X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FMainFrame.java;h=76d9ba7a74ac75f82b19655d741034ac654a2c37;hb=803a2b32992b5944b73c6dfcb80ceb58c09b81c1;hp=fb23501fc9573da6dbee75a90938785dee6fd552;hpb=bdf2d2a11d720d6457f52866af7ff909afe98db4;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrame.java b/forester/java/src/org/forester/archaeopteryx/MainFrame.java index fb23501..76d9ba7 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrame.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrame.java @@ -1,1824 +1,2729 @@ -// $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.ArrayList; -import java.util.LinkedList; -import java.util.List; -import java.util.Locale; -import java.util.NoSuchElementException; - -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.phylogeny.iterators.PhylogenyNodeIterator; -import org.forester.sdi.GSDI; -import org.forester.sdi.GSDIR; -import org.forester.sdi.SDIException; -import org.forester.util.ForesterConstants; -import org.forester.util.ForesterUtil; - -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 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"; - static final String RIGHT_LINE_UP_DOMAINS = "Right-align Domain Architectures"; - static final String LINE_UP_RENDERABLE_DATA = "Line Up Diagrams (such as Domain Architectures)"; - JMenuBar _jmenubar; - JMenu _file_jmenu; - JMenu _tools_menu; - JMenu _view_jmenu; - JMenu _options_jmenu; - JMenu _font_size_menu; - JMenu _help_jmenu; - JMenuItem[] _load_phylogeny_from_webservice_menu_items; - // Analysis menu - JMenu _analysis_menu; - JMenuItem _load_species_tree_item; - JMenuItem _gsdi_item; - JMenuItem _gsdir_item; - JMenuItem _lineage_inference; - // file menu: - JMenuItem _open_item; - JMenuItem _open_url_item; - JMenuItem _save_item; - JMenuItem _save_all_item; - JMenuItem _close_item; - JMenuItem _exit_item; - JMenuItem _new_item; - // 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; - JMenuItem _delete_selected_nodes_item; - JMenuItem _delete_not_selected_nodes_item; - // font size menu: - JMenuItem _super_tiny_fonts_item; - JMenuItem _tiny_fonts_item; - JMenuItem _small_fonts_item; - JMenuItem _medium_fonts_item; - JMenuItem _large_fonts_item; - // options menu: - // _ screen and print - JMenuItem _choose_font_mi; - JMenuItem _switch_colors_mi; - JCheckBoxMenuItem _label_direction_cbmi; - // _ screen display - JCheckBoxMenuItem _screen_antialias_cbmi; - JCheckBoxMenuItem _background_gradient_cbmi; - JRadioButtonMenuItem _non_lined_up_cladograms_rbmi; - JRadioButtonMenuItem _uniform_cladograms_rbmi; - JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi; - JCheckBoxMenuItem _color_by_taxonomic_group_cbmi; - JCheckBoxMenuItem _show_scale_cbmi; //TODO fix me - JCheckBoxMenuItem _show_overview_cbmi; - JCheckBoxMenuItem _show_domain_labels; - JCheckBoxMenuItem _show_annotation_ref_source; - JCheckBoxMenuItem _abbreviate_scientific_names; - JCheckBoxMenuItem _color_labels_same_as_parent_branch; - JMenuItem _overview_placment_mi; - JMenuItem _choose_minimal_confidence_mi; - JCheckBoxMenuItem _show_default_node_shapes_internal_cbmi; - JCheckBoxMenuItem _show_default_node_shapes_external_cbmi; - JMenuItem _cycle_node_shape_mi; - JMenuItem _cycle_node_fill_mi; - JMenuItem _choose_node_size_mi; - JCheckBoxMenuItem _show_confidence_stddev_cbmi; - JCheckBoxMenuItem _right_line_up_domains_cbmi; - JCheckBoxMenuItem _line_up_renderable_data_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 _textframes = new LinkedList(); ; - Configuration _configuration; - Options _options; - private Phylogeny _species_tree; - InferenceManager _inference_manager; - final ProcessPool _process_pool; - private String _previous_node_annotation_ref; - - MainFrame() { - _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 == _delete_selected_nodes_item ) { - if ( isSubtreeDisplayed() ) { - return; - } - deleteSelectedNodes( true ); - } - else if ( o == _delete_not_selected_nodes_item ) { - if ( isSubtreeDisplayed() ) { - return; - } - deleteSelectedNodes( false ); - } - else if ( o == _annotate_item ) { - annotateSequences(); - } - else if ( o == _switch_colors_mi ) { - switchColors(); - } - else if ( o == _display_basic_information_item ) { - 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 == _color_by_taxonomic_group_cbmi ) { - updateOptions( getOptions() ); - } - else if ( o == _show_confidence_stddev_cbmi ) { - updateOptions( getOptions() ); - } - else if ( o == _use_brackets_for_conf_in_nh_export_cbmi ) { - if ( _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) { - _use_internal_names_for_conf_in_nh_export_cbmi.setSelected( false ); - } - updateOptions( getOptions() ); - } - else if ( o == _use_internal_names_for_conf_in_nh_export_cbmi ) { - if ( _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) { - _use_brackets_for_conf_in_nh_export_cbmi.setSelected( false ); - } - updateOptions( getOptions() ); - } - else if ( o == _label_direction_cbmi ) { - updateOptions( getOptions() ); - } - else if ( o == _show_overview_cbmi ) { - updateOptions( getOptions() ); - if ( getCurrentTreePanel() != null ) { - getCurrentTreePanel().updateOvSizes(); - } - } - else if ( o == _line_up_renderable_data_cbmi ) { - if ( !_line_up_renderable_data_cbmi.isSelected() ) { - _right_line_up_domains_cbmi.setSelected( false ); - } - updateOptions( getOptions() ); - } - else if ( o == _right_line_up_domains_cbmi ) { - if ( _right_line_up_domains_cbmi.isSelected() ) { - _line_up_renderable_data_cbmi.setSelected( true ); - } - updateOptions( getOptions() ); - } - else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi ) - || ( o == _convex_type_cbmi ) || ( o == _euro_type_cbmi ) || ( o == _rounded_type_cbmi ) - || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) { - typeChanged( o ); - } - else if ( o == _about_item ) { - about(); - } - else if ( o == _help_item ) { - try { - AptxUtil.openWebsite( Constants.APTX_DOC_SITE, is_applet, applet ); - } - catch ( final IOException e1 ) { - ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() ); - } - } - 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(); - } - - private void deleteSelectedNodes( final boolean delete ) { - final Phylogeny phy = getMainPanel().getCurrentPhylogeny(); - if ( ( phy == null ) || ( phy.getNumberOfExternalNodes() < 2 ) ) { - return; - } - final List nodes = new ArrayList(); - if ( ( getCurrentTreePanel().getFoundNodes0() != null ) || ( getCurrentTreePanel().getFoundNodes1() != null ) ) { - final List all_selected_nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes(); - for( final PhylogenyNode n : all_selected_nodes ) { - if ( n.isExternal() ) { - nodes.add( n ); - } - } - } - String function = "Retain"; - if ( delete ) { - function = "Delete"; - } - if ( ( nodes == null ) || nodes.isEmpty() ) { - JOptionPane - .showMessageDialog( this, - "Need to select external nodes, either via direct selection or via the \"Search\" function", - "No external nodes selected to " + function.toLowerCase(), - JOptionPane.ERROR_MESSAGE ); - return; - } - final int todo = nodes.size(); - final int ext = phy.getNumberOfExternalNodes(); - int res = todo; - if ( delete ) { - res = ext - todo; - } - if ( res < 1 ) { - JOptionPane.showMessageDialog( this, - "Cannot delete all nodes", - "Attempt to delete all nodes ", - JOptionPane.ERROR_MESSAGE ); - return; - } - final int result = JOptionPane.showConfirmDialog( null, function + " " + todo - + " external node(s), from a total of " + ext + " external nodes," + "\nresulting in tree with " + res - + " nodes?", function + " external nodes", JOptionPane.OK_CANCEL_OPTION ); - if ( result == JOptionPane.OK_OPTION ) { - if ( !delete ) { - final List to_delete = new ArrayList(); - for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) { - final PhylogenyNode n = it.next(); - if ( !nodes.contains( n ) ) { - to_delete.add( n ); - } - } - for( final PhylogenyNode n : to_delete ) { - phy.deleteSubtree( n, true ); - } - } - else { - for( final PhylogenyNode n : nodes ) { - phy.deleteSubtree( n, true ); - } - } - resetSearch(); - getCurrentTreePanel().setNodeInPreorderToNull(); - phy.externalNodesHaveChanged(); - phy.clearHashIdToNodeMap(); - phy.recalculateNumberOfExternalDescendants( true ); - getCurrentTreePanel().resetNodeIdToDistToLeafMap(); - getCurrentTreePanel().setEdited( true ); - repaint(); - } - } - - void resetSearch() { - getMainPanel().getCurrentTreePanel().setFoundNodes0( null ); - getMainPanel().getCurrentTreePanel().setFoundNodes1( null ); - getMainPanel().getControlPanel().setSearchFoundCountsOnLabel0( 0 ); - getMainPanel().getControlPanel().getSearchFoundCountsLabel0().setVisible( false ); - getMainPanel().getControlPanel().getSearchTextField0().setText( "" ); - getMainPanel().getControlPanel().getSearchResetButton0().setEnabled( false ); - getMainPanel().getControlPanel().getSearchResetButton0().setVisible( false ); - getMainPanel().getControlPanel().setSearchFoundCountsOnLabel1( 0 ); - getMainPanel().getControlPanel().getSearchFoundCountsLabel1().setVisible( false ); - getMainPanel().getControlPanel().getSearchTextField1().setText( "" ); - getMainPanel().getControlPanel().getSearchResetButton1().setEnabled( false ); - getMainPanel().getControlPanel().getSearchResetButton1().setVisible( false ); - } - - 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( "Documentation" ) ); - _help_jmenu.addSeparator(); - _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) ); - _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" ); //TODO need to add this... - _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) ); - _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) ); - _help_jmenu.addSeparator(); - _help_jmenu.add( _about_item = new JMenuItem( "About" ) ); - customizeJMenuItem( _help_item ); - customizeJMenuItem( _website_item ); - customizeJMenuItem( _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 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 ( ( _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 ); - } - if ( ( _right_line_up_domains_cbmi != null ) && _right_line_up_domains_cbmi.isEnabled() ) { - options.setRightLineUpDomains( _right_line_up_domains_cbmi.isSelected() ); - } - if ( ( _line_up_renderable_data_cbmi != null ) && _line_up_renderable_data_cbmi.isEnabled() ) { - options.setLineUpRendarableNodeData( _line_up_renderable_data_cbmi.isSelected() ); - } - } - - 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 ) { - List nodes = null; - if ( ( getCurrentTreePanel().getFoundNodes0() != null ) - || ( getCurrentTreePanel().getFoundNodes1() != null ) ) { - nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes(); - } - 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 PhylogenyNode n : nodes ) { - ForesterUtil.ensurePresenceOfSequence( n ); - final Annotation ann = ForesterUtil.isEmpty( ref ) ? new Annotation() - : new Annotation( ref ); - if ( !ForesterUtil.isEmpty( desc ) ) { - ann.setDesc( desc ); - } - n.getNodeData().getSequence().addAnnotation( ann ); - } - } - getMainPanel().getControlPanel().showAnnotations(); - } - } - } - } - - private void chooseFont() { - final FontChooser fc = new FontChooser(); - fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() ); - fc.showDialog( 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) 2014 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( "Documentation:\n" ); - about.append( Constants.APTX_DOC_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 updateScreenTextAntialias( final List treepanels ) { - for( final TreePanel tree_panel : treepanels ) { - tree_panel.setTextAntialias(); - } - } -} +// $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.ArrayList; +import java.util.LinkedList; +import java.util.List; +import java.util.Locale; +import java.util.NoSuchElementException; + +import javax.swing.Box; +import javax.swing.JApplet; +import javax.swing.JCheckBoxMenuItem; +import javax.swing.JFileChooser; +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 javax.swing.filechooser.FileFilter; + +import org.forester.archaeopteryx.AptxUtil.GraphicsExportType; +import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE; +import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION; +import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE; +import org.forester.archaeopteryx.tools.AncestralTaxonomyInferrer; +import org.forester.archaeopteryx.tools.InferenceManager; +import org.forester.archaeopteryx.tools.ProcessPool; +import org.forester.archaeopteryx.tools.ProcessRunning; +import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION; +import org.forester.io.writers.PhylogenyWriter; +import org.forester.phylogeny.Phylogeny; +import org.forester.phylogeny.PhylogenyMethods; +import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY; +import org.forester.phylogeny.PhylogenyNode; +import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE; +import org.forester.phylogeny.data.Annotation; +import org.forester.phylogeny.data.NodeDataField; +import org.forester.phylogeny.data.NodeVisualData.NodeFill; +import org.forester.phylogeny.data.NodeVisualData.NodeShape; +import org.forester.phylogeny.iterators.PhylogenyNodeIterator; +import org.forester.sdi.GSDI; +import org.forester.sdi.GSDIR; +import org.forester.sdi.SDIException; +import org.forester.util.ForesterConstants; +import org.forester.util.ForesterUtil; +import org.forester.util.WindowsUtils; + +public abstract class MainFrame extends JFrame implements ActionListener { + + final static NHFilter nhfilter = new NHFilter(); + final static NHXFilter nhxfilter = new NHXFilter(); + final static XMLFilter xmlfilter = new XMLFilter(); + final static TolFilter tolfilter = new TolFilter(); + final static NexusFilter nexusfilter = new NexusFilter(); + final static PdfFilter pdffilter = new PdfFilter(); + final static GraphicsFileFilter graphicsfilefilter = new GraphicsFileFilter(); + final static MsaFileFilter msafilter = new MsaFileFilter(); + final static SequencesFileFilter seqsfilter = new SequencesFileFilter(); + final static DefaultFilter defaultfilter = new DefaultFilter(); + 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 = AptxConstants.PHYLOXML_REFERENCE; //TODO //FIXME + static final String APTX_REF_TOOL_TIP = AptxConstants.APTX_REFERENCE; + private static final long serialVersionUID = 3655000897845508358L; + final static Font menu_font = new Font( Configuration.getDefaultFontFamilyName(), + Font.PLAIN, + 10 ); + static final String TYPE_MENU_HEADER = "Type"; + static final String RECTANGULAR_TYPE_CBMI_LABEL = "Rectangular"; + static final String EURO_TYPE_CBMI_LABEL = "Euro Type"; + static final String CURVED_TYPE_CBMI_LABEL = "Curved"; + static final String TRIANGULAR_TYPE_CBMI_LABEL = "Triangular"; + static final String CONVEX_TYPE_CBMI_LABEL = "Convex"; + static final String ROUNDED_TYPE_CBMI_LABEL = "Rounded"; + static final String UNROOTED_TYPE_CBMI_LABEL = "Unrooted (alpha)"; //TODO + static final String CIRCULAR_TYPE_CBMI_LABEL = "Circular (alpha)"; //TODO + static final String OPTIONS_HEADER = "Options"; + static final String SEARCH_SUBHEADER = "Search:"; + static final String DISPLAY_SUBHEADER = "Display:"; + static final String SEARCH_TERMS_ONLY_LABEL = "Match Complete Terms Only"; + static final String SEARCH_REGEX_LABEL = "Search with Regular Expressions"; + static final String SEARCH_CASE_SENSITIVE_LABEL = "Case Sensitive"; + static final String INVERSE_SEARCH_RESULT_LABEL = "Negate Result"; + 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 SEARCH_WITH_REGEX_TIP = "To search using regular expressions (~Java/Perl syntax). For example, use \"^B.+\\d{2,}$\" to search for everything starting with a B and ending with at least two digits."; + static final String SCREEN_ANTIALIAS_LABEL = "Antialias"; + static final String COLOR_LABELS_LABEL = "Colorize Labels Same as Parent Branch"; + static final String BG_GRAD_LABEL = "Background Color Gradient"; + static final String DISPLAY_NODE_BOXES_LABEL_EXT = "Shapes for External Nodes"; + static final String DISPLAY_NODE_BOXES_LABEL_INT = "Shapes for Internal Nodes"; + static final String DISPLAY_NODE_BOXES_LABEL_MARKED = "Shapes for Nodes with Visual Data"; + static final String SHOW_OVERVIEW_LABEL = "Overview"; + static final String FONT_SIZE_MENU_LABEL = "Font Size"; + static final String NONUNIFORM_CLADOGRAMS_LABEL = "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"; + static final String RIGHT_LINE_UP_DOMAINS = "Right-align Domain Architectures"; + static final String LINE_UP_RENDERABLE_DATA = "Line Up Diagrams (such as Domain Architectures)"; + static final String INFER_ANCESTOR_TAXONOMIES = "Infer Ancestor Taxonomies"; + static final String OBTAIN_DETAILED_TAXONOMIC_INFORMATION = "Obtain Detailed Taxonomic Information"; + JMenuBar _jmenubar; + JMenu _file_jmenu; + JMenu _tools_menu; + JMenu _view_jmenu; + JMenu _options_jmenu; + JMenu _font_size_menu; + JMenu _help_jmenu; + JMenuItem[] _load_phylogeny_from_webservice_menu_items; + // Analysis menu + JMenu _analysis_menu; + JMenuItem _load_species_tree_item; + JMenuItem _gsdi_item; + JMenuItem _gsdir_item; + JMenuItem _lineage_inference; + // file menu: + JMenuItem _open_item; + JMenuItem _open_url_item; + JMenuItem _save_item; + JMenuItem _save_all_item; + JMenuItem _close_item; + JMenuItem _exit_item; + JMenuItem _new_item; + JMenuItem _print_item; + JMenuItem _write_to_pdf_item; + JMenuItem _write_to_jpg_item; + JMenuItem _write_to_gif_item; + JMenuItem _write_to_tif_item; + JMenuItem _write_to_png_item; + JMenuItem _write_to_bmp_item; + // tools menu: + JMenuItem _midpoint_root_item; + JMenuItem _taxcolor_item; + JMenuItem _confcolor_item; + JMenuItem _color_rank_jmi; + JMenuItem _collapse_species_specific_subtrees; + JMenuItem _obtain_detailed_taxonomic_information_jmi; + JMenuItem _obtain_detailed_taxonomic_information_deleting_jmi; + JMenuItem _obtain_seq_information_jmi; + JMenuItem _move_node_names_to_tax_sn_jmi; + JMenuItem _move_node_names_to_seq_names_jmi; + JMenuItem _extract_tax_code_from_node_names_jmi; + JMenuItem _annotate_item; + JMenuItem _remove_branch_color_item; + JMenuItem _remove_visual_styles_item; + JMenuItem _delete_selected_nodes_item; + JMenuItem _delete_not_selected_nodes_item; + // font size menu: + JMenuItem _super_tiny_fonts_item; + JMenuItem _tiny_fonts_item; + JMenuItem _small_fonts_item; + JMenuItem _medium_fonts_item; + JMenuItem _large_fonts_item; + // options menu: + // _ screen and print + JMenuItem _choose_font_mi; + JMenuItem _switch_colors_mi; + JCheckBoxMenuItem _label_direction_cbmi; + // _ screen display + JCheckBoxMenuItem _screen_antialias_cbmi; + JCheckBoxMenuItem _background_gradient_cbmi; + JRadioButtonMenuItem _non_lined_up_cladograms_rbmi; + JRadioButtonMenuItem _uniform_cladograms_rbmi; + JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi; + JCheckBoxMenuItem _color_by_taxonomic_group_cbmi; + JCheckBoxMenuItem _show_scale_cbmi; //TODO fix me + JCheckBoxMenuItem _show_overview_cbmi; + JCheckBoxMenuItem _show_domain_labels; + JCheckBoxMenuItem _show_annotation_ref_source; + JCheckBoxMenuItem _abbreviate_scientific_names; + JCheckBoxMenuItem _color_labels_same_as_parent_branch; + JMenuItem _overview_placment_mi; + JMenuItem _choose_minimal_confidence_mi; + JCheckBoxMenuItem _show_default_node_shapes_internal_cbmi; + JCheckBoxMenuItem _show_default_node_shapes_external_cbmi; + JCheckBoxMenuItem _show_default_node_shapes_for_marked_cbmi; + JMenuItem _cycle_node_shape_mi; + JMenuItem _cycle_node_fill_mi; + JMenuItem _choose_node_size_mi; + JMenuItem _cycle_data_return; + JCheckBoxMenuItem _show_confidence_stddev_cbmi; + JCheckBoxMenuItem _right_line_up_domains_cbmi; + JCheckBoxMenuItem _line_up_renderable_data_cbmi; + // _ print + JCheckBoxMenuItem _graphics_export_visible_only_cbmi; + JCheckBoxMenuItem _antialias_print_cbmi; + JCheckBoxMenuItem _print_black_and_white_cbmi; + //JMenuItem _print_size_mi; + JMenuItem _choose_pdf_width_mi; + // _ parsing + JCheckBoxMenuItem _internal_number_are_confidence_for_nh_parsing_cbmi; + JRadioButtonMenuItem _extract_taxonomy_no_rbmi; + JRadioButtonMenuItem _extract_taxonomy_agressive_rbmi; + JRadioButtonMenuItem _extract_taxonomy_pfam_strict_rbmi; + JRadioButtonMenuItem _extract_taxonomy_pfam_relaxed_rbmi; + JCheckBoxMenuItem _replace_underscores_cbmi; + JCheckBoxMenuItem _allow_errors_in_distance_to_parent_cbmi; + JCheckBoxMenuItem _use_brackets_for_conf_in_nh_export_cbmi; + JCheckBoxMenuItem _use_internal_names_for_conf_in_nh_export_cbmi; + JCheckBoxMenuItem _parse_beast_style_extended_nexus_tags_cbmi; + // _ search + JCheckBoxMenuItem _search_case_senstive_cbmi; + JCheckBoxMenuItem _search_whole_words_only_cbmi; + JCheckBoxMenuItem _inverse_search_result_cbmi; + JCheckBoxMenuItem _search_with_regex_cbmi; + JCheckBoxMenuItem _color_all_found_nodes_when_coloring_subtree_cbmi; + // type