Phylogeny[] phys, final String config_file_name, final String title ) {
- return new MainFrameApplication( phys, config_file_name, title );
- }
-
- static void setTextForGraphicsSizeChooserMenuItem( final JMenuItem mi, final Options o ) {
- mi.setText( "Enter Default Size for Graphics Export... (current: " + o.getPrintSizeX() + ", "
- + o.getPrintSizeY() + ")" );
- }
-
- static void setTextForPdfLineWidthChooserMenuItem( final JMenuItem mi, final Options o ) {
- mi.setText( "Enter Default Line Width for PDF Export... (current: " + o.getPrintLineWidth() + ")" );
- }
-
- static void warnIfNotPhyloXmlValidation( final Configuration c ) {
- if ( !c.isValidatePhyloXmlAgainstSchema() ) {
- JOptionPane
- .showMessageDialog( null,
- ForesterUtil
- .wordWrap( "phyloXML XSD-based validation is turned off [enable with line 'validate_against_phyloxml_xsd_schem: true' in configuration file]",
- 80 ),
- "Warning",
- JOptionPane.WARNING_MESSAGE );
- }
- }
-} // MainFrameApplication.
-
-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
+// $Id:\r
+// FORESTER -- software libraries and applications\r
+// for evolutionary biology research and applications.\r
+//\r
+// Copyright (C) 2008-2009 Christian M. Zmasek\r
+// Copyright (C) 2008-2009 Burnham Institute for Medical Research\r
+// Copyright (C) 2003-2007 Ethalinda K.S. Cannon\r
+// All rights reserved\r
+//\r
+// This library is free software; you can redistribute it and/or\r
+// modify it under the terms of the GNU Lesser General Public\r
+// License as published by the Free Software Foundation; either\r
+// version 2.1 of the License, or (at your option) any later version.\r
+//\r
+// This library is distributed in the hope that it will be useful,\r
+// but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU\r
+// Lesser General Public License for more details.\r
+//\r
+// You should have received a copy of the GNU Lesser General Public\r
+// License along with this library; if not, write to the Free Software\r
+// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+//\r
+// Contact: phylosoft @ gmail . com\r
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester\r
+\r
+package org.forester.archaeopteryx;\r
+\r
+import java.awt.BorderLayout;\r
+import java.awt.Font;\r
+import java.awt.event.ActionEvent;\r
+import java.awt.event.ComponentAdapter;\r
+import java.awt.event.ComponentEvent;\r
+import java.awt.event.WindowAdapter;\r
+import java.awt.event.WindowEvent;\r
+import java.io.File;\r
+import java.io.FileInputStream;\r
+import java.io.IOException;\r
+import java.io.InputStream;\r
+import java.net.MalformedURLException;\r
+import java.net.URL;\r
+import java.util.ArrayList;\r
+import java.util.HashSet;\r
+import java.util.List;\r
+import java.util.Set;\r
+\r
+import javax.swing.ButtonGroup;\r
+import javax.swing.JCheckBoxMenuItem;\r
+import javax.swing.JFileChooser;\r
+import javax.swing.JMenu;\r
+import javax.swing.JMenuBar;\r
+import javax.swing.JMenuItem;\r
+import javax.swing.JOptionPane;\r
+import javax.swing.JRadioButtonMenuItem;\r
+import javax.swing.UIManager;\r
+import javax.swing.UnsupportedLookAndFeelException;\r
+import javax.swing.WindowConstants;\r
+import javax.swing.event.ChangeEvent;\r
+import javax.swing.event.ChangeListener;\r
+import javax.swing.filechooser.FileFilter;\r
+import javax.swing.plaf.synth.SynthLookAndFeel;\r
+\r
+import org.forester.analysis.TaxonomyDataManager;\r
+import org.forester.archaeopteryx.AptxUtil.GraphicsExportType;\r
+import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;\r
+import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;\r
+import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;\r
+import org.forester.archaeopteryx.tools.AncestralTaxonomyInferrer;\r
+import org.forester.archaeopteryx.tools.InferenceManager;\r
+import org.forester.archaeopteryx.tools.PhyloInferenceDialog;\r
+import org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions;\r
+import org.forester.archaeopteryx.tools.PhylogeneticInferrer;\r
+import org.forester.archaeopteryx.tools.SequenceDataRetriver;\r
+import org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient;\r
+import org.forester.archaeopteryx.webservices.WebservicesManager;\r
+import org.forester.io.parsers.FastaParser;\r
+import org.forester.io.parsers.GeneralMsaParser;\r
+import org.forester.io.parsers.PhylogenyParser;\r
+import org.forester.io.parsers.nexus.NexusPhylogeniesParser;\r
+import org.forester.io.parsers.nhx.NHXParser;\r
+import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;\r
+import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;\r
+import org.forester.io.parsers.phyloxml.PhyloXmlParser;\r
+import org.forester.io.parsers.phyloxml.PhyloXmlUtil;\r
+import org.forester.io.parsers.tol.TolParser;\r
+import org.forester.io.parsers.util.ParserUtils;\r
+import org.forester.io.writers.PhylogenyWriter;\r
+import org.forester.io.writers.SequenceWriter;\r
+import org.forester.msa.Msa;\r
+import org.forester.msa.MsaFormatException;\r
+import org.forester.phylogeny.Phylogeny;\r
+import org.forester.phylogeny.PhylogenyMethods;\r
+import org.forester.phylogeny.PhylogenyNode;\r
+import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;\r
+import org.forester.phylogeny.data.Confidence;\r
+import org.forester.phylogeny.data.Taxonomy;\r
+import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;\r
+import org.forester.phylogeny.factories.PhylogenyFactory;\r
+import org.forester.phylogeny.iterators.PhylogenyNodeIterator;\r
+import org.forester.sequence.Sequence;\r
+import org.forester.util.BasicDescriptiveStatistics;\r
+import org.forester.util.BasicTable;\r
+import org.forester.util.BasicTableParser;\r
+import org.forester.util.DescriptiveStatistics;\r
+import org.forester.util.ForesterUtil;\r
+import org.forester.util.WindowsUtils;\r
+\r
+public final class MainFrameApplication extends MainFrame {\r
+\r
+ static final String INFER_ANCESTOR_TAXONOMIES = "Infer Ancestor Taxonomies";\r
+ static final String OBTAIN_DETAILED_TAXONOMIC_INFORMATION = "Obtain Detailed Taxonomic Information";\r
+ private final static int FRAME_X_SIZE = 800;\r
+ private final static int FRAME_Y_SIZE = 800;\r
+ // Filters for the file-open dialog (classes defined in this file)\r
+ private final static NHFilter nhfilter = new NHFilter();\r
+ private final static NHXFilter nhxfilter = new NHXFilter();\r
+ private final static XMLFilter xmlfilter = new XMLFilter();\r
+ private final static TolFilter tolfilter = new TolFilter();\r
+ private final static NexusFilter nexusfilter = new NexusFilter();\r
+ private final static PdfFilter pdffilter = new PdfFilter();\r
+ private final static GraphicsFileFilter graphicsfilefilter = new GraphicsFileFilter();\r
+ private final static MsaFileFilter msafilter = new MsaFileFilter();\r
+ private final static SequencesFileFilter seqsfilter = new SequencesFileFilter();\r
+ private final static DefaultFilter defaultfilter = new DefaultFilter();\r
+ private static final long serialVersionUID = -799735726778865234L;\r
+ private final JFileChooser _values_filechooser;\r
+ private final JFileChooser _sequences_filechooser;\r
+ private final JFileChooser _open_filechooser;\r
+ private final JFileChooser _msa_filechooser;\r
+ private final JFileChooser _seqs_pi_filechooser;\r
+ private final JFileChooser _open_filechooser_for_species_tree;\r
+ private final JFileChooser _save_filechooser;\r
+ private final JFileChooser _writetopdf_filechooser;\r
+ private final JFileChooser _writetographics_filechooser;\r
+ // Application-only print menu items\r
+ private JMenuItem _print_item;\r
+ private JMenuItem _write_to_pdf_item;\r
+ private JMenuItem _write_to_jpg_item;\r
+ private JMenuItem _write_to_gif_item;\r
+ private JMenuItem _write_to_tif_item;\r
+ private JMenuItem _write_to_png_item;\r
+ private JMenuItem _write_to_bmp_item;\r
+ private File _current_dir;\r
+ private ButtonGroup _radio_group_1;\r
+ private ButtonGroup _radio_group_2;\r
+ // Others:\r
+ double _min_not_collapse = Constants.MIN_NOT_COLLAPSE_DEFAULT;\r
+ // Phylogeny Inference menu\r
+ private JMenu _inference_menu;\r
+ private JMenuItem _inference_from_msa_item;\r
+ private JMenuItem _inference_from_seqs_item;\r
+ // Phylogeny Inference\r
+ private PhylogeneticInferenceOptions _phylogenetic_inference_options = null;\r
+ private Msa _msa = null;\r
+ private File _msa_file = null;\r
+ private List<Sequence> _seqs = null;\r
+ private File _seqs_file = null;\r
+ JMenuItem _read_values_jmi;\r
+ JMenuItem _read_seqs_jmi;\r
+\r
+ private MainFrameApplication( final Phylogeny[] phys, final Configuration config ) {\r
+ _configuration = config;\r
+ if ( _configuration == null ) {\r
+ throw new IllegalArgumentException( "configuration is null" );\r
+ }\r
+ setVisible( false );\r
+ setOptions( Options.createInstance( _configuration ) );\r
+ _mainpanel = new MainPanel( _configuration, this );\r
+ _open_filechooser = null;\r
+ _open_filechooser_for_species_tree = null;\r
+ _save_filechooser = null;\r
+ _writetopdf_filechooser = null;\r
+ _writetographics_filechooser = null;\r
+ _msa_filechooser = null;\r
+ _seqs_pi_filechooser = null;\r
+ _values_filechooser = null;\r
+ _sequences_filechooser = null;\r
+ _jmenubar = new JMenuBar();\r
+ buildFileMenu();\r
+ buildTypeMenu();\r
+ _contentpane = getContentPane();\r
+ _contentpane.setLayout( new BorderLayout() );\r
+ _contentpane.add( _mainpanel, BorderLayout.CENTER );\r
+ // App is this big\r
+ setSize( MainFrameApplication.FRAME_X_SIZE, MainFrameApplication.FRAME_Y_SIZE );\r
+ // The window listener\r
+ setDefaultCloseOperation( WindowConstants.DO_NOTHING_ON_CLOSE );\r
+ addWindowListener( new WindowAdapter() {\r
+\r
+ @Override\r
+ public void windowClosing( final WindowEvent e ) {\r
+ exit();\r
+ }\r
+ } );\r
+ // setVisible( true );\r
+ if ( ( phys != null ) && ( phys.length > 0 ) ) {\r
+ AptxUtil.addPhylogeniesToTabs( phys, "", null, _configuration, _mainpanel );\r
+ validate();\r
+ getMainPanel().getControlPanel().showWholeAll();\r
+ getMainPanel().getControlPanel().showWhole();\r
+ }\r
+ //activateSaveAllIfNeeded();\r
+ // ...and its children\r
+ _contentpane.repaint();\r
+ }\r
+\r
+ private MainFrameApplication( final Phylogeny[] phys, final Configuration config, final String title ) {\r
+ this( phys, config, title, null );\r
+ }\r
+\r
+ private MainFrameApplication( final Phylogeny[] phys,\r
+ final Configuration config,\r
+ final String title,\r
+ final File current_dir ) {\r
+ super();\r
+ _configuration = config;\r
+ if ( _configuration == null ) {\r
+ throw new IllegalArgumentException( "configuration is null" );\r
+ }\r
+ try {\r
+ boolean synth_exception = false;\r
+ if ( Constants.__SYNTH_LF ) {\r
+ try {\r
+ final SynthLookAndFeel synth = new SynthLookAndFeel();\r
+ synth.load( MainFrameApplication.class.getResourceAsStream( "/resources/synth_look_and_feel_1.xml" ),\r
+ MainFrameApplication.class );\r
+ UIManager.setLookAndFeel( synth );\r
+ }\r
+ catch ( final Exception ex ) {\r
+ synth_exception = true;\r
+ ForesterUtil.printWarningMessage( Constants.PRG_NAME,\r
+ "could not create synth look and feel: "\r
+ + ex.getLocalizedMessage() );\r
+ }\r
+ }\r
+ if ( !Constants.__SYNTH_LF || synth_exception ) {\r
+ if ( _configuration.isUseNativeUI() ) {\r
+ UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );\r
+ }\r
+ else {\r
+ UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );\r
+ }\r
+ }\r
+ //UIManager.setLookAndFeel( "com.sun.java.swing.plaf.nimbus.NimbusLookAndFeel" );\r
+ }\r
+ catch ( final UnsupportedLookAndFeelException e ) {\r
+ AptxUtil.dieWithSystemError( "unsupported look and feel: " + e.toString() );\r
+ }\r
+ catch ( final ClassNotFoundException e ) {\r
+ AptxUtil.dieWithSystemError( "class not found exception: " + e.toString() );\r
+ }\r
+ catch ( final InstantiationException e ) {\r
+ AptxUtil.dieWithSystemError( "instantiation exception: " + e.toString() );\r
+ }\r
+ catch ( final IllegalAccessException e ) {\r
+ AptxUtil.dieWithSystemError( "illegal access exception: " + e.toString() );\r
+ }\r
+ if ( ( current_dir != null ) && current_dir.canRead() && current_dir.isDirectory() ) {\r
+ setCurrentDir( current_dir );\r
+ }\r
+ // hide until everything is ready\r
+ setVisible( false );\r
+ setOptions( Options.createInstance( _configuration ) );\r
+ setInferenceManager( InferenceManager.createInstance( _configuration ) );\r
+ setPhylogeneticInferenceOptions( PhylogeneticInferenceOptions.createInstance( _configuration ) );\r
+ // _textframe = null; #~~~~\r
+ // set title\r
+ setTitle( Constants.PRG_NAME + " " + Constants.VERSION + " (" + Constants.PRG_DATE + ")" );\r
+ _mainpanel = new MainPanel( _configuration, this );\r
+ // The file dialogs\r
+ _open_filechooser = new JFileChooser();\r
+ _open_filechooser.setCurrentDirectory( new File( "." ) );\r
+ _open_filechooser.setMultiSelectionEnabled( false );\r
+ _open_filechooser.addChoosableFileFilter( MainFrameApplication.xmlfilter );\r
+ _open_filechooser.addChoosableFileFilter( MainFrameApplication.nhxfilter );\r
+ _open_filechooser.addChoosableFileFilter( MainFrameApplication.nhfilter );\r
+ _open_filechooser.addChoosableFileFilter( MainFrameApplication.nexusfilter );\r
+ _open_filechooser.addChoosableFileFilter( MainFrameApplication.tolfilter );\r
+ _open_filechooser.addChoosableFileFilter( _open_filechooser.getAcceptAllFileFilter() );\r
+ _open_filechooser.setFileFilter( MainFrameApplication.defaultfilter );\r
+ _open_filechooser_for_species_tree = new JFileChooser();\r
+ _open_filechooser_for_species_tree.setCurrentDirectory( new File( "." ) );\r
+ _open_filechooser_for_species_tree.setMultiSelectionEnabled( false );\r
+ _open_filechooser_for_species_tree.addChoosableFileFilter( MainFrameApplication.xmlfilter );\r
+ _open_filechooser_for_species_tree.addChoosableFileFilter( MainFrameApplication.tolfilter );\r
+ _open_filechooser_for_species_tree.setFileFilter( MainFrameApplication.xmlfilter );\r
+ _save_filechooser = new JFileChooser();\r
+ _save_filechooser.setCurrentDirectory( new File( "." ) );\r
+ _save_filechooser.setMultiSelectionEnabled( false );\r
+ _save_filechooser.setFileFilter( MainFrameApplication.xmlfilter );\r
+ _save_filechooser.addChoosableFileFilter( MainFrameApplication.nhfilter );\r
+ _save_filechooser.addChoosableFileFilter( MainFrameApplication.nexusfilter );\r
+ _save_filechooser.addChoosableFileFilter( _save_filechooser.getAcceptAllFileFilter() );\r
+ _writetopdf_filechooser = new JFileChooser();\r
+ _writetopdf_filechooser.addChoosableFileFilter( MainFrameApplication.pdffilter );\r
+ _writetographics_filechooser = new JFileChooser();\r
+ _writetographics_filechooser.addChoosableFileFilter( MainFrameApplication.graphicsfilefilter );\r
+ // Msa:\r
+ _msa_filechooser = new JFileChooser();\r
+ _msa_filechooser.setName( "Read Multiple Sequence Alignment File" );\r
+ _msa_filechooser.setCurrentDirectory( new File( "." ) );\r
+ _msa_filechooser.setMultiSelectionEnabled( false );\r
+ _msa_filechooser.addChoosableFileFilter( _msa_filechooser.getAcceptAllFileFilter() );\r
+ _msa_filechooser.addChoosableFileFilter( MainFrameApplication.msafilter );\r
+ // Seqs:\r
+ _seqs_pi_filechooser = new JFileChooser();\r
+ _seqs_pi_filechooser.setName( "Read Sequences File" );\r
+ _seqs_pi_filechooser.setCurrentDirectory( new File( "." ) );\r
+ _seqs_pi_filechooser.setMultiSelectionEnabled( false );\r
+ _seqs_pi_filechooser.addChoosableFileFilter( _seqs_pi_filechooser.getAcceptAllFileFilter() );\r
+ _seqs_pi_filechooser.addChoosableFileFilter( MainFrameApplication.seqsfilter );\r
+ // Expression\r
+ _values_filechooser = new JFileChooser();\r
+ _values_filechooser.setCurrentDirectory( new File( "." ) );\r
+ _values_filechooser.setMultiSelectionEnabled( false );\r
+ // Sequences\r
+ _sequences_filechooser = new JFileChooser();\r
+ _sequences_filechooser.setCurrentDirectory( new File( "." ) );\r
+ _sequences_filechooser.setMultiSelectionEnabled( false );\r
+ // build the menu bar\r
+ _jmenubar = new JMenuBar();\r
+ if ( !_configuration.isUseNativeUI() ) {\r
+ _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
+ }\r
+ buildFileMenu();\r
+ if ( Constants.__ALLOW_PHYLOGENETIC_INFERENCE ) {\r
+ buildPhylogeneticInferenceMenu();\r
+ }\r
+ buildAnalysisMenu();\r
+ buildToolsMenu();\r
+ buildViewMenu();\r
+ buildFontSizeMenu();\r
+ buildOptionsMenu();\r
+ buildTypeMenu();\r
+ buildHelpMenu();\r
+ setJMenuBar( _jmenubar );\r
+ _jmenubar.add( _help_jmenu );\r
+ _contentpane = getContentPane();\r
+ _contentpane.setLayout( new BorderLayout() );\r
+ _contentpane.add( _mainpanel, BorderLayout.CENTER );\r
+ // App is this big\r
+ setSize( MainFrameApplication.FRAME_X_SIZE, MainFrameApplication.FRAME_Y_SIZE );\r
+ // addWindowFocusListener( new WindowAdapter() {\r
+ //\r
+ // @Override\r
+ // public void windowGainedFocus( WindowEvent e ) {\r
+ // requestFocusInWindow();\r
+ // }\r
+ // } );\r
+ // The window listener\r
+ setDefaultCloseOperation( WindowConstants.DO_NOTHING_ON_CLOSE );\r
+ addWindowListener( new WindowAdapter() {\r
+\r
+ @Override\r
+ public void windowClosing( final WindowEvent e ) {\r
+ if ( isUnsavedDataPresent() ) {\r
+ final int r = JOptionPane.showConfirmDialog( null,\r
+ "Exit despite potentially unsaved changes?",\r
+ "Exit?",\r
+ JOptionPane.YES_NO_OPTION );\r
+ if ( r != JOptionPane.YES_OPTION ) {\r
+ return;\r
+ }\r
+ }\r
+ else {\r
+ final int r = JOptionPane.showConfirmDialog( null,\r
+ "Exit Archaeopteryx?",\r
+ "Exit?",\r
+ JOptionPane.YES_NO_OPTION );\r
+ if ( r != JOptionPane.YES_OPTION ) {\r
+ return;\r
+ }\r
+ }\r
+ exit();\r
+ }\r
+ } );\r
+ // The component listener\r
+ addComponentListener( new ComponentAdapter() {\r
+\r
+ @Override\r
+ public void componentResized( final ComponentEvent e ) {\r
+ if ( _mainpanel.getCurrentTreePanel() != null ) {\r
+ _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel()\r
+ .getWidth(),\r
+ _mainpanel.getCurrentTreePanel()\r
+ .getHeight(),\r
+ getOptions().isAllowFontSizeChange() );\r
+ }\r
+ }\r
+ } );\r
+ requestFocusInWindow();\r
+ // addKeyListener( this );\r
+ setVisible( true );\r
+ if ( ( phys != null ) && ( phys.length > 0 ) ) {\r
+ AptxUtil.addPhylogeniesToTabs( phys, title, null, _configuration, _mainpanel );\r
+ validate();\r
+ getMainPanel().getControlPanel().showWholeAll();\r
+ getMainPanel().getControlPanel().showWhole();\r
+ }\r
+ activateSaveAllIfNeeded();\r
+ // ...and its children\r
+ _contentpane.repaint();\r
+ System.gc();\r
+ }\r
+\r
+ private MainFrameApplication( final Phylogeny[] phys, final String config_file, final String title ) {\r
+ // Reads the config file (false, false => not url, not applet):\r
+ this( phys, new Configuration( config_file, false, false, true ), title );\r
+ }\r
+\r
+ @Override\r
+ public void actionPerformed( final ActionEvent e ) {\r
+ try {\r
+ super.actionPerformed( e );\r
+ final Object o = e.getSource();\r
+ // Handle app-specific actions here:\r
+ if ( o == _open_item ) {\r
+ readPhylogeniesFromFile();\r
+ }\r
+ if ( o == _open_url_item ) {\r
+ readPhylogeniesFromURL();\r
+ }\r
+ else if ( o == _save_item ) {\r
+ writeToFile( _mainpanel.getCurrentPhylogeny() );\r
+ // If subtree currently displayed, save it, instead of complete\r
+ // tree.\r
+ }\r
+ else if ( o == _new_item ) {\r
+ newTree();\r
+ }\r
+ else if ( o == _save_all_item ) {\r
+ writeAllToFile();\r
+ }\r
+ else if ( o == _close_item ) {\r
+ closeCurrentPane();\r
+ }\r
+ else if ( o == _write_to_pdf_item ) {\r
+ writeToPdf( _mainpanel.getCurrentPhylogeny() );\r
+ }\r
+ else if ( o == _write_to_jpg_item ) {\r
+ writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.JPG );\r
+ }\r
+ else if ( o == _write_to_png_item ) {\r
+ writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.PNG );\r
+ }\r
+ else if ( o == _write_to_gif_item ) {\r
+ writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.GIF );\r
+ }\r
+ else if ( o == _write_to_tif_item ) {\r
+ writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.TIFF );\r
+ }\r
+ else if ( o == _write_to_bmp_item ) {\r
+ writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.BMP );\r
+ }\r
+ else if ( o == _print_item ) {\r
+ print();\r
+ }\r
+ else if ( o == _load_species_tree_item ) {\r
+ readSpeciesTreeFromFile();\r
+ }\r
+ else if ( o == _lineage_inference ) {\r
+ if ( isSubtreeDisplayed() ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Subtree is shown.",\r
+ "Cannot infer ancestral taxonomies",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ executeLineageInference();\r
+ }\r
+ else if ( o == _obtain_detailed_taxonomic_information_jmi ) {\r
+ if ( isSubtreeDisplayed() ) {\r
+ return;\r
+ }\r
+ obtainDetailedTaxonomicInformation();\r
+ }\r
+ else if ( o == _obtain_detailed_taxonomic_information_deleting_jmi ) {\r
+ if ( isSubtreeDisplayed() ) {\r
+ return;\r
+ }\r
+ obtainDetailedTaxonomicInformationDelete();\r
+ }\r
+ else if ( o == _obtain_seq_information_jmi ) {\r
+ obtainSequenceInformation();\r
+ }\r
+ else if ( o == _read_values_jmi ) {\r
+ if ( isSubtreeDisplayed() ) {\r
+ return;\r
+ }\r
+ addExpressionValuesFromFile();\r
+ }\r
+ else if ( o == _read_seqs_jmi ) {\r
+ if ( isSubtreeDisplayed() ) {\r
+ return;\r
+ }\r
+ addSequencesFromFile();\r
+ }\r
+ else if ( o == _move_node_names_to_tax_sn_jmi ) {\r
+ moveNodeNamesToTaxSn();\r
+ }\r
+ else if ( o == _move_node_names_to_seq_names_jmi ) {\r
+ moveNodeNamesToSeqNames();\r
+ }\r
+ else if ( o == _extract_tax_code_from_node_names_jmi ) {\r
+ extractTaxDataFromNodeNames();\r
+ }\r
+ else if ( o == _graphics_export_visible_only_cbmi ) {\r
+ updateOptions( getOptions() );\r
+ }\r
+ else if ( o == _antialias_print_cbmi ) {\r
+ updateOptions( getOptions() );\r
+ }\r
+ else if ( o == _print_black_and_white_cbmi ) {\r
+ updateOptions( getOptions() );\r
+ }\r
+ else if ( o == _print_using_actual_size_cbmi ) {\r
+ updateOptions( getOptions() );\r
+ }\r
+ else if ( o == _graphics_export_using_actual_size_cbmi ) {\r
+ updateOptions( getOptions() );\r
+ }\r
+ else if ( o == _print_size_mi ) {\r
+ choosePrintSize();\r
+ }\r
+ else if ( o == _choose_pdf_width_mi ) {\r
+ choosePdfWidth();\r
+ }\r
+ else if ( o == _internal_number_are_confidence_for_nh_parsing_cbmi ) {\r
+ updateOptions( getOptions() );\r
+ }\r
+ else if ( o == _replace_underscores_cbmi ) {\r
+ if ( ( _extract_taxonomy_no_rbmi != null ) && !_extract_taxonomy_no_rbmi.isSelected() ) {\r
+ _extract_taxonomy_no_rbmi.setSelected( true );\r
+ }\r
+ updateOptions( getOptions() );\r
+ }\r
+ else if ( o == _allow_errors_in_distance_to_parent_cbmi ) {\r
+ updateOptions( getOptions() );\r
+ }\r
+ else if ( o == _collapse_below_threshold ) {\r
+ if ( isSubtreeDisplayed() ) {\r
+ return;\r
+ }\r
+ collapseBelowThreshold();\r
+ }\r
+ else if ( ( o == _extract_taxonomy_pfam_strict_rbmi ) || ( o == _extract_taxonomy_pfam_relaxed_rbmi )\r
+ || ( o == _extract_taxonomy_agressive_rbmi ) ) {\r
+ if ( _replace_underscores_cbmi != null ) {\r
+ _replace_underscores_cbmi.setSelected( false );\r
+ }\r
+ updateOptions( getOptions() );\r
+ }\r
+ else if ( o == _extract_taxonomy_no_rbmi ) {\r
+ updateOptions( getOptions() );\r
+ }\r
+ else if ( o == _inference_from_msa_item ) {\r
+ executePhyleneticInference( false );\r
+ }\r
+ else if ( o == _inference_from_seqs_item ) {\r
+ executePhyleneticInference( true );\r
+ }\r
+ _contentpane.repaint();\r
+ }\r
+ catch ( final Exception ex ) {\r
+ AptxUtil.unexpectedException( ex );\r
+ }\r
+ catch ( final Error err ) {\r
+ AptxUtil.unexpectedError( err );\r
+ }\r
+ }\r
+\r
+ public void end() {\r
+ _mainpanel.terminate();\r
+ _contentpane.removeAll();\r
+ setVisible( false );\r
+ dispose();\r
+ }\r
+\r
+ @Override\r
+ public MainPanel getMainPanel() {\r
+ return _mainpanel;\r
+ }\r
+\r
+ public Msa getMsa() {\r
+ return _msa;\r
+ }\r
+\r
+ public File getMsaFile() {\r
+ return _msa_file;\r
+ }\r
+\r
+ public List<Sequence> getSeqs() {\r
+ return _seqs;\r
+ }\r
+\r
+ public File getSeqsFile() {\r
+ return _seqs_file;\r
+ }\r
+\r
+ public void readMsaFromFile() {\r
+ // Set an initial directory if none set yet\r
+ final File my_dir = getCurrentDir();\r
+ _msa_filechooser.setMultiSelectionEnabled( false );\r
+ // Open file-open dialog and set current directory\r
+ if ( my_dir != null ) {\r
+ _msa_filechooser.setCurrentDirectory( my_dir );\r
+ }\r
+ final int result = _msa_filechooser.showOpenDialog( _contentpane );\r
+ // All done: get the msa\r
+ final File file = _msa_filechooser.getSelectedFile();\r
+ setCurrentDir( _msa_filechooser.getCurrentDirectory() );\r
+ if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
+ setMsaFile( null );\r
+ setMsa( null );\r
+ Msa msa = null;\r
+ try {\r
+ final InputStream is = new FileInputStream( file );\r
+ if ( FastaParser.isLikelyFasta( file ) ) {\r
+ msa = FastaParser.parseMsa( is );\r
+ }\r
+ else {\r
+ msa = GeneralMsaParser.parse( is );\r
+ }\r
+ }\r
+ catch ( final MsaFormatException e ) {\r
+ setArrowCursor();\r
+ JOptionPane.showMessageDialog( this,\r
+ e.getLocalizedMessage(),\r
+ "Multiple sequence alignment format error",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ catch ( final IOException e ) {\r
+ setArrowCursor();\r
+ JOptionPane.showMessageDialog( this,\r
+ e.getLocalizedMessage(),\r
+ "Failed to read multiple sequence alignment",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ catch ( final IllegalArgumentException e ) {\r
+ setArrowCursor();\r
+ JOptionPane.showMessageDialog( this,\r
+ e.getLocalizedMessage(),\r
+ "Unexpected error during reading of multiple sequence alignment",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ catch ( final Exception e ) {\r
+ setArrowCursor();\r
+ e.printStackTrace();\r
+ JOptionPane.showMessageDialog( this,\r
+ e.getLocalizedMessage(),\r
+ "Unexpected error during reading of multiple sequence alignment",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ if ( ( msa == null ) || ( msa.getNumberOfSequences() < 1 ) ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Multiple sequence alignment is empty",\r
+ "Illegal Multiple Sequence Alignment",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ if ( msa.getNumberOfSequences() < 4 ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Multiple sequence alignment needs to contain at least 3 sequences",\r
+ "Illegal multiple sequence alignment",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ if ( msa.getLength() < 2 ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Multiple sequence alignment needs to contain at least 2 residues",\r
+ "Illegal multiple sequence alignment",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ System.gc();\r
+ setMsaFile( _msa_filechooser.getSelectedFile() );\r
+ setMsa( msa );\r
+ }\r
+ }\r
+\r
+ public void readSeqsFromFileforPI() {\r
+ // Set an initial directory if none set yet\r
+ final File my_dir = getCurrentDir();\r
+ _seqs_pi_filechooser.setMultiSelectionEnabled( false );\r
+ // Open file-open dialog and set current directory\r
+ if ( my_dir != null ) {\r
+ _seqs_pi_filechooser.setCurrentDirectory( my_dir );\r
+ }\r
+ final int result = _seqs_pi_filechooser.showOpenDialog( _contentpane );\r
+ // All done: get the seqs\r
+ final File file = _seqs_pi_filechooser.getSelectedFile();\r
+ setCurrentDir( _seqs_pi_filechooser.getCurrentDirectory() );\r
+ if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
+ setSeqsFile( null );\r
+ setSeqs( null );\r
+ List<Sequence> seqs = null;\r
+ try {\r
+ if ( FastaParser.isLikelyFasta( new FileInputStream( file ) ) ) {\r
+ seqs = FastaParser.parse( new FileInputStream( file ) );\r
+ for( final Sequence seq : seqs ) {\r
+ System.out.println( SequenceWriter.toFasta( seq, 60 ) );\r
+ }\r
+ }\r
+ else {\r
+ //TODO error\r
+ }\r
+ }\r
+ catch ( final MsaFormatException e ) {\r
+ setArrowCursor();\r
+ JOptionPane.showMessageDialog( this,\r
+ e.getLocalizedMessage(),\r
+ "Multiple sequence file format error",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ catch ( final IOException e ) {\r
+ setArrowCursor();\r
+ JOptionPane.showMessageDialog( this,\r
+ e.getLocalizedMessage(),\r
+ "Failed to read multiple sequence file",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ catch ( final IllegalArgumentException e ) {\r
+ setArrowCursor();\r
+ JOptionPane.showMessageDialog( this,\r
+ e.getLocalizedMessage(),\r
+ "Unexpected error during reading of multiple sequence file",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ catch ( final Exception e ) {\r
+ setArrowCursor();\r
