From: cmzmasek Date: Wed, 13 Jul 2016 01:24:49 +0000 (-0700) Subject: in progress X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=803a2b32992b5944b73c6dfcb80ceb58c09b81c1;p=jalview.git in progress --- diff --git a/forester/java/src/org/forester/archaeopteryx/AptxConstants.java b/forester/java/src/org/forester/archaeopteryx/AptxConstants.java index 0508f65..f6049ce 100644 --- a/forester/java/src/org/forester/archaeopteryx/AptxConstants.java +++ b/forester/java/src/org/forester/archaeopteryx/AptxConstants.java @@ -38,8 +38,8 @@ public final class AptxConstants { final static boolean __ALLOW_PHYLOGENETIC_INFERENCE = true; public final static String PRG_NAME = "Archaeopteryx"; - final static String VERSION = "0.9913 beta"; - final static String PRG_DATE = "160701"; + final static String VERSION = "0.9914 beta"; + final static String PRG_DATE = "160712"; final static String DEFAULT_CONFIGURATION_FILE_NAME = "_aptx_configuration_file"; final static String[] DEFAULT_FONT_CHOICES = { "Arial Unicode MS", "Dialog", "SansSerif", "Sans", "Arial", "Helvetica" }; diff --git a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java index 5f94b35..958a952 100644 --- a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java +++ b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java @@ -72,6 +72,7 @@ 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.data.BranchWidth; import org.forester.phylogeny.data.Confidence; import org.forester.phylogeny.data.Taxonomy; import org.forester.phylogeny.iterators.PhylogenyNodeIterator; @@ -788,6 +789,19 @@ public final class AptxUtil { atv_control.setDrawPhylogram( false ); atv_control.setDrawPhylogramEnabled( false ); } + + if ( t.getFirstExternalNode().getBranchData().getBranchColor() != null + && atv_control.getUseVisualStylesCb() != null ) { + atv_control.getUseVisualStylesCb().setSelected( true ); + } + if ( t.getFirstExternalNode().getBranchData().getBranchWidth() != null + && t.getFirstExternalNode().getBranchData().getBranchWidth().getValue() + != BranchWidth.BRANCH_WIDTH_DEFAULT_VALUE + && atv_control.getUseBranchWidthsCb() != null ) { + atv_control.getUseBranchWidthsCb().setSelected( true ); + } + + if ( configuration.doGuessCheckOption( Configuration.display_as_phylogram ) ) { if ( atv_control.getDisplayAsPhylogramCb() != null ) { if ( has_bl ) { diff --git a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java index dcb7a4a..3c9990f 100644 --- a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java +++ b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java @@ -2480,4 +2480,8 @@ final class ControlPanel extends JPanel implements ActionListener { } return label; } + + public JCheckBox getUseBranchWidthsCb() { + return _width_branches; + } } diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrame.java b/forester/java/src/org/forester/archaeopteryx/MainFrame.java index 4cf0ac6..76d9ba7 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrame.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrame.java @@ -1,2722 +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.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; - // _ 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 == _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() ); - } - } - - 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 +// $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 diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java index 1d36727..fd79734 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java @@ -1,2207 +1,2210 @@ -// $Id: -// FORESTER -- software libraries and applications -// for evolutionary biology research and applications. -// -// Copyright (C) 2008-2009 Christian M. Zmasek -// Copyright (C) 2008-2009 Burnham Institute for Medical Research -// Copyright (C) 2003-2007 Ethalinda K.S. Cannon -// All rights reserved -// -// This library is free software; you can redistribute it and/or -// modify it under the terms of the GNU Lesser General Public -// License as published by the Free Software Foundation; either -// version 2.1 of the License, or (at your option) any later version. -// -// This library is distributed in the hope that it will be useful, -// but WITHOUT ANY WARRANTY; without even the implied warranty of -// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU -// Lesser General Public License for more details. -// -// You should have received a copy of the GNU Lesser General Public -// License along with this library; if not, write to the Free Software -// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA -// -// Contact: phylosoft @ gmail . com -// WWW: https://sites.google.com/site/cmzmasek/home/software/forester - -package org.forester.archaeopteryx; - -import java.awt.BorderLayout; -import java.awt.Font; -import java.awt.event.ActionEvent; -import java.awt.event.ComponentAdapter; -import java.awt.event.ComponentEvent; -import java.awt.event.WindowAdapter; -import java.awt.event.WindowEvent; -import java.io.File; -import java.io.FileInputStream; -import java.io.IOException; -import java.io.InputStream; -import java.net.MalformedURLException; -import java.net.URL; -import java.util.ArrayList; -import java.util.HashSet; -import java.util.List; -import java.util.Set; - -import javax.swing.ButtonGroup; -import javax.swing.JCheckBoxMenuItem; -import javax.swing.JFileChooser; -import javax.swing.JMenu; -import javax.swing.JMenuBar; -import javax.swing.JMenuItem; -import javax.swing.JOptionPane; -import javax.swing.JRadioButtonMenuItem; -import javax.swing.UIManager; -import javax.swing.UnsupportedLookAndFeelException; -import javax.swing.WindowConstants; -import javax.swing.event.ChangeEvent; -import javax.swing.event.ChangeListener; - -import org.forester.analysis.TaxonomyDataManager; -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.PhyloInferenceDialog; -import org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions; -import org.forester.archaeopteryx.tools.PhylogeneticInferrer; -import org.forester.archaeopteryx.tools.SequenceDataRetriver; -import org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient; -import