menu: + JMenu _type_menu; + JCheckBoxMenuItem _rectangular_type_cbmi; + JCheckBoxMenuItem _triangular_type_cbmi; + JCheckBoxMenuItem _curved_type_cbmi; + JCheckBoxMenuItem _convex_type_cbmi; + JCheckBoxMenuItem _euro_type_cbmi; + JCheckBoxMenuItem _rounded_type_cbmi; + JCheckBoxMenuItem _unrooted_type_cbmi; + JCheckBoxMenuItem _circular_type_cbmi; + // view as text menu: + JMenuItem _view_as_NH_item; + JMenuItem _view_as_XML_item; + JMenuItem _view_as_nexus_item; + JMenuItem _display_basic_information_item; + // help menu: + JMenuItem _about_item; + JMenuItem _help_item; + JMenuItem _website_item; + JMenuItem _phyloxml_website_item; + JMenuItem _phyloxml_ref_item; + JMenuItem _aptx_ref_item; + // + File _current_dir; + JFileChooser _writetopdf_filechooser; + JFileChooser _save_filechooser; + JFileChooser _writetographics_filechooser; + // process menu: + JMenu _process_menu; + MainPanel _mainpanel; + Container _contentpane; + final LinkedList _textframes = new LinkedList(); ; + Configuration _configuration; + Options _options; + private Phylogeny _species_tree; + InferenceManager _inference_manager; + final ProcessPool _process_pool; + private String _previous_node_annotation_ref; + + MainFrame() { + _process_pool = ProcessPool.createInstance(); + _writetopdf_filechooser = new JFileChooser(); + _writetopdf_filechooser.setMultiSelectionEnabled( false ); + _writetopdf_filechooser.addChoosableFileFilter( pdffilter ); + _writetographics_filechooser = new JFileChooser(); + _writetographics_filechooser.setMultiSelectionEnabled( false ); + _writetographics_filechooser.addChoosableFileFilter( graphicsfilefilter ); + _save_filechooser = new JFileChooser(); + _save_filechooser.setMultiSelectionEnabled( false ); + _save_filechooser.setFileFilter( xmlfilter ); + _save_filechooser.addChoosableFileFilter( nhfilter ); + _save_filechooser.addChoosableFileFilter( nexusfilter ); + _save_filechooser.addChoosableFileFilter( _save_filechooser.getAcceptAllFileFilter() ); + try { + final String home_dir = System.getProperty( "user.home" ); + _save_filechooser.setCurrentDirectory( new File( home_dir ) ); + _writetopdf_filechooser.setCurrentDirectory( new File( home_dir ) ); + _writetographics_filechooser.setCurrentDirectory( new File( home_dir ) ); + } + catch ( final Exception e ) { + e.printStackTrace(); + // Do nothing. Not important. + } + } + + /** + * 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 == _delete_selected_nodes_item ) { + if ( isSubtreeDisplayed() ) { + return; + } + deleteSelectedNodes( true ); + } + else if ( o == _delete_not_selected_nodes_item ) { + if ( isSubtreeDisplayed() ) { + return; + } + deleteSelectedNodes( false ); + } + else if ( o == _annotate_item ) { + annotateSequences(); + } + else if ( o == _switch_colors_mi ) { + switchColors(); + } + else if ( o == _display_basic_information_item ) { + if ( getCurrentTreePanel() != null ) { + displayBasicInformation( getCurrentTreePanel().getTreeFile() ); + } + } + else if ( o == _view_as_NH_item ) { + viewAsNH(); + } + else if ( o == _view_as_XML_item ) { + viewAsXML(); + } + else if ( o == _view_as_nexus_item ) { + viewAsNexus(); + } + else if ( o == _super_tiny_fonts_item ) { + if ( getCurrentTreePanel() != null ) { + getCurrentTreePanel().setSuperTinyFonts(); + getCurrentTreePanel().repaint(); + } + } + else if ( o == _tiny_fonts_item ) { + if ( getCurrentTreePanel() != null ) { + getCurrentTreePanel().setTinyFonts(); + getCurrentTreePanel().repaint(); + } + } + else if ( o == _small_fonts_item ) { + if ( getCurrentTreePanel() != null ) { + getCurrentTreePanel().setSmallFonts(); + getCurrentTreePanel().repaint(); + } + } + else if ( o == _medium_fonts_item ) { + if ( getCurrentTreePanel() != null ) { + getCurrentTreePanel().setMediumFonts(); + getCurrentTreePanel().repaint(); + } + } + else if ( o == _large_fonts_item ) { + if ( getCurrentTreePanel() != null ) { + getCurrentTreePanel().setLargeFonts(); + getCurrentTreePanel().repaint(); + } + } + else if ( o == _choose_font_mi ) { + chooseFont(); + } + else if ( o == _choose_minimal_confidence_mi ) { + chooseMinimalConfidence(); + } + else if ( o == _choose_node_size_mi ) { + chooseNodeSize( getOptions(), this ); + } + else if ( o == _overview_placment_mi ) { + MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() ); + } + else if ( o == _cycle_node_fill_mi ) { + MainFrame.cycleNodeFill( getOptions() ); + } + else if ( o == _cycle_node_shape_mi ) { + MainFrame.cycleNodeShape( getOptions() ); + } + else if ( o == _cycle_data_return ) { + MainFrame.cycleNodeDataReturn( getOptions(), getConfiguration() ); + } + else if ( o == _screen_antialias_cbmi ) { + updateOptions( getOptions() ); + updateScreenTextAntialias( getMainPanel().getTreePanels() ); + } + else if ( o == _background_gradient_cbmi ) { + updateOptions( getOptions() ); + } + else if ( o == _show_domain_labels ) { + updateOptions( getOptions() ); + } + else if ( o == _show_annotation_ref_source ) { + updateOptions( getOptions() ); + } + else if ( o == _abbreviate_scientific_names ) { + updateOptions( getOptions() ); + } + else if ( o == _color_labels_same_as_parent_branch ) { + updateOptions( getOptions() ); + } + else if ( o == _show_default_node_shapes_internal_cbmi ) { + updateOptions( getOptions() ); + } + else if ( o == _show_default_node_shapes_external_cbmi ) { + updateOptions( getOptions() ); + } + else if ( o == _show_default_node_shapes_for_marked_cbmi ) { + updateOptions( getOptions() ); + } + else if ( o == _non_lined_up_cladograms_rbmi ) { + updateOptions( getOptions() ); + showWhole(); + } + else if ( o == _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 ) { + if ( ( _search_with_regex_cbmi != null ) && _search_whole_words_only_cbmi.isSelected() ) { + _search_with_regex_cbmi.setSelected( false ); + } + updateOptions( getOptions() ); + getMainPanel().getControlPanel().search0(); + getMainPanel().getControlPanel().search1(); + } + else if ( o == _inverse_search_result_cbmi ) { + updateOptions( getOptions() ); + getMainPanel().getControlPanel().search0(); + getMainPanel().getControlPanel().search1(); + } + else if ( o == _search_with_regex_cbmi ) { + if ( ( _search_whole_words_only_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) { + _search_whole_words_only_cbmi.setSelected( false ); + } + if ( ( _search_case_senstive_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) { + _search_case_senstive_cbmi.setSelected( true ); + } + updateOptions( getOptions() ); + getMainPanel().getControlPanel().search0(); + getMainPanel().getControlPanel().search1(); + } + else if ( o == _color_all_found_nodes_when_coloring_subtree_cbmi ) { + updateOptions( getOptions() ); + } + else if ( o == _parse_beast_style_extended_nexus_tags_cbmi ) { + updateOptions( getOptions() ); + } + else if ( o == _show_scale_cbmi ) { + updateOptions( getOptions() ); + } + else if ( o == _color_by_taxonomic_group_cbmi ) { + updateOptions( getOptions() ); + } + else if ( o == _show_confidence_stddev_cbmi ) { + updateOptions( getOptions() ); + } + else if ( o == _use_brackets_for_conf_in_nh_export_cbmi ) { + if ( _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) { + _use_internal_names_for_conf_in_nh_export_cbmi.setSelected( false ); + } + updateOptions( getOptions() ); + } + else if ( o == _use_internal_names_for_conf_in_nh_export_cbmi ) { + if ( _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) { + _use_brackets_for_conf_in_nh_export_cbmi.setSelected( false ); + } + updateOptions( getOptions() ); + } + else if ( o == _label_direction_cbmi ) { + updateOptions( getOptions() ); + } + else if ( o == _show_overview_cbmi ) { + updateOptions( getOptions() ); + if ( getCurrentTreePanel() != null ) { + getCurrentTreePanel().updateOvSizes(); + } + } + else if ( o == _line_up_renderable_data_cbmi ) { + if ( !_line_up_renderable_data_cbmi.isSelected() ) { + _right_line_up_domains_cbmi.setSelected( false ); + } + updateOptions( getOptions() ); + } + else if ( o == _right_line_up_domains_cbmi ) { + if ( _right_line_up_domains_cbmi.isSelected() ) { + _line_up_renderable_data_cbmi.setSelected( true ); + } + updateOptions( getOptions() ); + } + else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi ) + || ( o == _convex_type_cbmi ) || ( o == _euro_type_cbmi ) || ( o == _rounded_type_cbmi ) + || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) { + typeChanged( o ); + } + else if ( o == _about_item ) { + about(); + } + else if ( o == _help_item ) { + try { + AptxUtil.openWebsite( AptxConstants.APTX_DOC_SITE, is_applet, applet ); + } + catch ( final IOException e1 ) { + ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() ); + } + } + else if ( o == _website_item ) { + try { + AptxUtil.openWebsite( AptxConstants.APTX_WEB_SITE, is_applet, applet ); + } + catch ( final IOException e1 ) { + ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() ); + } + } + else if ( o == _phyloxml_website_item ) { + try { + AptxUtil.openWebsite( AptxConstants.PHYLOXML_WEB_SITE, is_applet, applet ); + } + catch ( final IOException e1 ) { + ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() ); + } + } + else if ( o == _aptx_ref_item ) { + try { + AptxUtil.openWebsite( AptxConstants.APTX_REFERENCE_URL, is_applet, applet ); + } + catch ( final IOException e1 ) { + ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() ); + } + } + else if ( o == _phyloxml_ref_item ) { + try { + AptxUtil.openWebsite( AptxConstants.PHYLOXML_REFERENCE_URL, is_applet, applet ); + } + catch ( final IOException e1 ) { + ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() ); + } + } + else if ( o == _write_to_pdf_item ) { + final File curr_dir = writeToPdf( _mainpanel.getCurrentPhylogeny(), + getMainPanel(), + _writetopdf_filechooser, + _current_dir, + getContentPane(), + this ); + if ( curr_dir != null ) { + setCurrentDir( curr_dir ); + } + } + else if ( o == _save_all_item ) { + writeAllToFile(); + } + else if ( o == _write_to_jpg_item ) { + final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), + GraphicsExportType.JPG, + _mainpanel, + _writetographics_filechooser, + this, + getContentPane(), + _current_dir ); + if ( new_dir != null ) { + setCurrentDir( new_dir ); + } + } + else if ( o == _write_to_gif_item ) { + final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), + GraphicsExportType.GIF, + _mainpanel, + _writetographics_filechooser, + this, + getContentPane(), + _current_dir ); + if ( new_dir != null ) { + setCurrentDir( new_dir ); + } + } + else if ( o == _write_to_tif_item ) { + final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), + GraphicsExportType.TIFF, + _mainpanel, + _writetographics_filechooser, + this, + getContentPane(), + _current_dir ); + if ( new_dir != null ) { + setCurrentDir( new_dir ); + } + } + else if ( o == _write_to_bmp_item ) { + final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), + GraphicsExportType.BMP, + _mainpanel, + _writetographics_filechooser, + this, + getContentPane(), + _current_dir ); + if ( new_dir != null ) { + setCurrentDir( new_dir ); + } + } + else if ( o == _write_to_png_item ) { + final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), + GraphicsExportType.PNG, + _mainpanel, + _writetographics_filechooser, + this, + getContentPane(), + _current_dir ); + if ( new_dir != null ) { + setCurrentDir( new_dir ); + } + } + else if ( o == _print_item ) { + print( getCurrentTreePanel(), getOptions(), this ); + } + else if ( o == _save_item ) { + final File new_dir = writeToFile( _mainpanel.getCurrentPhylogeny(), + getMainPanel(), + _save_filechooser, + _current_dir, + getContentPane(), + this ); + if ( new_dir != null ) { + setCurrentDir( new_dir ); + } + } + else if ( o == _graphics_export_visible_only_cbmi ) { + updateOptions( getOptions() ); + } + else if ( o == _antialias_print_cbmi ) { + updateOptions( getOptions() ); + } + else if ( o == _print_black_and_white_cbmi ) { + updateOptions( getOptions() ); + } + else if ( o == _choose_pdf_width_mi ) { + choosePdfWidth(); + } + else if ( o == _lineage_inference ) { + if ( isSubtreeDisplayed() ) { + JOptionPane.showMessageDialog( this, + "Subtree is shown.", + "Cannot infer ancestral taxonomies", + JOptionPane.ERROR_MESSAGE ); + return; + } + executeLineageInference(); + } + else { + if ( _load_phylogeny_from_webservice_menu_items != null ) { + for( int i = 0; i < _load_phylogeny_from_webservice_menu_items.length; ++i ) { + if ( o == _load_phylogeny_from_webservice_menu_items[ i ] ) { + readPhylogeniesFromWebservice( i ); + } + } + } + } + _contentpane.repaint(); + } + + public Configuration getConfiguration() { + return _configuration; + } + + /** + * This method returns the current external node data which + * has been selected by the user by clicking the "Return ..." + * menu item. This method is expected to be called from Javascript or + * something like it. + * + * @return current external node data as String + */ + public String getCurrentExternalNodesDataBuffer() { + return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString(); + } + + public int getCurrentExternalNodesDataBufferChangeCounter() { + return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter(); + } + + public int getCurrentExternalNodesDataBufferLength() { + return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length(); + } + + public InferenceManager getInferenceManager() { + return _inference_manager; + } + + public MainPanel getMainPanel() { + return _mainpanel; + } + + public Options getOptions() { + return _options; + } + + public ProcessPool getProcessPool() { + return _process_pool; + } + + public void showTextFrame( final String s, final String title ) { + checkTextFrames(); + _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) ); + } + + public void showWhole() { + _mainpanel.getControlPanel().showWhole(); + } + + public void updateProcessMenu() { + // In general Swing is not thread safe. + // See "Swing's Threading Policy". + SwingUtilities.invokeLater( new Runnable() { + + @Override + public void run() { + doUpdateProcessMenu(); + } + } ); + } + + private void annotateSequences() { + if ( getCurrentTreePanel() != null ) { + List nodes = null; + if ( ( getCurrentTreePanel().getFoundNodes0() != null ) + || ( getCurrentTreePanel().getFoundNodes1() != null ) ) { + nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes(); + } + if ( ( nodes == null ) || nodes.isEmpty() ) { + JOptionPane + .showMessageDialog( 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 PhylogenyNode n : nodes ) { + ForesterUtil.ensurePresenceOfSequence( n ); + final Annotation ann = ForesterUtil.isEmpty( ref ) ? new Annotation() + : new Annotation( ref ); + if ( !ForesterUtil.isEmpty( desc ) ) { + ann.setDesc( desc ); + } + n.getNodeData().getSequence().addAnnotation( ann ); + } + } + getMainPanel().getControlPanel().showAnnotations(); + } + } + } + } + + private void chooseFont() { + final FontChooser fc = new FontChooser(); + fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() ); + fc.showDialog( this, "Select the Base Font" ); + getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() ); + getControlPanel().displayedPhylogenyMightHaveChanged( true ); + getMainPanel().getCurrentTreePanel().resetPreferredSize(); + getMainPanel().getCurrentTreePanel().updateOvSizes(); + + repaint(); + } + + 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 deleteSelectedNodes( final boolean delete ) { + final Phylogeny phy = getMainPanel().getCurrentPhylogeny(); + if ( ( phy == null ) || ( phy.getNumberOfExternalNodes() < 2 ) ) { + return; + } + final List nodes = new ArrayList(); + if ( ( getCurrentTreePanel().getFoundNodes0() != null ) || ( getCurrentTreePanel().getFoundNodes1() != null ) ) { + final List all_selected_nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes(); + for( final PhylogenyNode n : all_selected_nodes ) { + if ( n.isExternal() ) { + nodes.add( n ); + } + } + } + String function = "Retain"; + if ( delete ) { + function = "Delete"; + } + if ( ( nodes == null ) || nodes.isEmpty() ) { + JOptionPane + .showMessageDialog( this, + "Need to select external nodes, either via direct selection or via the \"Search\" function", + "No external nodes selected to " + function.toLowerCase(), + JOptionPane.ERROR_MESSAGE ); + return; + } + final int todo = nodes.size(); + final int ext = phy.getNumberOfExternalNodes(); + int res = todo; + if ( delete ) { + res = ext - todo; + } + if ( res < 1 ) { + JOptionPane.showMessageDialog( this, + "Cannot delete all nodes", + "Attempt to delete all nodes ", + JOptionPane.ERROR_MESSAGE ); + return; + } + final int result = JOptionPane.showConfirmDialog( null, function + " " + todo + + " external node(s), from a total of " + ext + " external nodes," + "\nresulting in tree with " + res + + " nodes?", function + " external nodes", JOptionPane.OK_CANCEL_OPTION ); + if ( result == JOptionPane.OK_OPTION ) { + if ( !delete ) { + final List to_delete = new ArrayList(); + for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) { + final PhylogenyNode n = it.next(); + if ( !nodes.contains( n ) ) { + to_delete.add( n ); + } + } + for( final PhylogenyNode n : to_delete ) { + phy.deleteSubtree( n, true ); + } + } + else { + for( final PhylogenyNode n : nodes ) { + phy.deleteSubtree( n, true ); + } + } + resetSearch(); + getCurrentTreePanel().setNodeInPreorderToNull(); + phy.externalNodesHaveChanged(); + phy.clearHashIdToNodeMap(); + phy.recalculateNumberOfExternalDescendants( true ); + getCurrentTreePanel().resetNodeIdToDistToLeafMap(); + getCurrentTreePanel().setEdited( true ); + repaint(); + } + } + + private void doUpdateProcessMenu() { + if ( _process_pool.size() > 0 ) { + if ( _process_menu == null ) { + _process_menu = createMenu( "", getConfiguration() ); + _process_menu.setForeground( Color.RED ); + } + _process_menu.removeAll(); + final String text = "processes running: " + _process_pool.size(); + _process_menu.setText( text ); + _jmenubar.add( _process_menu ); + for( int i = 0; i < _process_pool.size(); ++i ) { + final ProcessRunning p = _process_pool.getProcessByIndex( i ); + _process_menu.add( customizeJMenuItem( new JMenuItem( p.getName() + " [" + p.getStart() + "]" ) ) ); + } + } + else { + if ( _process_menu != null ) { + _process_menu.removeAll(); + _jmenubar.remove( _process_menu ); + } + } + _jmenubar.validate(); + _jmenubar.repaint(); + repaint(); + } + + private String getPreviousNodeAnnotationReference() { + return _previous_node_annotation_ref; + } + + private void removeBranchColors() { + if ( getMainPanel().getCurrentPhylogeny() != null ) { + AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() ); + } + } + + private void removeVisualStyles() { + if ( getMainPanel().getCurrentPhylogeny() != null ) { + AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() ); + } + } + + private void setPreviousNodeAnnotationReference( final String previous_node_annotation_ref ) { + _previous_node_annotation_ref = previous_node_annotation_ref; + } + + private void writeAllToFile() { + if ( ( getMainPanel().getTabbedPane() == null ) || ( getMainPanel().getTabbedPane().getTabCount() < 1 ) ) { + return; + } + final File my_dir = getCurrentDir(); + if ( my_dir != null ) { + _save_filechooser.setCurrentDirectory( my_dir ); + } + _save_filechooser.setSelectedFile( new File( "" ) ); + final int result = _save_filechooser.showSaveDialog( _contentpane ); + final File file = _save_filechooser.getSelectedFile(); + setCurrentDir( _save_filechooser.getCurrentDirectory() ); + if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) { + if ( file.exists() ) { + final int i = JOptionPane.showConfirmDialog( 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 trees = new ArrayList(); + for( int i = 0; i < count; ++i ) { + final Phylogeny phy = getMainPanel().getPhylogeny( i ); + if ( ForesterUtil.isEmpty( phy.getName() ) + && !ForesterUtil.isEmpty( getMainPanel().getTabbedPane().getTitleAt( i ) ) ) { + phy.setName( getMainPanel().getTabbedPane().getTitleAt( i ) ); + } + trees.add( phy ); + getMainPanel().getTreePanels().get( i ).setEdited( false ); + } + final PhylogenyWriter writer = new PhylogenyWriter(); + try { + writer.toPhyloXML( file, trees, 0, ForesterUtil.LINE_SEPARATOR ); + } + catch ( final IOException e ) { + JOptionPane.showMessageDialog( this, + "Failed to write to: " + file, + "Error", + JOptionPane.WARNING_MESSAGE ); + } + } + } + + void activateSaveAllIfNeeded() { + if ( ( getMainPanel().getTabbedPane() != null ) && ( getMainPanel().getTabbedPane().getTabCount() > 1 ) ) { + _save_all_item.setEnabled( true ); + } + else { + _save_all_item.setEnabled( false ); + } + } + + void buildFileMenu() { + _file_jmenu = MainFrame.createMenu( "File", getConfiguration() ); + _file_jmenu.add( _save_item = new JMenuItem( "Save Tree