+ e.printStackTrace();\r
+ JOptionPane.showMessageDialog( this,\r
+ e.getLocalizedMessage(),\r
+ "Unexpected error during reading of multiple sequence file",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ if ( ( seqs == null ) || ( seqs.size() < 1 ) ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Multiple sequence file is empty",\r
+ "Illegal multiple sequence file",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ if ( seqs.size() < 4 ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Multiple sequence file needs to contain at least 3 sequences",\r
+ "Illegal multiple sequence file",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ // if ( msa.getLength() < 2 ) {\r
+ // JOptionPane.showMessageDialog( this,\r
+ // "Multiple sequence alignment needs to contain at least 2 residues",\r
+ // "Illegal multiple sequence file",\r
+ // JOptionPane.ERROR_MESSAGE );\r
+ // return;\r
+ // }\r
+ System.gc();\r
+ setSeqsFile( _seqs_pi_filechooser.getSelectedFile() );\r
+ setSeqs( seqs );\r
+ }\r
+ }\r
+\r
+ void buildAnalysisMenu() {\r
+ _analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );\r
+ _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );\r
+ _analysis_menu.add( _gsdir_item = new JMenuItem( "GSDIR (GSDI with re-rooting)" ) );\r
+ _analysis_menu.add( _load_species_tree_item = new JMenuItem( "Load Species Tree..." ) );\r
+ customizeJMenuItem( _gsdi_item );\r
+ customizeJMenuItem( _gsdir_item );\r
+ customizeJMenuItem( _load_species_tree_item );\r
+ _analysis_menu.addSeparator();\r
+ _analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) );\r
+ customizeJMenuItem( _lineage_inference );\r
+ _lineage_inference.setToolTipText( "Inference of ancestor taxonomies/lineages" );\r
+ _jmenubar.add( _analysis_menu );\r
+ }\r
+\r
+ @Override\r
+ void buildFileMenu() {\r
+ _file_jmenu = MainFrame.createMenu( "File", getConfiguration() );\r
+ _file_jmenu.add( _open_item = new JMenuItem( "Read Tree from File..." ) );\r
+ _file_jmenu.addSeparator();\r
+ _file_jmenu.add( _open_url_item = new JMenuItem( "Read Tree from URL/Webservice..." ) );\r
+ _file_jmenu.addSeparator();\r
+ final WebservicesManager webservices_manager = WebservicesManager.getInstance();\r
+ _load_phylogeny_from_webservice_menu_items = new JMenuItem[ webservices_manager\r
+ .getAvailablePhylogeniesWebserviceClients().size() ];\r
+ for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {\r
+ final PhylogeniesWebserviceClient client = webservices_manager.getAvailablePhylogeniesWebserviceClient( i );\r
+ _load_phylogeny_from_webservice_menu_items[ i ] = new JMenuItem( client.getMenuName() );\r
+ _file_jmenu.add( _load_phylogeny_from_webservice_menu_items[ i ] );\r
+ }\r
+ if ( getConfiguration().isEditable() ) {\r
+ _file_jmenu.addSeparator();\r
+ _file_jmenu.add( _new_item = new JMenuItem( "New" ) );\r
+ _new_item.setToolTipText( "to create a new tree with one node, as source for manual tree construction" );\r
+ }\r
+ _file_jmenu.addSeparator();\r
+ _file_jmenu.add( _save_item = new JMenuItem( "Save Tree As..." ) );\r
+ _file_jmenu.add( _save_all_item = new JMenuItem( "Save All Trees As..." ) );\r
+ _save_all_item.setToolTipText( "Write all phylogenies to one file." );\r
+ _save_all_item.setEnabled( false );\r
+ _file_jmenu.addSeparator();\r
+ _file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) );\r
+ if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" ) || AptxUtil.canWriteFormat( "TIF" ) ) {\r
+ _file_jmenu.add( _write_to_tif_item = new JMenuItem( "Export to TIFF file..." ) );\r
+ }\r
+ _file_jmenu.add( _write_to_png_item = new JMenuItem( "Export to PNG file..." ) );\r
+ _file_jmenu.add( _write_to_jpg_item = new JMenuItem( "Export to JPG file..." ) );\r
+ if ( AptxUtil.canWriteFormat( "gif" ) ) {\r
+ _file_jmenu.add( _write_to_gif_item = new JMenuItem( "Export to GIF file..." ) );\r
+ }\r
+ if ( AptxUtil.canWriteFormat( "bmp" ) ) {\r
+ _file_jmenu.add( _write_to_bmp_item = new JMenuItem( "Export to BMP file..." ) );\r
+ }\r
+ _file_jmenu.addSeparator();\r
+ _file_jmenu.add( _print_item = new JMenuItem( "Print..." ) );\r
+ _file_jmenu.addSeparator();\r
+ _file_jmenu.add( _close_item = new JMenuItem( "Close Tab" ) );\r
+ _close_item.setToolTipText( "To close the current pane." );\r
+ _close_item.setEnabled( true );\r
+ _file_jmenu.addSeparator();\r
+ _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );\r
+ customizeJMenuItem( _open_item );\r
+ _open_item\r
+ .setFont( new Font( _open_item.getFont().getFontName(), Font.BOLD, _open_item.getFont().getSize() + 4 ) );\r
+ customizeJMenuItem( _open_url_item );\r
+ for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {\r
+ customizeJMenuItem( _load_phylogeny_from_webservice_menu_items[ i ] );\r
+ }\r
+ customizeJMenuItem( _save_item );\r
+ if ( getConfiguration().isEditable() ) {\r
+ customizeJMenuItem( _new_item );\r
+ }\r
+ customizeJMenuItem( _close_item );\r
+ customizeJMenuItem( _save_all_item );\r
+ customizeJMenuItem( _write_to_pdf_item );\r
+ customizeJMenuItem( _write_to_png_item );\r
+ customizeJMenuItem( _write_to_jpg_item );\r
+ customizeJMenuItem( _write_to_gif_item );\r
+ customizeJMenuItem( _write_to_tif_item );\r
+ customizeJMenuItem( _write_to_bmp_item );\r
+ customizeJMenuItem( _print_item );\r
+ customizeJMenuItem( _exit_item );\r
+ _jmenubar.add( _file_jmenu );\r
+ }\r
+\r
+ void buildOptionsMenu() {\r
+ _options_jmenu = MainFrame.createMenu( OPTIONS_HEADER, getConfiguration() );\r
+ _options_jmenu.addChangeListener( new ChangeListener() {\r
+\r
+ @Override\r
+ public void stateChanged( final ChangeEvent e ) {\r
+ MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );\r
+ MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );\r
+ MainFrame\r
+ .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );\r
+ MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame\r
+ .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );\r
+ setTextForGraphicsSizeChooserMenuItem( _print_size_mi, getOptions() );\r
+ setTextForPdfLineWidthChooserMenuItem( _choose_pdf_width_mi, getOptions() );\r
+ MainFrame.updateOptionsMenuDependingOnPhylogenyType( getMainPanel(),\r
+ _show_scale_cbmi,\r
+ _show_branch_length_values_cbmi,\r
+ _non_lined_up_cladograms_rbmi,\r
+ _uniform_cladograms_rbmi,\r
+ _ext_node_dependent_cladogram_rbmi,\r
+ _label_direction_cbmi );\r
+ MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );\r
+ MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );\r
+ MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );\r
+ }\r
+ } );\r
+ _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( DISPLAY_SUBHEADER ), getConfiguration() ) );\r
+ _options_jmenu\r
+ .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );\r
+ _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );\r
+ _options_jmenu.add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( NON_LINED_UP_CLADOGRAMS_LABEL ) );\r
+ _radio_group_1 = new ButtonGroup();\r
+ _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );\r
+ _radio_group_1.add( _uniform_cladograms_rbmi );\r
+ _radio_group_1.add( _non_lined_up_cladograms_rbmi );\r
+ ///////\r
+ _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( SHOW_OVERVIEW_LABEL ) );\r
+ _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( DISPLAY_SCALE_LABEL ) );\r
+ _options_jmenu\r
+ .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );\r
+ _options_jmenu\r
+ .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_INT ) );\r
+ _options_jmenu\r
+ .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_EXT ) );\r
+ if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {\r
+ _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( SHOW_DOMAIN_LABELS_LABEL ) );\r
+ }\r
+ _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( SHOW_ANN_REF_SOURCE_LABEL ) );\r
+ _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( SHOW_CONF_STDDEV_LABEL ) );\r
+ _options_jmenu.add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( COLOR_BY_TAXONOMIC_GROUP ) );\r
+ _options_jmenu.add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( COLOR_LABELS_LABEL ) );\r
+ _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );\r
+ _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( ABBREV_SN_LABEL ) );\r
+ _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( LABEL_DIRECTION_LABEL ) );\r
+ _label_direction_cbmi.setToolTipText( LABEL_DIRECTION_TIP );\r
+ _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( SCREEN_ANTIALIAS_LABEL ) );\r
+ _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( BG_GRAD_LABEL ) );\r
+ _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );\r
+ _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );\r
+ _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );\r
+ _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );\r
+ _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );\r
+ _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );\r
+ _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );\r
+ ///////\r
+ _options_jmenu.addSeparator();\r
+ _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( SEARCH_SUBHEADER ), getConfiguration() ) );\r
+ _options_jmenu.add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( SEARCH_CASE_SENSITIVE_LABEL ) );\r
+ _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( SEARCH_TERMS_ONLY_LABEL ) );\r
+ _options_jmenu.add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( INVERSE_SEARCH_RESULT_LABEL ) );\r
+ _options_jmenu.addSeparator();\r
+ _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Graphics Export & Printing:" ),\r
+ getConfiguration() ) );\r
+ _options_jmenu.add( _antialias_print_cbmi = new JCheckBoxMenuItem( "Antialias" ) );\r
+ _options_jmenu.add( _print_black_and_white_cbmi = new JCheckBoxMenuItem( "Export in Black and White" ) );\r
+ _options_jmenu\r
+ .add( _print_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PDF export and Printing" ) );\r
+ _options_jmenu\r
+ .add( _graphics_export_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PNG, JPG, and GIF export" ) );\r
+ _options_jmenu\r
+ .add( _graphics_export_visible_only_cbmi = new JCheckBoxMenuItem( "Limit to Visible ('Screenshot') for PNG, JPG, and GIF export" ) );\r
+ _options_jmenu.add( _print_size_mi = new JMenuItem( "" ) );\r
+ _options_jmenu.add( _choose_pdf_width_mi = new JMenuItem( "" ) );\r
+ _options_jmenu.addSeparator();\r
+ _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/NHX/Nexus Input:" ), getConfiguration() ) );\r
+ _options_jmenu\r
+ .add( _internal_number_are_confidence_for_nh_parsing_cbmi = new JCheckBoxMenuItem( "Internal Node Names are Confidence Values" ) );\r
+ _options_jmenu.add( _replace_underscores_cbmi = new JCheckBoxMenuItem( "Replace Underscores with Spaces" ) );\r
+ _options_jmenu\r
+ .add( _allow_errors_in_distance_to_parent_cbmi = new JCheckBoxMenuItem( "Ignore Distance Values Format Errors" ) );\r
+ //\r
+ _options_jmenu.add( _extract_taxonomy_no_rbmi = new JRadioButtonMenuItem( "No Taxonomy Extraction" ) );\r
+ _options_jmenu\r
+ .add( _extract_taxonomy_pfam_strict_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style Node Names" ) );\r
+ _options_jmenu\r
+ .add( _extract_taxonomy_pfam_relaxed_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style like Node Names" ) );\r
+ _options_jmenu\r
+ .add( _extract_taxonomy_agressive_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids/Scientific Names from Node Names" ) );\r
+ _extract_taxonomy_pfam_strict_rbmi\r
+ .setToolTipText( "To extract taxonomy codes/ids from node names in the form of e.g. \"BCL2_MOUSE/123-304\" or \"BCL2_10090/123-304\"" );\r
+ _extract_taxonomy_pfam_relaxed_rbmi\r
+ .setToolTipText( "To extract taxonomy codes/ids from node names in the form of e.g. \"bax_MOUSE\" or \"bax_10090\"" );\r
+ _extract_taxonomy_agressive_rbmi\r
+ .setToolTipText( "To extract taxonomy codes/ids or scientific names from node names in the form of e.g. \"MOUSE\" or \"10090\" or \"xyz_Nematostella_vectensis\"" );\r
+ _radio_group_2 = new ButtonGroup();\r
+ _radio_group_2.add( _extract_taxonomy_no_rbmi );\r
+ _radio_group_2.add( _extract_taxonomy_pfam_strict_rbmi );\r
+ _radio_group_2.add( _extract_taxonomy_pfam_relaxed_rbmi );\r
+ _radio_group_2.add( _extract_taxonomy_agressive_rbmi );\r
+ // \r
+ _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/Nexus Output:" ), getConfiguration() ) );\r
+ _options_jmenu\r
+ .add( _use_brackets_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_BRACKETS_FOR_CONF_IN_NH_LABEL ) );\r
+ _use_brackets_for_conf_in_nh_export_cbmi\r
+ .setToolTipText( "e.g. \"0.1[90]\" for a branch with support 90 and a length of 0.1" );\r
+ _options_jmenu\r
+ .add( _use_internal_names_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL ) );\r
+ customizeJMenuItem( _choose_font_mi );\r
+ customizeJMenuItem( _choose_minimal_confidence_mi );\r
+ customizeJMenuItem( _switch_colors_mi );\r
+ customizeJMenuItem( _print_size_mi );\r
+ customizeJMenuItem( _choose_pdf_width_mi );\r
+ customizeJMenuItem( _overview_placment_mi );\r
+ customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions()\r
+ .isShowDefaultNodeShapesExternal() );\r
+ customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()\r
+ .isShowDefaultNodeShapesInternal() );\r
+ customizeJMenuItem( _cycle_node_shape_mi );\r
+ customizeJMenuItem( _cycle_node_fill_mi );\r
+ customizeJMenuItem( _choose_node_size_mi );\r
+ customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );\r
+ customizeCheckBoxMenuItem( _color_by_taxonomic_group_cbmi, getOptions().isColorByTaxonomicGroup() );\r
+ customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );\r
+ customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );\r
+ customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );\r
+ customizeCheckBoxMenuItem( _show_annotation_ref_source, getOptions().isShowAnnotationRefSource() );\r
+ customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );\r
+ customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );\r
+ customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );\r
+ customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,\r
+ getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );\r
+ customizeRadioButtonMenuItem( _uniform_cladograms_rbmi,\r
+ getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );\r
+ customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,\r
+ getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );\r
+ customizeCheckBoxMenuItem( _show_branch_length_values_cbmi, getOptions().isShowBranchLengthValues() );\r
+ customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );\r
+ customizeCheckBoxMenuItem( _label_direction_cbmi,\r
+ getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );\r
+ customizeCheckBoxMenuItem( _antialias_print_cbmi, getOptions().isAntialiasPrint() );\r
+ customizeCheckBoxMenuItem( _print_black_and_white_cbmi, getOptions().isPrintBlackAndWhite() );\r
+ customizeCheckBoxMenuItem( _internal_number_are_confidence_for_nh_parsing_cbmi, getOptions()\r
+ .isInternalNumberAreConfidenceForNhParsing() );\r
+ customizeRadioButtonMenuItem( _extract_taxonomy_no_rbmi,\r
+ getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.NO );\r
+ customizeRadioButtonMenuItem( _extract_taxonomy_pfam_strict_rbmi,\r
+ getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );\r
+ customizeRadioButtonMenuItem( _extract_taxonomy_pfam_relaxed_rbmi,\r
+ getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );\r
+ customizeRadioButtonMenuItem( _extract_taxonomy_agressive_rbmi,\r
+ getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.AGGRESSIVE );\r
+ customizeCheckBoxMenuItem( _replace_underscores_cbmi, getOptions().isReplaceUnderscoresInNhParsing() );\r
+ customizeCheckBoxMenuItem( _allow_errors_in_distance_to_parent_cbmi, getOptions()\r
+ .isReplaceUnderscoresInNhParsing() );\r
+ customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );\r
+ customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );\r
+ customizeCheckBoxMenuItem( _graphics_export_visible_only_cbmi, getOptions().isGraphicsExportVisibleOnly() );\r
+ customizeCheckBoxMenuItem( _print_using_actual_size_cbmi, getOptions().isPrintUsingActualSize() );\r
+ customizeCheckBoxMenuItem( _graphics_export_using_actual_size_cbmi, getOptions()\r
+ .isGraphicsExportUsingActualSize() );\r
+ customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );\r
+ customizeCheckBoxMenuItem( _use_brackets_for_conf_in_nh_export_cbmi, getOptions()\r
+ .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );\r
+ customizeCheckBoxMenuItem( _use_internal_names_for_conf_in_nh_export_cbmi, getOptions()\r
+ .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );\r
+ _jmenubar.add( _options_jmenu );\r
+ }\r
+\r
+ void buildPhylogeneticInferenceMenu() {\r
+ final InferenceManager im = getInferenceManager();\r
+ _inference_menu = MainFrame.createMenu( "Inference", getConfiguration() );\r
+ _inference_menu.add( _inference_from_msa_item = new JMenuItem( "From Multiple Sequence Alignment..." ) );\r
+ customizeJMenuItem( _inference_from_msa_item );\r
+ _inference_from_msa_item.setToolTipText( "Basic phylogenetic inference from MSA" );\r
+ if ( im.canDoMsa() ) {\r
+ _inference_menu.add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences..." ) );\r
+ customizeJMenuItem( _inference_from_seqs_item );\r
+ _inference_from_seqs_item\r
+ .setToolTipText( "Basic phylogenetic inference including multiple sequence alignment" );\r
+ }\r
+ else {\r
+ _inference_menu\r
+ .add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences (no program found)" ) );\r
+ customizeJMenuItem( _inference_from_seqs_item );\r
+ _inference_from_seqs_item.setEnabled( false );\r
+ }\r
+ _jmenubar.add( _inference_menu );\r
+ }\r
+\r
+ void buildToolsMenu() {\r
+ _tools_menu = createMenu( "Tools", getConfiguration() );\r
+ _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );\r
+ customizeJMenuItem( _confcolor_item );\r
+ _tools_menu.add( _color_rank_jmi = new JMenuItem( "Colorize Subtrees via Taxonomic Rank" ) );\r
+ customizeJMenuItem( _color_rank_jmi );\r
+ _color_rank_jmi.setToolTipText( "for example, at \"Class\" level, colorize mammal specific subtree red" );\r
+ _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );\r
+ customizeJMenuItem( _taxcolor_item );\r
+ _tools_menu.addSeparator();\r
+ _tools_menu.add( _remove_visual_styles_item = new JMenuItem( "Delete All Visual Styles From Nodes" ) );\r
+ _remove_visual_styles_item\r
+ .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny." );\r
+ customizeJMenuItem( _remove_visual_styles_item );\r
+ _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete All Colors From Branches" ) );\r
+ _remove_branch_color_item.setToolTipText( "To remove all branch color values from the current phylogeny." );\r
+ customizeJMenuItem( _remove_branch_color_item );\r
+ _tools_menu.addSeparator();\r
+ _tools_menu.add( _annotate_item = new JMenuItem( "Annotate Sequences of Selected Nodes" ) );\r
+ customizeJMenuItem( _annotate_item );\r
+ _tools_menu.addSeparator();\r
+ _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );\r
+ customizeJMenuItem( _midpoint_root_item );\r
+ _tools_menu.addSeparator();\r
+ _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );\r
+ customizeJMenuItem( _collapse_species_specific_subtrees );\r
+ _tools_menu\r
+ .add( _collapse_below_threshold = new JMenuItem( "Collapse Branches with Confidence Below Threshold into Multifurcations" ) );\r
+ customizeJMenuItem( _collapse_below_threshold );\r
+ _collapse_below_threshold\r
+ .setToolTipText( "To collapse branches with confidence values below a threshold into multifurcations (in the case of multiple confidences per branch: without at least one confidence value above a threshold)" );\r
+ _tools_menu.addSeparator();\r
+ _tools_menu\r
+ .add( _extract_tax_code_from_node_names_jmi = new JMenuItem( "Extract Taxonomic Data from Node Names" ) );\r
+ customizeJMenuItem( _extract_tax_code_from_node_names_jmi );\r
+ _extract_tax_code_from_node_names_jmi\r
+ .setToolTipText( "To extract SwissProt/Uniprot taxonomic codes (mnemonics) from nodes names in the form of 'xyz_CAEEL', Uniprot/NCBI identifiers form of 'xyz_6239', or scientific names form of 'xyz_Caenorhabditis_elegans'" );\r
+ _tools_menu\r
+ .add( _move_node_names_to_tax_sn_jmi = new JMenuItem( "Transfer Node Names to Taxonomic Scientific Names" ) );\r
+ customizeJMenuItem( _move_node_names_to_tax_sn_jmi );\r
+ _move_node_names_to_tax_sn_jmi.setToolTipText( "To interpret node names as taxonomic scientific names" );\r
+ _tools_menu.add( _move_node_names_to_seq_names_jmi = new JMenuItem( "Transfer Node Names to Sequence Names" ) );\r
+ customizeJMenuItem( _move_node_names_to_seq_names_jmi );\r
+ _move_node_names_to_seq_names_jmi.setToolTipText( "To interpret node names as sequence (protein, gene) names" );\r
+ _tools_menu.addSeparator();\r
+ _tools_menu.add( _obtain_seq_information_jmi = new JMenuItem( "Obtain Sequence Information" ) );\r
+ customizeJMenuItem( _obtain_seq_information_jmi );\r
+ _obtain_seq_information_jmi.setToolTipText( "To add additional sequence information" );\r
+ _tools_menu\r
+ .add( _obtain_detailed_taxonomic_information_jmi = new JMenuItem( OBTAIN_DETAILED_TAXONOMIC_INFORMATION ) );\r
+ customizeJMenuItem( _obtain_detailed_taxonomic_information_jmi );\r
+ _obtain_detailed_taxonomic_information_jmi\r
+ .setToolTipText( "To add additional taxonomic information (from UniProt Taxonomy)" );\r
+ _tools_menu\r
+ .add( _obtain_detailed_taxonomic_information_deleting_jmi = new JMenuItem( "Obtain Detailed Taxonomic Information (deletes nodes!)" ) );\r
+ customizeJMenuItem( _obtain_detailed_taxonomic_information_deleting_jmi );\r
+ _obtain_detailed_taxonomic_information_deleting_jmi\r
+ .setToolTipText( "To add additional taxonomic information, deletes nodes for which taxonomy cannot found (from UniProt Taxonomy)" );\r
+ _tools_menu.addSeparator();\r
+ _tools_menu.add( _read_values_jmi = new JMenuItem( "Attach Vector/Expression Values" ) );\r
+ customizeJMenuItem( _read_values_jmi );\r
+ _read_values_jmi.setToolTipText( "To attach vector (e.g. gene expression) values to tree nodes (beta)" );\r
+ _jmenubar.add( _tools_menu );\r
+ _tools_menu.add( _read_seqs_jmi = new JMenuItem( "Attach Molecular Sequences" ) );\r
+ customizeJMenuItem( _read_seqs_jmi );\r
+ _read_seqs_jmi\r
+ .setToolTipText( "To attach molecular sequences to tree nodes (from Fasta-formatted file) (beta)" );\r
+ _jmenubar.add( _tools_menu );\r
+ }\r
+\r
+ @Override\r
+ void close() {\r
+ if ( isUnsavedDataPresent() ) {\r
+ final int r = JOptionPane.showConfirmDialog( this,\r
+ "Exit despite potentially unsaved changes?",\r
+ "Exit?",\r
+ JOptionPane.YES_NO_OPTION );\r
+ if ( r != JOptionPane.YES_OPTION ) {\r
+ return;\r
+ }\r
+ }\r
+ exit();\r
+ }\r
+\r
+ void executeLineageInference() {\r
+ if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) {\r
+ return;\r
+ }\r
+ if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Phylogeny is not rooted.",\r
+ "Cannot infer ancestral taxonomies",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ final AncestralTaxonomyInferrer inferrer = new AncestralTaxonomyInferrer( this,\r
+ _mainpanel.getCurrentTreePanel(),\r
+ _mainpanel.getCurrentPhylogeny()\r
+ .copy() );\r
+ new Thread( inferrer ).start();\r
+ }\r
+\r
+ void exit() {\r
+ removeAllTextFrames();\r
+ _mainpanel.terminate();\r
+ _contentpane.removeAll();\r
+ setVisible( false );\r
+ dispose();\r
+ System.exit( 0 );\r
+ }\r
+\r
+ void readPhylogeniesFromURL() {\r
+ URL url = null;\r
+ Phylogeny[] phys = null;\r
+ final String message = "Please enter a complete URL, for example \"http://purl.org/phylo/treebase/phylows/study/TB2:S15480?format=nexus\"";\r
+ final String url_string = JOptionPane.showInputDialog( this,\r
+ message,\r
+ "Use URL/webservice to obtain a phylogeny",\r
+ JOptionPane.QUESTION_MESSAGE );\r
+ boolean nhx_or_nexus = false;\r
+ if ( ( url_string != null ) && ( url_string.length() > 0 ) ) {\r
+ try {\r
+ url = new URL( url_string );\r
+ PhylogenyParser parser = null;\r
+ if ( url.getHost().toLowerCase().indexOf( "tolweb" ) >= 0 ) {\r
+ parser = new TolParser();\r
+ }\r
+ else {\r
+ parser = ParserUtils.createParserDependingOnUrlContents( url, getConfiguration()\r
+ .isValidatePhyloXmlAgainstSchema() );\r
+ }\r
+ if ( parser instanceof NexusPhylogeniesParser ) {\r
+ nhx_or_nexus = true;\r
+ }\r
+ else if ( parser instanceof NHXParser ) {\r
+ nhx_or_nexus = true;\r
+ }\r
+ if ( _mainpanel.getCurrentTreePanel() != null ) {\r
+ _mainpanel.getCurrentTreePanel().setWaitCursor();\r
+ }\r
+ else {\r
+ _mainpanel.setWaitCursor();\r
+ }\r
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();\r
+ phys = factory.create( url.openStream(), parser );\r
+ }\r
+ catch ( final MalformedURLException e ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Malformed URL: " + url + "\n" + e.getLocalizedMessage(),\r
+ "Malformed URL",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ }\r
+ catch ( final IOException e ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Could not read from " + url + "\n"\r
+ + ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),\r
+ "Failed to read URL",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ }\r
+ catch ( final Exception e ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),\r
+ "Unexpected Exception",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ }\r
+ finally {\r
+ if ( _mainpanel.getCurrentTreePanel() != null ) {\r
+ _mainpanel.getCurrentTreePanel().setArrowCursor();\r
+ }\r
+ else {\r
+ _mainpanel.setArrowCursor();\r
+ }\r
+ }\r
+ if ( ( phys != null ) && ( phys.length > 0 ) ) {\r
+ if ( nhx_or_nexus && getOptions().isInternalNumberAreConfidenceForNhParsing() ) {\r
+ for( final Phylogeny phy : phys ) {\r
+ \r
+ PhylogenyMethods.transferInternalNodeNamesToConfidence( phy, "" );\r
+ }\r
+ }\r
+ AptxUtil.addPhylogeniesToTabs( phys,\r
+ new File( url.getFile() ).getName(),\r
+ new File( url.getFile() ).toString(),\r
+ getConfiguration(),\r
+ getMainPanel() );\r
+ _mainpanel.getControlPanel().showWhole();\r
+ }\r
+ }\r
+ activateSaveAllIfNeeded();\r
+ System.gc();\r
+ }\r
+\r
+ void setMsa( final Msa msa ) {\r
+ _msa = msa;\r
+ }\r
+\r
+ void setMsaFile( final File msa_file ) {\r
+ _msa_file = msa_file;\r
+ }\r
+\r
+ void setSeqs( final List<Sequence> seqs ) {\r
+ _seqs = seqs;\r
+ }\r
+\r
+ void setSeqsFile( final File seqs_file ) {\r
+ _seqs_file = seqs_file;\r
+ }\r
+\r
+ void writePhylogenyToGraphicsFile( final String file_name, final GraphicsExportType type ) {\r
+ _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel().getWidth(),\r
+ _mainpanel.getCurrentTreePanel().getHeight(),\r
+ true );\r
+ String file_written_to = "";\r
+ boolean error = false;\r
+ try {\r
+ file_written_to = AptxUtil.writePhylogenyToGraphicsFile( file_name,\r
+ _mainpanel.getCurrentTreePanel().getWidth(),\r
+ _mainpanel.getCurrentTreePanel().getHeight(),\r
+ _mainpanel.getCurrentTreePanel(),\r
+ _mainpanel.getControlPanel(),\r
+ type,\r
+ getOptions() );\r
+ }\r
+ catch ( final IOException e ) {\r
+ error = true;\r
+ JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );\r
+ }\r
+ if ( !error ) {\r
+ if ( ( file_written_to != null ) && ( file_written_to.length() > 0 ) ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Wrote image to: " + file_written_to,\r
+ "Graphics Export",\r
+ JOptionPane.INFORMATION_MESSAGE );\r
+ }\r
+ else {\r
+ JOptionPane.showMessageDialog( this,\r
+ "There was an unknown problem when attempting to write to an image file: \""\r
+ + file_name + "\"",\r
+ "Error",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ }\r
+ }\r
+ _contentpane.repaint();\r
+ }\r
+\r
+ private void addExpressionValuesFromFile() {\r
+ if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Need to load evolutionary tree first",\r
+ "Can Not Read Expression Values",\r
+ JOptionPane.WARNING_MESSAGE );\r
+ return;\r
+ }\r
+ final File my_dir = getCurrentDir();\r
+ if ( my_dir != null ) {\r
+ _values_filechooser.setCurrentDirectory( my_dir );\r
+ }\r
+ final int result = _values_filechooser.showOpenDialog( _contentpane );\r
+ final File file = _values_filechooser.getSelectedFile();\r
+ if ( ( file != null ) && ( file.length() > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
+ BasicTable<String> t = null;\r
+ try {\r
+ t = BasicTableParser.parse( file, '\t' );\r
+ if ( t.getNumberOfColumns() < 2 ) {\r