org.forester.archaeopteryx.webservices.WebservicesManager; -import org.forester.io.parsers.FastaParser; -import org.forester.io.parsers.GeneralMsaParser; -import org.forester.io.parsers.PhylogenyParser; -import org.forester.io.parsers.nexus.NexusPhylogeniesParser; -import org.forester.io.parsers.nhx.NHXParser; -import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION; -import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException; -import org.forester.io.parsers.phyloxml.PhyloXmlParser; -import org.forester.io.parsers.phyloxml.PhyloXmlUtil; -import org.forester.io.parsers.tol.TolParser; -import org.forester.io.parsers.util.ParserUtils; -import org.forester.io.writers.SequenceWriter; -import org.forester.msa.Msa; -import org.forester.msa.MsaFormatException; -import org.forester.phylogeny.Phylogeny; -import org.forester.phylogeny.PhylogenyMethods; -import org.forester.phylogeny.PhylogenyNode; -import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE; -import org.forester.phylogeny.data.Confidence; -import org.forester.phylogeny.data.PhylogenyDataUtil; -import org.forester.phylogeny.data.Sequence; -import org.forester.phylogeny.data.Taxonomy; -import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory; -import org.forester.phylogeny.factories.PhylogenyFactory; -import org.forester.phylogeny.iterators.PhylogenyNodeIterator; -import org.forester.sequence.MolecularSequence; -import org.forester.util.BasicDescriptiveStatistics; -import org.forester.util.BasicTable; -import org.forester.util.BasicTableParser; -import org.forester.util.DescriptiveStatistics; -import org.forester.util.ForesterUtil; - -public final class MainFrameApplication extends MainFrame { - - private final static int FRAME_X_SIZE = 800; - private final static int FRAME_Y_SIZE = 800; - // Filters for the file-open dialog (classes defined in this file) - private static final long serialVersionUID = -799735726778865234L; - private static final boolean PREPROCESS_TREES = false; - private final JFileChooser _values_filechooser; - private final JFileChooser _sequences_filechooser; - private final JFileChooser _open_filechooser; - private final JFileChooser _msa_filechooser; - private final JFileChooser _seqs_pi_filechooser; - private final JFileChooser _open_filechooser_for_species_tree; - // Application-only print menu items - private JMenuItem _collapse_below_threshold; - private JMenuItem _collapse_below_branch_length; - private ButtonGroup _radio_group_1; - private ButtonGroup _radio_group_2; - // Others: - double _min_not_collapse = AptxConstants.MIN_NOT_COLLAPSE_DEFAULT; - double _min_not_collapse_bl = 0.001; - // Phylogeny Inference menu - private JMenu _inference_menu; - private JMenuItem _inference_from_msa_item; - private JMenuItem _inference_from_seqs_item; - // Phylogeny Inference - private PhylogeneticInferenceOptions _phylogenetic_inference_options = null; - private Msa _msa = null; - private File _msa_file = null; - private List _seqs = null; - private File _seqs_file = null; - JMenuItem _read_values_jmi; - JMenuItem _read_seqs_jmi; - - private MainFrameApplication( final Phylogeny[] phys, final Configuration config ) { - _configuration = config; - if ( _configuration == null ) { - throw new IllegalArgumentException( "configuration is null" ); - } - setVisible( false ); - setOptions( Options.createInstance( _configuration ) ); - _mainpanel = new MainPanel( _configuration, this ); - _open_filechooser = null; - _open_filechooser_for_species_tree = null; - _save_filechooser = null; - _writetopdf_filechooser = null; - _writetographics_filechooser = null; - _msa_filechooser = null; - _seqs_pi_filechooser = null; - _values_filechooser = null; - _sequences_filechooser = null; - _jmenubar = new JMenuBar(); - buildFileMenu(); - buildTypeMenu(); - _contentpane = getContentPane(); - _contentpane.setLayout( new BorderLayout() ); - _contentpane.add( _mainpanel, BorderLayout.CENTER ); - // App is this big - setSize( MainFrameApplication.FRAME_X_SIZE, MainFrameApplication.FRAME_Y_SIZE ); - // The window listener - setDefaultCloseOperation( WindowConstants.DO_NOTHING_ON_CLOSE ); - addWindowListener( new WindowAdapter() { - - @Override - public void windowClosing( final WindowEvent e ) { - exit(); - } - } ); - // setVisible( true ); - if ( ( phys != null ) && ( phys.length > 0 ) ) { - AptxUtil.addPhylogeniesToTabs( phys, "", null, _configuration, _mainpanel ); - validate(); - getMainPanel().getControlPanel().showWholeAll(); - getMainPanel().getControlPanel().showWhole(); - } - //activateSaveAllIfNeeded(); - // ...and its children - _contentpane.repaint(); - } - - private MainFrameApplication( final Phylogeny[] phys, final Configuration config, final String title ) { - this( phys, config, title, null ); - } - - private MainFrameApplication( final Phylogeny[] phys, - final Configuration config, - final String title, - final File current_dir ) { - super(); - _configuration = config; - if ( _configuration == null ) { - throw new IllegalArgumentException( "configuration is null" ); - } - try { - if ( _configuration.isUseNativeUI() ) { - UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() ); - } - else { - UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() ); - } - } - catch ( final UnsupportedLookAndFeelException e ) { - AptxUtil.dieWithSystemError( "unsupported look and feel: " + e.toString() ); - } - catch ( final ClassNotFoundException e ) { - AptxUtil.dieWithSystemError( "class not found exception: " + e.toString() ); - } - catch ( final InstantiationException e ) { - AptxUtil.dieWithSystemError( "instantiation exception: " + e.toString() ); - } - catch ( final IllegalAccessException e ) { - AptxUtil.dieWithSystemError( "illegal access exception: " + e.toString() ); - } - if ( ( current_dir != null ) && current_dir.canRead() && current_dir.isDirectory() ) { - setCurrentDir( current_dir ); - } - // hide until everything is ready - setVisible( false ); - setOptions( Options.createInstance( _configuration ) ); - setInferenceManager( InferenceManager.createInstance( _configuration ) ); - setPhylogeneticInferenceOptions( PhylogeneticInferenceOptions.createInstance( _configuration ) ); - // set title - setTitle( AptxConstants.PRG_NAME + " " + AptxConstants.VERSION + " (" + AptxConstants.PRG_DATE + ")" ); - _mainpanel = new MainPanel( _configuration, this ); - // The file dialogs - _open_filechooser = new JFileChooser(); - _open_filechooser.setMultiSelectionEnabled( true ); - _open_filechooser.addChoosableFileFilter( MainFrame.xmlfilter ); - _open_filechooser.addChoosableFileFilter( MainFrame.nhxfilter ); - _open_filechooser.addChoosableFileFilter( MainFrame.nhfilter ); - _open_filechooser.addChoosableFileFilter( MainFrame.nexusfilter ); - _open_filechooser.addChoosableFileFilter( MainFrame.tolfilter ); - _open_filechooser.addChoosableFileFilter( _open_filechooser.getAcceptAllFileFilter() ); - _open_filechooser.setFileFilter( MainFrame.defaultfilter ); - _open_filechooser_for_species_tree = new JFileChooser(); - _open_filechooser_for_species_tree.setMultiSelectionEnabled( false ); - _open_filechooser_for_species_tree.addChoosableFileFilter( MainFrame.xmlfilter ); - _open_filechooser_for_species_tree.addChoosableFileFilter( MainFrame.tolfilter ); - _open_filechooser_for_species_tree.setFileFilter( MainFrame.xmlfilter ); - // Msa: - _msa_filechooser = new JFileChooser(); - _msa_filechooser.setName( "Read Multiple Sequence Alignment File" ); - _msa_filechooser.setMultiSelectionEnabled( false ); - _msa_filechooser.addChoosableFileFilter( _msa_filechooser.getAcceptAllFileFilter() ); - _msa_filechooser.addChoosableFileFilter( MainFrame.msafilter ); - // Seqs: - _seqs_pi_filechooser = new JFileChooser(); - _seqs_pi_filechooser.setName( "Read Sequences File" ); - _seqs_pi_filechooser.setMultiSelectionEnabled( false ); - _seqs_pi_filechooser.addChoosableFileFilter( _seqs_pi_filechooser.getAcceptAllFileFilter() ); - _seqs_pi_filechooser.addChoosableFileFilter( MainFrame.seqsfilter ); - // Expression - _values_filechooser = new JFileChooser(); - _values_filechooser.setMultiSelectionEnabled( false ); - // Sequences - _sequences_filechooser = new JFileChooser(); - _sequences_filechooser.setMultiSelectionEnabled( false ); - try { - final String home_dir = System.getProperty( "user.home" ); - _open_filechooser.setCurrentDirectory( new File( home_dir ) ); - _open_filechooser_for_species_tree.setCurrentDirectory( new File( home_dir ) ); - _msa_filechooser.setCurrentDirectory( new File( home_dir ) ); - _seqs_pi_filechooser.setCurrentDirectory( new File( home_dir ) ); - _values_filechooser.setCurrentDirectory( new File( home_dir ) ); - _sequences_filechooser.setCurrentDirectory( new File( home_dir ) ); - } - catch ( final Exception e ) { - e.printStackTrace(); - // Do nothing. Not important. - } - // build the menu bar - _jmenubar = new JMenuBar(); - if ( !_configuration.isUseNativeUI() ) { - _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() ); - } - buildFileMenu(); - if ( AptxConstants.__ALLOW_PHYLOGENETIC_INFERENCE ) { - buildPhylogeneticInferenceMenu(); - } - buildAnalysisMenu(); - buildToolsMenu(); - buildViewMenu(); - buildFontSizeMenu(); - buildOptionsMenu(); - buildTypeMenu(); - buildHelpMenu(); - setJMenuBar( _jmenubar ); - _jmenubar.add( _help_jmenu ); - _contentpane = getContentPane(); - _contentpane.setLayout( new BorderLayout() ); - _contentpane.add( _mainpanel, BorderLayout.CENTER ); - // App is this big - setSize( MainFrameApplication.FRAME_X_SIZE, MainFrameApplication.FRAME_Y_SIZE ); - // addWindowFocusListener( new WindowAdapter() { - // - // @Override - // public void windowGainedFocus( WindowEvent e ) { - // requestFocusInWindow(); - // } - // } ); - // The window listener - setDefaultCloseOperation( WindowConstants.DO_NOTHING_ON_CLOSE ); - addWindowListener( new WindowAdapter() { - - @Override - public void windowClosing( final WindowEvent e ) { - if ( isUnsavedDataPresent() ) { - final int r = JOptionPane.showConfirmDialog( null, - "Exit despite potentially unsaved changes?", - "Exit?", - JOptionPane.YES_NO_OPTION ); - if ( r != JOptionPane.YES_OPTION ) { - return; - } - } - else { - final int r = JOptionPane.showConfirmDialog( null, - "Exit Archaeopteryx?", - "Exit?", - JOptionPane.YES_NO_OPTION ); - if ( r != JOptionPane.YES_OPTION ) { - return; - } - } - exit(); - } - } ); - // The component listener - addComponentListener( new ComponentAdapter() { - - @Override - public void componentResized( final ComponentEvent e ) { - if ( _mainpanel.getCurrentTreePanel() != null ) { - _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel() - .getWidth(), - _mainpanel.getCurrentTreePanel() - .getHeight() ); - } - } - } ); - requestFocusInWindow(); - // addKeyListener( this ); - setVisible( true ); - if ( ( phys != null ) && ( phys.length > 0 ) ) { - AptxUtil.addPhylogeniesToTabs( phys, title, null, _configuration, _mainpanel ); - validate(); - getMainPanel().getControlPanel().showWholeAll(); - getMainPanel().getControlPanel().showWhole(); - } - activateSaveAllIfNeeded(); - // ...and its children - _contentpane.repaint(); - System.gc(); - } - - private MainFrameApplication( final Phylogeny[] phys, final String config_file, final String title ) { - // Reads the config file (false, false => not url, not applet): - this( phys, new Configuration( config_file, false, false, true ), title ); - } - - @Override - public void actionPerformed( final ActionEvent e ) { - try { - super.actionPerformed( e ); - final Object o = e.getSource(); - // Handle app-specific actions here: - if ( o == _open_item ) { - readPhylogeniesFromFile(); - } - if ( o == _open_url_item ) { - readPhylogeniesFromURL(); - } - else if ( o == _new_item ) { - newTree(); - } - else if ( o == _close_item ) { - closeCurrentPane(); - } - else if ( o == _load_species_tree_item ) { - readSpeciesTreeFromFile(); - } - else if ( o == _obtain_detailed_taxonomic_information_jmi ) { - if ( isSubtreeDisplayed() ) { - return; - } - obtainDetailedTaxonomicInformation(); - } - else if ( o == _obtain_detailed_taxonomic_information_deleting_jmi ) { - if ( isSubtreeDisplayed() ) { - return; - } - obtainDetailedTaxonomicInformationDelete(); - } - else if ( o == _obtain_seq_information_jmi ) { - obtainSequenceInformation(); - } - else if ( o == _read_values_jmi ) { - if ( isSubtreeDisplayed() ) { - return; - } - addExpressionValuesFromFile(); - } - else if ( o == _read_seqs_jmi ) { - if ( isSubtreeDisplayed() ) { - return; - } - addSequencesFromFile(); - } - else if ( o == _move_node_names_to_tax_sn_jmi ) { - moveNodeNamesToTaxSn(); - } - else if ( o == _move_node_names_to_seq_names_jmi ) { - moveNodeNamesToSeqNames(); - } - else if ( o == _extract_tax_code_from_node_names_jmi ) { - extractTaxDataFromNodeNames(); - } - else if ( o == _internal_number_are_confidence_for_nh_parsing_cbmi ) { - updateOptions( getOptions() ); - } - else if ( o == _replace_underscores_cbmi ) { - if ( ( _extract_taxonomy_no_rbmi != null ) && !