As..." ) ); + _file_jmenu.addSeparator(); + _file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) ); + if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" ) || AptxUtil.canWriteFormat( "TIF" ) ) { + _file_jmenu.add( _write_to_tif_item = new JMenuItem( "Export to TIFF file..." ) ); + } + _file_jmenu.add( _write_to_png_item = new JMenuItem( "Export to PNG file..." ) ); + _file_jmenu.add( _write_to_jpg_item = new JMenuItem( "Export to JPG file..." ) ); + if ( AptxUtil.canWriteFormat( "gif" ) ) { + _file_jmenu.add( _write_to_gif_item = new JMenuItem( "Export to GIF file..." ) ); + } + if ( AptxUtil.canWriteFormat( "bmp" ) ) { + _file_jmenu.add( _write_to_bmp_item = new JMenuItem( "Export to BMP file..." ) ); + } + _file_jmenu.addSeparator(); + _file_jmenu.add( _print_item = new JMenuItem( "Print..." ) ); + _file_jmenu.addSeparator(); + _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) ); + customizeJMenuItem( _save_item ); + customizeJMenuItem( _write_to_pdf_item ); + customizeJMenuItem( _write_to_png_item ); + customizeJMenuItem( _write_to_jpg_item ); + customizeJMenuItem( _write_to_gif_item ); + customizeJMenuItem( _write_to_tif_item ); + customizeJMenuItem( _write_to_bmp_item ); + customizeJMenuItem( _print_item ); + customizeJMenuItem( _exit_item ); + _jmenubar.add( _file_jmenu ); + } + + void buildFontSizeMenu() { + _font_size_menu = createMenu( FONT_SIZE_MENU_LABEL, getConfiguration() ); + _font_size_menu.add( _super_tiny_fonts_item = new JMenuItem( "Super Tiny Fonts" ) ); + _font_size_menu.add( _tiny_fonts_item = new JMenuItem( "Tiny Fonts" ) ); + _font_size_menu.add( _small_fonts_item = new JMenuItem( "Small Fonts" ) ); + _font_size_menu.add( _medium_fonts_item = new JMenuItem( "Medium Fonts" ) ); + _font_size_menu.add( _large_fonts_item = new JMenuItem( "Large Fonts" ) ); + customizeJMenuItem( _super_tiny_fonts_item ); + customizeJMenuItem( _tiny_fonts_item ); + customizeJMenuItem( _small_fonts_item ); + customizeJMenuItem( _medium_fonts_item ); + customizeJMenuItem( _large_fonts_item ); + _jmenubar.add( _font_size_menu ); + } + + void buildHelpMenu() { + _help_jmenu = createMenu( "Help", getConfiguration() ); + _help_jmenu.add( _help_item = new JMenuItem( "Documentation" ) ); + _help_jmenu.addSeparator(); + _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) ); + _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" ); //TODO need to add this... + _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) ); + _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) ); + _help_jmenu.addSeparator(); + _help_jmenu.add( _about_item = new JMenuItem( "About" ) ); + customizeJMenuItem( _help_item ); + customizeJMenuItem( _website_item ); + customizeJMenuItem( _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 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 ); + } + } + } + + 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 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 ); + } + } + + 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(); + } + + 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; + } + } + + ControlPanel getControlPanel() { + return getMainPanel().getControlPanel(); + } + + File getCurrentDir() { + if ( ( _current_dir == null ) || !_current_dir.canRead() ) { + if ( ForesterUtil.isWindows() ) { + try { + _current_dir = new File( WindowsUtils.getCurrentUserDesktopPath() ); + } + catch ( final Exception e ) { + _current_dir = null; + } + } + } + if ( ( _current_dir == null ) || !_current_dir.canRead() ) { + if ( System.getProperty( "user.home" ) != null ) { + _current_dir = new File( System.getProperty( "user.home" ) ); + } + else if ( System.getProperty( "user.dir" ) != null ) { + _current_dir = new File( System.getProperty( "user.dir" ) ); + } + } + return _current_dir; + } + + TreePanel getCurrentTreePanel() { + return getMainPanel().getCurrentTreePanel(); + } + + JMenu getHelpMenu() { + return _help_jmenu; + } + + JCheckBoxMenuItem getlabelDirectionCbmi() { + return _label_direction_cbmi; + } + + JMenuBar getMenuBarOfMainFrame() { + return _jmenubar; + } + + final Phylogeny getSpeciesTree() { + return _species_tree; + } + + void initializeTypeMenu( final Options options ) { + setTypeMenuToAllUnselected(); + switch ( options.getPhylogenyGraphicsType() ) { + case CONVEX: + _convex_type_cbmi.setSelected( true ); + break; + case CURVED: + _curved_type_cbmi.setSelected( true ); + break; + case EURO_STYLE: + _euro_type_cbmi.setSelected( true ); + break; + case ROUNDED: + _rounded_type_cbmi.setSelected( true ); + break; + case TRIANGULAR: + _triangular_type_cbmi.setSelected( true ); + break; + case UNROOTED: + _unrooted_type_cbmi.setSelected( true ); + break; + case CIRCULAR: + _circular_type_cbmi.setSelected( true ); + break; + default: + _rectangular_type_cbmi.setSelected( true ); + break; + } + } + + boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) { + if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) { + return false; + } + else if ( ( getSpeciesTree() == null ) || getSpeciesTree().isEmpty() ) { + JOptionPane.showMessageDialog( 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 resetSearch() { + getMainPanel().getCurrentTreePanel().setFoundNodes0( null ); + getMainPanel().getCurrentTreePanel().setFoundNodes1( null ); + getMainPanel().getControlPanel().setSearchFoundCountsOnLabel0( 0 ); + getMainPanel().getControlPanel().getSearchFoundCountsLabel0().setVisible( false ); + getMainPanel().getControlPanel().getSearchTextField0().setText( "" ); + getMainPanel().getControlPanel().getSearchResetButton0().setEnabled( false ); + getMainPanel().getControlPanel().getSearchResetButton0().setVisible( false ); + getMainPanel().getControlPanel().setSearchFoundCountsOnLabel1( 0 ); + getMainPanel().getControlPanel().getSearchFoundCountsLabel1().setVisible( false ); + getMainPanel().getControlPanel().getSearchTextField1().setText( "" ); + getMainPanel().getControlPanel().getSearchResetButton1().setEnabled( false ); + getMainPanel().getControlPanel().getSearchResetButton1().setVisible( false ); + } + + void setConfiguration( final Configuration configuration ) { + _configuration = configuration; + } + + void setCurrentDir( final File current_dir ) { + _current_dir = current_dir; + } + + void setInferenceManager( final InferenceManager i ) { + _inference_manager = i; + } + + void setOptions( final Options options ) { + _options = options; + } + + void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) { + setTypeMenuToAllUnselected(); + switch ( type ) { + case CIRCULAR: + _circular_type_cbmi.setSelected( true ); + break; + case CONVEX: + _convex_type_cbmi.setSelected( true ); + break; + case CURVED: + _curved_type_cbmi.setSelected( true ); + break; + case EURO_STYLE: + _euro_type_cbmi.setSelected( true ); + break; + case ROUNDED: + _rounded_type_cbmi.setSelected( true ); + break; + case RECTANGULAR: + _rectangular_type_cbmi.setSelected( true ); + break; + case TRIANGULAR: + _triangular_type_cbmi.setSelected( true ); + break; + case UNROOTED: + _unrooted_type_cbmi.setSelected( true ); + break; + default: + throw new IllegalArgumentException( "unknown type: " + type ); + } + } + + final void setSpeciesTree( final Phylogeny species_tree ) { + _species_tree = species_tree; + } + + void setTypeMenuToAllUnselected() { + _convex_type_cbmi.setSelected( false ); + _curved_type_cbmi.setSelected( false ); + _euro_type_cbmi.setSelected( false ); + _rounded_type_cbmi.setSelected( false ); + _triangular_type_cbmi.setSelected( false ); + _rectangular_type_cbmi.setSelected( false ); + _unrooted_type_cbmi.setSelected( false ); + _circular_type_cbmi.setSelected( false ); + } + + void switchColors() { + final TreeColorSet colorset = _mainpanel.getTreeColorSet(); + final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset ); + csc.setVisible( true ); + } + + void taxColor() { + if ( _mainpanel.getCurrentTreePanel() != null ) { + _mainpanel.getCurrentTreePanel().taxColor(); + } + } + + void typeChanged( final Object o ) { + updateTypeCheckboxes( getOptions(), o ); + updateOptions( getOptions() ); + if ( getCurrentTreePanel() != null ) { + final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType(); + final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType(); + if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) + || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) + || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) + || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) { + getCurrentTreePanel().getControlPanel().showWhole(); + } + if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) { + getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true ); + } + else { + getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false ); + } + getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() ); + updateScreenTextAntialias( getMainPanel().getTreePanels() ); + if ( getCurrentTreePanel().getControlPanel().getDynamicallyHideData() != null ) { + if ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) { + getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( false ); + } + else { + getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( true ); + } + } + } + } + + void updateOptions( final Options options ) { + options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() ); + options.setBackgroundColorGradient( ( _background_gradient_cbmi != null ) + && _background_gradient_cbmi.isSelected() ); + options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() ); + options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null ) + && _show_annotation_ref_source.isSelected() ); + options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null ) + && _abbreviate_scientific_names.isSelected() ); + options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null ) + && _color_labels_same_as_parent_branch.isSelected() ); + options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null ) + && _show_default_node_shapes_internal_cbmi.isSelected() ); + options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null ) + && _show_default_node_shapes_external_cbmi.isSelected() ); + options.setShowDefaultNodeShapesForMarkedNodes( ( _show_default_node_shapes_for_marked_cbmi != null ) + && _show_default_node_shapes_for_marked_cbmi.isSelected() ); + if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) { + options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP ); + } + else if ( ( _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 ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) { + options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() ); + } + options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() ); + if ( ( _use_brackets_for_conf_in_nh_export_cbmi != null ) + && _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) { + options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS ); + } + else if ( ( _use_internal_names_for_conf_in_nh_export_cbmi != null ) + && _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) { + options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES ); + } + else { + options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE ); + } + options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null ) + && _print_black_and_white_cbmi.isSelected() ); + options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null ) + && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() ); + if ( ( _extract_taxonomy_pfam_strict_rbmi != null ) && _extract_taxonomy_pfam_strict_rbmi.isSelected() ) { + options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); + } + else if ( ( _extract_taxonomy_pfam_relaxed_rbmi != null ) && _extract_taxonomy_pfam_relaxed_rbmi.isSelected() ) { + options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + } + else if ( ( _extract_taxonomy_agressive_rbmi != null ) && _extract_taxonomy_agressive_rbmi.isSelected() ) { + options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE ); + } + else if ( ( _extract_taxonomy_no_rbmi != null ) && _extract_taxonomy_no_rbmi.isSelected() ) { + options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO ); + } + options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null ) + && _replace_underscores_cbmi.isSelected() ); + options.setAllowErrorsInDistanceToParent( ( _allow_errors_in_distance_to_parent_cbmi != null ) + && _allow_errors_in_distance_to_parent_cbmi.isSelected() ); + options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null ) + && _search_whole_words_only_cbmi.isSelected() ); + options.setSearchWithRegex( ( _search_with_regex_cbmi != null ) && _search_with_regex_cbmi.isSelected() ); + options.setInverseSearchResult( ( _inverse_search_result_cbmi != null ) + && _inverse_search_result_cbmi.isSelected() ); + if ( _graphics_export_visible_only_cbmi != null ) { + options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_cbmi.isSelected() ); + } + if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) { + options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ); + } + else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) { + options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR ); + } + else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) { + options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED ); + } + else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) { + options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX ); + } + else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) { + options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ); + } + else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) { + options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED ); + } + else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) { + options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED ); + } + else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) { + options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ); + } + if ( ( _right_line_up_domains_cbmi != null ) && _right_line_up_domains_cbmi.isEnabled() ) { + options.setRightLineUpDomains( _right_line_up_domains_cbmi.isSelected() ); + } + if ( ( _line_up_renderable_data_cbmi != null ) && _line_up_renderable_data_cbmi.isEnabled() ) { + options.setLineUpRendarableNodeData( _line_up_renderable_data_cbmi.isSelected() ); + } + if ( ( _color_all_found_nodes_when_coloring_subtree_cbmi != null ) && _color_all_found_nodes_when_coloring_subtree_cbmi.isEnabled() ) { + options.setColorAllFoundNodesWhenColoringSubtree( _color_all_found_nodes_when_coloring_subtree_cbmi.isSelected() ); + } + if ( ( _parse_beast_style_extended_nexus_tags_cbmi != null ) && _parse_beast_style_extended_nexus_tags_cbmi.isEnabled() ) { + options.setParseBeastStyleExtendedNexusTags(_parse_beast_style_extended_nexus_tags_cbmi.isSelected() ); + } + } + + void updateTypeCheckboxes( final Options options, final Object o ) { + setTypeMenuToAllUnselected(); + ( ( JCheckBoxMenuItem ) o ).setSelected( true ); + } + + void viewAsNexus() { + if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) { + String title = "Nexus"; + if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) { + title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title; + } + showTextFrame( _mainpanel.getCurrentPhylogeny().toNexus( getOptions().getNhConversionSupportValueStyle() ), + title ); + } + } + + void viewAsNH() { + if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) { + String title = "New Hampshire"; + if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) { + title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title; + } + showTextFrame( _mainpanel.getCurrentPhylogeny().toNewHampshire( getOptions() + .getNhConversionSupportValueStyle() ), + title ); + } + } + + void viewAsXML() { + if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) { + String title = "phyloXML"; + if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) { + title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title; + } + showTextFrame( _mainpanel.getCurrentPhylogeny().toPhyloXML( 0 ), title ); + } + } + + private static void cycleNodeDataReturn( final Options op, final Configuration conf ) { + switch ( op.getExtDescNodeDataToReturn() ) { + case UNKNOWN: + op.setExtDescNodeDataToReturn( NodeDataField.DOMAINS_ALL ); + break; + case DOMAINS_ALL: + op.setExtDescNodeDataToReturn( NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN ); + break; + case DOMAINS_COLLAPSED_PER_PROTEIN: + op.setExtDescNodeDataToReturn( NodeDataField.SEQ_ANNOTATIONS ); + break; + case SEQ_ANNOTATIONS: + op.setExtDescNodeDataToReturn( NodeDataField.GO_TERM_IDS ); + break; + case GO_TERM_IDS: + op.setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_MOL_SEQ_FASTA ); + break; + case SEQUENCE_MOL_SEQ_FASTA: + if ( ( conf != null ) && ( conf.getExtDescNodeDataToReturn() != null ) + && ( conf.getExtDescNodeDataToReturn() != NodeDataField.DOMAINS_ALL ) + && ( conf.getExtDescNodeDataToReturn() != NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN ) + && ( conf.getExtDescNodeDataToReturn() != NodeDataField.SEQ_ANNOTATIONS ) + && ( conf.getExtDescNodeDataToReturn() != NodeDataField.GO_TERM_IDS ) + && ( conf.getExtDescNodeDataToReturn() != NodeDataField.SEQUENCE_MOL_SEQ_FASTA ) ) { + op.setExtDescNodeDataToReturn( conf.getExtDescNodeDataToReturn() ); + } + else { + op.setExtDescNodeDataToReturn( NodeDataField.UNKNOWN ); + } + break; + default: + op.setExtDescNodeDataToReturn( NodeDataField.UNKNOWN ); + } + } + + /** + * Display the about box. + */ + static void about() { + final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + AptxConstants.VERSION + "\n" ); + about.append( "Copyright (C) 2016 Christian M Zmasek\n" ); + about.append( "All Rights Reserved\n" ); + about.append( "License: GNU Lesser General Public License (LGPL)\n" ); + about.append( "Last modified: " + AptxConstants.PRG_DATE + "\n" ); + about.append( "Based on: " + ForesterUtil.getForesterLibraryInformation() + "\n" ); + about.append( "phyloXML version : " + ForesterConstants.PHYLO_XML_VERSION + "\n" ); + about.append( "phyloXML location: " + ForesterConstants.PHYLO_XML_LOCATION + "\n" ); + if ( !ForesterUtil.isEmpty( ForesterUtil.JAVA_VERSION ) && !ForesterUtil.isEmpty( ForesterUtil.JAVA_VENDOR ) ) { + about.append( "[your Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]\n" ); + } + if ( !ForesterUtil.isEmpty( ForesterUtil.OS_NAME ) && !ForesterUtil.isEmpty( ForesterUtil.OS_ARCH ) + && !ForesterUtil.isEmpty( ForesterUtil.OS_VERSION ) ) { + about.append( "[your OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " " + + ForesterUtil.OS_VERSION + "]\n" ); + } + final Runtime rt = java.lang.Runtime.getRuntime(); + final long free_memory = rt.freeMemory() / 1000000; + final long total_memory = rt.totalMemory() / 1000000; + about.append( "[free memory: " + free_memory + "MB, total memory: " + total_memory + "MB]\n" ); + about.append( "[locale: " + Locale.getDefault() + "]\n" ); + about.append( "References:\n" ); + about.append( AptxConstants.PHYLOXML_REFERENCE_SHORT + "\n" ); + about.append( "For more information & download:\n" ); + about.append( AptxConstants.APTX_WEB_SITE + "\n" ); + about.append( "Documentation:\n" ); + about.append( AptxConstants.APTX_DOC_SITE + "\n" ); + about.append( "Comments: " + AptxConstants.AUTHOR_EMAIL ); + JOptionPane.showMessageDialog( null, about, AptxConstants.PRG_NAME, JOptionPane.PLAIN_MESSAGE ); + } + + static void chooseNodeSize( final Options options, final Component parent ) { + final String s = ( String ) JOptionPane.showInputDialog( parent, + "Please enter the default size for node shapes.