+ t = BasicTableParser.parse( file, ',' );\r
+ }\r
+ if ( t.getNumberOfColumns() < 2 ) {\r
+ t = BasicTableParser.parse( file, ' ' );\r
+ }\r
+ }\r
+ catch ( final IOException e ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ e.getMessage(),\r
+ "Could Not Read Expression Value Table",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ if ( t.getNumberOfColumns() < 2 ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Table contains " + t.getNumberOfColumns() + " column(s)",\r
+ "Problem with Expression Value Table",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ if ( t.getNumberOfRows() < 1 ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Table contains zero rows",\r
+ "Problem with Expression Value Table",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ final Phylogeny phy = getCurrentTreePanel().getPhylogeny();\r
+ if ( t.getNumberOfRows() != phy.getNumberOfExternalNodes() ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Table contains " + t.getNumberOfRows() + " rows, but tree contains "\r
+ + phy.getNumberOfExternalNodes() + " external nodes",\r
+ "Warning",\r
+ JOptionPane.WARNING_MESSAGE );\r
+ }\r
+ final DescriptiveStatistics stats = new BasicDescriptiveStatistics();\r
+ int not_found = 0;\r
+ for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {\r
+ final PhylogenyNode node = iter.next();\r
+ final String node_name = node.getName();\r
+ if ( !ForesterUtil.isEmpty( node_name ) ) {\r
+ int row = -1;\r
+ try {\r
+ row = t.findRow( node_name );\r
+ }\r
+ catch ( final IllegalArgumentException e ) {\r
+ JOptionPane\r
+ .showMessageDialog( this,\r
+ e.getMessage(),\r
+ "Error Mapping Node Identifiers to Expression Value Identifiers",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ if ( row < 0 ) {\r
+ if ( node.isExternal() ) {\r
+ not_found++;\r
+ }\r
+ continue;\r
+ }\r
+ final List<Double> l = new ArrayList<Double>();\r
+ for( int col = 1; col < t.getNumberOfColumns(); ++col ) {\r
+ double d = -100;\r
+ try {\r
+ d = Double.parseDouble( t.getValueAsString( col, row ) );\r
+ }\r
+ catch ( final NumberFormatException e ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Could not parse \"" + t.getValueAsString( col, row )\r
+ + "\" into a decimal value",\r
+ "Issue with Expression Value Table",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ stats.addValue( d );\r
+ l.add( d );\r
+ }\r
+ if ( !l.isEmpty() ) {\r
+ if ( node.getNodeData().getProperties() != null ) {\r
+ node.getNodeData().getProperties()\r
+ .removePropertiesWithGivenReferencePrefix( PhyloXmlUtil.VECTOR_PROPERTY_REF );\r
+ }\r
+ node.getNodeData().setVector( l );\r
+ }\r
+ }\r
+ }\r
+ if ( not_found > 0 ) {\r
+ JOptionPane.showMessageDialog( this, "Could not fine expression values for " + not_found\r
+ + " external node(s)", "Warning", JOptionPane.WARNING_MESSAGE );\r
+ }\r
+ getCurrentTreePanel().setStatisticsForExpressionValues( stats );\r
+ }\r
+ }\r
+\r
+ private void addSequencesFromFile() {\r
+ if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Need to load evolutionary tree first",\r
+ "Can Not Read Sequences",\r
+ JOptionPane.WARNING_MESSAGE );\r
+ return;\r
+ }\r
+ final File my_dir = getCurrentDir();\r
+ if ( my_dir != null ) {\r
+ _sequences_filechooser.setCurrentDirectory( my_dir );\r
+ }\r
+ final int result = _sequences_filechooser.showOpenDialog( _contentpane );\r
+ final File file = _sequences_filechooser.getSelectedFile();\r
+ List<Sequence> seqs = null;\r
+ if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
+ try {\r
+ if ( FastaParser.isLikelyFasta( new FileInputStream( file ) ) ) {\r
+ seqs = FastaParser.parse( new FileInputStream( file ) );\r
+ }\r
+ else {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Format does not appear to be Fasta",\r
+ "Multiple sequence file format error",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ }\r
+ catch ( final MsaFormatException e ) {\r
+ setArrowCursor();\r
+ JOptionPane.showMessageDialog( this,\r
+ e.getLocalizedMessage(),\r
+ "Multiple sequence file format error",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ catch ( final IOException e ) {\r
+ setArrowCursor();\r
+ JOptionPane.showMessageDialog( this,\r
+ e.getLocalizedMessage(),\r
+ "Failed to read multiple sequence file",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ catch ( final Exception e ) {\r
+ setArrowCursor();\r
+ e.printStackTrace();\r
+ JOptionPane.showMessageDialog( this,\r
+ e.getLocalizedMessage(),\r
+ "Unexpected error during reading of multiple sequence file",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ if ( ( seqs == null ) || ( seqs.size() < 1 ) ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Multiple sequence file is empty",\r
+ "Empty multiple sequence file",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ setArrowCursor();\r
+ return;\r
+ }\r
+ }\r
+ if ( seqs != null ) {\r
+ for( final Sequence seq : seqs ) {\r
+ System.out.println( seq.getIdentifier() );\r
+ }\r
+ final Phylogeny phy = getCurrentTreePanel().getPhylogeny();\r
+ int total_counter = 0;\r
+ int attached_counter = 0;\r
+ for( final Sequence seq : seqs ) {\r
+ ++total_counter;\r
+ final String seq_name = seq.getIdentifier();\r
+ if ( !ForesterUtil.isEmpty( seq_name ) ) {\r
+ List<PhylogenyNode> nodes = phy.getNodesViaSequenceName( seq_name );\r
+ if ( nodes.isEmpty() ) {\r
+ nodes = phy.getNodesViaSequenceSymbol( seq_name );\r
+ }\r
+ if ( nodes.isEmpty() ) {\r
+ nodes = phy.getNodesViaGeneName( seq_name );\r
+ }\r
+ if ( nodes.isEmpty() ) {\r
+ nodes = phy.getNodes( seq_name );\r
+ }\r
+ if ( nodes.size() > 1 ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Sequence name \"" + seq_name + "\" is not unique",\r
+ "Sequence name not unique",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ setArrowCursor();\r
+ return;\r
+ }\r
+ final String[] a = seq_name.split( "\\s" );\r
+ if ( nodes.isEmpty() && ( a.length > 1 ) ) {\r
+ final String seq_name_split = a[ 0 ];\r
+ nodes = phy.getNodesViaSequenceName( seq_name_split );\r
+ if ( nodes.isEmpty() ) {\r
+ nodes = phy.getNodesViaSequenceSymbol( seq_name_split );\r
+ }\r
+ if ( nodes.isEmpty() ) {\r
+ nodes = phy.getNodes( seq_name_split );\r
+ }\r
+ if ( nodes.size() > 1 ) {\r
+ JOptionPane.showMessageDialog( this, "Split sequence name \"" + seq_name_split\r
+ + "\" is not unique", "Sequence name not unique", JOptionPane.ERROR_MESSAGE );\r
+ setArrowCursor();\r
+ return;\r
+ }\r
+ }\r
+ if ( nodes.size() == 1 ) {\r
+ ++attached_counter;\r
+ final PhylogenyNode n = nodes.get( 0 );\r
+ if ( !n.getNodeData().isHasSequence() ) {\r
+ n.getNodeData().addSequence( new org.forester.phylogeny.data.Sequence() );\r
+ }\r
+ n.getNodeData().getSequence().setMolecularSequence( seq.getMolecularSequenceAsString() );\r
+ if ( ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) {\r
+ n.getNodeData().getSequence().setName( seq_name );\r
+ }\r
+ }\r
+ }\r
+ }\r
+ if ( attached_counter > 0 ) {\r
+ int ext_nodes = 0;\r
+ int ext_nodes_with_seq = 0;\r
+ for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {\r
+ ++ext_nodes;\r
+ final PhylogenyNode n = iter.next();\r
+ if ( n.getNodeData().isHasSequence()\r
+ && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getMolecularSequence() ) ) {\r
+ ++ext_nodes_with_seq;\r
+ }\r
+ }\r
+ final String s;\r
+ if ( ext_nodes == ext_nodes_with_seq ) {\r
+ s = "All " + ext_nodes_with_seq + " external nodes now have a molecular sequence attached to them.";\r
+ }\r
+ else {\r
+ s = ext_nodes_with_seq + " out of " + ext_nodes\r
+ + " external nodes now have a molecular sequence attached to them.";\r
+ }\r
+ if ( ( attached_counter == total_counter ) && ( ext_nodes == ext_nodes_with_seq ) ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Attached all " + total_counter + " sequences to tree nodes.\n" + s,\r
+ "All sequences attached",\r
+ JOptionPane.INFORMATION_MESSAGE );\r
+ }\r
+ else {\r
+ JOptionPane.showMessageDialog( this, "Attached " + attached_counter\r
+ + " sequences out of a total of " + total_counter + " sequences.\n" + s, attached_counter\r
+ + " sequences attached", JOptionPane.WARNING_MESSAGE );\r
+ }\r
+ }\r
+ else {\r
+ JOptionPane.showMessageDialog( this, "No maching tree node for any of the " + total_counter\r
+ + " sequences", "Could not attach any sequences", JOptionPane.ERROR_MESSAGE );\r
+ }\r
+ }\r
+ }\r
+\r
+ private void choosePdfWidth() {\r
+ final String s = ( String ) JOptionPane.showInputDialog( this,\r
+ "Please enter the default line width for PDF export.\n"\r
+ + "[current value: "\r
+ + getOptions().getPrintLineWidth() + "]\n",\r
+ "Line Width for PDF Export",\r
+ JOptionPane.QUESTION_MESSAGE,\r
+ null,\r
+ null,\r
+ getOptions().getPrintLineWidth() );\r
+ if ( !ForesterUtil.isEmpty( s ) ) {\r
+ boolean success = true;\r
+ float f = 0.0f;\r
+ final String m_str = s.trim();\r
+ if ( !ForesterUtil.isEmpty( m_str ) ) {\r
+ try {\r
+ f = Float.parseFloat( m_str );\r
+ }\r
+ catch ( final Exception ex ) {\r
+ success = false;\r
+ }\r
+ }\r
+ else {\r
+ success = false;\r
+ }\r
+ if ( success && ( f > 0.0 ) ) {\r
+ getOptions().setPrintLineWidth( f );\r
+ }\r
+ }\r
+ }\r
+\r
+ private void choosePrintSize() {\r
+ final String s = ( String ) JOptionPane.showInputDialog( this,\r
+ "Please enter values for width and height,\nseparated by a comma.\n"\r
+ + "[current values: "\r
+ + getOptions().getPrintSizeX() + ", "\r
+ + getOptions().getPrintSizeY() + "]\n"\r
+ + "[A4: " + Constants.A4_SIZE_X + ", "\r
+ + Constants.A4_SIZE_Y + "]\n" + "[US Letter: "\r
+ + Constants.US_LETTER_SIZE_X + ", "\r
+ + Constants.US_LETTER_SIZE_Y + "]",\r
+ "Default Size for Graphics Export",\r
+ JOptionPane.QUESTION_MESSAGE,\r
+ null,\r
+ null,\r
+ getOptions().getPrintSizeX() + ", "\r
+ + getOptions().getPrintSizeY() );\r
+ if ( !ForesterUtil.isEmpty( s ) && ( s.indexOf( ',' ) > 0 ) ) {\r
+ boolean success = true;\r
+ int x = 0;\r
+ int y = 0;\r
+ final String[] str_ary = s.split( "," );\r
+ if ( str_ary.length == 2 ) {\r
+ final String x_str = str_ary[ 0 ].trim();\r
+ final String y_str = str_ary[ 1 ].trim();\r
+ if ( !ForesterUtil.isEmpty( x_str ) && !ForesterUtil.isEmpty( y_str ) ) {\r
+ try {\r
+ x = Integer.parseInt( x_str );\r
+ y = Integer.parseInt( y_str );\r
+ }\r
+ catch ( final Exception ex ) {\r
+ success = false;\r
+ }\r
+ }\r
+ else {\r
+ success = false;\r
+ }\r
+ }\r
+ else {\r
+ success = false;\r
+ }\r
+ if ( success && ( x > 1 ) && ( y > 1 ) ) {\r
+ getOptions().setPrintSizeX( x );\r
+ getOptions().setPrintSizeY( y );\r
+ }\r
+ }\r
+ }\r
+\r
+ private void closeCurrentPane() {\r
+ if ( getMainPanel().getCurrentTreePanel() != null ) {\r
+ if ( getMainPanel().getCurrentTreePanel().isEdited() ) {\r
+ final int r = JOptionPane.showConfirmDialog( this,\r
+ "Close tab despite potentially unsaved changes?",\r
+ "Close Tab?",\r
+ JOptionPane.YES_NO_OPTION );\r
+ if ( r != JOptionPane.YES_OPTION ) {\r
+ return;\r
+ }\r
+ }\r
+ getMainPanel().closeCurrentPane();\r
+ activateSaveAllIfNeeded();\r
+ }\r
+ }\r
+\r
+ private void collapse( final Phylogeny phy, final double m ) {\r
+ final PhylogenyNodeIterator it = phy.iteratorPostorder();\r
+ final List<PhylogenyNode> to_be_removed = new ArrayList<PhylogenyNode>();\r
+ double min_support = Double.MAX_VALUE;\r
+ boolean conf_present = false;\r
+ while ( it.hasNext() ) {\r
+ final PhylogenyNode n = it.next();\r
+ if ( !n.isExternal() && !n.isRoot() ) {\r
+ final List<Confidence> c = n.getBranchData().getConfidences();\r
+ if ( ( c != null ) && ( c.size() > 0 ) ) {\r
+ conf_present = true;\r
+ double max = 0;\r
+ for( final Confidence confidence : c ) {\r
+ if ( confidence.getValue() > max ) {\r
+ max = confidence.getValue();\r
+ }\r
+ }\r
+ if ( max < getMinNotCollapseConfidenceValue() ) {\r
+ to_be_removed.add( n );\r
+ }\r
+ if ( max < min_support ) {\r
+ min_support = max;\r
+ }\r
+ }\r
+ }\r
+ }\r
+ if ( conf_present ) {\r
+ for( final PhylogenyNode node : to_be_removed ) {\r
+ PhylogenyMethods.removeNode( node, phy );\r
+ }\r
+ if ( to_be_removed.size() > 0 ) {\r
+ phy.externalNodesHaveChanged();\r
+ phy.clearHashIdToNodeMap();\r
+ phy.recalculateNumberOfExternalDescendants( true );\r
+ getCurrentTreePanel().resetNodeIdToDistToLeafMap();\r
+ getCurrentTreePanel().updateSetOfCollapsedExternalNodes();\r
+ getCurrentTreePanel().calculateLongestExtNodeInfo();\r
+ getCurrentTreePanel().setNodeInPreorderToNull();\r
+ getCurrentTreePanel().recalculateMaxDistanceToRoot();\r
+ getCurrentTreePanel().resetPreferredSize();\r
+ getCurrentTreePanel().setEdited( true );\r
+ getCurrentTreePanel().repaint();\r
+ repaint();\r
+ }\r
+ if ( to_be_removed.size() > 0 ) {\r
+ JOptionPane.showMessageDialog( this, "Collapsed " + to_be_removed.size()\r
+ + " branches with\nconfidence values below " + getMinNotCollapseConfidenceValue(), "Collapsed "\r
+ + to_be_removed.size() + " branches", JOptionPane.INFORMATION_MESSAGE );\r
+ }\r
+ else {\r
+ JOptionPane.showMessageDialog( this, "No branch collapsed,\nminimum confidence value per branch is "\r
+ + min_support, "No branch collapsed", JOptionPane.INFORMATION_MESSAGE );\r
+ }\r
+ }\r
+ else {\r
+ JOptionPane.showMessageDialog( this,\r
+ "No branch collapsed because no confidence values present",\r
+ "No confidence values present",\r
+ JOptionPane.INFORMATION_MESSAGE );\r
+ }\r
+ }\r
+\r
+ private void collapseBelowThreshold() {\r
+ if ( getCurrentTreePanel() != null ) {\r
+ final Phylogeny phy = getCurrentTreePanel().getPhylogeny();\r
+ if ( ( phy != null ) && !phy.isEmpty() ) {\r
+ final String s = ( String ) JOptionPane.showInputDialog( this,\r
+ "Please enter the minimum confidence value\n",\r
+ "Minimal Confidence Value",\r
+ JOptionPane.QUESTION_MESSAGE,\r
+ null,\r
+ null,\r
+ getMinNotCollapseConfidenceValue() );\r
+ if ( !ForesterUtil.isEmpty( s ) ) {\r
+ boolean success = true;\r
+ double m = 0.0;\r
+ final String m_str = s.trim();\r
+ if ( !ForesterUtil.isEmpty( m_str ) ) {\r
+ try {\r
+ m = Double.parseDouble( m_str );\r
+ }\r
+ catch ( final Exception ex ) {\r
+ success = false;\r
+ }\r
+ }\r
+ else {\r
+ success = false;\r
+ }\r
+ if ( success && ( m >= 0.0 ) ) {\r
+ setMinNotCollapseConfidenceValue( m );\r
+ collapse( phy, m );\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ private PhyloXmlParser createPhyloXmlParser() {\r
+ PhyloXmlParser xml_parser = null;\r
+ if ( getConfiguration().isValidatePhyloXmlAgainstSchema() ) {\r
+ try {\r
+ xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();\r
+ }\r
+ catch ( final Exception e ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ e.getLocalizedMessage(),\r
+ "failed to create validating XML parser",\r
+ JOptionPane.WARNING_MESSAGE );\r
+ }\r
+ }\r
+ if ( xml_parser == null ) {\r
+ xml_parser = PhyloXmlParser.createPhyloXmlParser();\r
+ }\r
+ return xml_parser;\r
+ }\r
+\r
+ private void executePhyleneticInference( final boolean from_unaligned_seqs ) {\r
+ final PhyloInferenceDialog dialog = new PhyloInferenceDialog( this,\r
+ getPhylogeneticInferenceOptions(),\r
+ from_unaligned_seqs );\r
+ dialog.activate();\r
+ if ( dialog.getValue() == JOptionPane.OK_OPTION ) {\r
+ if ( !from_unaligned_seqs ) {\r
+ if ( getMsa() != null ) {\r
+ final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getMsa(),\r
+ getPhylogeneticInferenceOptions()\r
+ .copy(), this );\r
+ new Thread( inferrer ).start();\r
+ }\r
+ else {\r
+ JOptionPane.showMessageDialog( this,\r
+ "No multiple sequence alignment selected",\r
+ "Phylogenetic Inference Not Launched",\r
+ JOptionPane.WARNING_MESSAGE );\r
+ }\r
+ }\r
+ else {\r
+ if ( getSeqs() != null ) {\r
+ final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getSeqs(),\r
+ getPhylogeneticInferenceOptions()\r
+ .copy(), this );\r
+ new Thread( inferrer ).start();\r
+ }\r
+ else {\r
+ JOptionPane.showMessageDialog( this,\r
+ "No input sequences selected",\r
+ "Phylogenetic Inference Not Launched",\r
+ JOptionPane.WARNING_MESSAGE );\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ private void extractTaxDataFromNodeNames() throws PhyloXmlDataFormatException {\r
+ final StringBuilder sb = new StringBuilder();\r
+ final StringBuilder sb_failed = new StringBuilder();\r
+ int counter = 0;\r
+ int counter_failed = 0;\r
+ if ( getCurrentTreePanel() != null ) {\r
+ final Phylogeny phy = getCurrentTreePanel().getPhylogeny();\r
+ if ( ( phy != null ) && !phy.isEmpty() ) {\r
+ final PhylogenyNodeIterator it = phy.iteratorExternalForward();\r
+ while ( it.hasNext() ) {\r
+ final PhylogenyNode n = it.next();\r
+ final String name = n.getName().trim();\r
+ if ( !ForesterUtil.isEmpty( name ) ) {\r
+ final String nt = ParserUtils.extractTaxonomyDataFromNodeName( n,\r
+ TAXONOMY_EXTRACTION.AGGRESSIVE );\r
+ if ( !ForesterUtil.isEmpty( nt ) ) {\r
+ if ( counter < 15 ) {\r
+ sb.append( name + ": " + nt + "\n" );\r
+ }\r
+ else if ( counter == 15 ) {\r
+ sb.append( "...\n" );\r
+ }\r
+ counter++;\r
+ }\r
+ else {\r
+ if ( counter_failed < 15 ) {\r
+ sb_failed.append( name + "\n" );\r
+ }\r
+ else if ( counter_failed == 15 ) {\r
+ sb_failed.append( "...\n" );\r
+ }\r
+ counter_failed++;\r
+ }\r
+ }\r
+ }\r
+ if ( counter > 0 ) {\r
+ String failed = "";\r
+ String all = "all ";\r
+ if ( counter_failed > 0 ) {\r
+ all = "";\r
+ failed = "\nCould not extract taxonomic data for " + counter_failed\r
+ + " named external nodes:\n" + sb_failed;\r
+ }\r
+ JOptionPane.showMessageDialog( this,\r
+ "Extracted taxonomic data from " + all + counter\r
+ + " named external nodes:\n" + sb.toString() + failed,\r
+ "Taxonomic Data Extraction Completed",\r
+ counter_failed > 0 ? JOptionPane.WARNING_MESSAGE\r
+ : JOptionPane.INFORMATION_MESSAGE );\r
+ }\r
+ else {\r
+ JOptionPane\r
+ .showMessageDialog( this,\r
+ "Could not extract any taxonomic data.\nMaybe node names are empty\n"\r
+ + "or not in the forms \"XYZ_CAEEL\", \"XYZ_6239\", or \"XYZ_Caenorhabditis_elegans\"\n"\r
+ + "or nodes already have taxonomic data?\n",\r
+ "No Taxonomic Data Extracted",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ private ControlPanel getControlPanel() {\r
+ return getMainPanel().getControlPanel();\r
+ }\r
+\r
+ private File getCurrentDir() {\r
+ if ( ( _current_dir == null ) || !_current_dir.canRead() ) {\r
+ if ( ForesterUtil.isWindows() ) {\r
+ try {\r
+ _current_dir = new File( WindowsUtils.getCurrentUserDesktopPath() );\r
+ }\r
+ catch ( final Exception e ) {\r
+ _current_dir = null;\r
+ }\r
+ }\r
+ }\r
+ if ( ( _current_dir == null ) || !_current_dir.canRead() ) {\r
+ if ( System.getProperty( "user.home" ) != null ) {\r
+ _current_dir = new File( System.getProperty( "user.home" ) );\r
+ }\r
+ else if ( System.getProperty( "user.dir" ) != null ) {\r
+ _current_dir = new File( System.getProperty( "user.dir" ) );\r
+ }\r
+ }\r
+ return _current_dir;\r
+ }\r
+\r
+ private double getMinNotCollapseConfidenceValue() {\r
+ return _min_not_collapse;\r
+ }\r
+\r
+ private PhylogeneticInferenceOptions getPhylogeneticInferenceOptions() {\r
+ if ( _phylogenetic_inference_options == null ) {\r
+ _phylogenetic_inference_options = new PhylogeneticInferenceOptions();\r
+ }\r
+ return _phylogenetic_inference_options;\r
+ }\r
+\r
+ private boolean isUnsavedDataPresent() {\r
+ final List<TreePanel> tps = getMainPanel().getTreePanels();\r
+ for( final TreePanel tp : tps ) {\r
+ if ( tp.isEdited() ) {\r
+ return true;\r
+ }\r
+ }\r
+ return false;\r
+ }\r
+\r
+ private void moveNodeNamesToSeqNames() throws PhyloXmlDataFormatException {\r
+ if ( getCurrentTreePanel() != null ) {\r
+ final Phylogeny phy = getCurrentTreePanel().getPhylogeny();\r
+ if ( ( phy != null ) && !phy.isEmpty() ) {\r
+ PhylogenyMethods\r
+ .transferNodeNameToField( phy, PhylogenyMethods.PhylogenyNodeField.SEQUENCE_NAME, false );\r
+ }\r
+ }\r
+ }\r
+\r
+ private void moveNodeNamesToTaxSn() throws PhyloXmlDataFormatException {\r
+ if ( getCurrentTreePanel() != null ) {\r
+ final Phylogeny phy = getCurrentTreePanel().getPhylogeny();\r
+ if ( ( phy != null ) && !phy.isEmpty() ) {\r
+ PhylogenyMethods.transferNodeNameToField( phy,\r
+ PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME,\r
+ false );\r
+ }\r
+ }\r
+ }\r
+\r
+ private void newTree() {\r
+ final Phylogeny[] phys = new Phylogeny[ 1 ];\r
+ final Phylogeny phy = new Phylogeny();\r
+ final PhylogenyNode node = new PhylogenyNode();\r
+ phy.setRoot( node );\r
+ phy.setRooted( true );\r
+ phys[ 0 ] = phy;\r
+ AptxUtil.addPhylogeniesToTabs( phys, "", "", getConfiguration(), getMainPanel() );\r
+ _mainpanel.getControlPanel().showWhole();\r
+ _mainpanel.getCurrentTreePanel().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );\r
+ _mainpanel.getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );\r
+ if ( getMainPanel().getMainFrame() == null ) {\r
+ // Must be "E" applet version.\r
+ ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() )\r
+ .setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );\r
+ }\r
+ else {\r
+ getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );\r
+ }\r
+ activateSaveAllIfNeeded();\r
+ System.gc();\r
+ }\r
+\r
+ private void obtainDetailedTaxonomicInformation() {\r
+ if ( getCurrentTreePanel() != null ) {\r
+ final Phylogeny phy = getCurrentTreePanel().getPhylogeny();\r
+ if ( ( phy != null ) && !phy.isEmpty() ) {\r
+ final TaxonomyDataManager t = new TaxonomyDataManager( this,\r
+ _mainpanel.getCurrentTreePanel(),\r
+ phy.copy(),\r
+ false,\r
+ true );\r
+ new Thread( t ).start();\r
+ }\r
+ }\r
+ }\r
+\r
+ private void obtainDetailedTaxonomicInformationDelete() {\r
+ if ( getCurrentTreePanel() != null ) {\r
+ final Phylogeny phy = getCurrentTreePanel().getPhylogeny();\r
+ if ( ( phy != null ) && !phy.isEmpty() ) {\r
+ final TaxonomyDataManager t = new TaxonomyDataManager( this,\r
+ _mainpanel.getCurrentTreePanel(),\r
+ phy.copy(),\r
+ true,\r
+ true );\r
+ new Thread( t ).start();\r
+ }\r
+ }\r
+ }\r
+\r
+ private void obtainSequenceInformation() {\r
+ if ( getCurrentTreePanel() != null ) {\r
+ final Phylogeny phy = getCurrentTreePanel().getPhylogeny();\r
+ if ( ( phy != null ) && !phy.isEmpty() ) {\r
+ final SequenceDataRetriver u = new SequenceDataRetriver( this,\r
+ _mainpanel.getCurrentTreePanel(),\r
+ phy.copy() );\r
+ new Thread( u ).start();\r
+ }\r
+ }\r
+ }\r
+\r
+ private void print() {\r
+ if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null )\r
+ || getCurrentTreePanel().getPhylogeny().isEmpty() ) {\r
+ return;\r
+ }\r
+ if ( !getOptions().isPrintUsingActualSize() ) {\r
+ getCurrentTreePanel().calcParametersForPainting( getOptions().getPrintSizeX() - 80,\r
+ getOptions().getPrintSizeY() - 140,\r
+ true );\r
+ getCurrentTreePanel().resetPreferredSize();\r
+ getCurrentTreePanel().repaint();\r
+ }\r
+ final String job_name = Constants.PRG_NAME;\r
+ boolean error = false;\r
+ String printer_name = null;\r
+ try {\r
+ printer_name = Printer.print( getCurrentTreePanel(), job_name );\r
+ }\r
+ catch ( final Exception e ) {\r
+ error = true;\r
+ JOptionPane.showMessageDialog( this, e.getMessage(), "Printing Error", JOptionPane.ERROR_MESSAGE );\r
+ }\r
+ if ( !error && ( printer_name != null ) ) {\r
+ String msg = "Printing data sent to printer";\r
+ if ( printer_name.length() > 1 ) {\r
+ msg += " [" + printer_name + "]";\r
+ }\r
+ JOptionPane.showMessageDialog( this, msg, "Printing...", JOptionPane.INFORMATION_MESSAGE );\r
+ }\r
+ if ( !getOptions().isPrintUsingActualSize() ) {\r
+ getControlPanel().showWhole();\r
+ }\r
+ }\r
+\r
+ private void printPhylogenyToPdf( final String file_name ) {\r
+ if ( !getOptions().isPrintUsingActualSize() ) {\r
+ getCurrentTreePanel().calcParametersForPainting( getOptions().getPrintSizeX(),\r
+ getOptions().getPrintSizeY(),\r
+ true );\r
+ getCurrentTreePanel().resetPreferredSize();\r
+ getCurrentTreePanel().repaint();\r
+ }\r
+ String pdf_written_to = "";\r
+ boolean error = false;\r
+ try {\r
+ if ( getOptions().isPrintUsingActualSize() ) {\r
+ pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name,\r
+ getCurrentTreePanel(),\r
+ getCurrentTreePanel().getWidth(),\r
+ getCurrentTreePanel().getHeight() );\r
+ }\r
+ else {\r
+ pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name, getCurrentTreePanel(), getOptions()\r
+ .getPrintSizeX(), getOptions().getPrintSizeY() );\r
+ }\r
+ }\r
+ catch ( final IOException e ) {\r
+ error = true;\r
+ JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );\r
+ }\r
+ if ( !error ) {\r
+ if ( !ForesterUtil.isEmpty( pdf_written_to ) ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Wrote PDF to: " + pdf_written_to,\r
+ "Information",\r
+ JOptionPane.INFORMATION_MESSAGE );\r
+ }\r
+ else {\r
+ JOptionPane.showMessageDialog( this,\r
+ "There was an unknown problem when attempting to write to PDF file: \""\r
+ + file_name + "\"",\r
+ "Error",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ }\r
+ }\r
+ if ( !getOptions().isPrintUsingActualSize() ) {\r
+ getControlPanel().showWhole();\r
+ }\r
+ }\r
+\r
+ private void readPhylogeniesFromFile() {\r
+ boolean exception = false;\r
+ Phylogeny[] phys = null;\r
+ // Set an initial directory if none set yet\r
+ final File my_dir = getCurrentDir();\r
+ _open_filechooser.setMultiSelectionEnabled( true );\r
+ // Open file-open dialog and set current directory\r
+ if ( my_dir != null ) {\r
+ _open_filechooser.setCurrentDirectory( my_dir );\r
+ }\r
+ final int result = _open_filechooser.showOpenDialog( _contentpane );\r
+ // All done: get the file\r
+ final File[] files = _open_filechooser.getSelectedFiles();\r
+ setCurrentDir( _open_filechooser.getCurrentDirectory() );\r
+ boolean nhx_or_nexus = false;\r
+ if ( ( files != null ) && ( files.length > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
+ for( final File file : files ) {\r
+ if ( ( file != null ) && !file.isDirectory() ) {\r
+ if ( _mainpanel.getCurrentTreePanel() != null ) {\r
+ _mainpanel.getCurrentTreePanel().setWaitCursor();\r
+ }\r
+ else {\r
+ _mainpanel.setWaitCursor();\r
+ }\r
+ if ( ( _open_filechooser.getFileFilter() == MainFrameApplication.nhfilter )\r
+ || ( _open_filechooser.getFileFilter() == MainFrameApplication.nhxfilter ) ) {\r
+ try {\r
+ final NHXParser nhx = new NHXParser();\r
+ setSpecialOptionsForNhxParser( nhx );\r
+ phys = PhylogenyMethods.readPhylogenies( nhx, file );\r
+ nhx_or_nexus = true;\r
+ }\r
+ catch ( final Exception e ) {\r
+ exception = true;\r
+ exceptionOccuredDuringOpenFile( e );\r
+ }\r
+ }\r
+ else if ( _open_filechooser.getFileFilter() == MainFrameApplication.xmlfilter ) {\r
+ warnIfNotPhyloXmlValidation( getConfiguration() );\r
+ try {\r
+ final PhyloXmlParser xml_parser = createPhyloXmlParser();\r
+ phys = PhylogenyMethods.readPhylogenies( xml_parser, file );\r
+ }\r
+ catch ( final Exception e ) {\r
+ exception = true;\r
+ exceptionOccuredDuringOpenFile( e );\r
+ }\r
+ }\r
+ else if ( _open_filechooser.getFileFilter() == MainFrameApplication.tolfilter ) {\r
+ try {\r
+ phys = PhylogenyMethods.readPhylogenies( new TolParser(), file );\r
+ }\r
+ catch ( final Exception e ) {\r
+ exception = true;\r
+ exceptionOccuredDuringOpenFile( e );\r
+ }\r
+ }\r
+ else if ( _open_filechooser.getFileFilter() == MainFrameApplication.nexusfilter ) {\r
+ try {\r
+ final NexusPhylogeniesParser nex = new NexusPhylogeniesParser();\r
+ setSpecialOptionsForNexParser( nex );\r
+ phys = PhylogenyMethods.readPhylogenies( nex, file );\r
+ nhx_or_nexus = true;\r
+ }\r
+ catch ( final Exception e ) {\r
+ exception = true;\r
+ exceptionOccuredDuringOpenFile( e );\r
+ }\r
+ }\r
+ // "*.*":\r
+ else {\r
+ try {\r
+ final PhylogenyParser parser = ParserUtils\r
+ .createParserDependingOnFileType( file, getConfiguration()\r
+ .isValidatePhyloXmlAgainstSchema() );\r
+ if ( parser instanceof NexusPhylogeniesParser ) {\r
+ final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) parser;\r
+ setSpecialOptionsForNexParser( nex );\r
+ nhx_or_nexus = true;\r
+ }\r
+ else if ( parser instanceof NHXParser ) {\r
+ final NHXParser nhx = ( NHXParser ) parser;\r
+ setSpecialOptionsForNhxParser( nhx );\r
+ nhx_or_nexus = true;\r
+ }\r
+ else if ( parser instanceof PhyloXmlParser ) {\r
+ warnIfNotPhyloXmlValidation( getConfiguration() );\r
+ }\r
+ phys = PhylogenyMethods.readPhylogenies( parser, file );\r
+ }\r
+ catch ( final Exception e ) {\r
+ exception = true;\r
+ exceptionOccuredDuringOpenFile( e );\r
+ }\r
+ }\r
+ if ( _mainpanel.getCurrentTreePanel() != null ) {\r
+ _mainpanel.getCurrentTreePanel().setArrowCursor();\r
+ }\r
+ else {\r
+ _mainpanel.setArrowCursor();\r
+ }\r