_extract_taxonomy_no_rbmi.isSelected() ) { - _extract_taxonomy_no_rbmi.setSelected( true ); - } - updateOptions( getOptions() ); - } - else if ( o == _allow_errors_in_distance_to_parent_cbmi ) { - updateOptions( getOptions() ); - } - else if ( o == _collapse_below_threshold ) { - if ( isSubtreeDisplayed() ) { - return; - } - collapseBelowThreshold(); - } - else if ( o == _collapse_below_branch_length ) { - if ( isSubtreeDisplayed() ) { - return; - } - collapseBelowBranchLengthThreshold(); - } - else if ( ( o == _extract_taxonomy_pfam_strict_rbmi ) || ( o == _extract_taxonomy_pfam_relaxed_rbmi ) - || ( o == _extract_taxonomy_agressive_rbmi ) ) { - if ( _replace_underscores_cbmi != null ) { - _replace_underscores_cbmi.setSelected( false ); - } - updateOptions( getOptions() ); - } - else if ( o == _extract_taxonomy_no_rbmi ) { - updateOptions( getOptions() ); - } - else if ( o == _inference_from_msa_item ) { - executePhyleneticInference( false ); - } - else if ( o == _inference_from_seqs_item ) { - executePhyleneticInference( true ); - } - _contentpane.repaint(); - } - catch ( final Exception ex ) { - AptxUtil.unexpectedException( ex ); - } - catch ( final Error err ) { - AptxUtil.unexpectedError( err ); - } - } - - public void end() { - _mainpanel.terminate(); - _contentpane.removeAll(); - setVisible( false ); - dispose(); - } - - @Override - public MainPanel getMainPanel() { - return _mainpanel; - } - - public Msa getMsa() { - return _msa; - } - - public File getMsaFile() { - return _msa_file; - } - - public List getSeqs() { - return _seqs; - } - - public File getSeqsFile() { - return _seqs_file; - } - - public void readMsaFromFile() { - // Set an initial directory if none set yet - final File my_dir = getCurrentDir(); - _msa_filechooser.setMultiSelectionEnabled( false ); - // Open file-open dialog and set current directory - if ( my_dir != null ) { - _msa_filechooser.setCurrentDirectory( my_dir ); - } - final int result = _msa_filechooser.showOpenDialog( _contentpane ); - // All done: get the msa - final File file = _msa_filechooser.getSelectedFile(); - setCurrentDir( _msa_filechooser.getCurrentDirectory() ); - if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) { - setMsaFile( null ); - setMsa( null ); - Msa msa = null; - try { - final InputStream is = new FileInputStream( file ); - if ( FastaParser.isLikelyFasta( file ) ) { - msa = FastaParser.parseMsa( is ); - } - else { - msa = GeneralMsaParser.parse( is ); - } - } - catch ( final MsaFormatException e ) { - setArrowCursor(); - JOptionPane.showMessageDialog( this, - e.getLocalizedMessage(), - "Multiple sequence alignment format error", - JOptionPane.ERROR_MESSAGE ); - return; - } - catch ( final IOException e ) { - setArrowCursor(); - JOptionPane.showMessageDialog( this, - e.getLocalizedMessage(), - "Failed to read multiple sequence alignment", - JOptionPane.ERROR_MESSAGE ); - return; - } - catch ( final IllegalArgumentException e ) { - setArrowCursor(); - JOptionPane.showMessageDialog( this, - e.getLocalizedMessage(), - "Unexpected error during reading of multiple sequence alignment", - JOptionPane.ERROR_MESSAGE ); - return; - } - catch ( final Exception e ) { - setArrowCursor(); - e.printStackTrace(); - JOptionPane.showMessageDialog( this, - e.getLocalizedMessage(), - "Unexpected error during reading of multiple sequence alignment", - JOptionPane.ERROR_MESSAGE ); - return; - } - if ( ( msa == null ) || ( msa.getNumberOfSequences() < 1 ) ) { - JOptionPane.showMessageDialog( this, - "Multiple sequence alignment is empty", - "Illegal Multiple Sequence Alignment", - JOptionPane.ERROR_MESSAGE ); - return; - } - if ( msa.getNumberOfSequences() < 4 ) { - JOptionPane.showMessageDialog( this, - "Multiple sequence alignment needs to contain at least 3 sequences", - "Illegal multiple sequence alignment", - JOptionPane.ERROR_MESSAGE ); - return; - } - if ( msa.getLength() < 2 ) { - JOptionPane.showMessageDialog( this, - "Multiple sequence alignment needs to contain at least 2 residues", - "Illegal multiple sequence alignment", - JOptionPane.ERROR_MESSAGE ); - return; - } - System.gc(); - setMsaFile( _msa_filechooser.getSelectedFile() ); - setMsa( msa ); - } - } - - public void readSeqsFromFileforPI() { - // Set an initial directory if none set yet - final File my_dir = getCurrentDir(); - _seqs_pi_filechooser.setMultiSelectionEnabled( false ); - // Open file-open dialog and set current directory - if ( my_dir != null ) { - _seqs_pi_filechooser.setCurrentDirectory( my_dir ); - } - final int result = _seqs_pi_filechooser.showOpenDialog( _contentpane ); - // All done: get the seqs - final File file = _seqs_pi_filechooser.getSelectedFile(); - setCurrentDir( _seqs_pi_filechooser.getCurrentDirectory() ); - if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) { - setSeqsFile( null ); - setSeqs( null ); - List seqs = null; - try { - if ( FastaParser.isLikelyFasta( new FileInputStream( file ) ) ) { - seqs = FastaParser.parse( new FileInputStream( file ) ); - for( final MolecularSequence seq : seqs ) { - System.out.println( SequenceWriter.toFasta( seq, 60 ) ); - } - } - else { - //TODO error - } - } - catch ( final MsaFormatException e ) { - setArrowCursor(); - JOptionPane.showMessageDialog( this, - e.getLocalizedMessage(), - "Multiple sequence file format error", - JOptionPane.ERROR_MESSAGE ); - return; - } - catch ( final IOException e ) { - setArrowCursor(); - JOptionPane.showMessageDialog( this, - e.getLocalizedMessage(), - "Failed