\n" + + "[current value: " + + options.getDefaultNodeShapeSize() + "]\n", + "Node Shape Size", + JOptionPane.QUESTION_MESSAGE, + null, + null, + options.getDefaultNodeShapeSize() ); + if ( !ForesterUtil.isEmpty( s ) ) { + boolean success = true; + double m = 0.0; + final String m_str = s.trim(); + if ( !ForesterUtil.isEmpty( m_str ) ) { + try { + m = Double.parseDouble( m_str ); + } + catch ( final Exception ex ) { + success = false; + } + } + else { + success = false; + } + if ( success && ( m >= 0.0 ) ) { + final short size = ForesterUtil.roundToShort( m ); + if ( size >= 0.0 ) { + options.setDefaultNodeShapeSize( size ); + } + } + } + } + + static String createCurrentFontDesc( final TreeFontSet tree_font_set ) { + return tree_font_set.getLargeFont().getFamily() + " " + tree_font_set.getLargeFont().getSize(); + } + + static JMenu createMenu( final String title, final Configuration conf ) { + final JMenu jmenu = new JMenu( title ); + if ( !conf.isUseNativeUI() ) { + jmenu.setFont( MainFrame.menu_font ); + jmenu.setBackground( conf.getGuiMenuBackgroundColor() ); + jmenu.setForeground( conf.getGuiMenuTextColor() ); + } + return jmenu; + } + + static JMenuItem customizeMenuItemAsLabel( final JMenuItem label, final Configuration configuration ) { + label.setFont( MainFrame.menu_font.deriveFont( Font.BOLD ) ); + if ( !configuration.isUseNativeUI() ) { + label.setBackground( configuration.getGuiMenuBackgroundColor() ); + label.setForeground( configuration.getGuiMenuTextColor() ); + label.setOpaque( true ); + } + label.setSelected( false ); + label.setEnabled( false ); + return label; + } + + static void cycleNodeFill( final Options op ) { + switch ( op.getDefaultNodeFill() ) { + case GRADIENT: + op.setDefaultNodeFill( NodeFill.SOLID ); + break; + case NONE: + op.setDefaultNodeFill( NodeFill.GRADIENT ); + break; + case SOLID: + op.setDefaultNodeFill( NodeFill.NONE ); + break; + default: + throw new RuntimeException( "unknown fill: " + op.getDefaultNodeFill() ); + } + } + + static void cycleNodeShape( final Options op ) { + switch ( op.getDefaultNodeShape() ) { + case CIRCLE: + op.setDefaultNodeShape( NodeShape.RECTANGLE ); + break; + case RECTANGLE: + op.setDefaultNodeShape( NodeShape.CIRCLE ); + break; + default: + throw new RuntimeException( "unknown shape: " + op.getDefaultNodeShape() ); + } + } + + static void cycleOverview( final Options op, final TreePanel tree_panel ) { + switch ( op.getOvPlacement() ) { + case LOWER_LEFT: + op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT ); + break; + case LOWER_RIGHT: + op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT ); + break; + case UPPER_LEFT: + op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT ); + break; + case UPPER_RIGHT: + op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT ); + break; + default: + throw new RuntimeException( "unknown placement: " + op.getOvPlacement() ); + } + if ( tree_panel != null ) { + tree_panel.updateOvSettings(); + } + } + + static void exceptionOccuredDuringSaveAs( final Exception e, final TreePanel tp, final Component comp ) { + try { + tp.setArrowCursor(); + } + catch ( final Exception ex ) { + // Do nothing. + } + JOptionPane.showMessageDialog( comp, "Exception" + e, "Error during File|SaveAs", JOptionPane.ERROR_MESSAGE ); + } + + static void print( final TreePanel tp, final Options op, final Component c ) { + if ( ( tp == null ) || ( tp.getPhylogeny() == null ) || tp.getPhylogeny().isEmpty() ) { + return; + } + final String job_name = AptxConstants.PRG_NAME; + boolean error = false; + String printer_name = null; + try { + printer_name = Printer.print( tp, job_name ); + } + catch ( final Exception e ) { + error = true; + JOptionPane.showMessageDialog( c, e.getMessage(), "Printing Error", JOptionPane.ERROR_MESSAGE ); + } + if ( !error && ( printer_name != null ) ) { + String msg = "Printing data sent to printer"; + if ( printer_name.length() > 1 ) { + msg += " [" + printer_name + "]"; + } + JOptionPane.showMessageDialog( c, msg, "Printing...", JOptionPane.INFORMATION_MESSAGE ); + } + if ( !op.isPrintUsingActualSize() ) { + tp.getControlPanel().showWhole(); + } + } + + static void printPhylogenyToPdf( final String file_name, + final Options opts, + final TreePanel tp, + final Component comp ) { + + String pdf_written_to = ""; + boolean error = false; + try { + if ( opts.isPrintUsingActualSize() ) { + pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name, tp, tp.getWidth() , tp.getHeight() ); + } + else { + // Never false. + } + } + catch ( final IOException e ) { + error = true; + JOptionPane.showMessageDialog( comp, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE ); + } + if ( !error ) { + if ( !ForesterUtil.isEmpty( pdf_written_to ) ) { + JOptionPane.showMessageDialog( comp, + "Wrote PDF to: " + pdf_written_to, + "Information", + JOptionPane.INFORMATION_MESSAGE ); + } + else { + JOptionPane.showMessageDialog( comp, + "There was an unknown problem when attempting to write to PDF file: \"" + + file_name + "\"", + "Error", + JOptionPane.ERROR_MESSAGE ); + } + } + if ( !opts.isPrintUsingActualSize() ) { + tp.getControlPanel().showWhole(); + } + } + + static void setCycleDataReturnMenuItem( final JMenuItem mi, final Options options ) { + if ( ( options != null ) && ( options.getExtDescNodeDataToReturn() != null ) ) { + mi.setText( "Cycle Node Return Data... (current: " + options.getExtDescNodeDataToReturn().toString() + ")" ); + } + else { + mi.setText( "Cycle Node Return Data..." ); + } + } + + static void setCycleNodeFillMenuItem( final JMenuItem mi, final Options options ) { + if ( ( options != null ) && ( options.getDefaultNodeFill() != null ) ) { + mi.setText( "Cycle Node Shape Fill Type... (current: " + + options.getDefaultNodeFill().toString().toLowerCase() + ")" ); + } + else { + mi.setText( "Cycle Node Shape Fill Type..." ); + } + } + + static void setCycleNodeShapeMenuItem( final JMenuItem mi, final Options options ) { + if ( ( options != null ) && ( options.getDefaultNodeShape() != null ) ) { + mi.setText( "Cycle Node Shape Fill Type... (current: " + + options.getDefaultNodeShape().toString().toLowerCase() + ")" ); + } + else { + mi.setText( "Cycle Node Shape Fill Type..." ); + } + } + + static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) { + if ( ( options != null ) && ( options.getOvPlacement() != null ) ) { + mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" ); + } + else { + mi.setText( "Cycle Overview Placement..." ); + } + } + + static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) { + if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) { + mi.setText( "Select Color Scheme... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName() + + ")" ); + } + else { + mi.setText( "Select Color Scheme..." ); + } + } + + static void setTextForFontChooserMenuItem( final JMenuItem mi, final String font_desc ) { + mi.setText( "Select Default Font... (current: " + font_desc + ")" ); + } + + static void setTextForPdfLineWidthChooserMenuItem( final JMenuItem mi, final Options o ) { + mi.setText( "Enter Default Line Width for PDF Export... (current: " + o.getPrintLineWidth() + ")" ); + } + + static void setTextMinSupportMenuItem( final JMenuItem mi, final Options options, final TreePanel current_tree_panel ) { + if ( ( current_tree_panel == null ) || ( current_tree_panel.getPhylogeny() == null ) ) { + mi.setEnabled( true ); + } + else if ( AptxUtil.isHasAtLeastOneBranchWithSupportValues( current_tree_panel.getPhylogeny() ) ) { + mi.setEnabled( true ); + } + else { + mi.setEnabled( false ); + } + mi.setText( "Enter Min Confidence Value... (current: " + options.getMinConfidenceValue() + ")" ); + } + + static void setTextNodeSizeMenuItem( final JMenuItem mi, final Options options ) { + mi.setText( "Enter Default Node Shape Size... (current: " + options.getDefaultNodeShapeSize() + ")" ); + } + + static void updateScreenTextAntialias( final List treepanels ) { + for( final TreePanel tree_panel : treepanels ) { + tree_panel.setTextAntialias(); + } + } + + static boolean writeAsNewHampshire( final TreePanel tp, final Options op, boolean exception, final File file ) { + try { + final PhylogenyWriter writer = new PhylogenyWriter(); + writer.toNewHampshire( tp.getPhylogeny(), true, op.getNhConversionSupportValueStyle(), file ); + } + catch ( final Exception e ) { + exception = true; + exceptionOccuredDuringSaveAs( e, tp, tp ); + } + return exception; + } + + static boolean writeAsNexus( final TreePanel tp, final Options op, boolean exception, final File file ) { + try { + final PhylogenyWriter writer = new PhylogenyWriter(); + writer.toNexus( file, tp.getPhylogeny(), op.getNhConversionSupportValueStyle() ); + } + catch ( final Exception e ) { + exception = true; + exceptionOccuredDuringSaveAs( e, tp, tp ); + } + return exception; + } + + static boolean writeAsPhyloXml( final TreePanel tp, final Options op, boolean exception, final File file ) { + try { + final PhylogenyWriter writer = new PhylogenyWriter(); + writer.toPhyloXML( file, tp.getPhylogeny(), 0 ); + } + catch ( final Exception e ) { + exception = true; + exceptionOccuredDuringSaveAs( e, tp, tp ); + } + return exception; + } + + static void writePhylogenyToGraphicsFile( final String file_name, + final GraphicsExportType type, + final MainPanel mp, + final Component comp, + final Container contentpane ) { + mp.getCurrentTreePanel().calcParametersForPainting( mp.getCurrentTreePanel().getWidth(), + mp.getCurrentTreePanel().getHeight() ); + String file_written_to = ""; + boolean error = false; + try { + file_written_to = AptxUtil.writePhylogenyToGraphicsFile( file_name, + mp.getCurrentTreePanel().getWidth(), + mp.getCurrentTreePanel().getHeight(), + mp.getCurrentTreePanel(), + mp.getControlPanel(), + type, + mp.getOptions() ); + } + catch ( final IOException e ) { + error = true; + JOptionPane.showMessageDialog( comp, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE ); + } + if ( !error ) { + if ( ( file_written_to != null ) && ( file_written_to.length() > 0 ) ) { + JOptionPane.showMessageDialog( comp, + "Wrote image to: " + file_written_to, + "Graphics Export", + JOptionPane.INFORMATION_MESSAGE ); + } + else { + JOptionPane.showMessageDialog( comp, + "There was an unknown problem when attempting to write to an image file: \"" + + file_name + "\"", + "Error", + JOptionPane.ERROR_MESSAGE ); + } + } + contentpane.repaint(); + } + + static File writeToFile( final Phylogeny t, + final MainPanel mp, + final JFileChooser save_filechooser, + final File current_dir, + final Container contentpane, + final Component comp ) { + File new_file = null; + if ( t == null ) { + return null; + } + String initial_filename = null; + if ( mp.getCurrentTreePanel().getTreeFile() != null ) { + try { + initial_filename = mp.getCurrentTreePanel().getTreeFile().getCanonicalPath(); + } + catch ( final IOException e ) { + initial_filename = null; + } + } + if ( !ForesterUtil.isEmpty( initial_filename ) ) { + save_filechooser.setSelectedFile( new File( initial_filename ) ); + } + else { + save_filechooser.setSelectedFile( new File( "" ) ); + } + final File my_dir = current_dir; + if ( my_dir != null ) { + save_filechooser.setCurrentDirectory( my_dir ); + } + final int result = save_filechooser.showSaveDialog( contentpane ); + final File file = save_filechooser.getSelectedFile(); + new_file = save_filechooser.getCurrentDirectory(); + boolean exception = false; + if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) { + if ( file.exists() ) { + final int i = JOptionPane.showConfirmDialog( comp, + file + " already exists.