+ if ( !exception && ( phys != null ) && ( phys.length > 0 ) ) {\r
+ boolean one_desc = false;\r
+ if ( nhx_or_nexus ) {\r
+ for( final Phylogeny phy : phys ) {\r
+ if ( getOptions().isInternalNumberAreConfidenceForNhParsing() ) {\r
+ PhylogenyMethods.transferInternalNodeNamesToConfidence( phy, "" );\r
+ }\r
+ if ( PhylogenyMethods.getMinimumDescendentsPerInternalNodes( phy ) == 1 ) {\r
+ one_desc = true;\r
+ break;\r
+ }\r
+ }\r
+ }\r
+ AptxUtil.addPhylogeniesToTabs( phys,\r
+ file.getName(),\r
+ file.getAbsolutePath(),\r
+ getConfiguration(),\r
+ getMainPanel() );\r
+ _mainpanel.getControlPanel().showWhole();\r
+ if ( nhx_or_nexus && one_desc ) {\r
+ JOptionPane\r
+ .showMessageDialog( this,\r
+ "One or more trees contain (a) node(s) with one descendant, "\r
+ + ForesterUtil.LINE_SEPARATOR\r
+ + "possibly indicating illegal parentheses within node names.",\r
+ "Warning: Possible Error in New Hampshire Formatted Data",\r
+ JOptionPane.WARNING_MESSAGE );\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }\r
+ activateSaveAllIfNeeded();\r
+ System.gc();\r
+ }\r
+\r
+ private void readSpeciesTreeFromFile() {\r
+ Phylogeny t = null;\r
+ boolean exception = false;\r
+ final File my_dir = getCurrentDir();\r
+ _open_filechooser_for_species_tree.setSelectedFile( new File( "" ) );\r
+ if ( my_dir != null ) {\r
+ _open_filechooser_for_species_tree.setCurrentDirectory( my_dir );\r
+ }\r
+ final int result = _open_filechooser_for_species_tree.showOpenDialog( _contentpane );\r
+ final File file = _open_filechooser_for_species_tree.getSelectedFile();\r
+ if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
+ if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrameApplication.xmlfilter ) {\r
+ try {\r
+ final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( PhyloXmlParser\r
+ .createPhyloXmlParserXsdValidating(), file );\r
+ t = trees[ 0 ];\r
+ }\r
+ catch ( final Exception e ) {\r
+ exception = true;\r
+ exceptionOccuredDuringOpenFile( e );\r
+ }\r
+ }\r
+ else if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrameApplication.tolfilter ) {\r
+ try {\r
+ final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new TolParser(), file );\r
+ t = trees[ 0 ];\r
+ }\r
+ catch ( final Exception e ) {\r
+ exception = true;\r
+ exceptionOccuredDuringOpenFile( e );\r
+ }\r
+ }\r
+ // "*.*":\r
+ else {\r
+ try {\r
+ final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( PhyloXmlParser\r
+ .createPhyloXmlParserXsdValidating(), file );\r
+ t = trees[ 0 ];\r
+ }\r
+ catch ( final Exception e ) {\r
+ exception = true;\r
+ exceptionOccuredDuringOpenFile( e );\r
+ }\r
+ }\r
+ if ( !exception && ( t != null ) && !t.isRooted() ) {\r
+ exception = true;\r
+ t = null;\r
+ JOptionPane.showMessageDialog( this,\r
+ "Species tree is not rooted",\r
+ "Species tree not loaded",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ }\r
+ if ( !exception && ( t != null ) ) {\r
+ final Set<Taxonomy> tax_set = new HashSet<Taxonomy>();\r
+ for( final PhylogenyNodeIterator it = t.iteratorExternalForward(); it.hasNext(); ) {\r
+ final PhylogenyNode node = it.next();\r
+ if ( !node.getNodeData().isHasTaxonomy() ) {\r
+ exception = true;\r
+ t = null;\r
+ JOptionPane\r
+ .showMessageDialog( this,\r
+ "Species tree contains external node(s) without taxonomy information",\r
+ "Species tree not loaded",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ break;\r
+ }\r
+ else {\r
+ if ( tax_set.contains( node.getNodeData().getTaxonomy() ) ) {\r
+ exception = true;\r
+ t = null;\r
+ JOptionPane.showMessageDialog( this,\r
+ "Taxonomy ["\r
+ + node.getNodeData().getTaxonomy().asSimpleText()\r
+ + "] is not unique in species tree",\r
+ "Species tree not loaded",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ break;\r
+ }\r
+ else {\r
+ tax_set.add( node.getNodeData().getTaxonomy() );\r
+ }\r
+ }\r
+ }\r
+ }\r
+ if ( !exception && ( t != null ) ) {\r
+ setSpeciesTree( t );\r
+ JOptionPane.showMessageDialog( this,\r
+ "Species tree successfully loaded",\r
+ "Species tree loaded",\r
+ JOptionPane.INFORMATION_MESSAGE );\r
+ }\r
+ _contentpane.repaint();\r
+ System.gc();\r
+ }\r
+ }\r
+\r
+ private void setArrowCursor() {\r
+ try {\r
+ _mainpanel.getCurrentTreePanel().setArrowCursor();\r
+ }\r
+ catch ( final Exception ex ) {\r
+ // Do nothing.\r
+ }\r
+ }\r
+\r
+ private void setCurrentDir( final File current_dir ) {\r
+ _current_dir = current_dir;\r
+ }\r
+\r
+ private void setMinNotCollapseConfidenceValue( final double min_not_collapse ) {\r
+ _min_not_collapse = min_not_collapse;\r
+ }\r
+\r
+ private void setPhylogeneticInferenceOptions( final PhylogeneticInferenceOptions phylogenetic_inference_options ) {\r
+ _phylogenetic_inference_options = phylogenetic_inference_options;\r
+ }\r
+\r
+ private void setSpecialOptionsForNexParser( final NexusPhylogeniesParser nex ) {\r
+ nex.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );\r
+ nex.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() );\r
+ }\r
+\r
+ private void setSpecialOptionsForNhxParser( final NHXParser nhx ) {\r
+ nhx.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );\r
+ nhx.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() );\r
+ nhx.setAllowErrorsInDistanceToParent( getOptions().isAllowErrorsInDistanceToParent() );\r
+ }\r
+\r
+ private void writeAllToFile() {\r
+ if ( ( getMainPanel().getTabbedPane() == null ) || ( getMainPanel().getTabbedPane().getTabCount() < 1 ) ) {\r
+ return;\r
+ }\r
+ final File my_dir = getCurrentDir();\r
+ if ( my_dir != null ) {\r
+ _save_filechooser.setCurrentDirectory( my_dir );\r
+ }\r
+ _save_filechooser.setSelectedFile( new File( "" ) );\r
+ final int result = _save_filechooser.showSaveDialog( _contentpane );\r
+ final File file = _save_filechooser.getSelectedFile();\r
+ setCurrentDir( _save_filechooser.getCurrentDirectory() );\r
+ if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
+ if ( file.exists() ) {\r
+ final int i = JOptionPane.showConfirmDialog( this,\r
+ file + " already exists. Overwrite?",\r
+ "Warning",\r
+ JOptionPane.OK_CANCEL_OPTION,\r
+ JOptionPane.WARNING_MESSAGE );\r
+ if ( i != JOptionPane.OK_OPTION ) {\r
+ return;\r
+ }\r
+ else {\r
+ try {\r
+ file.delete();\r
+ }\r
+ catch ( final Exception e ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Failed to delete: " + file,\r
+ "Error",\r
+ JOptionPane.WARNING_MESSAGE );\r
+ }\r
+ }\r
+ }\r
+ final int count = getMainPanel().getTabbedPane().getTabCount();\r
+ final List<Phylogeny> trees = new ArrayList<Phylogeny>();\r
+ for( int i = 0; i < count; ++i ) {\r
+ final Phylogeny phy = getMainPanel().getPhylogeny( i );\r
+ if ( ForesterUtil.isEmpty( phy.getName() )\r
+ && !ForesterUtil.isEmpty( getMainPanel().getTabbedPane().getTitleAt( i ) ) ) {\r
+ phy.setName( getMainPanel().getTabbedPane().getTitleAt( i ) );\r
+ }\r
+ trees.add( phy );\r
+ getMainPanel().getTreePanels().get( i ).setEdited( false );\r
+ }\r
+ final PhylogenyWriter writer = new PhylogenyWriter();\r
+ try {\r
+ writer.toPhyloXML( file, trees, 0, ForesterUtil.LINE_SEPARATOR );\r
+ }\r
+ catch ( final IOException e ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Failed to write to: " + file,\r
+ "Error",\r
+ JOptionPane.WARNING_MESSAGE );\r
+ }\r
+ }\r
+ }\r
+\r
+ private boolean writeAsNewHampshire( final Phylogeny t, boolean exception, final File file ) {\r
+ try {\r
+ final PhylogenyWriter writer = new PhylogenyWriter();\r
+ writer.toNewHampshire( t, true, getOptions().getNhConversionSupportValueStyle(), file );\r
+ }\r
+ catch ( final Exception e ) {\r
+ exception = true;\r
+ exceptionOccuredDuringSaveAs( e );\r
+ }\r
+ return exception;\r
+ }\r
+\r
+ private boolean writeAsNexus( final Phylogeny t, boolean exception, final File file ) {\r
+ try {\r
+ final PhylogenyWriter writer = new PhylogenyWriter();\r
+ writer.toNexus( file, t, getOptions().getNhConversionSupportValueStyle() );\r
+ }\r
+ catch ( final Exception e ) {\r
+ exception = true;\r
+ exceptionOccuredDuringSaveAs( e );\r
+ }\r
+ return exception;\r
+ }\r
+\r
+ private boolean writeAsPhyloXml( final Phylogeny t, boolean exception, final File file ) {\r
+ try {\r
+ final PhylogenyWriter writer = new PhylogenyWriter();\r
+ writer.toPhyloXML( file, t, 0 );\r
+ }\r
+ catch ( final Exception e ) {\r
+ exception = true;\r
+ exceptionOccuredDuringSaveAs( e );\r
+ }\r
+ return exception;\r
+ }\r
+\r
+ private void writeToFile( final Phylogeny t ) {\r
+ if ( t == null ) {\r
+ return;\r
+ }\r
+ String initial_filename = null;\r
+ if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {\r
+ try {\r
+ initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().getCanonicalPath();\r
+ }\r
+ catch ( final IOException e ) {\r
+ initial_filename = null;\r
+ }\r
+ }\r
+ if ( !ForesterUtil.isEmpty( initial_filename ) ) {\r
+ _save_filechooser.setSelectedFile( new File( initial_filename ) );\r
+ }\r
+ else {\r
+ _save_filechooser.setSelectedFile( new File( "" ) );\r
+ }\r
+ final File my_dir = getCurrentDir();\r
+ if ( my_dir != null ) {\r
+ _save_filechooser.setCurrentDirectory( my_dir );\r
+ }\r
+ final int result = _save_filechooser.showSaveDialog( _contentpane );\r
+ final File file = _save_filechooser.getSelectedFile();\r
+ setCurrentDir( _save_filechooser.getCurrentDirectory() );\r
+ boolean exception = false;\r
+ if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
+ if ( file.exists() ) {\r
+ final int i = JOptionPane.showConfirmDialog( this,\r
+ file + " already exists.\nOverwrite?",\r
+ "Overwrite?",\r
+ JOptionPane.OK_CANCEL_OPTION,\r
+ JOptionPane.QUESTION_MESSAGE );\r
+ if ( i != JOptionPane.OK_OPTION ) {\r
+ return;\r
+ }\r
+ else {\r
+ final File to = new File( file.getAbsoluteFile().toString() + Constants.BACKUP_FILE_SUFFIX );\r
+ try {\r
+ ForesterUtil.copyFile( file, to );\r
+ }\r
+ catch ( final Exception e ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Failed to create backup copy " + to,\r
+ "Failed to Create Backup Copy",\r
+ JOptionPane.WARNING_MESSAGE );\r
+ }\r
+ try {\r
+ file.delete();\r
+ }\r
+ catch ( final Exception e ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Failed to delete: " + file,\r
+ "Failed to Delete",\r
+ JOptionPane.WARNING_MESSAGE );\r
+ }\r
+ }\r
+ }\r
+ if ( _save_filechooser.getFileFilter() == MainFrameApplication.nhfilter ) {\r
+ exception = writeAsNewHampshire( t, exception, file );\r
+ }\r
+ else if ( _save_filechooser.getFileFilter() == MainFrameApplication.xmlfilter ) {\r
+ exception = writeAsPhyloXml( t, exception, file );\r
+ }\r
+ else if ( _save_filechooser.getFileFilter() == MainFrameApplication.nexusfilter ) {\r
+ exception = writeAsNexus( t, exception, file );\r
+ }\r
+ // "*.*":\r
+ else {\r
+ final String file_name = file.getName().trim().toLowerCase();\r
+ if ( file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )\r
+ || file_name.endsWith( ".tree" ) ) {\r
+ exception = writeAsNewHampshire( t, exception, file );\r
+ }\r
+ else if ( file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) ) {\r
+ exception = writeAsNexus( t, exception, file );\r
+ }\r
+ // XML is default:\r
+ else {\r
+ exception = writeAsPhyloXml( t, exception, file );\r
+ }\r
+ }\r
+ if ( !exception ) {\r
+ getMainPanel().setTitleOfSelectedTab( file.getName() );\r
+ getMainPanel().getCurrentTreePanel().setTreeFile( file );\r
+ getMainPanel().getCurrentTreePanel().setEdited( false );\r
+ }\r
+ }\r
+ }\r
+\r
+ private void writeToGraphicsFile( final Phylogeny t, final GraphicsExportType type ) {\r
+ if ( ( t == null ) || t.isEmpty() ) {\r
+ return;\r
+ }\r
+ String initial_filename = "";\r
+ if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {\r
+ initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().toString();\r
+ }\r
+ if ( initial_filename.indexOf( '.' ) > 0 ) {\r
+ initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );\r
+ }\r
+ initial_filename = initial_filename + "." + type;\r
+ _writetographics_filechooser.setSelectedFile( new File( initial_filename ) );\r
+ final File my_dir = getCurrentDir();\r
+ if ( my_dir != null ) {\r
+ _writetographics_filechooser.setCurrentDirectory( my_dir );\r
+ }\r
+ final int result = _writetographics_filechooser.showSaveDialog( _contentpane );\r
+ File file = _writetographics_filechooser.getSelectedFile();\r
+ setCurrentDir( _writetographics_filechooser.getCurrentDirectory() );\r
+ if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
+ if ( !file.toString().toLowerCase().endsWith( type.toString() ) ) {\r
+ file = new File( file.toString() + "." + type );\r
+ }\r
+ if ( file.exists() ) {\r
+ final int i = JOptionPane.showConfirmDialog( this,\r
+ file + " already exists. Overwrite?",\r
+ "Warning",\r
+ JOptionPane.OK_CANCEL_OPTION,\r
+ JOptionPane.WARNING_MESSAGE );\r
+ if ( i != JOptionPane.OK_OPTION ) {\r
+ return;\r
+ }\r
+ else {\r
+ try {\r
+ file.delete();\r
+ }\r
+ catch ( final Exception e ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Failed to delete: " + file,\r
+ "Error",\r
+ JOptionPane.WARNING_MESSAGE );\r
+ }\r
+ }\r
+ }\r
+ writePhylogenyToGraphicsFile( file.toString(), type );\r
+ }\r
+ }\r
+\r
+ private void writeToPdf( final Phylogeny t ) {\r
+ if ( ( t == null ) || t.isEmpty() ) {\r
+ return;\r
+ }\r
+ String initial_filename = "";\r
+ if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {\r
+ initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().toString();\r
+ }\r
+ if ( initial_filename.indexOf( '.' ) > 0 ) {\r
+ initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );\r
+ }\r
+ initial_filename = initial_filename + ".pdf";\r
+ _writetopdf_filechooser.setSelectedFile( new File( initial_filename ) );\r
+ final File my_dir = getCurrentDir();\r
+ if ( my_dir != null ) {\r
+ _writetopdf_filechooser.setCurrentDirectory( my_dir );\r
+ }\r
+ final int result = _writetopdf_filechooser.showSaveDialog( _contentpane );\r
+ File file = _writetopdf_filechooser.getSelectedFile();\r
+ setCurrentDir( _writetopdf_filechooser.getCurrentDirectory() );\r
+ if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
+ if ( !file.toString().toLowerCase().endsWith( ".pdf" ) ) {\r
+ file = new File( file.toString() + ".pdf" );\r
+ }\r
+ if ( file.exists() ) {\r
+ final int i = JOptionPane.showConfirmDialog( this,\r
+ file + " already exists. Overwrite?",\r
+ "WARNING",\r
+ JOptionPane.OK_CANCEL_OPTION,\r
+ JOptionPane.WARNING_MESSAGE );\r
+ if ( i != JOptionPane.OK_OPTION ) {\r
+ return;\r
+ }\r
+ }\r
+ printPhylogenyToPdf( file.toString() );\r
+ }\r
+ }\r
+\r
+ public static MainFrameApplication createInstance( final Phylogeny[] phys, final Configuration config ) {\r
+ return new MainFrameApplication( phys, config );\r
+ }\r
+\r
+ public static MainFrame createInstance( final Phylogeny[] phys,\r
+ final Configuration config,\r
+ final String title,\r
+ final File current_dir ) {\r
+ return new MainFrameApplication( phys, config, title, current_dir );\r
+ }\r
+\r
+ static MainFrame createInstance( final Phylogeny[] phys, final Configuration config, final String title ) {\r
+ return new MainFrameApplication( phys, config, title );\r
+ }\r
+\r
+ static MainFrame createInstance( final Phylogeny[] phys, final String config_file_name, final String title ) {\r
+ return new MainFrameApplication( phys, config_file_name, title );\r
+ }\r
+\r
+ static void setTextForGraphicsSizeChooserMenuItem( final JMenuItem mi, final Options o ) {\r
+ mi.setText( "Enter Default Size for Graphics Export... (current: " + o.getPrintSizeX() + ", "\r
+ + o.getPrintSizeY() + ")" );\r
+ }\r
+\r
+ static void setTextForPdfLineWidthChooserMenuItem( final JMenuItem mi, final Options o ) {\r
+ mi.setText( "Enter Default Line Width for PDF Export... (current: " + o.getPrintLineWidth() + ")" );\r
+ }\r
+\r
+ static void warnIfNotPhyloXmlValidation( final Configuration c ) {\r
+ if ( !c.isValidatePhyloXmlAgainstSchema() ) {\r
+ JOptionPane\r
+ .showMessageDialog( null,\r
+ ForesterUtil\r
+ .wordWrap( "phyloXML XSD-based validation is turned off [enable with line 'validate_against_phyloxml_xsd_schem: true' in configuration file]",\r
+ 80 ),\r
+ "Warning",\r
+ JOptionPane.WARNING_MESSAGE );\r
+ }\r
+ }\r
+} // MainFrameApplication.\r
+\r
+class DefaultFilter extends FileFilter {\r
+\r
+ @Override\r
+ public boolean accept( final File f ) {\r
+ final String file_name = f.getName().trim().toLowerCase();\r
+ return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )\r
+ || file_name.endsWith( ".nwk" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".ph" )\r
+ || file_name.endsWith( ".tr" ) || file_name.endsWith( ".dnd" ) || file_name.endsWith( ".tree" )\r
+ || file_name.endsWith( ".nhx" ) || file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" )\r
+ || file_name.endsWith( "phylo.xml" ) || file_name.endsWith( ".pxml" ) || file_name.endsWith( ".nexus" )\r
+ || file_name.endsWith( ".nx" ) || file_name.endsWith( ".nex" ) || file_name.endsWith( ".tre" )\r
+ || file_name.endsWith( ".zip" ) || file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" )\r
+ || file_name.endsWith( ".con" ) || f.isDirectory();\r
+ }\r
+\r
+ @Override\r
+ public String getDescription() {\r
+ return "All supported files (*.xml, *.phyloxml, *phylo.xml, *.nhx, *.nh, *.newick, *.nex, *.nexus, *.phy, *.tre, *.tree, *.tol, ...)";\r
+ }\r
+}\r
+\r
+class GraphicsFileFilter extends FileFilter {\r
+\r
+ @Override\r
+ public boolean accept( final File f ) {\r
+ final String file_name = f.getName().trim().toLowerCase();\r
+ return file_name.endsWith( ".jpg" ) || file_name.endsWith( ".jpeg" ) || file_name.endsWith( ".png" )\r
+ || file_name.endsWith( ".gif" ) || file_name.endsWith( ".bmp" ) || f.isDirectory();\r
+ }\r
+\r
+ @Override\r
+ public String getDescription() {\r
+ return "Image files (*.jpg, *.jpeg, *.png, *.gif, *.bmp)";\r
+ }\r
+}\r
+\r
+class MsaFileFilter extends FileFilter {\r
+\r
+ @Override\r
+ public boolean accept( final File f ) {\r
+ final String file_name = f.getName().trim().toLowerCase();\r
+ return file_name.endsWith( ".msa" ) || file_name.endsWith( ".aln" ) || file_name.endsWith( ".fasta" )\r
+ || file_name.endsWith( ".fas" ) || file_name.endsWith( ".fa" ) || f.isDirectory();\r
+ }\r
+\r
+ @Override\r
+ public String getDescription() {\r
+ return "Multiple sequence alignment files (*.msa, *.aln, *.fasta, *.fa, *.fas)";\r
+ }\r
+}\r
+\r
+class NexusFilter extends FileFilter {\r
+\r
+ @Override\r
+ public boolean accept( final File f ) {\r
+ final String file_name = f.getName().trim().toLowerCase();\r
+ return file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) || file_name.endsWith( ".nx" )\r
+ || file_name.endsWith( ".tre" ) || f.isDirectory();\r
+ }\r
+\r
+ @Override\r
+ public String getDescription() {\r
+ return "Nexus files (*.nex, *.nexus, *.nx, *.tre)";\r
+ }\r
+} // NexusFilter\r
+\r
+class NHFilter extends FileFilter {\r
+\r
+ @Override\r
+ public boolean accept( final File f ) {\r
+ final String file_name = f.getName().trim().toLowerCase();\r
+ return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )\r
+ || file_name.endsWith( ".tr" ) || file_name.endsWith( ".tree" ) || file_name.endsWith( ".dnd" )\r
+ || file_name.endsWith( ".ph" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".nwk" )\r
+ || f.isDirectory();\r
+ }\r
+\r
+ @Override\r
+ public String getDescription() {\r
+ return "New Hampshire - Newick files (*.nh, *.newick, *.phy, *.tree, *.dnd, *.tr, *.ph, *.phb, *.nwk)";\r
+ }\r
+} // NHFilter\r
+\r
+class NHXFilter extends FileFilter {\r
+\r
+ @Override\r
+ public boolean accept( final File f ) {\r
+ final String file_name = f.getName().trim().toLowerCase();\r
+ return file_name.endsWith( ".nhx" ) || f.isDirectory();\r
+ }\r
+\r
+ @Override\r
+ public String getDescription() {\r
+ return "NHX files (*.nhx) [deprecated]";\r
+ }\r
+}\r
+\r
+class PdfFilter extends FileFilter {\r
+\r
+ @Override\r
+ public boolean accept( final File f ) {\r
+ return f.getName().trim().toLowerCase().endsWith( ".pdf" ) || f.isDirectory();\r
+ }\r
+\r
+ @Override\r
+ public String getDescription() {\r
+ return "PDF files (*.pdf)";\r
+ }\r
+} // PdfFilter\r
+\r
+class SequencesFileFilter extends FileFilter {\r
+\r
+ @Override\r
+ public boolean accept( final File f ) {\r
+ final String file_name = f.getName().trim().toLowerCase();\r
+ return file_name.endsWith( ".fasta" ) || file_name.endsWith( ".fa" ) || file_name.endsWith( ".fas" )\r
+ || file_name.endsWith( ".seqs" ) || f.isDirectory();\r
+ }\r
+\r
+ @Override\r
+ public String getDescription() {\r
+ return "Sequences files (*.fasta, *.fa, *.fas, *.seqs )";\r
+ }\r
+}\r
+\r
+class TolFilter extends FileFilter {\r
+\r
+ @Override\r
+ public boolean accept( final File f ) {\r
+ final String file_name = f.getName().trim().toLowerCase();\r
+ return ( file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" ) || file_name.endsWith( ".zip" ) || f\r
+ .isDirectory() ) && ( !file_name.endsWith( ".xml.zip" ) );\r
+ }\r
+\r
+ @Override\r
+ public String getDescription() {\r
+ return "Tree of Life files (*.tol, *.tolxml)";\r
+ }\r
+} // TolFilter\r
+\r
+class XMLFilter extends FileFilter {\r
+\r
+ @Override\r
+ public boolean accept( final File f ) {\r
+ final String file_name = f.getName().trim().toLowerCase();\r
+ return file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" ) || file_name.endsWith( "phylo.xml" )\r
+ || file_name.endsWith( ".pxml" ) || file_name.endsWith( ".zip" ) || f.isDirectory();\r
+ }\r
+\r
+ @Override\r
+ public String getDescription() {\r
+ return "phyloXML files (*.xml, *.phyloxml, *phylo.xml, *.pxml, *.zip)";\r
+ }\r
+} // XMLFilter\r
-// $Id:
-// FORESTER -- software libraries and applications
-// for evolutionary biology research and applications.
-//
-// Copyright (C) 2008-2009 Christian M. Zmasek
-// Copyright (C) 2008-2009 Burnham Institute for Medical Research
-// All rights reserved
-//
-// This library is free software; you can redistribute it and/or
-// modify it under the terms of the GNU Lesser General Public
-// License as published by the Free Software Foundation; either
-// version 2.1 of the License, or (at your option) any later version.
-//
-// This library is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
-// Lesser General Public License for more details.
-//
-// You should have received a copy of the GNU Lesser General Public
-// License along with this library; if not, write to the Free Software
-// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-//
-// Contact: phylosoft @ gmail . com
-// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
-
-package org.forester.phylogeny;
-
-import java.awt.Color;
-import java.io.File;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.Comparator;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-import org.forester.io.parsers.FastaParser;
-import org.forester.io.parsers.PhylogenyParser;
-import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
-import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
-import org.forester.io.parsers.util.PhylogenyParserException;
-import org.forester.phylogeny.data.Accession;
-import org.forester.phylogeny.data.Annotation;
-import org.forester.phylogeny.data.BranchColor;
-import org.forester.phylogeny.data.BranchWidth;
-import org.forester.phylogeny.data.Confidence;
-import org.forester.phylogeny.data.DomainArchitecture;
-import org.forester.phylogeny.data.Event;
-import org.forester.phylogeny.data.Identifier;
-import org.forester.phylogeny.data.PhylogenyDataUtil;
-import org.forester.phylogeny.data.Sequence;
-import org.forester.phylogeny.data.Taxonomy;
-import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
-import org.forester.phylogeny.factories.PhylogenyFactory;
-import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
-import org.forester.util.BasicDescriptiveStatistics;
-import org.forester.util.DescriptiveStatistics;
-import org.forester.util.ForesterUtil;
-
-public class PhylogenyMethods {
-
- private PhylogenyMethods() {
- // Hidden constructor.
- }
-
- @Override
- public Object clone() throws CloneNotSupportedException {
- throw new CloneNotSupportedException();
- }
-
- public static boolean extractFastaInformation( final Phylogeny phy ) {
- boolean could_extract = false;
- for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
- final PhylogenyNode node = iter.next();
- if ( !ForesterUtil.isEmpty( node.getName() ) ) {
- final Matcher name_m = FastaParser.FASTA_DESC_LINE.matcher( node.getName() );
- if ( name_m.lookingAt() ) {
- could_extract = true;
- final String acc_source = name_m.group( 1 );
- final String acc = name_m.group( 2 );
- final String seq_name = name_m.group( 3 );
- final String tax_sn = name_m.group( 4 );
- if ( !ForesterUtil.isEmpty( acc_source ) && !ForesterUtil.isEmpty( acc ) ) {
- ForesterUtil.ensurePresenceOfSequence( node );
- node.getNodeData().getSequence( 0 ).setAccession( new Accession( acc, acc_source ) );
- }
- if ( !ForesterUtil.isEmpty( seq_name ) ) {
- ForesterUtil.ensurePresenceOfSequence( node );
- node.getNodeData().getSequence( 0 ).setName( seq_name );
- }
- if ( !ForesterUtil.isEmpty( tax_sn ) ) {
- ForesterUtil.ensurePresenceOfTaxonomy( node );
- node.getNodeData().getTaxonomy( 0 ).setScientificName( tax_sn );
- }
- }
- }
- }
- return could_extract;
- }
-
- public static DescriptiveStatistics calculatBranchLengthStatistics( final Phylogeny phy ) {
- final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
- for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
- final PhylogenyNode n = iter.next();
- if ( !n.isRoot() && ( n.getDistanceToParent() >= 0.0 ) ) {
- stats.addValue( n.getDistanceToParent() );
- }
- }
- return stats;
- }
-
- public static List<DescriptiveStatistics> calculatConfidenceStatistics( final Phylogeny phy ) {
- final List<DescriptiveStatistics> stats = new ArrayList<DescriptiveStatistics>();
- for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
- final PhylogenyNode n = iter.next();
- if ( !n.isExternal() && !n.isRoot() ) {
- if ( n.getBranchData().isHasConfidences() ) {
- for( int i = 0; i < n.getBranchData().getConfidences().size(); ++i ) {
- final Confidence c = n.getBranchData().getConfidences().get( i );
- if ( ( i > ( stats.size() - 1 ) ) || ( stats.get( i ) == null ) ) {
- stats.add( i, new BasicDescriptiveStatistics() );
- }
- if ( !ForesterUtil.isEmpty( c.getType() ) ) {
- if ( !ForesterUtil.isEmpty( stats.get( i ).getDescription() ) ) {
- if ( !stats.get( i ).getDescription().equalsIgnoreCase( c.getType() ) ) {
- throw new IllegalArgumentException( "support values in node [" + n.toString()
- + "] appear inconsistently ordered" );
- }
- }
- stats.get( i ).setDescription( c.getType() );
- }
- stats.get( i ).addValue( ( ( c != null ) && ( c.getValue() >= 0 ) ) ? c.getValue() : 0 );
- }
- }
- }
- }
- return stats;
- }
-
- /**
- * Calculates the distance between PhylogenyNodes node1 and node2.
- *
- *
- * @param node1
- * @param node2
- * @return distance between node1 and node2
- */
- public static double calculateDistance( final PhylogenyNode node1, final PhylogenyNode node2 ) {
- final PhylogenyNode lca = calculateLCA( node1, node2 );
- final PhylogenyNode n1 = node1;
- final PhylogenyNode n2 = node2;
- return ( PhylogenyMethods.getDistance( n1, lca ) + PhylogenyMethods.getDistance( n2, lca ) );
- }
-
- /**
- * Returns the LCA of PhylogenyNodes node1 and node2.
- *
- *
- * @param node1
- * @param node2
- * @return LCA of node1 and node2
- */
- public final static PhylogenyNode calculateLCA( PhylogenyNode node1, PhylogenyNode node2 ) {
- if ( node1 == null ) {
- throw new IllegalArgumentException( "first argument (node) is null" );
- }
- if ( node2 == null ) {
- throw new IllegalArgumentException( "second argument (node) is null" );
- }
- if ( node1 == node2 ) {
- return node1;
- }
- if ( ( node1.getParent() == node2.getParent() ) ) {
- return node1.getParent();
- }
- int depth1 = node1.calculateDepth();
- int depth2 = node2.calculateDepth();
- while ( ( depth1 > -1 ) && ( depth2 > -1 ) ) {
- if ( depth1 > depth2 ) {
- node1 = node1.getParent();
- depth1--;
- }
- else if ( depth2 > depth1 ) {
- node2 = node2.getParent();
- depth2--;
- }
- else {
- if ( node1 == node2 ) {
- return node1;
- }
- node1 = node1.getParent();
- node2 = node2.getParent();
- depth1--;
- depth2--;
- }
- }
- throw new IllegalArgumentException( "illegal attempt to calculate LCA of two nodes which do not share a common root" );
- }
-
- /**
- * Returns the LCA of PhylogenyNodes node1 and node2.
- * Precondition: ids are in pre-order (or level-order).