to read multiple sequence file", - JOptionPane.ERROR_MESSAGE ); - return; - } - catch ( final IllegalArgumentException e ) { - setArrowCursor(); - JOptionPane.showMessageDialog( this, - e.getLocalizedMessage(), - "Unexpected error during reading of multiple sequence file", - JOptionPane.ERROR_MESSAGE ); - return; - } - catch ( final Exception e ) { - setArrowCursor(); - e.printStackTrace(); - JOptionPane.showMessageDialog( this, - e.getLocalizedMessage(), - "Unexpected error during reading of multiple sequence file", - JOptionPane.ERROR_MESSAGE ); - return; - } - if ( ( seqs == null ) || ( seqs.size() < 1 ) ) { - JOptionPane.showMessageDialog( this, - "Multiple sequence file is empty", - "Illegal multiple sequence file", - JOptionPane.ERROR_MESSAGE ); - return; - } - if ( seqs.size() < 4 ) { - JOptionPane.showMessageDialog( this, - "Multiple sequence file needs to contain at least 3 sequences", - "Illegal multiple sequence file", - JOptionPane.ERROR_MESSAGE ); - return; - } - // if ( msa.getLength() < 2 ) { - // JOptionPane.showMessageDialog( this, - // "Multiple sequence alignment needs to contain at least 2 residues", - // "Illegal multiple sequence file", - // JOptionPane.ERROR_MESSAGE ); - // return; - // } - System.gc(); - setSeqsFile( _seqs_pi_filechooser.getSelectedFile() ); - setSeqs( seqs ); - } - } - - private void addExpressionValuesFromFile() { - if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) { - JOptionPane.showMessageDialog( this, - "Need to load evolutionary tree first", - "Can Not Read Expression Values", - JOptionPane.WARNING_MESSAGE ); - return; - } - final File my_dir = getCurrentDir(); - if ( my_dir != null ) { - _values_filechooser.setCurrentDirectory( my_dir ); - } - final int result = _values_filechooser.showOpenDialog( _contentpane ); - final File file = _values_filechooser.getSelectedFile(); - if ( ( file != null ) && ( file.length() > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) { - BasicTable t = null; - try { - t = BasicTableParser.parse( file, '\t' ); - if ( t.getNumberOfColumns() < 2 ) { - t = BasicTableParser.parse( file, ',' ); - } - if ( t.getNumberOfColumns() < 2 ) { - t = BasicTableParser.parse( file, ' ' ); - } - } - catch ( final IOException e ) { - JOptionPane.showMessageDialog( this, - e.getMessage(), - "Could Not Read Expression Value Table", - JOptionPane.ERROR_MESSAGE ); - return; - } - if ( t.getNumberOfColumns() < 2 ) { - JOptionPane.showMessageDialog( this, - "Table contains " + t.getNumberOfColumns() + " column(s)", - "Problem with Expression Value Table", - JOptionPane.ERROR_MESSAGE ); - return; - } - if ( t.getNumberOfRows() < 1 ) { - JOptionPane.showMessageDialog( this, - "Table contains zero rows", - "Problem with Expression Value Table", - JOptionPane.ERROR_MESSAGE ); - return; - } - final Phylogeny phy = getCurrentTreePanel().getPhylogeny(); - if ( t.getNumberOfRows() != phy.getNumberOfExternalNodes() ) { - JOptionPane.showMessageDialog( this, - "Table contains " + t.getNumberOfRows() + " rows, but tree contains " - + phy.getNumberOfExternalNodes() + " external nodes", - "Warning", - JOptionPane.WARNING_MESSAGE ); - } - final DescriptiveStatistics stats = new BasicDescriptiveStatistics(); - int not_found = 0; - for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) { - final PhylogenyNode node = iter.next(); - final String node_name = node.getName(); - if ( !ForesterUtil.isEmpty( node_name ) ) { - int row = -1; - try { - row = t.findRow( node_name ); - } - catch ( final IllegalArgumentException e ) { - JOptionPane - .showMessageDialog( this, - e.getMessage(), - "Error Mapping Node Identifiers to Expression Value Identifiers", - JOptionPane.ERROR_MESSAGE ); - return; - } - if ( row < 0 ) { - if ( node.isExternal() ) { - not_found++; - } - continue; - } - final List l = new ArrayList(); - for( int col = 1; col < t.getNumberOfColumns(); ++col ) { - double d = -100; - try { - d = Double.parseDouble( t.getValueAsString( col, row ) ); - } - catch ( final NumberFormatException e ) { - JOptionPane.showMessageDialog( this, - "Could not parse \"" + t.getValueAsString( col, row ) - + "\" into a decimal value", - "Issue with Expression Value Table", - JOptionPane.ERROR_MESSAGE ); - return; - } - stats.addValue( d ); - l.add( d ); - } - if ( !l.isEmpty() ) { - if ( node.getNodeData().getProperties() != null ) { - node.getNodeData().getProperties() - .removePropertiesWithGivenReferencePrefix( PhyloXmlUtil.VECTOR_PROPERTY_REF ); - } - node.getNodeData().setVector( l ); - } - } - } - if ( not_found > 0 ) { - JOptionPane.showMessageDialog( this, "Could not fine expression values for " + not_found - + " external node(s)", "Warning", JOptionPane.WARNING_MESSAGE ); - } - getCurrentTreePanel().setStatisticsForExpressionValues( stats ); - } - } - - private void addSequencesFromFile() { - if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) { - JOptionPane.showMessageDialog( this, - "Need to load evolutionary tree first", - "Can Not Read Sequences", - JOptionPane.WARNING_MESSAGE ); - return; - } - final File my_dir = getCurrentDir(); - if ( my_dir != null ) { - _sequences_filechooser.setCurrentDirectory( my_dir ); - } - final int result = _sequences_filechooser.showOpenDialog( _contentpane ); - final File file = _sequences_filechooser.getSelectedFile(); - List seqs = null; - if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) { - try { - final FileInputStream fis1 = new FileInputStream( file ); - if ( FastaParser.isLikelyFasta( fis1 ) ) { - final FileInputStream fis2 = new FileInputStream( file ); - seqs = FastaParser.parse( fis2 ); - try { - fis2.close(); - } - catch ( final Exception e ) { - // Ignore. - } - } - else { - JOptionPane.showMessageDialog( this, - "Format does not appear to be Fasta", - "Multiple sequence file format error", - JOptionPane.ERROR_MESSAGE ); - return; - } - try { - fis1.close(); - } - catch ( final Exception e ) { - // Ignore. - } - } - catch ( final MsaFormatException e ) { - setArrowCursor(); - JOptionPane.showMessageDialog( this, - e.getLocalizedMessage(), - "Multiple sequence file format