\nOverwrite?", + "Overwrite?", + JOptionPane.OK_CANCEL_OPTION, + JOptionPane.QUESTION_MESSAGE ); + if ( i != JOptionPane.OK_OPTION ) { + return null; + } + else { + final File to = new File( file.getAbsoluteFile().toString() + AptxConstants.BACKUP_FILE_SUFFIX ); + try { + ForesterUtil.copyFile( file, to ); + } + catch ( final Exception e ) { + JOptionPane.showMessageDialog( comp, + "Failed to create backup copy " + to, + "Failed to Create Backup Copy", + JOptionPane.WARNING_MESSAGE ); + } + try { + file.delete(); + } + catch ( final Exception e ) { + JOptionPane.showMessageDialog( comp, + "Failed to delete: " + file, + "Failed to Delete", + JOptionPane.WARNING_MESSAGE ); + } + } + } + if ( save_filechooser.getFileFilter() == MainFrame.nhfilter ) { + exception = writeAsNewHampshire( mp.getCurrentTreePanel(), mp.getOptions(), exception, file ); + } + else if ( save_filechooser.getFileFilter() == MainFrame.xmlfilter ) { + exception = writeAsPhyloXml( mp.getCurrentTreePanel(), mp.getOptions(), exception, file ); + } + else if ( save_filechooser.getFileFilter() == MainFrame.nexusfilter ) { + exception = writeAsNexus( mp.getCurrentTreePanel(), mp.getOptions(), exception, file ); + } + // "*.*": + else { + final String file_name = file.getName().trim().toLowerCase(); + if ( file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" ) + || file_name.endsWith( ".tree" ) ) { + exception = writeAsNewHampshire( mp.getCurrentTreePanel(), mp.getOptions(), exception, file ); + } + else if ( file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) ) { + exception = writeAsNexus( mp.getCurrentTreePanel(), mp.getOptions(), exception, file ); + } + // XML is default: + else { + exception = writeAsPhyloXml( mp.getCurrentTreePanel(), mp.getOptions(), exception, file ); + } + } + if ( !exception ) { + mp.setTitleOfSelectedTab( file.getName() ); + mp.getCurrentTreePanel().setTreeFile( file ); + mp.getCurrentTreePanel().setEdited( false ); + } + } + return new_file; + } + + static File writeToGraphicsFile( final Phylogeny t, + final GraphicsExportType type, + final MainPanel mp, + final JFileChooser writetographics_filechooser, + final Component component, + final Container contentpane, + final File current_dir ) { + File new_dir = null; + if ( ( t == null ) || t.isEmpty() ) { + return null; + } + String initial_filename = ""; + if ( mp.getCurrentTreePanel().getTreeFile() != null ) { + initial_filename = mp.getCurrentTreePanel().getTreeFile().toString(); + } + if ( initial_filename.indexOf( '.' ) > 0 ) { + initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) ); + } + initial_filename = initial_filename + "." + type; + writetographics_filechooser.setSelectedFile( new File( initial_filename ) ); + final File my_dir = current_dir; + if ( my_dir != null ) { + writetographics_filechooser.setCurrentDirectory( my_dir ); + } + final int result = writetographics_filechooser.showSaveDialog( contentpane ); + File file = writetographics_filechooser.getSelectedFile(); + //setCurrentDir( writetographics_filechooser.getCurrentDirectory() ); + new_dir = writetographics_filechooser.getCurrentDirectory(); + if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) { + if ( !file.toString().toLowerCase().endsWith( type.toString() ) ) { + file = new File( file.toString() + "." + type ); + } + if ( file.exists() ) { + final int i = JOptionPane.showConfirmDialog( component, + file + " already exists. Overwrite?", + "Warning", + JOptionPane.OK_CANCEL_OPTION, + JOptionPane.WARNING_MESSAGE ); + if ( i != JOptionPane.OK_OPTION ) { + return null; + } + else { + try { + file.delete(); + } + catch ( final Exception e ) { + JOptionPane.showMessageDialog( component, + "Failed to delete: " + file, + "Error", + JOptionPane.WARNING_MESSAGE ); + } + } + } + writePhylogenyToGraphicsFile( file.toString(), type, mp, component, contentpane ); + } + return new_dir; + } + + static File writeToPdf( final Phylogeny t, + final MainPanel mp, + final JFileChooser writetopdf_filechooser, + final File curr_dir, + final Container contentpane, + final Component component ) { + if ( ( t == null ) || t.isEmpty() ) { + return null; + } + String initial_filename = ""; + if ( mp.getCurrentTreePanel().getTreeFile() != null ) { + initial_filename = mp.getCurrentTreePanel().getTreeFile().toString(); + } + if ( initial_filename.indexOf( '.' ) > 0 ) { + initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) ); + } + initial_filename = initial_filename + ".pdf"; + writetopdf_filechooser.setSelectedFile( new File( initial_filename ) ); + final File my_dir = curr_dir; + if ( my_dir != null ) { + writetopdf_filechooser.setCurrentDirectory( my_dir ); + } + final int result = writetopdf_filechooser.showSaveDialog( contentpane ); + File file = writetopdf_filechooser.getSelectedFile(); + // setCurrentDir( writetopdf_filechooser.getCurrentDirectory() ); + final File new_current_dir = writetopdf_filechooser.getCurrentDirectory(); + if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) { + if ( !file.toString().toLowerCase().endsWith( ".pdf" ) ) { + file = new File( file.toString() + ".pdf" ); + } + if ( file.exists() ) { + final int i = JOptionPane.showConfirmDialog( component, + file + " already exists. Overwrite?", + "WARNING", + JOptionPane.OK_CANCEL_OPTION, + JOptionPane.WARNING_MESSAGE ); + if ( i != JOptionPane.OK_OPTION ) { + return null; + } + } + printPhylogenyToPdf( file.toString(), mp.getOptions(), mp.getCurrentTreePanel(), component ); + } + return new_current_dir; + } +} + +class DefaultFilter extends FileFilter { + + @Override + public boolean accept( final File f ) { + final String file_name = f.getName().trim().toLowerCase(); + return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" ) + || file_name.endsWith( ".nwk" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".ph" ) + || file_name.endsWith( ".tr" ) || file_name.endsWith( ".dnd" ) || file_name.endsWith( ".tree" ) + || file_name.endsWith( ".nhx" ) || file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" ) + || file_name.endsWith( "phylo.xml" ) || file_name.endsWith( ".pxml" ) || file_name.endsWith( ".nexus" ) + || file_name.endsWith( ".nx" ) || file_name.endsWith( ".nex" ) || file_name.endsWith( ".tre" ) + || file_name.endsWith( ".zip" ) || file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" ) + || file_name.endsWith( ".con" ) || f.isDirectory(); + } + + @Override + public String getDescription() { + return "All supported files (*.xml, *.phyloxml, *phylo.xml, *.nhx, *.nh, *.newick, *.nex, *.nexus, *.phy, *.tre, *.tree, *.tol, ...)"; + } +} + +class GraphicsFileFilter extends FileFilter { + + @Override + public boolean accept( final File f ) { + final String file_name = f.getName().trim().toLowerCase(); + return file_name.endsWith( ".jpg" ) || file_name.endsWith( ".jpeg" ) || file_name.endsWith( ".png" ) + || file_name.endsWith( ".gif" ) || file_name.endsWith( ".bmp" ) || f.isDirectory(); + } + + @Override + public String getDescription() { + return "Image files (*.jpg, *.jpeg, *.png, *.gif, *.bmp)"; + } +} + +class MsaFileFilter extends FileFilter { + + @Override + public boolean accept( final File f ) { + final String file_name = f.getName().trim().toLowerCase(); + return file_name.endsWith( ".msa" ) || file_name.endsWith( ".aln" ) || file_name.endsWith( ".fasta" ) + || file_name.endsWith( ".fas" ) || file_name.endsWith( ".fa" ) || f.isDirectory(); + } + + @Override + public String getDescription() { + return "Multiple sequence alignment files (*.msa, *.aln, *.fasta, *.fa, *.fas)"; + } +} + +class NexusFilter extends FileFilter { + + @Override + public boolean accept( final File f ) { + final String file_name = f.getName().trim().toLowerCase(); + return file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) || file_name.endsWith( ".nx" ) + || file_name.endsWith( ".tre" ) || f.isDirectory(); + } + + @Override + public String getDescription() { + return "Nexus files (*.nex, *.nexus, *.nx, *.tre)"; + } +} // NexusFilter + +class NHFilter extends FileFilter { + + @Override + public boolean accept( final File f ) { + final String file_name = f.getName().trim().toLowerCase(); + return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" ) + || file_name.endsWith( ".tr" ) || file_name.endsWith( ".tree" ) || file_name.endsWith( ".dnd" ) + || file_name.endsWith( ".ph" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".nwk" ) + || f.isDirectory(); + } + + @Override + public String getDescription() { + return "New Hampshire - Newick files (*.nh, *.newick, *.phy, *.tree, *.dnd, *.tr, *.ph, *.phb, *.nwk)"; + } +} // NHFilter + +class NHXFilter extends FileFilter { + + @Override + public boolean accept( final File f ) { + final String file_name = f.getName().trim().toLowerCase(); + return file_name.endsWith( ".nhx" ) || f.isDirectory(); + } + + @Override + public String getDescription() { + return "NHX files (*.nhx) [deprecated]"; + } +} + +class PdfFilter extends FileFilter { + + @Override + public boolean accept( final File f ) { + return f.getName().trim().toLowerCase().endsWith( ".pdf" ) || f.isDirectory(); + } + + @Override + public String getDescription() { + return "PDF files (*.pdf)"; + } +} // PdfFilter + +class SequencesFileFilter extends FileFilter { + + @Override + public boolean accept( final File f ) { + final String file_name = f.getName().trim().toLowerCase(); + return file_name.endsWith( ".fasta" ) || file_name.endsWith( ".fa" ) || file_name.endsWith( ".fas" ) + || file_name.endsWith( ".seqs" ) || f.isDirectory(); + } + + @Override + public String getDescription() { + return "Sequences files (*.fasta, *.fa, *.fas, *.seqs )"; + } +} + +class TolFilter extends FileFilter { + + @Override + public boolean accept( final File f ) { + final String file_name = f.getName().trim().toLowerCase(); + return ( file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" ) || file_name.endsWith( ".zip" ) || f + .isDirectory() ) && ( !file_name.endsWith( ".xml.zip" ) ); + } + + @Override + public String getDescription() { + return "Tree of Life files (*.tol, *.tolxml)"; + } +} // TolFilter + +class XMLFilter extends FileFilter { + + @Override + public boolean accept( final File f ) { + final String file_name = f.getName().trim().toLowerCase(); + return file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" ) || file_name.endsWith( "phylo.xml" ) + || file_name.endsWith( ".pxml" ) || file_name.endsWith( ".zip" ) || f.isDirectory(); + } + + @Override + public String getDescription() { + return "phyloXML files (*.xml, *.phyloxml, *phylo.xml, *.pxml, *.zip)"; + } +} // XMLFilter