- *
- *
- * @param node1
- * @param node2
- * @return LCA of node1 and node2
- */
- public final static PhylogenyNode calculateLCAonTreeWithIdsInPreOrder( PhylogenyNode node1, PhylogenyNode node2 ) {
- if ( node1 == null ) {
- throw new IllegalArgumentException( "first argument (node) is null" );
- }
- if ( node2 == null ) {
- throw new IllegalArgumentException( "second argument (node) is null" );
- }
- while ( node1 != node2 ) {
- if ( node1.getId() > node2.getId() ) {
- node1 = node1.getParent();
- }
- else {
- node2 = node2.getParent();
- }
- }
- return node1;
- }
-
- public static short calculateMaxBranchesToLeaf( final PhylogenyNode node ) {
- if ( node.isExternal() ) {
- return 0;
- }
- short max = 0;
- for( PhylogenyNode d : node.getAllExternalDescendants() ) {
- short steps = 0;
- while ( d != node ) {
- if ( d.isCollapse() ) {
- steps = 0;
- }
- else {
- steps++;
- }
- d = d.getParent();
- }
- if ( max < steps ) {
- max = steps;
- }
- }
- return max;
- }
-
- public static int calculateMaxDepth( final Phylogeny phy ) {
- int max = 0;
- for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
- final PhylogenyNode node = iter.next();
- final int steps = node.calculateDepth();
- if ( steps > max ) {
- max = steps;
- }
- }
- return max;
- }
-
- public static double calculateMaxDistanceToRoot( final Phylogeny phy ) {
- double max = 0.0;
- for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
- final PhylogenyNode node = iter.next();
- final double d = node.calculateDistanceToRoot();
- if ( d > max ) {
- max = d;
- }
- }
- return max;
- }
-
- public static int calculateNumberOfExternalNodesWithoutTaxonomy( final PhylogenyNode node ) {
- final List<PhylogenyNode> descs = node.getAllExternalDescendants();
- int x = 0;
- for( final PhylogenyNode n : descs ) {
- if ( !n.getNodeData().isHasTaxonomy() || n.getNodeData().getTaxonomy().isEmpty() ) {
- x++;
- }
- }
- return x;
- }
-
- public static DescriptiveStatistics calculatNumberOfDescendantsPerNodeStatistics( final Phylogeny phy ) {
- final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
- for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
- final PhylogenyNode n = iter.next();
- if ( !n.isExternal() ) {
- stats.addValue( n.getNumberOfDescendants() );
- }
- }
- return stats;
- }
-
- public final static void collapseSubtreeStructure( final PhylogenyNode n ) {
- final List<PhylogenyNode> eds = n.getAllExternalDescendants();
- final List<Double> d = new ArrayList<Double>();
- for( final PhylogenyNode ed : eds ) {
- d.add( calculateDistanceToAncestor( n, ed ) );
- }
- for( int i = 0; i < eds.size(); ++i ) {
- n.setChildNode( i, eds.get( i ) );
- eds.get( i ).setDistanceToParent( d.get( i ) );
- }
- }
-
- public static int countNumberOfOneDescendantNodes( final Phylogeny phy ) {
- int count = 0;
- for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
- final PhylogenyNode n = iter.next();
- if ( !n.isExternal() && ( n.getNumberOfDescendants() == 1 ) ) {
- count++;
- }
- }
- return count;
- }
-
- public static int countNumberOfPolytomies( final Phylogeny phy ) {
- int count = 0;
- for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
- final PhylogenyNode n = iter.next();
- if ( !n.isExternal() && ( n.getNumberOfDescendants() > 2 ) ) {
- count++;
- }
- }
- return count;
- }
-
- public static final HashMap<String, PhylogenyNode> createNameToExtNodeMap( final Phylogeny phy ) {
- final HashMap<String, PhylogenyNode> nodes = new HashMap<String, PhylogenyNode>();
- final List<PhylogenyNode> ext = phy.getExternalNodes();
- for( final PhylogenyNode n : ext ) {
- nodes.put( n.getName(), n );
- }
- return nodes;
- }
-
- public static void deleteExternalNodesNegativeSelection( final Set<Long> to_delete, final Phylogeny phy ) {
- for( final Long id : to_delete ) {
- phy.deleteSubtree( phy.getNode( id ), true );
- }
- phy.clearHashIdToNodeMap();
- phy.externalNodesHaveChanged();
- }
-
- public static void deleteExternalNodesNegativeSelection( final String[] node_names_to_delete, final Phylogeny p )
- throws IllegalArgumentException {
- for( final String element : node_names_to_delete ) {
- if ( ForesterUtil.isEmpty( element ) ) {
- continue;
- }
- List<PhylogenyNode> nodes = null;
- nodes = p.getNodes( element );
- final Iterator<PhylogenyNode> it = nodes.iterator();
- while ( it.hasNext() ) {
- final PhylogenyNode n = it.next();
- if ( !n.isExternal() ) {
- throw new IllegalArgumentException( "attempt to delete non-external node \"" + element + "\"" );
- }
- p.deleteSubtree( n, true );
- }
- }
- p.clearHashIdToNodeMap();
- p.externalNodesHaveChanged();
- }
-
- public static List<String> deleteExternalNodesPositiveSelection( final String[] node_names_to_keep,
- final Phylogeny p ) {
- final PhylogenyNodeIterator it = p.iteratorExternalForward();
- final String[] to_delete = new String[ p.getNumberOfExternalNodes() ];
- int i = 0;
- Arrays.sort( node_names_to_keep );
- while ( it.hasNext() ) {
- final String curent_name = it.next().getName();
- if ( Arrays.binarySearch( node_names_to_keep, curent_name ) < 0 ) {
- to_delete[ i++ ] = curent_name;
- }
- }
- PhylogenyMethods.deleteExternalNodesNegativeSelection( to_delete, p );
- final List<String> deleted = new ArrayList<String>();
- for( final String n : to_delete ) {
- if ( !ForesterUtil.isEmpty( n ) ) {
- deleted.add( n );
- }
- }
- return deleted;
- }
-
- public static void deleteExternalNodesPositiveSelectionT( final List<Taxonomy> species_to_keep, final Phylogeny phy ) {
- final Set<Long> to_delete = new HashSet<Long>();
- for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
- final PhylogenyNode n = it.next();
- if ( n.getNodeData().isHasTaxonomy() ) {
- if ( !species_to_keep.contains( n.getNodeData().getTaxonomy() ) ) {
- to_delete.add( n.getId() );
- }
- }
- else {
- throw new IllegalArgumentException( "node " + n.getId() + " has no taxonomic data" );
- }
- }
- deleteExternalNodesNegativeSelection( to_delete, phy );
- }
-
- final public static void deleteInternalNodesWithOnlyOneDescendent( final Phylogeny phy ) {
- final ArrayList<PhylogenyNode> to_delete = new ArrayList<PhylogenyNode>();
- for( final PhylogenyNodeIterator iter = phy.iteratorPostorder(); iter.hasNext(); ) {
- final PhylogenyNode n = iter.next();
- if ( ( !n.isExternal() ) && ( n.getNumberOfDescendants() == 1 ) ) {
- to_delete.add( n );
- }
- }
- for( final PhylogenyNode d : to_delete ) {
- PhylogenyMethods.removeNode( d, phy );
- }
- phy.clearHashIdToNodeMap();
- phy.externalNodesHaveChanged();
- }
-
- final public static void deleteNonOrthologousExternalNodes( final Phylogeny phy, final PhylogenyNode n ) {
- if ( n.isInternal() ) {
- throw new IllegalArgumentException( "node is not external" );
- }
- final ArrayList<PhylogenyNode> to_delete = new ArrayList<PhylogenyNode>();
- for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
- final PhylogenyNode i = it.next();
- if ( !PhylogenyMethods.getEventAtLCA( n, i ).isSpeciation() ) {
- to_delete.add( i );
- }
- }
- for( final PhylogenyNode d : to_delete ) {
- phy.deleteSubtree( d, true );
- }
- phy.clearHashIdToNodeMap();
- phy.externalNodesHaveChanged();
- }
-
- public final static List<List<PhylogenyNode>> divideIntoSubTrees( final Phylogeny phy,
- final double min_distance_to_root ) {
- if ( min_distance_to_root <= 0 ) {
- throw new IllegalArgumentException( "attempt to use min distance to root of: " + min_distance_to_root );
- }
- final List<List<PhylogenyNode>> l = new ArrayList<List<PhylogenyNode>>();
- setAllIndicatorsToZero( phy );
- for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
- final PhylogenyNode n = it.next();
- if ( n.getIndicator() != 0 ) {
- continue;
- }
- l.add( divideIntoSubTreesHelper( n, min_distance_to_root ) );
- if ( l.isEmpty() ) {
- throw new RuntimeException( "this should not have happened" );
- }
- }
- return l;
- }
-
- public static List<PhylogenyNode> getAllDescendants( final PhylogenyNode node ) {
- final List<PhylogenyNode> descs = new ArrayList<PhylogenyNode>();
- final Set<Long> encountered = new HashSet<Long>();
- if ( !node.isExternal() ) {
- final List<PhylogenyNode> exts = node.getAllExternalDescendants();
- for( PhylogenyNode current : exts ) {
- descs.add( current );
- while ( current != node ) {
- current = current.getParent();
- if ( encountered.contains( current.getId() ) ) {
- continue;
- }
- descs.add( current );
- encountered.add( current.getId() );
- }
- }
- }
- return descs;
- }
-
- /**
- *
- * Convenience method
- *
- * @param node
- * @return
- */
- public static Color getBranchColorValue( final PhylogenyNode node ) {
- if ( node.getBranchData().getBranchColor() == null ) {
- return null;
- }
- return node.getBranchData().getBranchColor().getValue();
- }
-
- /**
- * Convenience method
- */
- public static double getBranchWidthValue( final PhylogenyNode node ) {
- if ( !node.getBranchData().isHasBranchWidth() ) {
- return BranchWidth.BRANCH_WIDTH_DEFAULT_VALUE;
- }
- return node.getBranchData().getBranchWidth().getValue();
- }
-
- /**
- * Convenience method
- */
- public static double getConfidenceValue( final PhylogenyNode node ) {
- if ( !node.getBranchData().isHasConfidences() ) {
- return Confidence.CONFIDENCE_DEFAULT_VALUE;
- }
- return node.getBranchData().getConfidence( 0 ).getValue();
- }
-
- /**
- * Convenience method
- */
- public static double[] getConfidenceValuesAsArray( final PhylogenyNode node ) {
- if ( !node.getBranchData().isHasConfidences() ) {
- return new double[ 0 ];
- }
- final double[] values = new double[ node.getBranchData().getConfidences().size() ];
- int i = 0;
- for( final Confidence c : node.getBranchData().getConfidences() ) {
- values[ i++ ] = c.getValue();
- }
- return values;
- }
-
- final public static Event getEventAtLCA( final PhylogenyNode n1, final PhylogenyNode n2 ) {
- return calculateLCA( n1, n2 ).getNodeData().getEvent();
- }
-
- /**
- * Returns taxonomy t if all external descendants have
- * the same taxonomy t, null otherwise.
- *
- */
- public static Taxonomy getExternalDescendantsTaxonomy( final PhylogenyNode node ) {
- final List<PhylogenyNode> descs = node.getAllExternalDescendants();
- Taxonomy tax = null;
- for( final PhylogenyNode n : descs ) {
- if ( !n.getNodeData().isHasTaxonomy() || n.getNodeData().getTaxonomy().isEmpty() ) {
- return null;
- }
- else if ( tax == null ) {
- tax = n.getNodeData().getTaxonomy();
- }
- else if ( n.getNodeData().getTaxonomy().isEmpty() || !tax.isEqual( n.getNodeData().getTaxonomy() ) ) {
- return null;
- }
- }
- return tax;
- }
-
- public static PhylogenyNode getFurthestDescendant( final PhylogenyNode node ) {
- final List<PhylogenyNode> children = node.getAllExternalDescendants();
- PhylogenyNode farthest = null;
- double longest = -Double.MAX_VALUE;
- for( final PhylogenyNode child : children ) {
- if ( PhylogenyMethods.getDistance( child, node ) > longest ) {
- farthest = child;
- longest = PhylogenyMethods.getDistance( child, node );
- }
- }
- return farthest;
- }
-
- // public static PhylogenyMethods getInstance() {
- // if ( PhylogenyMethods._instance == null ) {
- // PhylogenyMethods._instance = new PhylogenyMethods();
- // }
- // return PhylogenyMethods._instance;
- // }
- /**
- * Returns the largest confidence value found on phy.
- */
- static public double getMaximumConfidenceValue( final Phylogeny phy ) {
- double max = -Double.MAX_VALUE;
- for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
- final double s = PhylogenyMethods.getConfidenceValue( iter.next() );
- if ( ( s != Confidence.CONFIDENCE_DEFAULT_VALUE ) && ( s > max ) ) {
- max = s;
- }
- }
- return max;
- }
-
- static public int getMinimumDescendentsPerInternalNodes( final Phylogeny phy ) {
- int min = Integer.MAX_VALUE;
- int d = 0;
- PhylogenyNode n;
- for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) {
- n = it.next();
- if ( n.isInternal() ) {
- d = n.getNumberOfDescendants();
- if ( d < min ) {
- min = d;
- }
- }
- }
- return min;
- }
-
- /**
- * Convenience method for display purposes.
- * Not intended for algorithms.
- */
- public static String getSpecies( final PhylogenyNode node ) {
- if ( !node.getNodeData().isHasTaxonomy() ) {
- return "";
- }
- else if ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) ) {
- return node.getNodeData().getTaxonomy().getScientificName();
- }
- if ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
- return node.getNodeData().getTaxonomy().getTaxonomyCode();
- }
- else {
- return node.getNodeData().getTaxonomy().getCommonName();
- }
- }
-
- /**
- * Convenience method for display purposes.
- * Not intended for algorithms.
- */
- public static String getTaxonomyIdentifier( final PhylogenyNode node ) {
- if ( !node.getNodeData().isHasTaxonomy() || ( node.getNodeData().getTaxonomy().getIdentifier() == null ) ) {
- return "";
- }
- return node.getNodeData().getTaxonomy().getIdentifier().getValue();
- }
-
- public final static boolean isAllDecendentsAreDuplications( final PhylogenyNode n ) {
- if ( n.isExternal() ) {
- return true;
- }
- else {
- if ( n.isDuplication() ) {
- for( final PhylogenyNode desc : n.getDescendants() ) {
- if ( !isAllDecendentsAreDuplications( desc ) ) {
- return false;
- }
- }
- return true;
- }
- else {
- return false;
- }
- }
- }
-
- public static boolean isHasExternalDescendant( final PhylogenyNode node ) {
- for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
- if ( node.getChildNode( i ).isExternal() ) {
- return true;
- }
- }
- return false;
- }
-
- /*
- * This is case insensitive.
- *
- */
- public synchronized static boolean isTaxonomyHasIdentifierOfGivenProvider( final Taxonomy tax,
- final String[] providers ) {
- if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() ) ) {
- final String my_tax_prov = tax.getIdentifier().getProvider();
- for( final String provider : providers ) {
- if ( provider.equalsIgnoreCase( my_tax_prov ) ) {
- return true;
- }
- }
- return false;
- }
- else {
- return false;
- }
- }
-
- public static void midpointRoot( final Phylogeny phylogeny ) {
- if ( ( phylogeny.getNumberOfExternalNodes() < 2 ) || ( calculateMaxDistanceToRoot( phylogeny ) <= 0 ) ) {
- return;
- }
- int counter = 0;
- final int total_nodes = phylogeny.getNodeCount();
- while ( true ) {
- if ( ++counter > total_nodes ) {
- throw new RuntimeException( "this should not have happened: midpoint rooting does not converge" );
- }
- PhylogenyNode a = null;
- double da = 0;
- double db = 0;
- for( int i = 0; i < phylogeny.getRoot().getNumberOfDescendants(); ++i ) {
- final PhylogenyNode f = getFurthestDescendant( phylogeny.getRoot().getChildNode( i ) );
- final double df = getDistance( f, phylogeny.getRoot() );
- if ( df > 0 ) {
- if ( df > da ) {
- db = da;
- da = df;
- a = f;
- }
- else if ( df > db ) {
- db = df;
- }
- }
- }
- final double diff = da - db;
- if ( diff < 0.000001 ) {
- break;
- }
- double x = da - ( diff / 2.0 );
- while ( ( x > a.getDistanceToParent() ) && !a.isRoot() ) {
- x -= ( a.getDistanceToParent() > 0 ? a.getDistanceToParent() : 0 );
- a = a.getParent();
- }
- phylogeny.reRoot( a, x );
- }
- phylogeny.recalculateNumberOfExternalDescendants( true );
- }
-
- public static void normalizeBootstrapValues( final Phylogeny phylogeny,
- final double max_bootstrap_value,
- final double max_normalized_value ) {
- for( final PhylogenyNodeIterator iter = phylogeny.iteratorPreorder(); iter.hasNext(); ) {
- final PhylogenyNode node = iter.next();
- if ( node.isInternal() ) {
- final double confidence = getConfidenceValue( node );
- if ( confidence != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
- if ( confidence >= max_bootstrap_value ) {
- setBootstrapConfidence( node, max_normalized_value );
- }
- else {
- setBootstrapConfidence( node, ( confidence * max_normalized_value ) / max_bootstrap_value );
- }
- }
- }
- }
- }
-
- public static List<PhylogenyNode> obtainAllNodesAsList( final Phylogeny phy ) {
- final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
- if ( phy.isEmpty() ) {
- return nodes;
- }
- for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
- nodes.add( iter.next() );
- }
- return nodes;
- }
-
- /**
- * Returns a map of distinct taxonomies of
- * all external nodes of node.
- * If at least one of the external nodes has no taxonomy,
- * null is returned.
- *
- */
- public static Map<Taxonomy, Integer> obtainDistinctTaxonomyCounts( final PhylogenyNode node ) {
- final List<PhylogenyNode> descs = node.getAllExternalDescendants();
- final Map<Taxonomy, Integer> tax_map = new HashMap<Taxonomy, Integer>();
- for( final PhylogenyNode n : descs ) {
- if ( !n.getNodeData().isHasTaxonomy() || n.getNodeData().getTaxonomy().isEmpty() ) {
- return null;
- }
- final Taxonomy t = n.getNodeData().getTaxonomy();
- if ( tax_map.containsKey( t ) ) {
- tax_map.put( t, tax_map.get( t ) + 1 );
- }
- else {
- tax_map.put( t, 1 );
- }
- }
- return tax_map;
- }
-
- /**
- * Arranges the order of childern for each node of this Phylogeny in such a
- * way that either the branch with more children is on top (right) or on
- * bottom (left), dependent on the value of boolean order.
- *
- * @param order
- * decides in which direction to order
- * @param pri
- */
- public static void orderAppearance( final PhylogenyNode n,
- final boolean order,
- final boolean order_ext_alphabetically,
- final DESCENDANT_SORT_PRIORITY pri ) {
- if ( n.isExternal() ) {
- return;
- }
- else {
- PhylogenyNode temp = null;
- if ( ( n.getNumberOfDescendants() == 2 )
- && ( n.getChildNode1().getNumberOfExternalNodes() != n.getChildNode2().getNumberOfExternalNodes() )
- && ( ( n.getChildNode1().getNumberOfExternalNodes() < n.getChildNode2().getNumberOfExternalNodes() ) == order ) ) {
- temp = n.getChildNode1();
- n.setChild1( n.getChildNode2() );
- n.setChild2( temp );
- }
- else if ( order_ext_alphabetically ) {
- boolean all_ext = true;
- for( final PhylogenyNode i : n.getDescendants() ) {
- if ( !i.isExternal() ) {
- all_ext = false;
- break;
- }
- }
- if ( all_ext ) {
- PhylogenyMethods.sortNodeDescendents( n, pri );
- }
- }
- for( int i = 0; i < n.getNumberOfDescendants(); ++i ) {
- orderAppearance( n.getChildNode( i ), order, order_ext_alphabetically, pri );
- }
- }
- }
-
- public static void postorderBranchColorAveragingExternalNodeBased( final Phylogeny p ) {
- for( final PhylogenyNodeIterator iter = p.iteratorPostorder(); iter.hasNext(); ) {
- final PhylogenyNode node = iter.next();
- double red = 0.0;
- double green = 0.0;
- double blue = 0.0;
- int n = 0;
- if ( node.isInternal() ) {
- //for( final PhylogenyNodeIterator iterator = node.iterateChildNodesForward(); iterator.hasNext(); ) {
- for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
- final PhylogenyNode child_node = node.getChildNode( i );
- final Color child_color = getBranchColorValue( child_node );
- if ( child_color != null ) {
- ++n;
- red += child_color.getRed();
- green += child_color.getGreen();
- blue += child_color.getBlue();
- }
- }
- setBranchColorValue( node,
- new Color( ForesterUtil.roundToInt( red / n ),
- ForesterUtil.roundToInt( green / n ),
- ForesterUtil.roundToInt( blue / n ) ) );
- }
- }
- }
-
- public static final void preOrderReId( final Phylogeny phy ) {
- if ( phy.isEmpty() ) {
- return;
- }
- phy.setIdToNodeMap( null );
- long i = PhylogenyNode.getNodeCount();
- for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) {
- it.next().setId( i++ );
- }
- PhylogenyNode.setNodeCount( i );
- }
-
- public final static Phylogeny[] readPhylogenies( final PhylogenyParser parser, final File file ) throws IOException {
- final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
- final Phylogeny[] trees = factory.create( file, parser );
- if ( ( trees == null ) || ( trees.length == 0 ) ) {
- throw new PhylogenyParserException( "Unable to parse phylogeny from file: " + file );
- }
- return trees;
- }
-
- public final static Phylogeny[] readPhylogenies( final PhylogenyParser parser, final List<File> files )
- throws IOException {
- final List<Phylogeny> tree_list = new ArrayList<Phylogeny>();
- for( final File file : files ) {
- final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
- final Phylogeny[] trees = factory.create( file, parser );
- if ( ( trees == null ) || ( trees.length == 0 ) ) {
- throw new PhylogenyParserException( "Unable to parse phylogeny from file: " + file );
- }
- tree_list.addAll( Arrays.asList( trees ) );
- }
- return tree_list.toArray( new Phylogeny[ tree_list.size() ] );
- }
-
- public static void removeNode( final PhylogenyNode remove_me, final Phylogeny phylogeny ) {
- if ( remove_me.isRoot() ) {
- if ( remove_me.getNumberOfDescendants() == 1 ) {
- final PhylogenyNode desc = remove_me.getDescendants().get( 0 );
- desc.setDistanceToParent( addPhylogenyDistances( remove_me.getDistanceToParent(),
- desc.getDistanceToParent() ) );
- desc.setParent( null );
- phylogeny.setRoot( desc );
- phylogeny.clearHashIdToNodeMap();
- }
- else {
- throw new IllegalArgumentException( "attempt to remove a root node with more than one descendants" );
- }
- }
- else if ( remove_me.isExternal() ) {
- phylogeny.deleteSubtree( remove_me, false );
- phylogeny.clearHashIdToNodeMap();
- phylogeny.externalNodesHaveChanged();
- }
- else {
- final PhylogenyNode parent = remove_me.getParent();
- final List<PhylogenyNode> descs = remove_me.getDescendants();
- parent.removeChildNode( remove_me );
- for( final PhylogenyNode desc : descs ) {
- parent.addAsChild( desc );
- desc.setDistanceToParent( addPhylogenyDistances( remove_me.getDistanceToParent(),
- desc.getDistanceToParent() ) );
- }
- remove_me.setParent( null );
- phylogeny.clearHashIdToNodeMap();
- phylogeny.externalNodesHaveChanged();
- }
- }
-
- public static List<PhylogenyNode> searchData( final String query,
- final Phylogeny phy,
- final boolean case_sensitive,
- final boolean partial,
- final boolean search_domains ) {
- final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
- if ( phy.isEmpty() || ( query == null ) ) {
- return nodes;
- }
- if ( ForesterUtil.isEmpty( query ) ) {
- return nodes;
- }
- for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
- final PhylogenyNode node = iter.next();
- boolean match = false;
- if ( match( node.getName(), query, case_sensitive, partial ) ) {
- match = true;
- }
- else if ( node.getNodeData().isHasTaxonomy()
- && match( node.getNodeData().getTaxonomy().getTaxonomyCode(), query, case_sensitive, partial ) ) {
- match = true;
- }
- else if ( node.getNodeData().isHasTaxonomy()
- && match( node.getNodeData().getTaxonomy().getCommonName(), query, case_sensitive, partial ) ) {
- match = true;
- }
- else if ( node.getNodeData().isHasTaxonomy()
- && match( node.getNodeData().getTaxonomy().getScientificName(), query, case_sensitive, partial ) ) {
- match = true;
- }
- else if ( node.getNodeData().isHasTaxonomy()
- && ( node.getNodeData().getTaxonomy().getIdentifier() != null )
- && match( node.getNodeData().getTaxonomy().getIdentifier().getValue(),
- query,
- case_sensitive,
- partial ) ) {
- match = true;
- }
- else if ( node.getNodeData().isHasTaxonomy() && !node.getNodeData().getTaxonomy().getSynonyms().isEmpty() ) {
- final List<String> syns = node.getNodeData().getTaxonomy().getSynonyms();
- I: for( final String syn : syns ) {
- if ( match( syn, query, case_sensitive, partial ) ) {
- match = true;
- break I;
- }
- }
- }
- if ( !match && node.getNodeData().isHasSequence()
- && match( node.getNodeData().getSequence().getName(), query, case_sensitive, partial ) ) {
- match = true;
- }
- if ( !match && node.getNodeData().isHasSequence()
- && match( node.getNodeData().getSequence().getGeneName(), query, case_sensitive, partial ) ) {
- match = true;
- }
- if ( !match && node.getNodeData().isHasSequence()
- && match( node.getNodeData().getSequence().getSymbol(), query, case_sensitive, partial ) ) {
- match = true;
- }
- if ( !match
- && node.getNodeData().isHasSequence()
- && ( node.getNodeData().getSequence().getAccession() != null )
- && match( node.getNodeData().getSequence().getAccession().getValue(),
- query,
- case_sensitive,
- partial ) ) {
- match = true;
- }
- if ( search_domains && !match && node.getNodeData().isHasSequence()
- && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
- final DomainArchitecture da = node.getNodeData().getSequence().getDomainArchitecture();
- I: for( int i = 0; i < da.getNumberOfDomains(); ++i ) {
- if ( match( da.getDomain( i ).getName(), query, case_sensitive, partial ) ) {
- match = true;
- break I;
- }
- }
- }
- //
- if ( !match && node.getNodeData().isHasSequence()
- && ( node.getNodeData().getSequence().getAnnotations() != null ) ) {
- for( final Annotation ann : node.getNodeData().getSequence().getAnnotations() ) {
- if ( match( ann.getDesc(), query, case_sensitive, partial ) ) {
- match = true;
- break;
- }
- if ( match( ann.getRef(), query, case_sensitive, partial ) ) {
- match = true;
- break;
- }
- }
- }
- if ( !match && node.getNodeData().isHasSequence()
- && ( node.getNodeData().getSequence().getCrossReferences() != null ) ) {
- for( final Accession x : node.getNodeData().getSequence().getCrossReferences() ) {
- if ( match( x.getComment(), query, case_sensitive, partial ) ) {
- match = true;
- break;
- }
- if ( match( x.getSource(), query, case_sensitive, partial ) ) {
- match = true;
- break;
- }
- if ( match( x.getValue(), query, case_sensitive, partial ) ) {
- match = true;
- break;
- }
- }
- }
- //
- if ( !match && ( node.getNodeData().getBinaryCharacters() != null ) ) {
- Iterator<String> it = node.getNodeData().getBinaryCharacters().getPresentCharacters().iterator();
- I: while ( it.hasNext() ) {
- if ( match( it.next(), query, case_sensitive, partial ) ) {
- match = true;
- break I;
- }
- }
- it = node.getNodeData().getBinaryCharacters().getGainedCharacters().iterator();
- I: while ( it.hasNext() ) {
- if ( match( it.next(), query, case_sensitive, partial ) ) {
- match = true;
- break I;
- }
- }
- }
- if ( match ) {
- nodes.add( node );
- }
- }
- return nodes;
- }
-
- public static List<PhylogenyNode> searchDataLogicalAnd( final String[] queries,
- final Phylogeny phy,
- final boolean case_sensitive,
- final boolean partial,
- final boolean search_domains ) {
- final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
- if ( phy.isEmpty() || ( queries == null ) || ( queries.length < 1 ) ) {
- return nodes;
- }
- for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
- final PhylogenyNode node = iter.next();
- boolean all_matched = true;
- for( final String query : queries ) {
- boolean match = false;
- if ( ForesterUtil.isEmpty( query ) ) {
- continue;
- }
- if ( match( node.getName(), query, case_sensitive, partial ) ) {
- match = true;
- }
- else if ( node.getNodeData().isHasTaxonomy()
- && match( node.getNodeData().getTaxonomy().getTaxonomyCode(), query, case_sensitive, partial ) ) {
- match = true;
- }
- else if ( node.getNodeData().isHasTaxonomy()
- && match( node.getNodeData().getTaxonomy().getCommonName(), query, case_sensitive, partial ) ) {
- match = true;
- }
- else if ( node.getNodeData().isHasTaxonomy()
- && match( node.getNodeData().getTaxonomy().getScientificName(), query, case_sensitive, partial ) ) {
- match = true;
- }
- else if ( node.getNodeData().isHasTaxonomy()
- && ( node.getNodeData().getTaxonomy().getIdentifier() != null )
- && match( node.getNodeData().getTaxonomy().getIdentifier().getValue(),
- query,
- case_sensitive,
- partial ) ) {
- match = true;
- }
- else if ( node.getNodeData().isHasTaxonomy()
- && !node.getNodeData().getTaxonomy().getSynonyms().isEmpty() ) {
- final List<String> syns = node.getNodeData().getTaxonomy().getSynonyms();
- I: for( final String syn : syns ) {
- if ( match( syn, query, case_sensitive, partial ) ) {
- match = true;
- break I;
- }
- }
- }
- if ( !match && node.getNodeData().isHasSequence()
- && match( node.getNodeData().getSequence().getName(), query, case_sensitive, partial ) ) {
- match = true;
- }
- if ( !match && node.getNodeData().isHasSequence()
- && match( node.getNodeData().getSequence().getGeneName(), query, case_sensitive, partial ) ) {
- match = true;
- }
- if ( !match && node.getNodeData().isHasSequence()
- && match( node.getNodeData().getSequence().getSymbol(), query, case_sensitive, partial ) ) {
- match = true;
- }
- if ( !match
- && node.getNodeData().isHasSequence()
- && ( node.getNodeData().getSequence().getAccession() != null )
- && match( node.getNodeData().getSequence().getAccession().getValue(),
- query,
- case_sensitive,
- partial ) ) {
- match = true;
- }
- if ( search_domains && !match && node.getNodeData().isHasSequence()
- && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
- final DomainArchitecture da = node.getNodeData().getSequence().getDomainArchitecture();
- I: for( int i = 0; i < da.getNumberOfDomains(); ++i ) {
- if ( match( da.getDomain( i ).getName(), query, case_sensitive, partial ) ) {
- match = true;
- break I;
- }
- }
- }
- //
- if ( !match && node.getNodeData().isHasSequence()
- && ( node.getNodeData().getSequence().getAnnotations() != null ) ) {
- for( final Annotation ann : node.getNodeData().getSequence().getAnnotations() ) {
- if ( match( ann.getDesc(), query, case_sensitive, partial ) ) {
- match = true;
- break;
- }
- if ( match( ann.getRef(), query, case_sensitive, partial ) ) {
- match = true;
- break;
- }
- }
- }
- if ( !match && node.getNodeData().isHasSequence()
- && ( node.getNodeData().getSequence().getCrossReferences() != null ) ) {
- for( final Accession x : node.getNodeData().getSequence().getCrossReferences() ) {
- if ( match( x.getComment(), query, case_sensitive, partial ) ) {
- match = true;
- break;
- }
- if ( match( x.getSource(), query, case_sensitive, partial ) ) {
- match = true;
- break;
- }
- if ( match( x.getValue(), query, case_sensitive, partial ) ) {
- match = true;
- break;
- }
- }
- }
- //
- if ( !match && ( node.getNodeData().getBinaryCharacters() != null ) ) {
- Iterator<String> it = node.getNodeData().getBinaryCharacters().getPresentCharacters().iterator();
- I: while ( it.hasNext() ) {
- if ( match( it.next(), query, case_sensitive, partial ) ) {
- match = true;
- break I;
- }
- }
- it = node.getNodeData().getBinaryCharacters().getGainedCharacters().iterator();
- I: while ( it.hasNext() ) {
- if ( match( it.next(), query, case_sensitive, partial ) ) {
- match = true;
- break I;
- }
- }
- }
- if ( !match ) {
- all_matched = false;
- break;
- }
- }
- if ( all_matched ) {
- nodes.add( node );
- }
- }
- return nodes;
- }
-
- public static void setAllIndicatorsToZero( final Phylogeny phy ) {
- for( final PhylogenyNodeIterator it = phy.iteratorPostorder(); it.hasNext(); ) {
- it.next().setIndicator( ( byte ) 0 );
- }
- }
-
- /**
- * Convenience method.
- * Sets value for the first confidence value (created if not present, values overwritten otherwise).
- */
- public static void setBootstrapConfidence( final PhylogenyNode node, final double bootstrap_confidence_value ) {
- setConfidence( node, bootstrap_confidence_value, "bootstrap" );
- }
-
- public static void setBranchColorValue( final PhylogenyNode node, final Color color ) {
- if ( node.getBranchData().getBranchColor() == null ) {
- node.getBranchData().setBranchColor( new BranchColor() );
- }
- node.getBranchData().getBranchColor().setValue( color );
- }
-
- /**
- * Convenience method
- */
- public static void setBranchWidthValue( final PhylogenyNode node, final double branch_width_value ) {
- node.getBranchData().setBranchWidth( new BranchWidth( branch_width_value ) );
- }
-
- /**
- * Convenience method.
- * Sets value for the first confidence value (created if not present, values overwritten otherwise).