error", - JOptionPane.ERROR_MESSAGE ); - return; - } - catch ( final IOException e ) { - setArrowCursor(); - JOptionPane.showMessageDialog( this, - e.getLocalizedMessage(), - "Failed to read multiple sequence file", - JOptionPane.ERROR_MESSAGE ); - return; - } - catch ( final Exception e ) { - setArrowCursor(); - e.printStackTrace(); - JOptionPane.showMessageDialog( this, - e.getLocalizedMessage(), - "Unexpected error during reading of multiple sequence file", - JOptionPane.ERROR_MESSAGE ); - return; - } - if ( ( seqs == null ) || ( seqs.size() < 1 ) ) { - JOptionPane.showMessageDialog( this, - "Multiple sequence file is empty", - "Empty multiple sequence file", - JOptionPane.ERROR_MESSAGE ); - setArrowCursor(); - return; - } - } - if ( seqs != null ) { - for( final MolecularSequence seq : seqs ) { - System.out.println( seq.getIdentifier() ); - } - final Phylogeny phy = getCurrentTreePanel().getPhylogeny(); - int total_counter = 0; - int attached_counter = 0; - for( final MolecularSequence seq : seqs ) { - ++total_counter; - final String seq_name = seq.getIdentifier(); - if ( !ForesterUtil.isEmpty( seq_name ) ) { - List nodes = phy.getNodesViaSequenceName( seq_name ); - if ( nodes.isEmpty() ) { - nodes = phy.getNodesViaSequenceSymbol( seq_name ); - } - if ( nodes.isEmpty() ) { - nodes = phy.getNodesViaGeneName( seq_name ); - } - if ( nodes.isEmpty() ) { - nodes = phy.getNodes( seq_name ); - } - if ( nodes.size() > 1 ) { - JOptionPane.showMessageDialog( this, - "Sequence name \"" + seq_name + "\" is not unique", - "Sequence name not unique", - JOptionPane.ERROR_MESSAGE ); - setArrowCursor(); - return; - } - final String[] a = seq_name.split( "\\s" ); - if ( nodes.isEmpty() && ( a.length > 1 ) ) { - final String seq_name_split = a[ 0 ]; - nodes = phy.getNodesViaSequenceName( seq_name_split ); - if ( nodes.isEmpty() ) { - nodes = phy.getNodesViaSequenceSymbol( seq_name_split ); - } - if ( nodes.isEmpty() ) { - nodes = phy.getNodes( seq_name_split ); - } - if ( nodes.size() > 1 ) { - JOptionPane.showMessageDialog( this, "Split sequence name \"" + seq_name_split - + "\" is not unique", "Sequence name not unique", JOptionPane.ERROR_MESSAGE ); - setArrowCursor(); - return; - } - } - if ( nodes.size() == 1 ) { - ++attached_counter; - final PhylogenyNode n = nodes.get( 0 ); - if ( !n.getNodeData().isHasSequence() ) { - n.getNodeData().addSequence( new org.forester.phylogeny.data.Sequence() ); - } - n.getNodeData().getSequence().setMolecularSequence( seq.getMolecularSequenceAsString() ); - if ( ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) { - n.getNodeData().getSequence().setName( seq_name ); - } - } - } - } - if ( attached_counter > 0 ) { - int ext_nodes = 0; - int ext_nodes_with_seq = 0; - for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) { - ++ext_nodes; - final PhylogenyNode n = iter.next(); - if ( n.getNodeData().isHasSequence() - && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getMolecularSequence() ) ) { - ++ext_nodes_with_seq; - } - } - final String s; - if ( ext_nodes == ext_nodes_with_seq ) { - s = "All " + ext_nodes_with_seq + " external nodes now have a molecular sequence attached to them."; - } - else { - s = ext_nodes_with_seq + " out of " + ext_nodes - + " external nodes now have a molecular sequence attached to them."; - } - if ( ( attached_counter == total_counter ) && ( ext_nodes == ext_nodes_with_seq ) ) { - JOptionPane.showMessageDialog( this, - "Attached all " + total_counter + " sequences to tree nodes.\n" + s, - "All sequences attached", - JOptionPane.INFORMATION_MESSAGE ); - } - else { - JOptionPane.showMessageDialog( this, "Attached " + attached_counter - + " sequences out of a total of " + total_counter + " sequences.\n" + s, attached_counter - + " sequences attached", JOptionPane.WARNING_MESSAGE ); - } - } - else { - JOptionPane.showMessageDialog( this, "No maching tree node for any of the " + total_counter - + " sequences", "Could not attach any sequences", JOptionPane.ERROR_MESSAGE ); - } - } - } - - private void closeCurrentPane() { - if ( getMainPanel().getCurrentTreePanel() != null ) { - if ( getMainPanel().getCurrentTreePanel().isEdited() ) { - final int r = JOptionPane.showConfirmDialog( this, - "Close tab despite potentially unsaved changes?", - "Close Tab?", - JOptionPane.YES_NO_OPTION ); - if ( r != JOptionPane.YES_OPTION ) { - return; - } - } - getMainPanel().closeCurrentPane(); - activateSaveAllIfNeeded(); - } - } - - private void collapse( final Phylogeny phy ) { - final PhylogenyNodeIterator it = phy.iteratorPostorder(); - final List to_be_removed = new ArrayList(); - double min_support = Double.MAX_VALUE; - boolean conf_present = false; - while ( it.hasNext() ) { - final PhylogenyNode n = it.next(); - if ( !n.isExternal() && !n.isRoot() ) { - final List c = n.getBranchData().getConfidences(); - if ( ( c != null ) && ( c.size() > 0 ) ) { - conf_present = true; - double max = 0; - for( final Confidence confidence : c ) { - if ( confidence.getValue() > max ) { - max = confidence.getValue(); - } - } - if ( max < getMinNotCollapseConfidenceValue() ) { - to_be_removed.add( n ); - } - if ( max < min_support ) { - min_support = max; - } - } - } - } - if ( conf_present ) { - for( final PhylogenyNode node : to_be_removed ) { - PhylogenyMethods.removeNode( node, phy ); - } - if ( to_be_removed.size() > 0 ) { - phy.externalNodesHaveChanged(); - phy.clearHashIdToNodeMap(); - phy.recalculateNumberOfExternalDescendants( true ); - getCurrentTreePanel().resetNodeIdToDistToLeafMap(); - getCurrentTreePanel().updateSetOfCollapsedExternalNodes(); - getCurrentTreePanel().calculateLongestExtNodeInfo(); - getCurrentTreePanel().setNodeInPreorderToNull(); - getCurrentTreePanel().recalculateMaxDistanceToRoot(); - getCurrentTreePanel().resetPreferredSize(); - getCurrentTreePanel().setEdited( true ); - getCurrentTreePanel().repaint(); - repaint(); - } - if ( to_be_removed.size() > 0 ) { - JOptionPane.showMessageDialog( this, "Collapsed " + to_be_removed.size() - + " branches with\nconfidence values below " + getMinNotCollapseConfidenceValue(), "Collapsed " - + to_be_removed.size() + " branches", JOptionPane.INFORMATION_MESSAGE ); - } - else { - JOptionPane.showMessageDialog( this, "No branch collapsed,\nminimum confidence value per branch is " - + min_support, "No branch collapsed", JOptionPane.INFORMATION_MESSAGE ); - } - } - else { - JOptionPane.showMessageDialog( this, - "No branch collapsed because no confidence values present", - "No confidence values present", - JOptionPane.INFORMATION_MESSAGE ); - } - } - - private void collapseBelowBranchLengthThreshold() { - if ( getCurrentTreePanel() != null ) { - final Phylogeny phy = getCurrentTreePanel().getPhylogeny(); - if ( ( phy != null ) && !phy.isEmpty() ) { - final String s = ( String ) JOptionPane - .showInputDialog( this, - "Please enter the minimum branch length value\n", - "Minimal Branch Length Value", - JOptionPane.QUESTION_MESSAGE, - null, - null, - getMinNotCollapseBlValue() ); - 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 ) ) { - setMinNotCollapseBlValue( m ); - collapseBl( phy ); - } - } - } - } - } - - private void collapseBelowThreshold() { - if ( getCurrentTreePanel() != null ) { - final Phylogeny phy = getCurrentTreePanel().getPhylogeny(); - if ( ( phy != null ) && !phy.isEmpty() ) { - final String s = ( String ) JOptionPane.showInputDialog( this, - "Please enter the minimum confidence value\n", - "Minimal Confidence Value", - JOptionPane.QUESTION_MESSAGE, - null, - null, - getMinNotCollapseConfidenceValue() ); - if ( !ForesterUtil.isEmpty( s ) ) { - boolean success = true; - double m = 0.0; - final String m_str = s.trim(); - if ( !ForesterUtil.isEmpty( m_str ) ) { - try { - m = Double.parseDouble( m_str ); - } - catch ( final Exception ex ) { - success = false; - } - } - else { - success = false; - } - if ( success && ( m >= 0.0 ) ) { - setMinNotCollapseConfidenceValue( m ); - collapse( phy ); - } - } - } - } - } - - private void collapseBl( final Phylogeny phy ) { - final PhylogenyNodeIterator it = phy.iteratorPostorder(); - final List to_be_removed = new ArrayList(); - double min_bl = Double.MAX_VALUE; - boolean bl_present = false; - while ( it.hasNext() ) { - final PhylogenyNode n = it.next(); - if ( !n.isExternal() && !n.isRoot() ) { - final double bl = n.getDistanceToParent(); - if ( bl != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) { - bl_present = true; - if ( bl < getMinNotCollapseBlValue() ) { - to_be_removed.add( n ); - } - if ( bl < min_bl ) { - min_bl = bl; - } - } - } - } - if ( bl_present ) { - for( final PhylogenyNode node : to_be_removed ) { - PhylogenyMethods.removeNode( node, phy ); - } - if ( to_be_removed.size() > 0 ) { - phy.externalNodesHaveChanged(); - phy.clearHashIdToNodeMap(); - phy.recalculateNumberOfExternalDescendants( true ); - getCurrentTreePanel().resetNodeIdToDistToLeafMap(); - getCurrentTreePanel().updateSetOfCollapsedExternalNodes(); - getCurrentTreePanel().calculateLongestExtNodeInfo(); - getCurrentTreePanel().setNodeInPreorderToNull(); - getCurrentTreePanel().recalculateMaxDistanceToRoot(); - getCurrentTreePanel().resetPreferredSize(); - getCurrentTreePanel().setEdited( true ); - getCurrentTreePanel().repaint(); - repaint(); - } - if ( to_be_removed.size() > 0 ) { - JOptionPane.showMessageDialog( this, "Collapsed " + to_be_removed.size() - + " branches with\nbranch length values below " + getMinNotCollapseBlValue(), "Collapsed " - + to_be_removed.size() + " branches", JOptionPane.INFORMATION_MESSAGE ); - } - else { - JOptionPane.showMessageDialog( this, - "No branch collapsed,\nminimum branch length is " + min_bl, - "No branch collapsed", - JOptionPane.INFORMATION_MESSAGE ); - } - } - else { - JOptionPane.showMessageDialog( this, - "No branch collapsed because no branch length values present", - "No branch length values present", - JOptionPane.INFORMATION_MESSAGE ); - } - } - - private PhyloXmlParser createPhyloXmlParser() { - PhyloXmlParser xml_parser = null; - if ( getConfiguration().isValidatePhyloXmlAgainstSchema() ) { - try { - xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating(); - } - catch ( final Exception e ) { - JOptionPane.showMessageDialog( this, - e.getLocalizedMessage(), - "failed to create validating XML parser", - JOptionPane.WARNING_MESSAGE ); - } - } - if ( xml_parser == null ) { - xml_parser = PhyloXmlParser.createPhyloXmlParser(); - } - return xml_parser; - } - - private void executePhyleneticInference( final boolean from_unaligned_seqs ) { - final PhyloInferenceDialog dialog = new PhyloInferenceDialog( this, - getPhylogeneticInferenceOptions(), - from_unaligned_seqs ); - dialog.activate(); - if ( dialog.getValue() == JOptionPane.OK_OPTION ) { - if ( !from_unaligned_seqs ) { - if ( getMsa() != null ) { - final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getMsa(), - getPhylogeneticInferenceOptions() - .copy(), this ); - new Thread( inferrer ).start(); - } - else { - JOptionPane.showMessageDialog( this, - "No multiple sequence alignment selected", - "Phylogenetic Inference Not Launched", - JOptionPane.WARNING_MESSAGE ); - } - } - else { - if ( getSeqs() != null ) { - final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getSeqs(), - getPhylogeneticInferenceOptions() - .copy(), this ); - new Thread( inferrer ).start(); - } - else { - JOptionPane.showMessageDialog( this, - "No input sequences selected", - "Phylogenetic Inference Not Launched", - JOptionPane.WARNING_MESSAGE ); - } - } - } - } - - private void extractTaxDataFromNodeNames() throws PhyloXmlDataFormatException { - final StringBuilder sb = new StringBuilder(); - final StringBuilder sb_failed = new StringBuilder(); - int counter = 0; - int counter_failed = 0; - if ( getCurrentTreePanel() != null ) { - final Phylogeny phy = getCurrentTreePanel().getPhylogeny(); - if ( ( phy != null ) && !phy.isEmpty() ) { - final PhylogenyNodeIterator it = phy.iteratorExternalForward(); - while ( it.hasNext() ) { - final PhylogenyNode n = it.next(); - final String name = n.getName().trim(); - if ( !ForesterUtil.isEmpty( name ) ) { - final String nt = ParserUtils.extractTaxonomyDataFromNodeName( n, - TAXONOMY_EXTRACTION.AGGRESSIVE ); - if ( !ForesterUtil.isEmpty( nt ) ) { - if ( counter < 15 ) { - sb.append( name + ": " + nt + "\n" ); - } - else if ( counter == 15 ) { - sb.append( "...