- */
- public static void setConfidence( final PhylogenyNode node, final double confidence_value ) {
- setConfidence( node, confidence_value, "" );
- }
-
- /**
- * Convenience method.
- * Sets value for the first confidence value (created if not present, values overwritten otherwise).
- */
- public static void setConfidence( final PhylogenyNode node, final double confidence_value, final String type ) {
- Confidence c = null;
- if ( node.getBranchData().getNumberOfConfidences() > 0 ) {
- c = node.getBranchData().getConfidence( 0 );
- }
- else {
- c = new Confidence();
- node.getBranchData().addConfidence( c );
- }
- c.setType( type );
- c.setValue( confidence_value );
- }
-
- public static void setScientificName( final PhylogenyNode node, final String scientific_name ) {
- if ( !node.getNodeData().isHasTaxonomy() ) {
- node.getNodeData().setTaxonomy( new Taxonomy() );
- }
- node.getNodeData().getTaxonomy().setScientificName( scientific_name );
- }
-
- /**
- * Convenience method to set the taxonomy code of a phylogeny node.
- *
- *
- * @param node
- * @param taxonomy_code
- * @throws PhyloXmlDataFormatException
- */
- public static void setTaxonomyCode( final PhylogenyNode node, final String taxonomy_code )
- throws PhyloXmlDataFormatException {
- if ( !node.getNodeData().isHasTaxonomy() ) {
- node.getNodeData().setTaxonomy( new Taxonomy() );
- }
- node.getNodeData().getTaxonomy().setTaxonomyCode( taxonomy_code );
- }
-
- final static public void sortNodeDescendents( final PhylogenyNode node, final DESCENDANT_SORT_PRIORITY pri ) {
- class PhylogenyNodeSortTaxonomyPriority implements Comparator<PhylogenyNode> {
-
- @Override
- public int compare( final PhylogenyNode n1, final PhylogenyNode n2 ) {
- if ( n1.getNodeData().isHasTaxonomy() && n2.getNodeData().isHasTaxonomy() ) {
- if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getScientificName() ) )
- && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getScientificName() ) ) ) {
- return n1.getNodeData().getTaxonomy().getScientificName().toLowerCase()
- .compareTo( n2.getNodeData().getTaxonomy().getScientificName().toLowerCase() );
- }
- if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getTaxonomyCode() ) )
- && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) {
- return n1.getNodeData().getTaxonomy().getTaxonomyCode()
- .compareTo( n2.getNodeData().getTaxonomy().getTaxonomyCode() );
- }
- if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getCommonName() ) )
- && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getCommonName() ) ) ) {
- return n1.getNodeData().getTaxonomy().getCommonName().toLowerCase()
- .compareTo( n2.getNodeData().getTaxonomy().getCommonName().toLowerCase() );
- }
- }
- if ( n1.getNodeData().isHasSequence() && n2.getNodeData().isHasSequence() ) {
- if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getName() ) )
- && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getName() ) ) ) {
- return n1.getNodeData().getSequence().getName().toLowerCase()
- .compareTo( n2.getNodeData().getSequence().getName().toLowerCase() );
- }
- if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getSymbol() ) )
- && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getSymbol() ) ) ) {
- return n1.getNodeData().getSequence().getSymbol()
- .compareTo( n2.getNodeData().getSequence().getSymbol() );
- }
- if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getGeneName() ) )
- && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getGeneName() ) ) ) {
- return n1.getNodeData().getSequence().getGeneName()
- .compareTo( n2.getNodeData().getSequence().getGeneName() );
- }
- if ( ( n1.getNodeData().getSequence().getAccession() != null )
- && ( n2.getNodeData().getSequence().getAccession() != null )
- && !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getAccession().getValue() )
- && !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getAccession().getValue() ) ) {
- return n1.getNodeData().getSequence().getAccession().getValue()
- .compareTo( n2.getNodeData().getSequence().getAccession().getValue() );
- }
- }
- if ( ( !ForesterUtil.isEmpty( n1.getName() ) ) && ( !ForesterUtil.isEmpty( n2.getName() ) ) ) {
- return n1.getName().toLowerCase().compareTo( n2.getName().toLowerCase() );
- }
- return 0;
- }
- }
- class PhylogenyNodeSortSequencePriority implements Comparator<PhylogenyNode> {
-
- @Override
- public int compare( final PhylogenyNode n1, final PhylogenyNode n2 ) {
- if ( n1.getNodeData().isHasSequence() && n2.getNodeData().isHasSequence() ) {
- if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getName() ) )
- && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getName() ) ) ) {
- return n1.getNodeData().getSequence().getName().toLowerCase()
- .compareTo( n2.getNodeData().getSequence().getName().toLowerCase() );
- }
- if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getSymbol() ) )
- && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getSymbol() ) ) ) {
- return n1.getNodeData().getSequence().getSymbol()
- .compareTo( n2.getNodeData().getSequence().getSymbol() );
- }
- if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getGeneName() ) )
- && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getGeneName() ) ) ) {
- return n1.getNodeData().getSequence().getGeneName()
- .compareTo( n2.getNodeData().getSequence().getGeneName() );
- }
- if ( ( n1.getNodeData().getSequence().getAccession() != null )
- && ( n2.getNodeData().getSequence().getAccession() != null )
- && !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getAccession().getValue() )
- && !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getAccession().getValue() ) ) {
- return n1.getNodeData().getSequence().getAccession().getValue()
- .compareTo( n2.getNodeData().getSequence().getAccession().getValue() );
- }
- }
- if ( n1.getNodeData().isHasTaxonomy() && n2.getNodeData().isHasTaxonomy() ) {
- if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getScientificName() ) )
- && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getScientificName() ) ) ) {
- return n1.getNodeData().getTaxonomy().getScientificName().toLowerCase()
- .compareTo( n2.getNodeData().getTaxonomy().getScientificName().toLowerCase() );
- }
- if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getTaxonomyCode() ) )
- && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) {
- return n1.getNodeData().getTaxonomy().getTaxonomyCode()
- .compareTo( n2.getNodeData().getTaxonomy().getTaxonomyCode() );
- }
- if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getCommonName() ) )
- && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getCommonName() ) ) ) {
- return n1.getNodeData().getTaxonomy().getCommonName().toLowerCase()
- .compareTo( n2.getNodeData().getTaxonomy().getCommonName().toLowerCase() );
- }
- }
- if ( ( !ForesterUtil.isEmpty( n1.getName() ) ) && ( !ForesterUtil.isEmpty( n2.getName() ) ) ) {
- return n1.getName().toLowerCase().compareTo( n2.getName().toLowerCase() );
- }
- return 0;
- }
- }
- class PhylogenyNodeSortNodeNamePriority implements Comparator<PhylogenyNode> {
-
- @Override
- public int compare( final PhylogenyNode n1, final PhylogenyNode n2 ) {
- if ( ( !ForesterUtil.isEmpty( n1.getName() ) ) && ( !ForesterUtil.isEmpty( n2.getName() ) ) ) {
- return n1.getName().toLowerCase().compareTo( n2.getName().toLowerCase() );
- }
- if ( n1.getNodeData().isHasTaxonomy() && n2.getNodeData().isHasTaxonomy() ) {
- if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getScientificName() ) )
- && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getScientificName() ) ) ) {
- return n1.getNodeData().getTaxonomy().getScientificName().toLowerCase()
- .compareTo( n2.getNodeData().getTaxonomy().getScientificName().toLowerCase() );
- }
- if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getTaxonomyCode() ) )
- && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) {
- return n1.getNodeData().getTaxonomy().getTaxonomyCode()
- .compareTo( n2.getNodeData().getTaxonomy().getTaxonomyCode() );
- }
- if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getCommonName() ) )
- && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getCommonName() ) ) ) {
- return n1.getNodeData().getTaxonomy().getCommonName().toLowerCase()
- .compareTo( n2.getNodeData().getTaxonomy().getCommonName().toLowerCase() );
- }
- }
- if ( n1.getNodeData().isHasSequence() && n2.getNodeData().isHasSequence() ) {
- if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getName() ) )
- && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getName() ) ) ) {
- return n1.getNodeData().getSequence().getName().toLowerCase()
- .compareTo( n2.getNodeData().getSequence().getName().toLowerCase() );
- }
- if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getSymbol() ) )
- && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getSymbol() ) ) ) {
- return n1.getNodeData().getSequence().getSymbol()
- .compareTo( n2.getNodeData().getSequence().getSymbol() );
- }
- if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getGeneName() ) )
- && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getGeneName() ) ) ) {
- return n1.getNodeData().getSequence().getGeneName()
- .compareTo( n2.getNodeData().getSequence().getGeneName() );
- }
- if ( ( n1.getNodeData().getSequence().getAccession() != null )
- && ( n2.getNodeData().getSequence().getAccession() != null )
- && !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getAccession().getValue() )
- && !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getAccession().getValue() ) ) {
- return n1.getNodeData().getSequence().getAccession().getValue()
- .compareTo( n2.getNodeData().getSequence().getAccession().getValue() );
- }
- }
- return 0;
- }
- }
- Comparator<PhylogenyNode> c;
- switch ( pri ) {
- case SEQUENCE:
- c = new PhylogenyNodeSortSequencePriority();
- break;
- case NODE_NAME:
- c = new PhylogenyNodeSortNodeNamePriority();
- break;
- default:
- c = new PhylogenyNodeSortTaxonomyPriority();
- }
- final List<PhylogenyNode> descs = node.getDescendants();
- Collections.sort( descs, c );
- int i = 0;
- for( final PhylogenyNode desc : descs ) {
- node.setChildNode( i++, desc );
- }
- }
-
- /**
- * Removes from Phylogeny to_be_stripped all external Nodes which are
- * associated with a species NOT found in Phylogeny reference.
- *
- * @param reference
- * a reference Phylogeny
- * @param to_be_stripped
- * Phylogeny to be stripped
- * @return nodes removed from to_be_stripped
- */
- public static List<PhylogenyNode> taxonomyBasedDeletionOfExternalNodes( final Phylogeny reference,
- final Phylogeny to_be_stripped ) {
- final Set<String> ref_ext_taxo = new HashSet<String>();
- for( final PhylogenyNodeIterator it = reference.iteratorExternalForward(); it.hasNext(); ) {
- final PhylogenyNode n = it.next();
- if ( !n.getNodeData().isHasTaxonomy() ) {
- throw new IllegalArgumentException( "no taxonomic data in node: " + n );
- }
- if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
- ref_ext_taxo.add( n.getNodeData().getTaxonomy().getScientificName() );
- }
- if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
- ref_ext_taxo.add( n.getNodeData().getTaxonomy().getTaxonomyCode() );
- }
- if ( ( n.getNodeData().getTaxonomy().getIdentifier() != null )
- && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getIdentifier().getValue() ) ) {
- ref_ext_taxo.add( n.getNodeData().getTaxonomy().getIdentifier().getValuePlusProvider() );
- }
- }
- final ArrayList<PhylogenyNode> nodes_to_delete = new ArrayList<PhylogenyNode>();
- for( final PhylogenyNodeIterator it = to_be_stripped.iteratorExternalForward(); it.hasNext(); ) {
- final PhylogenyNode n = it.next();
- if ( !n.getNodeData().isHasTaxonomy() ) {
- nodes_to_delete.add( n );
- }
- else if ( !( ref_ext_taxo.contains( n.getNodeData().getTaxonomy().getScientificName() ) )
- && !( ref_ext_taxo.contains( n.getNodeData().getTaxonomy().getTaxonomyCode() ) )
- && !( ( n.getNodeData().getTaxonomy().getIdentifier() != null ) && ref_ext_taxo.contains( n
- .getNodeData().getTaxonomy().getIdentifier().getValuePlusProvider() ) ) ) {
- nodes_to_delete.add( n );
- }
- }
- for( final PhylogenyNode n : nodes_to_delete ) {
- to_be_stripped.deleteSubtree( n, true );
- }
- to_be_stripped.clearHashIdToNodeMap();
- to_be_stripped.externalNodesHaveChanged();
- return nodes_to_delete;
- }
-
- final static public void transferInternalNamesToBootstrapSupport( final Phylogeny phy ) {
- final PhylogenyNodeIterator it = phy.iteratorPostorder();
- while ( it.hasNext() ) {
- final PhylogenyNode n = it.next();
- if ( !n.isExternal() && !ForesterUtil.isEmpty( n.getName() ) ) {
- double value = -1;
- try {
- value = Double.parseDouble( n.getName() );
- }
- catch ( final NumberFormatException e ) {
- throw new IllegalArgumentException( "failed to parse number from [" + n.getName() + "]: "
- + e.getLocalizedMessage() );
- }
- if ( value >= 0.0 ) {
- n.getBranchData().addConfidence( new Confidence( value, "bootstrap" ) );
- n.setName( "" );
- }
- }
- }
- }
-
- final static public boolean isInternalNamesLookLikeConfidences( final Phylogeny phy ) {
- final PhylogenyNodeIterator it = phy.iteratorPostorder();
- while ( it.hasNext() ) {
- final PhylogenyNode n = it.next();
- if ( !n.isExternal() && !n.isRoot() ) {
- if ( !ForesterUtil.isEmpty( n.getName() ) ) {
- double value = -1;
- try {
- value = Double.parseDouble( n.getName() );
- }
- catch ( final NumberFormatException e ) {
- return false;
- }
- if ( ( value < 0.0 ) || ( value > 100 ) ) {
- return false;
- }
- }
- }
- }
- return true;
- }
-
- final static public void transferInternalNodeNamesToConfidence( final Phylogeny phy, final String confidence_type ) {
- final PhylogenyNodeIterator it = phy.iteratorPostorder();
- while ( it.hasNext() ) {
- transferInternalNodeNameToConfidence( confidence_type, it.next() );
- }
- }
-
- private static void transferInternalNodeNameToConfidence( final String confidence_type, final PhylogenyNode n ) {
- if ( !n.isExternal() && !n.getBranchData().isHasConfidences() ) {
- if ( !ForesterUtil.isEmpty( n.getName() ) ) {
- double d = -1.0;
- try {
- d = Double.parseDouble( n.getName() );
- }
- catch ( final Exception e ) {
- d = -1.0;
- }
- if ( d >= 0.0 ) {
- n.getBranchData().addConfidence( new Confidence( d, confidence_type ) );
- n.setName( "" );
- }
- }
- }
- }
-
- final static public void transferNodeNameToField( final Phylogeny phy,
- final PhylogenyNodeField field,
- final boolean external_only ) throws PhyloXmlDataFormatException {
- final PhylogenyNodeIterator it = phy.iteratorPostorder();
- while ( it.hasNext() ) {
- final PhylogenyNode n = it.next();
- if ( external_only && n.isInternal() ) {
- continue;
- }
- final String name = n.getName().trim();
- if ( !ForesterUtil.isEmpty( name ) ) {
- switch ( field ) {
- case TAXONOMY_CODE:
- n.setName( "" );
- setTaxonomyCode( n, name );
- break;
- case TAXONOMY_SCIENTIFIC_NAME:
- n.setName( "" );
- if ( !n.getNodeData().isHasTaxonomy() ) {
- n.getNodeData().setTaxonomy( new Taxonomy() );
- }
- n.getNodeData().getTaxonomy().setScientificName( name );
- break;
- case TAXONOMY_COMMON_NAME:
- n.setName( "" );
- if ( !n.getNodeData().isHasTaxonomy() ) {
- n.getNodeData().setTaxonomy( new Taxonomy() );
- }
- n.getNodeData().getTaxonomy().setCommonName( name );
- break;
- case SEQUENCE_SYMBOL:
- n.setName( "" );
- if ( !n.getNodeData().isHasSequence() ) {
- n.getNodeData().setSequence( new Sequence() );
- }
- n.getNodeData().getSequence().setSymbol( name );
- break;
- case SEQUENCE_NAME:
- n.setName( "" );
- if ( !n.getNodeData().isHasSequence() ) {
- n.getNodeData().setSequence( new Sequence() );
- }
- n.getNodeData().getSequence().setName( name );
- break;
- case TAXONOMY_ID_UNIPROT_1: {
- if ( !n.getNodeData().isHasTaxonomy() ) {
- n.getNodeData().setTaxonomy( new Taxonomy() );
- }
- String id = name;
- final int i = name.indexOf( '_' );
- if ( i > 0 ) {
- id = name.substring( 0, i );
- }
- else {
- n.setName( "" );
- }
- n.getNodeData().getTaxonomy()
- .setIdentifier( new Identifier( id, PhyloXmlUtil.UNIPROT_TAX_PROVIDER ) );
- break;
- }
- case TAXONOMY_ID_UNIPROT_2: {
- if ( !n.getNodeData().isHasTaxonomy() ) {
- n.getNodeData().setTaxonomy( new Taxonomy() );
- }
- String id = name;
- final int i = name.indexOf( '_' );
- if ( i > 0 ) {
- id = name.substring( i + 1, name.length() );
- }
- else {
- n.setName( "" );
- }
- n.getNodeData().getTaxonomy()
- .setIdentifier( new Identifier( id, PhyloXmlUtil.UNIPROT_TAX_PROVIDER ) );
- break;
- }
- case TAXONOMY_ID: {
- if ( !n.getNodeData().isHasTaxonomy() ) {
- n.getNodeData().setTaxonomy( new Taxonomy() );
- }
- n.getNodeData().getTaxonomy().setIdentifier( new Identifier( name ) );
- break;
- }
- }
- }
- }
- }
-
- static double addPhylogenyDistances( final double a, final double b ) {
- if ( ( a >= 0.0 ) && ( b >= 0.0 ) ) {
- return a + b;
- }
- else if ( a >= 0.0 ) {
- return a;
- }
- else if ( b >= 0.0 ) {
- return b;
- }
- return PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT;
- }
-
- static double calculateDistanceToAncestor( final PhylogenyNode anc, PhylogenyNode desc ) {
- double d = 0;
- boolean all_default = true;
- while ( anc != desc ) {
- if ( desc.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
- d += desc.getDistanceToParent();
- if ( all_default ) {
- all_default = false;
- }
- }
- desc = desc.getParent();
- }
- if ( all_default ) {
- return PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT;
- }
- return d;
- }
-
- /**
- * Deep copies the phylogeny originating from this node.
- */
- static PhylogenyNode copySubTree( final PhylogenyNode source ) {
- if ( source == null ) {
- return null;
- }
- else {
- final PhylogenyNode newnode = source.copyNodeData();
- if ( !source.isExternal() ) {
- for( int i = 0; i < source.getNumberOfDescendants(); ++i ) {
- newnode.setChildNode( i, PhylogenyMethods.copySubTree( source.getChildNode( i ) ) );
- }
- }
- return newnode;
- }
- }
-
- /**
- * Shallow copies the phylogeny originating from this node.
- */
- static PhylogenyNode copySubTreeShallow( final PhylogenyNode source ) {
- if ( source == null ) {
- return null;
- }
- else {
- final PhylogenyNode newnode = source.copyNodeDataShallow();
- if ( !source.isExternal() ) {
- for( int i = 0; i < source.getNumberOfDescendants(); ++i ) {
- newnode.setChildNode( i, PhylogenyMethods.copySubTreeShallow( source.getChildNode( i ) ) );
- }
- }
- return newnode;
- }
- }
-
- private final static List<PhylogenyNode> divideIntoSubTreesHelper( final PhylogenyNode node,
- final double min_distance_to_root ) {
- final List<PhylogenyNode> l = new ArrayList<PhylogenyNode>();
- final PhylogenyNode r = moveTowardsRoot( node, min_distance_to_root );
- for( final PhylogenyNode ext : r.getAllExternalDescendants() ) {
- if ( ext.getIndicator() != 0 ) {
- throw new RuntimeException( "this should not have happened" );
- }
- ext.setIndicator( ( byte ) 1 );
- l.add( ext );
- }
- return l;
- }
-
- /**
- * Calculates the distance between PhylogenyNodes n1 and n2.
- * PRECONDITION: n1 is a descendant of n2.
- *
- * @param n1
- * a descendant of n2
- * @param n2
- * @return distance between n1 and n2
- */
- private static double getDistance( PhylogenyNode n1, final PhylogenyNode n2 ) {
- double d = 0.0;
- while ( n1 != n2 ) {
- if ( n1.getDistanceToParent() > 0.0 ) {
- d += n1.getDistanceToParent();
- }
- n1 = n1.getParent();
- }
- return d;
- }
-
- private static boolean match( final String s,
- final String query,
- final boolean case_sensitive,
- final boolean partial ) {
- if ( ForesterUtil.isEmpty( s ) || ForesterUtil.isEmpty( query ) ) {
- return false;
- }
- String my_s = s.trim();
- String my_query = query.trim();
- if ( !case_sensitive ) {
- my_s = my_s.toLowerCase();
- my_query = my_query.toLowerCase();
- }
- if ( partial ) {
- return my_s.indexOf( my_query ) >= 0;
- }
- else {
- return Pattern.compile( "(\\b|_)" + Pattern.quote( my_query ) + "(\\b|_)" ).matcher( my_s ).find();
- }
- }
-
- private final static PhylogenyNode moveTowardsRoot( final PhylogenyNode node, final double min_distance_to_root ) {
- PhylogenyNode n = node;
- PhylogenyNode prev = node;
- while ( min_distance_to_root < n.calculateDistanceToRoot() ) {
- prev = n;
- n = n.getParent();
- }
- return prev;
- }
-
- public static enum DESCENDANT_SORT_PRIORITY {
- NODE_NAME, SEQUENCE, TAXONOMY;
- }
-
- public static enum PhylogenyNodeField {
- CLADE_NAME,
- SEQUENCE_NAME,
- SEQUENCE_SYMBOL,
- TAXONOMY_CODE,
- TAXONOMY_COMMON_NAME,
- TAXONOMY_ID,
- TAXONOMY_ID_UNIPROT_1,
- TAXONOMY_ID_UNIPROT_2,
- TAXONOMY_SCIENTIFIC_NAME;
- }
-}
+// $Id:\r
+// FORESTER -- software libraries and applications\r
+// for evolutionary biology research and applications.\r
+//\r
+// Copyright (C) 2008-2009 Christian M. Zmasek\r
+// Copyright (C) 2008-2009 Burnham Institute for Medical Research\r
+// All rights reserved\r
+//\r
+// This library is free software; you can redistribute it and/or\r
+// modify it under the terms of the GNU Lesser General Public\r
+// License as published by the Free Software Foundation; either\r
+// version 2.1 of the License, or (at your option) any later version.\r
+//\r
+// This library is distributed in the hope that it will be useful,\r
+// but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU\r
+// Lesser General Public License for more details.\r
+//\r
+// You should have received a copy of the GNU Lesser General Public\r
+// License along with this library; if not, write to the Free Software\r
+// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+//\r
+// Contact: phylosoft @ gmail . com\r
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester\r
+\r
+package org.forester.phylogeny;\r
+\r
+import java.awt.Color;\r
+import java.io.File;\r
+import java.io.IOException;\r
+import java.util.ArrayList;\r
+import java.util.Arrays;\r
+import java.util.Collections;\r
+import java.util.Comparator;\r
+import java.util.HashMap;\r
+import java.util.HashSet;\r
+import java.util.Iterator;\r
+import java.util.List;\r
+import java.util.Map;\r
+import java.util.Set;\r
+import java.util.regex.Matcher;\r
+import java.util.regex.Pattern;\r
+\r
+import org.forester.io.parsers.FastaParser;\r
+import org.forester.io.parsers.PhylogenyParser;\r
+import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;\r
+import org.forester.io.parsers.phyloxml.PhyloXmlUtil;\r
+import org.forester.io.parsers.util.PhylogenyParserException;\r
+import org.forester.phylogeny.data.Accession;\r
+import org.forester.phylogeny.data.Annotation;\r
+import org.forester.phylogeny.data.BranchColor;\r
+import org.forester.phylogeny.data.BranchWidth;\r
+import org.forester.phylogeny.data.Confidence;\r
+import org.forester.phylogeny.data.DomainArchitecture;\r
+import org.forester.phylogeny.data.Event;\r
+import org.forester.phylogeny.data.Identifier;\r
+import org.forester.phylogeny.data.PhylogenyDataUtil;\r
+import org.forester.phylogeny.data.Sequence;\r
+import org.forester.phylogeny.data.Taxonomy;\r
+import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;\r
+import org.forester.phylogeny.factories.PhylogenyFactory;\r
+import org.forester.phylogeny.iterators.PhylogenyNodeIterator;\r
+import org.forester.util.BasicDescriptiveStatistics;\r
+import org.forester.util.DescriptiveStatistics;\r
+import org.forester.util.ForesterUtil;\r
+\r
+public class PhylogenyMethods {\r
+\r
+ private PhylogenyMethods() {\r
+ // Hidden constructor.\r
+ }\r
+\r
+ @Override\r
+ public Object clone() throws CloneNotSupportedException {\r
+ throw new CloneNotSupportedException();\r
+ }\r
+\r
+ public static boolean extractFastaInformation( final Phylogeny phy ) {\r
+ boolean could_extract = false;\r
+ for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {\r
+ final PhylogenyNode node = iter.next();\r
+ if ( !ForesterUtil.isEmpty( node.getName() ) ) {\r
+ final Matcher name_m = FastaParser.FASTA_DESC_LINE.matcher( node.getName() );\r
+ if ( name_m.lookingAt() ) {\r
+ could_extract = true;\r
+ final String acc_source = name_m.group( 1 );\r
+ final String acc = name_m.group( 2 );\r
+ final String seq_name = name_m.group( 3 );\r
+ final String tax_sn = name_m.group( 4 );\r
+ if ( !ForesterUtil.isEmpty( acc_source ) && !ForesterUtil.isEmpty( acc ) ) {\r
+ ForesterUtil.ensurePresenceOfSequence( node );\r
+ node.getNodeData().getSequence( 0 ).setAccession( new Accession( acc, acc_source ) );\r
+ }\r
+ if ( !ForesterUtil.isEmpty( seq_name ) ) {\r
+ ForesterUtil.ensurePresenceOfSequence( node );\r
+ node.getNodeData().getSequence( 0 ).setName( seq_name );\r
+ }\r
+ if ( !ForesterUtil.isEmpty( tax_sn ) ) {\r
+ ForesterUtil.ensurePresenceOfTaxonomy( node );\r
+ node.getNodeData().getTaxonomy( 0 ).setScientificName( tax_sn );\r
+ }\r
+ }\r
+ }\r
+ }\r
+ return could_extract;\r
+ }\r
+\r
+ public static DescriptiveStatistics calculatBranchLengthStatistics( final Phylogeny phy ) {\r
+ final DescriptiveStatistics stats = new BasicDescriptiveStatistics();\r
+ for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {\r
+ final PhylogenyNode n = iter.next();\r
+ if ( !n.isRoot() && ( n.getDistanceToParent() >= 0.0 ) ) {\r
+ stats.addValue( n.getDistanceToParent() );\r
+ }\r
+ }\r
+ return stats;\r
+ }\r
+\r
+ public static List<DescriptiveStatistics> calculatConfidenceStatistics( final Phylogeny phy ) {\r
+ final List<DescriptiveStatistics> stats = new ArrayList<DescriptiveStatistics>();\r
+ for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {\r
+ final PhylogenyNode n = iter.next();\r
+ if ( !n.isExternal() && !n.isRoot() ) {\r
+ if ( n.getBranchData().isHasConfidences() ) {\r
+ for( int i = 0; i < n.getBranchData().getConfidences().size(); ++i ) {\r
+ final Confidence c = n.getBranchData().getConfidences().get( i );\r
+ if ( ( i > ( stats.size() - 1 ) ) || ( stats.get( i ) == null ) ) {\r
+ stats.add( i, new BasicDescriptiveStatistics() );\r
+ }\r
+ if ( !ForesterUtil.isEmpty( c.getType() ) ) {\r
+ if ( !ForesterUtil.isEmpty( stats.get( i ).getDescription() ) ) {\r
+ if ( !stats.get( i ).getDescription().equalsIgnoreCase( c.getType() ) ) {\r
+ throw new IllegalArgumentException( "support values in node [" + n.toString()\r
+ + "] appear inconsistently ordered" );\r
+ }\r
+ }\r
+ stats.get( i ).setDescription( c.getType() );\r
+ }\r
+ stats.get( i ).addValue( ( ( c != null ) && ( c.getValue() >= 0 ) ) ? c.getValue() : 0 );\r
+ }\r
+ }\r
+ }\r
+ }\r
+ return stats;\r
+ }\r
+\r
+ /**\r
+ * Calculates the distance between PhylogenyNodes node1 and node2.\r
+ * \r
+ * \r
+ * @param node1\r
+ * @param node2\r
+ * @return distance between node1 and node2\r
+ */\r
+ public static double calculateDistance( final PhylogenyNode node1, final PhylogenyNode node2 ) {\r
+ final PhylogenyNode lca = calculateLCA( node1, node2 );\r
+ final PhylogenyNode n1 = node1;\r
+ final PhylogenyNode n2 = node2;\r
+ return ( PhylogenyMethods.getDistance( n1, lca ) + PhylogenyMethods.getDistance( n2, lca ) );\r
+ }\r
+\r
+ /**\r
+ * Returns the LCA of PhylogenyNodes node1 and node2.\r
+ * \r
+ * \r
+ * @param node1\r
+ * @param node2\r
+ * @return LCA of node1 and node2\r
+ */\r
+ public final static PhylogenyNode calculateLCA( PhylogenyNode node1, PhylogenyNode node2 ) {\r
+ if ( node1 == null ) {\r
+ throw new IllegalArgumentException( "first argument (node) is null" );\r
+ }\r
+ if ( node2 == null ) {\r
+ throw new IllegalArgumentException( "second argument (node) is null" );\r
+ }\r
+ if ( node1 == node2 ) {\r
+ return node1;\r
+ }\r
+ if ( ( node1.getParent() == node2.getParent() ) ) {\r
+ return node1.getParent();\r
+ }\r
+ int depth1 = node1.calculateDepth();\r
+ int depth2 = node2.calculateDepth();\r
+ while ( ( depth1 > -1 ) && ( depth2 > -1 ) ) {\r
+ if ( depth1 > depth2 ) {\r
+ node1 = node1.getParent();\r
+ depth1--;\r
+ }\r
+ else if ( depth2 > depth1 ) {\r
+ node2 = node2.getParent();\r
+ depth2--;\r
+ }\r
+ else {\r
+ if ( node1 == node2 ) {\r
+ return node1;\r
+ }\r
+ node1 = node1.getParent();\r
+ node2 = node2.getParent();\r
+ depth1--;\r
+ depth2--;\r
+ }\r
+ }\r
+ throw new IllegalArgumentException( "illegal attempt to calculate LCA of two nodes which do not share a common root" );\r
+ }\r
+\r
+ /**\r
+ * Returns the LCA of PhylogenyNodes node1 and node2.\r
+ * Precondition: ids are in pre-order (or level-order).\r
+ * \r
+ * \r
+ * @param node1\r
+ * @param node2\r
+ * @return LCA of node1 and node2\r
+ */\r
+ public final static PhylogenyNode calculateLCAonTreeWithIdsInPreOrder( PhylogenyNode node1, PhylogenyNode node2 ) {\r
+ if ( node1 == null ) {\r
+ throw new IllegalArgumentException( "first argument (node) is null" );\r
+ }\r
+ if ( node2 == null ) {\r
+ throw new IllegalArgumentException( "second argument (node) is null" );\r
+ }\r
+ while ( node1 != node2 ) {\r
+ if ( node1.getId() > node2.getId() ) {\r
+ node1 = node1.getParent();\r
+ }\r
+ else {\r
+ node2 = node2.getParent();\r
+ }\r
+ }\r
+ return node1;\r
+ }\r
+\r
+ public static short calculateMaxBranchesToLeaf( final PhylogenyNode node ) {\r
+ if ( node.isExternal() ) {\r
+ return 0;\r
+ }\r
+ short max = 0;\r
+ for( PhylogenyNode d : node.getAllExternalDescendants() ) {\r
+ short steps = 0;\r
+ while ( d != node ) {\r
+ if ( d.isCollapse() ) {\r
+ steps = 0;\r
+ }\r
+ else {\r
+ steps++;\r
+ }\r
+ d = d.getParent();\r
+ }\r
+ if ( max < steps ) {\r
+ max = steps;\r
+ }\r
+ }\r
+ return max;\r
+ }\r
+\r
+ public static int calculateMaxDepth( final Phylogeny phy ) {\r
+ int max = 0;\r
+ for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {\r
+ final PhylogenyNode node = iter.next();\r
+ final int steps = node.calculateDepth();\r
+ if ( steps > max ) {\r
+ max = steps;\r
+ }\r
+ }\r
+ return max;\r
+ }\r
+\r
+ public static double calculateMaxDistanceToRoot( final Phylogeny phy ) {\r
+ double max = 0.0;\r
+ for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {\r
+ final PhylogenyNode node = iter.next();\r
+ final double d = node.calculateDistanceToRoot();\r
+ if ( d > max ) {\r
+ max = d;\r
+ }\r
+ }\r
+ return max;\r
+ }\r
+\r
+ public static int calculateNumberOfExternalNodesWithoutTaxonomy( final PhylogenyNode node ) {\r
+ final List<PhylogenyNode> descs = node.getAllExternalDescendants();\r
+ int x = 0;\r
+ for( final PhylogenyNode n : descs ) {\r
+ if ( !n.getNodeData().isHasTaxonomy() || n.getNodeData().getTaxonomy().isEmpty() ) {\r
+ x++;\r
+ }\r
+ }\r
+ return x;\r
+ }\r
+\r
+ public static DescriptiveStatistics calculatNumberOfDescendantsPerNodeStatistics( final Phylogeny phy ) {\r
+ final DescriptiveStatistics stats = new BasicDescriptiveStatistics();\r
+ for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {\r
+ final PhylogenyNode n = iter.next();\r
+ if ( !n.isExternal() ) {\r
+ stats.addValue( n.getNumberOfDescendants() );\r
+ }\r
+ }\r
+ return stats;\r
+ }\r
+\r
+ public final static void collapseSubtreeStructure( final PhylogenyNode n ) {\r
+ final List<PhylogenyNode> eds = n.getAllExternalDescendants();\r
+ final List<Double> d = new ArrayList<Double>();\r
+ for( final PhylogenyNode ed : eds ) {\r
+ d.add( calculateDistanceToAncestor( n, ed ) );\r
+ }\r
+ for( int i = 0; i < eds.size(); ++i ) {\r
+ n.setChildNode( i, eds.get( i ) );\r
+ eds.get( i ).setDistanceToParent( d.get( i ) );\r
+ }\r
+ }\r
+\r
+ public static int countNumberOfOneDescendantNodes( final Phylogeny phy ) {\r
+ int count = 0;\r
+ for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {\r
+ final PhylogenyNode n = iter.next();\r
+ if ( !n.isExternal() && ( n.getNumberOfDescendants() == 1 ) ) {\r
+ count++;\r
+ }\r
+ }\r
+ return count;\r
+ }\r
+\r
+ public static int countNumberOfPolytomies( final Phylogeny phy ) {\r
+ int count = 0;\r
+ for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {\r
+ final PhylogenyNode n = iter.next();\r
+ if ( !n.isExternal() && ( n.getNumberOfDescendants() > 2 ) ) {\r
+ count++;\r
+ }\r
+ }\r
+ return count;\r
+ }\r
+\r
+ public static final HashMap<String, PhylogenyNode> createNameToExtNodeMap( final Phylogeny phy ) {\r
+ final HashMap<String, PhylogenyNode> nodes = new HashMap<String, PhylogenyNode>();\r
+ final List<PhylogenyNode> ext = phy.getExternalNodes();\r
+ for( final PhylogenyNode n : ext ) {\r
+ nodes.put( n.getName(), n );\r
+ }\r
+ return nodes;\r
+ }\r
+\r
+ public static void deleteExternalNodesNegativeSelection( final Set<Long> to_delete, final Phylogeny phy ) {\r
+ for( final Long id : to_delete ) {\r
+ phy.deleteSubtree( phy.getNode( id ), true );\r
+ }\r
+ phy.clearHashIdToNodeMap();\r
+ phy.externalNodesHaveChanged();\r
+ }\r
+\r
+ public static void deleteExternalNodesNegativeSelection( final String[] node_names_to_delete, final Phylogeny p )\r
+ throws IllegalArgumentException {\r
+ for( final String element : node_names_to_delete ) {\r
+ if ( ForesterUtil.isEmpty( element ) ) {\r
+ continue;\r
+ }\r
+ List<PhylogenyNode> nodes = null;\r
+ nodes = p.getNodes( element );\r
+ final Iterator<PhylogenyNode> it = nodes.iterator();\r
+ while ( it.hasNext() ) {\r
+ final PhylogenyNode n = it.next();\r
+ if ( !n.isExternal() ) {\r
+ throw new IllegalArgumentException( "attempt to delete non-external node \"" + element + "\"" );\r
+ }\r
+ p.deleteSubtree( n, true );\r
+ }\r
+ }\r
+ p.clearHashIdToNodeMap();\r
+ p.externalNodesHaveChanged();\r
+ }\r
+\r
+ public static List<String> deleteExternalNodesPositiveSelection( final String[] node_names_to_keep,\r
+ final Phylogeny p ) {\r
+ final PhylogenyNodeIterator it = p.iteratorExternalForward();\r
+ final String[] to_delete = new String[ p.getNumberOfExternalNodes() ];\r
+ int i = 0;\r
+ Arrays.sort( node_names_to_keep );\r
+ while ( it.hasNext() ) {\r
+ final String curent_name = it.next().getName();\r
+ if ( Arrays.binarySearch( node_names_to_keep, curent_name ) < 0 ) {\r
+ to_delete[ i++ ] = curent_name;\r
+ }\r
+ }\r
+ PhylogenyMethods.deleteExternalNodesNegativeSelection( to_delete, p );\r
+ final List<String> deleted = new ArrayList<String>();\r
+ for( final String n : to_delete ) {\r
+ if ( !ForesterUtil.isEmpty( n ) ) {\r
+ deleted.add( n );\r
+ }\r
+ }\r
+ return deleted;\r
+ }\r
+\r
+ public static void deleteExternalNodesPositiveSelectionT( final List<Taxonomy> species_to_keep, final Phylogeny phy ) {\r
+ final Set<Long> to_delete = new HashSet<Long>();\r
+ for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {\r
+ final PhylogenyNode n = it.next();\r
+ if ( n.getNodeData().isHasTaxonomy() ) {\r
+ if ( !species_to_keep.contains( n.getNodeData().getTaxonomy() ) ) {\r
+ to_delete.add( n.getId() );\r
+ }\r
+ }\r
+ else {\r
+ throw new IllegalArgumentException( "node " + n.getId() + " has no taxonomic data" );\r
+ }\r
+ }\r
+ deleteExternalNodesNegativeSelection( to_delete, phy );\r
+ }\r
+\r
+ final public static void deleteInternalNodesWithOnlyOneDescendent( final Phylogeny phy ) {\r
+ final ArrayList<PhylogenyNode> to_delete = new ArrayList<PhylogenyNode>();\r
+ for( final PhylogenyNodeIterator iter = phy.iteratorPostorder(); iter.hasNext(); ) {\r
+ final PhylogenyNode n = iter.next();\r
+ if ( ( !n.isExternal() ) && ( n.getNumberOfDescendants() == 1 ) ) {\r
+ to_delete.add( n );\r
+ }\r
+ }\r
+ for( final PhylogenyNode d : to_delete ) {\r
+ PhylogenyMethods.removeNode( d, phy );\r
+ }\r
+ phy.clearHashIdToNodeMap();\r
+ phy.externalNodesHaveChanged();\r
+ }\r
+\r
+ final public static void deleteNonOrthologousExternalNodes( final Phylogeny phy, final PhylogenyNode n ) {\r
+ if ( n.isInternal() ) {\r
+ throw new IllegalArgumentException( "node is not external" );\r
+ }\r
+ final ArrayList<PhylogenyNode> to_delete = new ArrayList<PhylogenyNode>();\r
+ for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {\r
+ final PhylogenyNode i = it.next();\r
+ if ( !PhylogenyMethods.getEventAtLCA( n, i ).isSpeciation() ) {\r
+ to_delete.add( i );\r
+ }\r
+ }\r
+ for( final PhylogenyNode d : to_delete ) {\r
+ phy.deleteSubtree( d, true );\r
+ }\r
+ phy.clearHashIdToNodeMap();\r
+ phy.externalNodesHaveChanged();\r
+ }\r
+\r
+ public final static List<List<PhylogenyNode>> divideIntoSubTrees( final Phylogeny phy,\r
+ final double min_distance_to_root ) {\r
+ if ( min_distance_to_root <= 0 ) {\r
+ throw new IllegalArgumentException( "attempt to use min distance to root of: " + min_distance_to_root );\r
+ }\r
+ final List<List<PhylogenyNode>> l = new ArrayList<List<PhylogenyNode>>();\r
+ setAllIndicatorsToZero( phy );\r
+ for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {\r
+ final PhylogenyNode n = it.next();\r
+ if ( n.getIndicator() != 0 ) {\r
+ continue;\r
+ }\r
+ l.add( divideIntoSubTreesHelper( n, min_distance_to_root ) );\r
+ if ( l.isEmpty() ) {\r
+ throw new RuntimeException( "this should not have happened" );\r
+ }\r
+ }\r
+ return l;\r
+ }\r
+\r
+ public static List<PhylogenyNode> getAllDescendants( final PhylogenyNode node ) {\r
+ final List<PhylogenyNode> descs = new ArrayList<PhylogenyNode>();\r
+ final Set<Long> encountered = new HashSet<Long>();\r
+ if ( !node.isExternal() ) {\r
+ final List<PhylogenyNode> exts = node.getAllExternalDescendants();\r
+ for( PhylogenyNode current : exts ) {\r
+ descs.add( current );\r
+ while ( current != node ) {\r
+ current = current.getParent();\r
+ if ( encountered.contains( current.getId() ) ) {\r
+ continue;\r
+ }\r
+ descs.add( current );\r
+ encountered.add( current.getId() );\r
+ }\r
+ }\r
+ }\r
+ return descs;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * Convenience method\r
+ * \r
+ * @param node\r
+ * @return\r
+ */\r
+ public static Color getBranchColorValue( final PhylogenyNode node ) {\r
+ if ( node.getBranchData().getBranchColor() == null ) {\r
+ return null;\r
+ }\r
+ return node.getBranchData().getBranchColor().getValue();\r
+ }\r
+\r
+ /**\r
+ * Convenience method\r
+ */\r
+ public static double getBranchWidthValue( final PhylogenyNode node ) {\r
+ if ( !node.getBranchData().isHasBranchWidth() ) {\r
+ return BranchWidth.BRANCH_WIDTH_DEFAULT_VALUE;\r
+ }\r
+ return node.getBranchData().getBranchWidth().getValue();\r
+ }\r
+\r
+ /**\r
+ * Convenience method\r
+ */\r
+ public static double getConfidenceValue( final PhylogenyNode node ) {\r
+ if ( !node.getBranchData().isHasConfidences() ) {\r
+ return Confidence.CONFIDENCE_DEFAULT_VALUE;\r
+ }\r
+ return node.getBranchData().getConfidence( 0 ).getValue();\r
+ }\r
+\r
+ /**\r
+ * Convenience method\r
+ */\r
+ public static double[] getConfidenceValuesAsArray( final PhylogenyNode node ) {\r
+ if ( !node.getBranchData().isHasConfidences() ) {\r
+ return new double[ 0 ];\r
+ }\r
+ final double[] values = new double[ node.getBranchData().getConfidences().size() ];\r
+ int i = 0;\r
+ for( final Confidence c : node.getBranchData().getConfidences() ) {\r
+ values[ i++ ] = c.getValue();\r
+ }\r
+ return values;\r
+ }\r
+\r
+ final public static Event getEventAtLCA( final PhylogenyNode n1, final PhylogenyNode n2 ) {\r
+ return calculateLCA( n1, n2 ).getNodeData().getEvent();\r
+ }\r
+\r
+ /**\r
+ * Returns taxonomy t if all external descendants have \r
+ * the same taxonomy t, null otherwise.\r
+ * \r
+ */\r
+ public static Taxonomy getExternalDescendantsTaxonomy( final PhylogenyNode node ) {\r
+ final List<PhylogenyNode> descs = node.getAllExternalDescendants();\r
+ Taxonomy tax = null;\r
+ for( final PhylogenyNode n : descs ) {\r
+ if ( !n.getNodeData().isHasTaxonomy() || n.getNodeData().getTaxonomy().isEmpty() ) {\r
+ return null;\r
+ }\r
+ else if ( tax == null ) {\r
+ tax = n.getNodeData().getTaxonomy();\r
+ }\r
+ else if ( n.getNodeData().getTaxonomy().isEmpty() || !tax.isEqual( n.getNodeData().getTaxonomy() ) ) {\r
+ return null;\r
+ }\r
+ }\r
+ return tax;\r
+ }\r
+\r
+ public static PhylogenyNode getFurthestDescendant( final PhylogenyNode node ) {\r
+ final List<PhylogenyNode> children = node.getAllExternalDescendants();\r
+ PhylogenyNode farthest = null;\r
+ double longest = -Double.MAX_VALUE;\r
+ for( final PhylogenyNode child : children ) {\r
+ if ( PhylogenyMethods.getDistance( child, node ) > longest ) {\r
+ farthest = child;\r
+ longest = PhylogenyMethods.getDistance( child, node );\r
+ }\r
+ }\r
+ return farthest;\r
+ }\r
+\r
+ // public static PhylogenyMethods getInstance() {\r
+ // if ( PhylogenyMethods._instance == null ) {\r
+ // PhylogenyMethods._instance = new PhylogenyMethods();\r
+ // }\r
+ // return PhylogenyMethods._instance;\r
+ // }\r
+ /**\r
+ * Returns the largest confidence value found on phy.\r
+ */\r
+ static public double getMaximumConfidenceValue( final Phylogeny phy ) {\r
+ double max = -Double.MAX_VALUE;\r
+ for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {\r
+ final double s = PhylogenyMethods.getConfidenceValue( iter.next() );\r
+ if ( ( s != Confidence.CONFIDENCE_DEFAULT_VALUE ) && ( s > max ) ) {\r
+ max = s;\r
+ }\r
+ }\r
+ return max;\r
+ }\r
+\r
+ static public int getMinimumDescendentsPerInternalNodes( final Phylogeny phy ) {\r
+ int min = Integer.MAX_VALUE;\r
+ int d = 0;\r
+ PhylogenyNode n;\r
+ for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) {\r
+ n = it.next();\r
+ if ( n.isInternal() ) {\r
+ d = n.getNumberOfDescendants();\r
+ if ( d < min ) {\r
+ min = d;\r
+ }\r
+ }\r
+ }\r
+ return min;\r
+ }\r
+\r
+ /**\r
+ * Convenience method for display purposes.\r
+ * Not intended for algorithms.\r
+ */\r
+ public static String getSpecies( final PhylogenyNode node ) {\r
+ if ( !node.getNodeData().isHasTaxonomy() ) {\r
+ return "";\r
+ }\r
+ else if ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) ) {\r
+ return node.getNodeData().getTaxonomy().getScientificName();\r
+ }\r
+ if ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {\r
+ return node.getNodeData().getTaxonomy().getTaxonomyCode();\r
+ }\r
+ else {\r
+ return node.getNodeData().getTaxonomy().getCommonName();\r
+ }\r
+ }\r
+\r
+ /**\r
+ * Convenience method for display purposes.\r
+ * Not intended for algorithms.\r
+ */\r
+ public static String getTaxonomyIdentifier( final PhylogenyNode node ) {\r
+ if ( !node.getNodeData().isHasTaxonomy() || ( node.getNodeData().getTaxonomy().getIdentifier() == null ) ) {\r
+ return "";\r
+ }\r
+ return node.getNodeData().getTaxonomy().getIdentifier().getValue();\r
+ }\r
+\r
+ public final static boolean isAllDecendentsAreDuplications( final PhylogenyNode n ) {\r
+ if ( n.isExternal() ) {\r
+ return true;\r
+ }\r
+ else {\r
+ if ( n.isDuplication() ) {\r
+ for( final PhylogenyNode desc : n.getDescendants() ) {\r
+ if ( !isAllDecendentsAreDuplications( desc ) ) {\r
+ return false;\r
+ }\r
+ }\r
+ return true;\r
+ }\r
+ else {\r
+ return false;\r
+ }\r
+ }\r
+ }\r
+\r
+ public static boolean isHasExternalDescendant( final PhylogenyNode node ) {\r
+ for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {\r
+ if ( node.getChildNode( i ).isExternal() ) {\r
+ return true;\r
+ }\r
+ }\r
+ return false;\r
+ }\r
+\r
+ /*\r
+ * This is case insensitive.\r
+ * \r
+ */\r
+ public synchronized static boolean isTaxonomyHasIdentifierOfGivenProvider( final Taxonomy tax,\r
+ final String[] providers ) {\r
+ if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() ) ) {\r
+ final String my_tax_prov = tax.getIdentifier().getProvider();\r
+ for( final String provider : providers ) {\r
+ if ( provider.equalsIgnoreCase( my_tax_prov ) ) {\r
+ return true;\r
+ }\r
+ }\r
+ return false;\r
+ }\r
+ else {\r
+ return false;\r
+ }\r
+ }\r
+\r
+ public static void midpointRoot( final Phylogeny phylogeny ) {\r
+ if ( ( phylogeny.getNumberOfExternalNodes() < 2 ) || ( calculateMaxDistanceToRoot( phylogeny ) <= 0 ) ) {\r
+ return;\r
+ }\r
+ int counter = 0;\r
+ final int total_nodes = phylogeny.getNodeCount();\r
+ while ( true ) {\r
+ if ( ++counter > total_nodes ) {\r
+ throw new RuntimeException( "this should not have happened: midpoint rooting does not converge" );\r
+ }\r
+ PhylogenyNode a = null;\r
+ double da = 0;\r
+ double db = 0;\r
+ for( int i = 0; i < phylogeny.getRoot().getNumberOfDescendants(); ++i ) {\r
+ final PhylogenyNode f = getFurthestDescendant( phylogeny.getRoot().getChildNode( i ) );\r
+ final double df = getDistance( f, phylogeny.getRoot() );\r
+ if ( df > 0 ) {\r
+ if ( df > da ) {\r
+ db = da;\r
+ da = df;\r
+ a = f;\r
+ }\r
+ else if ( df > db ) {\r
+ db = df;\r
+ }\r
+ }\r
+ }\r
+ final double diff = da - db;\r
+ if ( diff < 0.000001 ) {\r
+ break;\r
+ }\r
+ double x = da - ( diff / 2.0 );\r
+ while ( ( x > a.getDistanceToParent() ) && !a.isRoot() ) {\r
+ x -= ( a.getDistanceToParent() > 0 ? a.getDistanceToParent() : 0 );\r
+ a = a.getParent();\r
+ }\r
+ phylogeny.reRoot( a, x );\r
+ }\r
+ phylogeny.recalculateNumberOfExternalDescendants( true );\r
+ }\r
+\r
+ public static void normalizeBootstrapValues( final Phylogeny phylogeny,\r
+ final double max_bootstrap_value,\r
+ final double max_normalized_value ) {\r
+ for( final PhylogenyNodeIterator iter = phylogeny.iteratorPreorder(); iter.hasNext(); ) {\r
+ final PhylogenyNode node = iter.next();\r
+ if ( node.isInternal() ) {\r
+ final double confidence = getConfidenceValue( node );\r
+ if ( confidence != Confidence.CONFIDENCE_DEFAULT_VALUE ) {\r
+ if ( confidence >= max_bootstrap_value ) {\r
+ setBootstrapConfidence( node, max_normalized_value );\r
+ }\r
+ else {\r
+ setBootstrapConfidence( node, ( confidence * max_normalized_value ) / max_bootstrap_value );\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ public static List<PhylogenyNode> obtainAllNodesAsList( final Phylogeny phy ) {\r
+ final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();\r
+ if ( phy.isEmpty() ) {\r
+ return nodes;\r
+ }\r
+ for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {\r
+ nodes.add( iter.next() );\r
+ }\r
+ return nodes;\r
+ }\r
+\r
+ /**\r
+ * Returns a map of distinct taxonomies of\r
+ * all external nodes of node.\r
+ * If at least one of the external nodes has no taxonomy,\r
+ * null is returned.\r
+ * \r
+ */\r
+ public static Map<Taxonomy, Integer> obtainDistinctTaxonomyCounts( final PhylogenyNode node ) {\r
+ final List<PhylogenyNode> descs = node.getAllExternalDescendants();\r
+ final Map<Taxonomy, Integer> tax_map = new HashMap<Taxonomy, Integer>();\r
+ for( final PhylogenyNode n : descs ) {\r
+ if ( !n.getNodeData().isHasTaxonomy() || n.getNodeData().getTaxonomy().isEmpty() ) {\r
+ return null;\r
+ }\r
+ final Taxonomy t = n.getNodeData().getTaxonomy();\r
+ if ( tax_map.containsKey( t ) ) {\r
+ tax_map.put( t, tax_map.get( t ) + 1 );\r
+ }\r
+ else {\r
+ tax_map.put( t, 1 );\r
+ }\r
+ }\r
+ return tax_map;\r
+ }\r
+\r
+ /**\r
+ * Arranges the order of childern for each node of this Phylogeny in such a\r
+ * way that either the branch with more children is on top (right) or on\r
+ * bottom (left), dependent on the value of boolean order.\r
+ * \r
+ * @param order\r
+ * decides in which direction to order\r
+ * @param pri \r
+ */\r
+ public static void orderAppearance( final PhylogenyNode n,\r
+ final boolean order,\r
+ final boolean order_ext_alphabetically,\r
+ final DESCENDANT_SORT_PRIORITY pri ) {\r
+ if ( n.isExternal() ) {\r
+ return;\r
+ }\r
+ else {\r
+ PhylogenyNode temp = null;\r
+ if ( ( n.getNumberOfDescendants() == 2 )\r
+ && ( n.getChildNode1().getNumberOfExternalNodes() != n.getChildNode2().getNumberOfExternalNodes() )\r
+ && ( ( n.getChildNode1().getNumberOfExternalNodes() < n.getChildNode2().getNumberOfExternalNodes() ) == order ) ) {\r
+ temp = n.getChildNode1();\r
+ n.setChild1( n.getChildNode2() );\r
+ n.setChild2( temp );\r
+ }\r
+ else if ( order_ext_alphabetically ) {\r
+ boolean all_ext = true;\r
+ for( final PhylogenyNode i : n.getDescendants() ) {\r
+ if ( !i.isExternal() ) {\r
+ all_ext = false;\r
+ break;\r
+ }\r
+ }\r
+ if ( all_ext ) {\r
+ PhylogenyMethods.sortNodeDescendents( n, pri );\r
+ }\r
+ }\r
+ for( int i = 0; i < n.getNumberOfDescendants(); ++i ) {\r
+ orderAppearance( n.getChildNode( i ), order, order_ext_alphabetically, pri );\r
+ }\r
+ }\r
+ }\r
+\r
+ public static void postorderBranchColorAveragingExternalNodeBased( final Phylogeny p ) {\r
+ for( final PhylogenyNodeIterator iter = p.iteratorPostorder(); iter.hasNext(); ) {\r
+ final PhylogenyNode node = iter.next();\r
+ double red = 0.0;\r
+ double green = 0.0;\r
+ double blue = 0.0;\r
+ int n = 0;\r
+ if ( node.isInternal() ) {\r
+ //for( final PhylogenyNodeIterator iterator = node.iterateChildNodesForward(); iterator.hasNext(); ) {\r
+ for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {\r
+ final PhylogenyNode child_node = node.getChildNode( i );\r
+ final Color child_color = getBranchColorValue( child_node );\r
+ if ( child_color != null ) {\r
+ ++n;\r
+ red += child_color.getRed();\r
+ green += child_color.getGreen();\r
+ blue += child_color.getBlue();\r
+ }\r
+ }\r
+ setBranchColorValue( node,\r
+ new Color( ForesterUtil.roundToInt( red / n ),\r
+ ForesterUtil.roundToInt( green / n ),\r
+ ForesterUtil.roundToInt( blue / n ) ) );\r
+ }\r
+ }\r
+ }\r
+\r
+ public static final void preOrderReId( final Phylogeny phy ) {\r
+ if ( phy.isEmpty() ) {\r
+ return;\r
+ }\r
+ phy.setIdToNodeMap( null );\r
+ long i = PhylogenyNode.getNodeCount();\r
+ for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) {\r
+ it.next().setId( i++ );\r
+ }\r
+ PhylogenyNode.setNodeCount( i );\r
+ }\r
+\r
+ public final static Phylogeny[] readPhylogenies( final PhylogenyParser parser, final File file ) throws IOException {\r
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();\r
+ final Phylogeny[] trees = factory.create( file, parser );\r
+ if ( ( trees == null ) || ( trees.length == 0 ) ) {\r
+ throw new PhylogenyParserException( "Unable to parse phylogeny from file: " + file );\r
+ }\r
+ return trees;\r
+ }\r
+\r
+ public final static Phylogeny[] readPhylogenies( final PhylogenyParser parser, final List<File> files )\r
+ throws IOException {\r
+ final List<Phylogeny> tree_list = new ArrayList<Phylogeny>();\r
+ for( final File file : files ) {\r
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();\r
+ final Phylogeny[] trees = factory.create( file, parser );\r
+ if ( ( trees == null ) || ( trees.length == 0 ) ) {\r
+ throw new PhylogenyParserException( "Unable to parse phylogeny from file: " + file );\r
+ }\r
+ tree_list.addAll( Arrays.asList( trees ) );\r
+ }\r
+ return tree_list.toArray( new Phylogeny[ tree_list.size() ] );\r
+ }\r
+\r
+ public static void removeNode( final PhylogenyNode remove_me, final Phylogeny phylogeny ) {\r
+ if ( remove_me.isRoot() ) {\r
+ if ( remove_me.getNumberOfDescendants() == 1 ) {\r
+ final PhylogenyNode desc = remove_me.getDescendants().get( 0 );\r
+ desc.setDistanceToParent( addPhylogenyDistances( remove_me.getDistanceToParent(),\r
+ desc.getDistanceToParent() ) );\r
+ desc.setParent( null );\r
+ phylogeny.setRoot( desc );\r
+ phylogeny.clearHashIdToNodeMap();\r
+ }\r
+ else {\r
+ throw new IllegalArgumentException( "attempt to remove a root node with more than one descendants" );\r
+ }\r
+ }\r
+ else if ( remove_me.isExternal() ) {\r
+ phylogeny.deleteSubtree( remove_me, false );\r
+ phylogeny.clearHashIdToNodeMap();\r
+ phylogeny.externalNodesHaveChanged();\r
+ }\r
+ else {\r
+ final PhylogenyNode parent = remove_me.getParent();\r
+ final List<PhylogenyNode> descs = remove_me.getDescendants();\r
+ parent.removeChildNode( remove_me );\r
+ for( final PhylogenyNode desc : descs ) {\r
+ parent.addAsChild( desc );\r
+ desc.setDistanceToParent( addPhylogenyDistances( remove_me.getDistanceToParent(),\r
+ desc.getDistanceToParent() ) );\r
+ }\r
+ remove_me.setParent( null );\r
+ phylogeny.clearHashIdToNodeMap();\r
+ phylogeny.externalNodesHaveChanged();\r
+ }\r
+ }\r
+\r
+ public static List<PhylogenyNode> searchData( final String query,\r
+ final Phylogeny phy,\r
+ final boolean case_sensitive,\r
+ final boolean partial,\r
+ final boolean search_domains ) {\r
+ final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();\r
+ if ( phy.isEmpty() || ( query == null ) ) {\r
+ return nodes;\r
+ }\r
+ if ( ForesterUtil.isEmpty( query ) ) {\r
+ return nodes;\r
+ }\r
+ for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {\r
+ final PhylogenyNode node = iter.next();\r
+ boolean match = false;\r
+ if ( match( node.getName(), query, case_sensitive, partial ) ) {\r
+ match = true;\r
+ }\r
+ else if ( node.getNodeData().isHasTaxonomy()\r
+ && match( node.getNodeData().getTaxonomy().getTaxonomyCode(), query, case_sensitive, partial ) ) {\r
+ match = true;\r
+ }\r
+ else if ( node.getNodeData().isHasTaxonomy()\r
+ && match( node.getNodeData().getTaxonomy().getCommonName(), query, case_sensitive, partial ) ) {\r
+ match = true;\r
+ }\r
+ else if ( node.getNodeData().isHasTaxonomy()\r
+ && match( node.getNodeData().getTaxonomy().getScientificName(), query, case_sensitive, partial ) ) {\r
+ match = true;\r
+ }\r
+ else if ( node.getNodeData().isHasTaxonomy()\r
+ && ( node.getNodeData().getTaxonomy().getIdentifier() != null )\r
+ && match( node.getNodeData().getTaxonomy().getIdentifier().getValue(),\r
+ query,\r
+ case_sensitive,\r
+ partial ) ) {\r
+ match = true;\r
+ }\r
+ else if ( node.getNodeData().isHasTaxonomy() && !node.getNodeData().getTaxonomy().getSynonyms().isEmpty() ) {\r
+ final List<String> syns = node.getNodeData().getTaxonomy().getSynonyms();\r
+ I: for( final String syn : syns ) {\r
+ if ( match( syn, query, case_sensitive, partial ) ) {\r
+ match = true;\r
+ break I;\r
+ }\r
+ }\r
+ }\r
+ if ( !match && node.getNodeData().isHasSequence()\r
+ && match( node.getNodeData().getSequence().getName(), query, case_sensitive, partial ) ) {\r
+ match = true;\r
+ }\r
+ if ( !match && node.getNodeData().isHasSequence()\r
+ && match( node.getNodeData().getSequence().getGeneName(), query, case_sensitive, partial ) ) {\r
+ match = true;\r
+ }\r
+ if ( !match && node.getNodeData().isHasSequence()\r
+ && match( node.getNodeData().getSequence().getSymbol(), query, case_sensitive, partial ) ) {\r
+ match = true;\r
+ }\r
+ if ( !match\r
+ && node.getNodeData().isHasSequence()\r
+ && ( node.getNodeData().getSequence().getAccession() != null )\r
+ && match( node.getNodeData().getSequence().getAccession().getValue(),\r
+ query,\r
+ case_sensitive,\r
+ partial ) ) {\r
+ match = true;\r
+ }\r
+ if ( search_domains && !match && node.getNodeData().isHasSequence()\r
+ && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {\r
+ final DomainArchitecture da = node.getNodeData().getSequence().getDomainArchitecture();\r
+ I: for( int i = 0; i < da.getNumberOfDomains(); ++i ) {\r
+ if ( match( da.getDomain( i ).getName(), query, case_sensitive, partial ) ) {\r
+ match = true;\r
+ break I;\r
+ }\r
+ }\r
+ }\r
+ //\r
+ if ( !match && node.getNodeData().isHasSequence()\r
+ && ( node.getNodeData().getSequence().getAnnotations() != null ) ) {\r
+ for( final Annotation ann : node.getNodeData().getSequence().getAnnotations() ) {\r
+ if ( match( ann.getDesc(), query, case_sensitive, partial ) ) {\r
+ match = true;\r
+ break;\r
+ }\r
+ if ( match( ann.getRef(), query, case_sensitive, partial ) ) {\r
+ match = true;\r
+ break;\r
+ }\r
+ }\r
+ }\r
+ if ( !match && node.getNodeData().isHasSequence()\r
+ && ( node.getNodeData().getSequence().getCrossReferences() != null ) ) {\r
+ for( final Accession x : node.getNodeData().getSequence().getCrossReferences() ) {\r
+ if ( match( x.getComment(), query, case_sensitive, partial ) ) {\r
+ match = true;\r
+ break;\r
+ }\r
+ if ( match( x.getSource(), query, case_sensitive, partial ) ) {\r
+ match = true;\r
+ break;\r
+ }\r
+ if ( match( x.getValue(), query, case_sensitive, partial ) ) {\r
+ match = true;\r
+ break;\r
+ }\r
+ }\r
+ }\r
+ //\r
+ if ( !match && ( node.getNodeData().getBinaryCharacters() != null ) ) {\r
+ Iterator<String> it = node.getNodeData().getBinaryCharacters().getPresentCharacters().iterator();\r
+ I: while ( it.hasNext() ) {\r
+ if ( match( it.next(), query, case_sensitive, partial ) ) {\r
+ match = true;\r
+ break I;\r
+ }\r
+ }\r
+ it = node.getNodeData().getBinaryCharacters().getGainedCharacters().iterator();\r
+ I: while ( it.hasNext() ) {\r
+ if ( match( it.next(), query, case_sensitive, partial ) ) {\r
+ match = true;\r
+ break I;\r
+ }\r
+ }\r
+ }\r
+ if ( match ) {\r
+ nodes.add( node );\r
+ }\r
+ }\r
+ return nodes;\r
+ }\r
+\r
+ public static List<PhylogenyNode> searchDataLogicalAnd( final String[] queries,\r
+ final Phylogeny phy,\r
+ final boolean case_sensitive,\r
+ final boolean partial,\r
+ final boolean search_domains ) {\r
+ final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();\r
+ if ( phy.isEmpty() || ( queries == null ) || ( queries.length < 1 ) ) {\r
+ return nodes;\r
+ }\r
+ for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {\r
+ final PhylogenyNode node = iter.next();\r
+ boolean all_matched = true;\r
+ for( final String query : queries ) {\r
+ boolean match = false;\r
+ if ( ForesterUtil.isEmpty( query ) ) {\r
+ continue;\r
+ }\r
+ if ( match( node.getName(), query, case_sensitive, partial ) ) {\r
+ match = true;\r
+ }\r
+ else if ( node.getNodeData().isHasTaxonomy()\r
+ && match( node.getNodeData().getTaxonomy().getTaxonomyCode(), query, case_sensitive, partial ) ) {\r
+ match = true;\r
+ }\r
+ else if ( node.getNodeData().isHasTaxonomy()\r
+ && match( node.getNodeData().getTaxonomy().getCommonName(), query, case_sensitive, partial ) ) {\r
+ match = true;\r
+ }\r
+ else if ( node.getNodeData().isHasTaxonomy()\r
+ && match( node.getNodeData().getTaxonomy().getScientificName(), query, case_sensitive, partial ) ) {\r
+ match = true;\r
+ }\r
+ else if ( node.getNodeData().isHasTaxonomy()\r
+ && ( node.getNodeData().getTaxonomy().getIdentifier() != null )\r
+ && match( node.getNodeData().getTaxonomy().getIdentifier().getValue(),\r
+ query,\r
+ case_sensitive,\r
+ partial ) ) {\r
+ match = true;\r
+ }\r
+ else if ( node.getNodeData().isHasTaxonomy()\r
+ && !node.getNodeData().getTaxonomy().getSynonyms().isEmpty() ) {\r
+ final List<String> syns = node.getNodeData().getTaxonomy().getSynonyms();\r
+ I: for( final String syn : syns ) {\r
+ if ( match( syn, query, case_sensitive, partial ) ) {\r
+ match = true;\r
+ break I;\r
+ }\r
+ }\r
+ }\r
+ if ( !match && node.getNodeData().isHasSequence()\r
+ && match( node.getNodeData().getSequence().getName(), query, case_sensitive, partial ) ) {\r
+ match = true;\r
+ }\r
+ if ( !match && node.getNodeData().isHasSequence()\r
+ && match( node.getNodeData().getSequence().getGeneName(), query, case_sensitive, partial ) ) {\r
+ match = true;\r
+ }\r
+ if ( !match && node.getNodeData().isHasSequence()\r
+ && match( node.getNodeData().getSequence().getSymbol(), query, case_sensitive, partial ) ) {\r
+ match = true;\r
+ }\r
+ if ( !match\r
+ && node.getNodeData().isHasSequence()\r
+ && ( node.getNodeData().getSequence().getAccession() != null )\r
+ && match( node.getNodeData().getSequence().getAccession().getValue(),\r
+ query,\r
+ case_sensitive,\r
+ partial ) ) {\r
+ match = true;\r
+ }\r
+ if ( search_domains && !match && node.getNodeData().isHasSequence()\r
+ && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {\r
+ final DomainArchitecture da = node.getNodeData().getSequence().getDomainArchitecture();\r
+ I: for( int i = 0; i < da.getNumberOfDomains(); ++i ) {\r
+ if ( match( da.getDomain( i ).getName(), query, case_sensitive, partial ) ) {\r
+ match = true;\r
+ break I;\r
+ }\r
+ }\r
+ }\r
+ //\r
+ if ( !match && node.getNodeData().isHasSequence()\r
+ && ( node.getNodeData().getSequence().getAnnotations() != null ) ) {\r
+ for( final Annotation ann : node.getNodeData().getSequence().getAnnotations() ) {\r
+ if ( match( ann.getDesc(), query, case_sensitive, partial ) ) {\r
+ match = true;\r
+ break;\r
+ }\r
+ if ( match( ann.getRef(), query, case_sensitive, partial ) ) {\r
+ match = true;\r
+ break;\r
+ }\r
+ }\r
+ }\r
+ if ( !match && node.getNodeData().isHasSequence()\r
+ && ( node.getNodeData().getSequence().getCrossReferences() != null ) ) {\r
+ for( final Accession x : node.getNodeData().getSequence().getCrossReferences() ) {\r
+ if ( match( x.getComment(), query, case_sensitive, partial ) ) {\r
+ match = true;\r
+ break;\r
+ }\r
+ if ( match( x.getSource(), query, case_sensitive, partial ) ) {\r
+ match = true;\r
+ break;\r
+ }\r
+ if ( match( x.getValue(), query, case_sensitive, partial ) ) {\r
+ match = true;\r
+ break;\r
+ }\r
+ }\r
+ }\r
+ //\r
+ if ( !match && ( node.getNodeData().getBinaryCharacters() != null ) ) {\r
+ Iterator<String> it = node.getNodeData().getBinaryCharacters().getPresentCharacters().iterator();\r
+ I: while ( it.hasNext() ) {\r
+ if ( match( it.next(), query, case_sensitive, partial ) ) {\r
+ match = true;\r
+ break I;\r
+ }\r
+ }\r
+ it = node.getNodeData().getBinaryCharacters().getGainedCharacters().iterator();\r
+ I: while ( it.hasNext() ) {\r
+ if ( match( it.next(), query, case_sensitive, partial ) ) {\r
+ match = true;\r
+ break I;\r
+ }\r
+ }\r
+ }\r
+ if ( !match ) {\r
+ all_matched = false;\r
+ break;\r
+ }\r
+ }\r
+ if ( all_matched ) {\r
+ nodes.add( node );\r
+ }\r
+ }\r
+ return nodes;\r
+ }\r
+\r
+ public static void setAllIndicatorsToZero( final Phylogeny phy ) {\r
+ for( final PhylogenyNodeIterator it = phy.iteratorPostorder(); it.hasNext(); ) {\r
+ it.next().setIndicator( ( byte ) 0 );\r
+ }\r
+ }\r
+\r
+ /**\r
+ * Convenience method.\r
+ * Sets value for the first confidence value (created if not present, values overwritten otherwise). \r
+ */\r
+ public static void setBootstrapConfidence( final PhylogenyNode node, final double bootstrap_confidence_value ) {\r
+ setConfidence( node, bootstrap_confidence_value, "bootstrap" );\r
+ }\r
+\r
+ public static void setBranchColorValue( final PhylogenyNode node, final Color color ) {\r
+ if ( node.getBranchData().getBranchColor() == null ) {\r
+ node.getBranchData().setBranchColor( new BranchColor() );\r
+ }\r
+ node.getBranchData().getBranchColor().setValue( color );\r
+ }\r
+\r
+ /**\r
+ * Convenience method\r
+ */\r
+ public static void setBranchWidthValue( final PhylogenyNode node, final double branch_width_value ) {\r
+ node.getBranchData().setBranchWidth( new BranchWidth( branch_width_value ) );\r
+ }\r
+\r
+ /**\r
+ * Convenience method.\r
+ * Sets value for the first confidence value (created if not present, values overwritten otherwise). \r
+ */\r
+ public static void setConfidence( final PhylogenyNode node, final double confidence_value ) {\r
+ setConfidence( node, confidence_value, "" );\r
+ }\r
+\r
+ /**\r
+ * Convenience method.\r
+ * Sets value for the first confidence value (created if not present, values overwritten otherwise). \r
+ */\r
+ public static void setConfidence( final PhylogenyNode node, final double confidence_value, final String type ) {\r
+ Confidence c = null;\r
+ if ( node.getBranchData().getNumberOfConfidences() > 0 ) {\r
+ c = node.getBranchData().getConfidence( 0 );\r
+ }\r
+ else {\r
+ c = new Confidence();\r
+ node.getBranchData().addConfidence( c );\r
+ }\r
+ c.setType( type );\r
+ c.setValue( confidence_value );\r
+ }\r
+\r
+ public static void setScientificName( final PhylogenyNode node, final String scientific_name ) {\r
+ if ( !node.getNodeData().isHasTaxonomy() ) {\r
+ node.getNodeData().setTaxonomy( new Taxonomy() );\r
+ }\r
+ node.getNodeData().getTaxonomy().setScientificName( scientific_name );\r
+ }\r
+\r
+ /**\r
+ * Convenience method to set the taxonomy code of a phylogeny node.\r
+ * \r
+ * \r
+ * @param node\r
+ * @param taxonomy_code\r
+ * @throws PhyloXmlDataFormatException \r
+ */\r
+ public static void setTaxonomyCode( final PhylogenyNode node, final String taxonomy_code )\r
+ throws PhyloXmlDataFormatException {\r
+ if ( !node.getNodeData().isHasTaxonomy() ) {\r
+ node.getNodeData().setTaxonomy( new Taxonomy() );\r
+ }\r
+ node.getNodeData().getTaxonomy().setTaxonomyCode( taxonomy_code );\r
+ }\r
+\r
+ final static public void sortNodeDescendents( final PhylogenyNode node, final DESCENDANT_SORT_PRIORITY pri ) {\r
+ class PhylogenyNodeSortTaxonomyPriority implements Comparator<PhylogenyNode> {\r
+\r
+ @Override\r
+ public int compare( final PhylogenyNode n1, final PhylogenyNode n2 ) {\r
+ if ( n1.getNodeData().isHasTaxonomy() && n2.getNodeData().isHasTaxonomy() ) {\r
+ if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getScientificName() ) )\r
+ && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getScientificName() ) ) ) {\r
+ return n1.getNodeData().getTaxonomy().getScientificName().toLowerCase()\r
+ .compareTo( n2.getNodeData().getTaxonomy().getScientificName().toLowerCase() );\r
+ }\r
+ if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getTaxonomyCode() ) )\r
+ && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) {\r
+ return n1.getNodeData().getTaxonomy().getTaxonomyCode()\r
+ .compareTo( n2.getNodeData().getTaxonomy().getTaxonomyCode() );\r
+ }\r
+ if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getCommonName() ) )\r
+ && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getCommonName() ) ) ) {\r
+ return n1.getNodeData().getTaxonomy().getCommonName().toLowerCase()\r
+ .compareTo( n2.getNodeData().getTaxonomy().getCommonName().toLowerCase() );\r
+ }\r
+ }\r
+ if ( n1.getNodeData().isHasSequence() && n2.getNodeData().isHasSequence() ) {\r
+ if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getName() ) )\r
+ && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getName() ) ) ) {\r
+ return n1.getNodeData().getSequence().getName().toLowerCase()\r
+ .compareTo( n2.getNodeData().getSequence().getName().toLowerCase() );\r
+ }\r
+ if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getSymbol() ) )\r
+ && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getSymbol() ) ) ) {\r
+ return n1.getNodeData().getSequence().getSymbol()\r
+ .compareTo( n2.getNodeData().getSequence().getSymbol() );\r
+ }\r
+ if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getGeneName() ) )\r
+ && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getGeneName() ) ) ) {\r
+ return n1.getNodeData().getSequence().getGeneName()\r
+ .compareTo( n2.getNodeData().getSequence().getGeneName() );\r
+ }\r
+ if ( ( n1.getNodeData().getSequence().getAccession() != null )\r
+ && ( n2.getNodeData().getSequence().getAccession() != null )\r
+ && !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getAccession().getValue() )\r
+ && !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getAccession().getValue() ) ) {\r
+ return n1.getNodeData().getSequence().getAccession().getValue()\r
+ .compareTo( n2.getNodeData().getSequence().getAccession().getValue() );\r
+ }\r
+ }\r
+ if ( ( !ForesterUtil.isEmpty( n1.getName() ) ) && ( !ForesterUtil.isEmpty( n2.getName() ) ) ) {\r
+ return n1.getName().toLowerCase().compareTo( n2.getName().toLowerCase() );\r
+ }\r
+ return 0;\r
+ }\r
+ }\r
+ class PhylogenyNodeSortSequencePriority implements Comparator<PhylogenyNode> {\r
+\r
+ @Override\r
+ public int compare( final PhylogenyNode n1, final PhylogenyNode n2 ) {\r
+ if ( n1.getNodeData().isHasSequence() && n2.getNodeData().isHasSequence() ) {\r
+ if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getName() ) )\r
+ && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getName() ) ) ) {\r
+ return n1.getNodeData().getSequence().getName().toLowerCase()\r
+ .compareTo( n2.getNodeData().getSequence().getName().toLowerCase() );\r
+ }\r
+ if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getSymbol() ) )\r
+ && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getSymbol() ) ) ) {\r
+ return n1.getNodeData().getSequence().getSymbol()\r
+ .compareTo( n2.getNodeData().getSequence().getSymbol() );\r
+ }\r
+ if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getGeneName() ) )\r
+ && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getGeneName() ) ) ) {\r
+ return n1.getNodeData().getSequence().getGeneName()\r
+ .compareTo( n2.getNodeData().getSequence().getGeneName() );\r
+ }\r
+ if ( ( n1.getNodeData().getSequence().getAccession() != null )\r
+ && ( n2.getNodeData().getSequence().getAccession() != null )\r
+ && !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getAccession().getValue() )\r
+ && !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getAccession().getValue() ) ) {\r
+ return n1.getNodeData().getSequence().getAccession().getValue()\r
+ .compareTo( n2.getNodeData().getSequence().getAccession().getValue() );\r
+ }\r
+ }\r
+ if ( n1.getNodeData().isHasTaxonomy() && n2.getNodeData().isHasTaxonomy() ) {\r
+ if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getScientificName() ) )\r
+ && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getScientificName() ) ) ) {\r
+ return n1.getNodeData().getTaxonomy().getScientificName().toLowerCase()\r
+ .compareTo( n2.getNodeData().getTaxonomy().getScientificName().toLowerCase() );\r
+ }\r
+ if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getTaxonomyCode() ) )\r
+ && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) {\r
+ return n1.getNodeData().getTaxonomy().getTaxonomyCode()\r
+ .compareTo( n2.getNodeData().getTaxonomy().getTaxonomyCode() );\r
+ }\r
+ if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getCommonName() ) )\r
+ && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getCommonName() ) ) ) {\r
+ return n1.getNodeData().getTaxonomy().getCommonName().toLowerCase()\r
+ .compareTo( n2.getNodeData().getTaxonomy().getCommonName().toLowerCase() );\r
+ }\r
+ }\r
+ if ( ( !ForesterUtil.isEmpty( n1.getName() ) ) && ( !ForesterUtil.isEmpty( n2.getName() ) ) ) {\r
+ return n1.getName().toLowerCase().compareTo( n2.getName().toLowerCase() );\r
+ }\r
+ return 0;\r
+ }\r
+ }\r
+ class PhylogenyNodeSortNodeNamePriority implements Comparator<PhylogenyNode> {\r
+\r
+ @Override\r
+ public int compare( final PhylogenyNode n1, final PhylogenyNode n2 ) {\r
+ if ( ( !ForesterUtil.isEmpty( n1.getName() ) ) && ( !ForesterUtil.isEmpty( n2.getName() ) ) ) {\r
+ return n1.getName().toLowerCase().compareTo( n2.getName().toLowerCase() );\r
+ }\r
+ if ( n1.getNodeData().isHasTaxonomy() && n2.getNodeData().isHasTaxonomy() ) {\r
+ if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getScientificName() ) )\r
+ && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getScientificName() ) ) ) {\r
+ return n1.getNodeData().getTaxonomy().getScientificName().toLowerCase()\r
+ .compareTo( n2.getNodeData().getTaxonomy().getScientificName().toLowerCase() );\r
+ }\r
+ if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getTaxonomyCode() ) )\r
+ && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) {\r
+ return n1.getNodeData().getTaxonomy().getTaxonomyCode()\r
+ .compareTo( n2.getNodeData().getTaxonomy().getTaxonomyCode() );\r
+ }\r
+ if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getCommonName() ) )\r
+ && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getCommonName() ) ) ) {\r
+ return n1.getNodeData().getTaxonomy().getCommonName().toLowerCase()\r
+ .compareTo( n2.getNodeData().getTaxonomy().getCommonName().toLowerCase() );\r
+ }\r
+ }\r
+ if ( n1.getNodeData().isHasSequence() && n2.getNodeData().isHasSequence() ) {\r
+ if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getName() ) )\r
+ && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getName() ) ) ) {\r
+ return n1.getNodeData().getSequence().getName().toLowerCase()\r
+ .compareTo( n2.getNodeData().getSequence().getName().toLowerCase() );\r
+ }\r
+ if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getSymbol() ) )\r
+ && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getSymbol() ) ) ) {\r
+ return n1.getNodeData().getSequence().getSymbol()\r
+ .compareTo( n2.getNodeData().getSequence().getSymbol() );\r
+ }\r
+ if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getGeneName() ) )\r
+ && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getGeneName() ) ) ) {\r
+ return n1.getNodeData().getSequence().getGeneName()\r
+ .compareTo( n2.getNodeData().getSequence().getGeneName() );\r
+ }\r
+ if ( ( n1.getNodeData().getSequence().getAccession() != null )\r
+ && ( n2.getNodeData().getSequence().getAccession() != null )\r
+ && !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getAccession().getValue() )\r
+ && !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getAccession().getValue() ) ) {\r
+ return n1.getNodeData().getSequence().getAccession().getValue()\r
+ .compareTo( n2.getNodeData().getSequence().getAccession().getValue() );\r
+ }\r
+ }\r
+ return 0;\r
+ }\r
+ }\r
+ Comparator<PhylogenyNode> c;\r
+ switch ( pri ) {\r
+ case SEQUENCE:\r
+ c = new PhylogenyNodeSortSequencePriority();\r
+ break;\r
+ case NODE_NAME:\r
+ c = new PhylogenyNodeSortNodeNamePriority();\r
+ break;\r
+ default:\r
+ c = new PhylogenyNodeSortTaxonomyPriority();\r
+ }\r
+ final List<PhylogenyNode> descs = node.getDescendants();\r
+ Collections.sort( descs, c );\r
+ int i = 0;\r
+ for( final PhylogenyNode desc : descs ) {\r
+ node.setChildNode( i++, desc );\r
+ }\r
+ }\r
+\r
+ /**\r
+ * Removes from Phylogeny to_be_stripped all external Nodes which are\r
+ * associated with a species NOT found in Phylogeny reference.\r
+ * \r
+ * @param reference\r
+ * a reference Phylogeny\r
+ * @param to_be_stripped\r
+ * Phylogeny to be stripped\r
+ * @return nodes removed from to_be_stripped\r
+ */\r
+ public static List<PhylogenyNode> taxonomyBasedDeletionOfExternalNodes( final Phylogeny reference,\r
+ final Phylogeny to_be_stripped ) {\r
+ final Set<String> ref_ext_taxo = new HashSet<String>();\r
+ for( final PhylogenyNodeIterator it = reference.iteratorExternalForward(); it.hasNext(); ) {\r
+ final PhylogenyNode n = it.next();\r
+ if ( !n.getNodeData().isHasTaxonomy() ) {\r
+ throw new IllegalArgumentException( "no taxonomic data in node: " + n );\r
+ }\r
+ if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {\r
+ ref_ext_taxo.add( n.getNodeData().getTaxonomy().getScientificName() );\r
+ }\r
+ if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {\r
+ ref_ext_taxo.add( n.getNodeData().getTaxonomy().getTaxonomyCode() );\r
+ }\r
+ if ( ( n.getNodeData().getTaxonomy().getIdentifier() != null )\r
+ && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getIdentifier().getValue() ) ) {\r
+ ref_ext_taxo.add( n.getNodeData().getTaxonomy().getIdentifier().getValuePlusProvider() );\r
+ }\r
+ }\r
+ final ArrayList<PhylogenyNode> nodes_to_delete = new ArrayList<PhylogenyNode>();\r
+ for( final PhylogenyNodeIterator it = to_be_stripped.iteratorExternalForward(); it.hasNext(); ) {\r
+ final PhylogenyNode n = it.next();\r
+ if ( !n.getNodeData().isHasTaxonomy() ) {\r
+ nodes_to_delete.add( n );\r
+ }\r
+ else if ( !( ref_ext_taxo.contains( n.getNodeData().getTaxonomy().getScientificName() ) )\r
+ && !( ref_ext_taxo.contains( n.getNodeData().getTaxonomy().getTaxonomyCode() ) )\r
+ && !( ( n.getNodeData().getTaxonomy().getIdentifier() != null ) && ref_ext_taxo.contains( n\r
+ .getNodeData().getTaxonomy().getIdentifier().getValuePlusProvider() ) ) ) {\r
+ nodes_to_delete.add( n );\r
+ }\r
+ }\r
+ for( final PhylogenyNode n : nodes_to_delete ) {\r
+ to_be_stripped.deleteSubtree( n, true );\r
+ }\r
+ to_be_stripped.clearHashIdToNodeMap();\r
+ to_be_stripped.externalNodesHaveChanged();\r
+ return nodes_to_delete;\r
+ }\r
+\r
+ final static public void transferInternalNamesToBootstrapSupport( final Phylogeny phy ) {\r
+ final PhylogenyNodeIterator it = phy.iteratorPostorder();\r
+ while ( it.hasNext() ) {\r
+ final PhylogenyNode n = it.next();\r
+ if ( !n.isExternal() && !ForesterUtil.isEmpty( n.getName() ) ) {\r
+ double value = -1;\r
+ try {\r
+ value = Double.parseDouble( n.getName() );\r
+ }\r
+ catch ( final NumberFormatException e ) {\r
+ throw new IllegalArgumentException( "failed to parse number from [" + n.getName() + "]: "\r
+ + e.getLocalizedMessage() );\r
+ }\r
+ if ( value >= 0.0 ) {\r
+ n.getBranchData().addConfidence( new Confidence( value, "bootstrap" ) );\r
+ n.setName( "" );\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ final static public boolean isInternalNamesLookLikeConfidences( final Phylogeny phy ) {\r
+ final PhylogenyNodeIterator it = phy.iteratorPostorder();\r
+ while ( it.hasNext() ) {\r
+ final PhylogenyNode n = it.next();\r
+ if ( !n.isExternal() && !n.isRoot() ) {\r
+ if ( !ForesterUtil.isEmpty( n.getName() ) ) {\r
+ double value = -1;\r
+ try {\r
+ value = Double.parseDouble( n.getName() );\r
+ }\r
+ catch ( final NumberFormatException e ) {\r
+ return false;\r
+ }\r
+ if ( ( value < 0.0 ) || ( value > 100 ) ) {\r
+ return false;\r
+ }\r
+ }\r
+ }\r
+ }\r
+ return true;\r
+ }\r
+\r
+ final static public void transferInternalNodeNamesToConfidence( final Phylogeny phy, final String confidence_type ) {\r
+ final PhylogenyNodeIterator it = phy.iteratorPostorder();\r
+ while ( it.hasNext() ) {\r
+ transferInternalNodeNameToConfidence( confidence_type, it.next() );\r
+ }\r
+ }\r
+\r
+ private static void transferInternalNodeNameToConfidence( final String confidence_type, final PhylogenyNode n ) {\r
+ if ( !n.isExternal() && !n.getBranchData().isHasConfidences() ) {\r
+ if ( !ForesterUtil.isEmpty( n.getName() ) ) {\r
+ double d = -1.0;\r
+ try {\r
+ d = Double.parseDouble( n.getName() );\r
+ }\r
+ catch ( final Exception e ) {\r
+ d = -1.0;\r
+ }\r
+ if ( d >= 0.0 ) {\r
+ n.getBranchData().addConfidence( new Confidence( d, confidence_type ) );\r
+ n.setName( "" );\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ final static public void transferNodeNameToField( final Phylogeny phy,\r
+ final PhylogenyNodeField field,\r
+ final boolean external_only ) throws PhyloXmlDataFormatException {\r
+ final PhylogenyNodeIterator it = phy.iteratorPostorder();\r
+ while ( it.hasNext() ) {\r
+ final PhylogenyNode n = it.next();\r
+ if ( external_only && n.isInternal() ) {\r
+ continue;\r
+ }\r
+ final String name = n.getName().trim();\r
+ if ( !ForesterUtil.isEmpty( name ) ) {\r
+ switch ( field ) {\r
+ case TAXONOMY_CODE:\r
+ n.setName( "" );\r
+ setTaxonomyCode( n, name );\r
+ break;\r
+ case TAXONOMY_SCIENTIFIC_NAME:\r
+ n.setName( "" );\r
+ if ( !n.getNodeData().isHasTaxonomy() ) {\r
+ n.getNodeData().setTaxonomy( new Taxonomy() );\r
+ }\r
+ n.getNodeData().getTaxonomy().setScientificName( name );\r
+ break;\r
+ case TAXONOMY_COMMON_NAME:\r
+ n.setName( "" );\r
+ if ( !n.getNodeData().isHasTaxonomy() ) {\r
+ n.getNodeData().setTaxonomy( new Taxonomy() );\r
+ }\r
+ n.getNodeData().getTaxonomy().setCommonName( name );\r
+ break;\r
+ case SEQUENCE_SYMBOL:\r
+ n.setName( "" );\r
+ if ( !n.getNodeData().isHasSequence() ) {\r
+ n.getNodeData().setSequence( new Sequence() );\r
+ }\r
+ n.getNodeData().getSequence().setSymbol( name );\r
+ break;\r
+ case SEQUENCE_NAME:\r
+ n.setName( "" );\r
+ if ( !n.getNodeData().isHasSequence() ) {\r
+ n.getNodeData().setSequence( new Sequence() );\r
+ }\r
+ n.getNodeData().getSequence().setName( name );\r
+ break;\r
+ case TAXONOMY_ID_UNIPROT_1: {\r
+ if ( !n.getNodeData().isHasTaxonomy() ) {\r
+ n.getNodeData().setTaxonomy( new Taxonomy() );\r
+ }\r
+ String id = name;\r
+ final int i = name.indexOf( '_' );\r
+ if ( i > 0 ) {\r
+ id = name.substring( 0, i );\r
+ }\r
+ else {\r
+ n.setName( "" );\r
+ }\r
+ n.getNodeData().getTaxonomy()\r
+ .setIdentifier( new Identifier( id, PhyloXmlUtil.UNIPROT_TAX_PROVIDER ) );\r
+ break;\r
+ }\r
+ case TAXONOMY_ID_UNIPROT_2: {\r
+ if ( !n.getNodeData().isHasTaxonomy() ) {\r
+ n.getNodeData().setTaxonomy( new Taxonomy() );\r
+ }\r
+ String id = name;\r
+ final int i = name.indexOf( '_' );\r
+ if ( i > 0 ) {\r
+ id = name.substring( i + 1, name.length() );\r
+ }\r
+ else {\r
+ n.setName( "" );\r
+ }\r
+ n.getNodeData().getTaxonomy()\r
+ .setIdentifier( new Identifier( id, PhyloXmlUtil.UNIPROT_TAX_PROVIDER ) );\r
+ break;\r
+ }\r
+ case TAXONOMY_ID: {\r
+ if ( !n.getNodeData().isHasTaxonomy() ) {\r
+ n.getNodeData().setTaxonomy( new Taxonomy() );\r
+ }\r
+ n.getNodeData().getTaxonomy().setIdentifier( new Identifier( name ) );\r
+ break;\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ static double addPhylogenyDistances( final double a, final double b ) {\r
+ if ( ( a >= 0.0 ) && ( b >= 0.0 ) ) {\r
+ return a + b;\r
+ }\r
+ else if ( a >= 0.0 ) {\r
+ return a;\r
+ }\r
+ else if ( b >= 0.0 ) {\r
+ return b;\r
+ }\r
+ return PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT;\r
+ }\r
+\r
+ static double calculateDistanceToAncestor( final PhylogenyNode anc, PhylogenyNode desc ) {\r
+ double d = 0;\r
+ boolean all_default = true;\r
+ while ( anc != desc ) {\r
+ if ( desc.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {\r
+ d += desc.getDistanceToParent();\r
+ if ( all_default ) {\r
+ all_default = false;\r
+ }\r
+ }\r
+ desc = desc.getParent();\r
+ }\r
+ if ( all_default ) {\r
+ return PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT;\r
+ }\r
+ return d;\r
+ }\r
+\r
+ /**\r
+ * Deep copies the phylogeny originating from this node.\r
+ */\r
+ static PhylogenyNode copySubTree( final PhylogenyNode source ) {\r
+ if ( source == null ) {\r
+ return null;\r
+ }\r
+ else {\r
+ final PhylogenyNode newnode = source.copyNodeData();\r
+ if ( !source.isExternal() ) {\r
+ for( int i = 0; i < source.getNumberOfDescendants(); ++i ) {\r
+ newnode.setChildNode( i, PhylogenyMethods.copySubTree( source.getChildNode( i ) ) );\r
+ }\r
+ }\r
+ return newnode;\r
+ }\r
+ }\r
+\r
+ /**\r
+ * Shallow copies the phylogeny originating from this node.\r
+ */\r
+ static PhylogenyNode copySubTreeShallow( final PhylogenyNode source ) {\r
+ if ( source == null ) {\r
+ return null;\r
+ }\r
+ else {\r
+ final PhylogenyNode newnode = source.copyNodeDataShallow();\r
+ if ( !source.isExternal() ) {\r
+ for( int i = 0; i < source.getNumberOfDescendants(); ++i ) {\r
+ newnode.setChildNode( i, PhylogenyMethods.copySubTreeShallow( source.getChildNode( i ) ) );\r
+ }\r
+ }\r
+ return newnode;\r
+ }\r
+ }\r
+\r
+ private final static List<PhylogenyNode> divideIntoSubTreesHelper( final PhylogenyNode node,\r
+ final double min_distance_to_root ) {\r
+ final List<PhylogenyNode> l = new ArrayList<PhylogenyNode>();\r
+ final PhylogenyNode r = moveTowardsRoot( node, min_distance_to_root );\r
+ for( final PhylogenyNode ext : r.getAllExternalDescendants() ) {\r
+ if ( ext.getIndicator() != 0 ) {\r
+ throw new RuntimeException( "this should not have happened" );\r
+ }\r
+ ext.setIndicator( ( byte ) 1 );\r
+ l.add( ext );\r
+ }\r
+ return l;\r
+ }\r
+\r
+ /**\r
+ * Calculates the distance between PhylogenyNodes n1 and n2.\r
+ * PRECONDITION: n1 is a descendant of n2.\r
+ * \r
+ * @param n1\r
+ * a descendant of n2\r
+ * @param n2\r
+ * @return distance between n1 and n2\r
+ */\r
+ private static double getDistance( PhylogenyNode n1, final PhylogenyNode n2 ) {\r
+ double d = 0.0;\r
+ while ( n1 != n2 ) {\r
+ if ( n1.getDistanceToParent() > 0.0 ) {\r
+ d += n1.getDistanceToParent();\r
+ }\r
+ n1 = n1.getParent();\r
+ }\r
+ return d;\r
+ }\r
+\r
+ private static boolean match( final String s,\r
+ final String query,\r
+ final boolean case_sensitive,\r
+ final boolean partial ) {\r
+ if ( ForesterUtil.isEmpty( s ) || ForesterUtil.isEmpty( query ) ) {\r
+ return false;\r
+ }\r
+ String my_s = s.trim();\r
+ String my_query = query.trim();\r
+ if ( !case_sensitive ) {\r
+ my_s = my_s.toLowerCase();\r
+ my_query = my_query.toLowerCase();\r
+ }\r
+ if ( partial ) {\r
+ return my_s.indexOf( my_query ) >= 0;\r
+ }\r
+ else {\r
+ return Pattern.compile( "(\\b|_)" + Pattern.quote( my_query ) + "(\\b|_)" ).matcher( my_s ).find();\r
+ }\r
+ }\r
+\r
+ private final static PhylogenyNode moveTowardsRoot( final PhylogenyNode node, final double min_distance_to_root ) {\r
+ PhylogenyNode n = node;\r
+ PhylogenyNode prev = node;\r
+ while ( min_distance_to_root < n.calculateDistanceToRoot() ) {\r
+ prev = n;\r
+ n = n.getParent();\r
+ }\r
+ return prev;\r
+ }\r
+\r
+ public static enum DESCENDANT_SORT_PRIORITY {\r
+ NODE_NAME, SEQUENCE, TAXONOMY;\r
+ }\r
+\r
+ public static enum PhylogenyNodeField {\r
+ CLADE_NAME,\r
+ SEQUENCE_NAME,\r
+ SEQUENCE_SYMBOL,\r
+ TAXONOMY_CODE,\r
+ TAXONOMY_COMMON_NAME,\r
+ TAXONOMY_ID,\r
+ TAXONOMY_ID_UNIPROT_1,\r
+ TAXONOMY_ID_UNIPROT_2,\r
+ TAXONOMY_SCIENTIFIC_NAME;\r
+ }\r
+}\r
public final class ForesterConstants {
- public final static String FORESTER_VERSION = "1.033";
- public final static String FORESTER_DATE = "140514";
+ public final static String FORESTER_VERSION = "1.034";
+ public final static String FORESTER_DATE = "140605";
public final static String PHYLO_XML_VERSION = "1.10";
public final static String PHYLO_XML_LOCATION = "http://www.phyloxml.org";
public final static String PHYLO_XML_XSD = "phyloxml.xsd";
git://source.jalview.org / jalview.git / commitdiff