\n" ); - } - counter++; - } - else { - if ( counter_failed < 15 ) { - sb_failed.append( name + "\n" ); - } - else if ( counter_failed == 15 ) { - sb_failed.append( "...\n" ); - } - counter_failed++; - } - } - } - if ( counter > 0 ) { - String failed = ""; - String all = "all "; - if ( counter_failed > 0 ) { - all = ""; - failed = "\nCould not extract taxonomic data for " + counter_failed - + " named external nodes:\n" + sb_failed; - } - JOptionPane.showMessageDialog( this, - "Extracted taxonomic data from " + all + counter - + " named external nodes:\n" + sb.toString() + failed, - "Taxonomic Data Extraction Completed", - counter_failed > 0 ? JOptionPane.WARNING_MESSAGE - : JOptionPane.INFORMATION_MESSAGE ); - } - else { - JOptionPane - .showMessageDialog( this, - "Could not extract any taxonomic data.\nMaybe node names are empty\n" - + "or not in the forms \"XYZ_CAEEL\", \"XYZ_6239\", or \"XYZ_Caenorhabditis_elegans\"\n" - + "or nodes already have taxonomic data?\n", - "No Taxonomic Data Extracted", - JOptionPane.ERROR_MESSAGE ); - } - } - } - } - - private double getMinNotCollapseBlValue() { - return _min_not_collapse_bl; - } - - private double getMinNotCollapseConfidenceValue() { - return _min_not_collapse; - } - - private PhylogeneticInferenceOptions getPhylogeneticInferenceOptions() { - if ( _phylogenetic_inference_options == null ) { - _phylogenetic_inference_options = new PhylogeneticInferenceOptions(); - } - return _phylogenetic_inference_options; - } - - private boolean isUnsavedDataPresent() { - final List tps = getMainPanel().getTreePanels(); - for( final TreePanel tp : tps ) { - if ( tp.isEdited() ) { - return true; - } - } - return false; - } - - private void moveNodeNamesToSeqNames() throws PhyloXmlDataFormatException { - if ( getCurrentTreePanel() != null ) { - final Phylogeny phy = getCurrentTreePanel().getPhylogeny(); - if ( ( phy != null ) && !phy.isEmpty() ) { - PhylogenyMethods - .transferNodeNameToField( phy, PhylogenyMethods.PhylogenyNodeField.SEQUENCE_NAME, false ); - } - } - } - - private void moveNodeNamesToTaxSn() throws PhyloXmlDataFormatException { - if ( getCurrentTreePanel() != null ) { - final Phylogeny phy = getCurrentTreePanel().getPhylogeny(); - if ( ( phy != null ) && !phy.isEmpty() ) { - PhylogenyMethods.transferNodeNameToField( phy, - PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME, - false ); - } - } - } - - private void newTree() { - final Phylogeny[] phys = new Phylogeny[ 1 ]; - final Phylogeny phy = new Phylogeny(); - final PhylogenyNode node = new PhylogenyNode(); - phy.setRoot( node ); - phy.setRooted( true ); - phys[ 0 ] = phy; - AptxUtil.addPhylogeniesToTabs( phys, "", "", getConfiguration(), getMainPanel() ); - _mainpanel.getControlPanel().showWhole(); - _mainpanel.getCurrentTreePanel().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ); - _mainpanel.getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ); - if ( getMainPanel().getMainFrame() == null ) { - // Must be "E" applet version. - ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() ) - .setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ); - } - else { - getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ); - } - activateSaveAllIfNeeded(); - System.gc(); - } - - private void obtainDetailedTaxonomicInformation() { - if ( getCurrentTreePanel() != null ) { - final Phylogeny phy = getCurrentTreePanel().getPhylogeny(); - if ( ( phy != null ) && !phy.isEmpty() ) { - final TaxonomyDataManager t = new TaxonomyDataManager( this, - _mainpanel.getCurrentTreePanel(), - phy.copy(), - false, - true ); - new Thread( t ).start(); - } - } - } - - private void obtainDetailedTaxonomicInformationDelete() { - if ( getCurrentTreePanel() != null ) { - final Phylogeny phy = getCurrentTreePanel().getPhylogeny(); - if ( ( phy != null ) && !phy.isEmpty() ) { - final TaxonomyDataManager t = new TaxonomyDataManager( this, - _mainpanel.getCurrentTreePanel(), - phy.copy(), - true, - true ); - new Thread( t ).start(); - } - } - } - - private void obtainSequenceInformation() { - if ( getCurrentTreePanel() != null ) { - final Phylogeny phy = getCurrentTreePanel().getPhylogeny(); - if ( ( phy != null ) && !phy.isEmpty() ) { - final SequenceDataRetriver u = new SequenceDataRetriver( this, - _mainpanel.getCurrentTreePanel(), - phy.copy() ); - new Thread( u ).start(); - } - } - } - - private void preProcessTreesUponReading( final Phylogeny[] phys ) { - for( final Phylogeny phy : phys ) { - if ( ( phy != null ) && !phy.isEmpty() ) { - for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) { - final PhylogenyNode n = it.next(); - if ( n.isExternal() ) { - if ( n.getNodeData().isHasSequence() ) { - final Sequence s = n.getNodeData().getSequence(); - if ( ForesterUtil.isEmpty( s.getGeneName() ) || s.getGeneName().startsWith( "LOC" ) ) { - if ( ( s.getAccession() != null ) - && !ForesterUtil.isEmpty( s.getAccession().getValue() ) ) { - s.setGeneName( s.getAccession().getValue() ); - } - else if ( !ForesterUtil.isEmpty( n.getName() ) ) { - s.setGeneName( n.getName() ); - } - } - } - } - } - } - } - } - - private void readPhylogeniesFromFile() { - boolean exception = false; - Phylogeny[] phys = null; - // Set an initial directory if none set yet - final File my_dir = getCurrentDir(); - // Open file-open dialog and set current directory - if ( my_dir != null ) { - _open_filechooser.setCurrentDirectory( my_dir ); - } - final int result = _open_filechooser.showOpenDialog( _contentpane ); - // All done: get the file - final File[] files = _open_filechooser.getSelectedFiles(); - setCurrentDir( _open_filechooser.getCurrentDirectory() ); - boolean nhx_or_nexus = false; - if ( ( files != null ) && ( files.length > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) { - for( final File file : files ) { - if ( ( file != null ) && !file.isDirectory() ) { - if ( _mainpanel.getCurrentTreePanel() != null ) { - _mainpanel.getCurrentTreePanel().setWaitCursor(); - } - else { - _mainpanel.setWaitCursor(); - } - if ( ( _open_filechooser.getFileFilter() == MainFrame.nhfilter ) - || ( _open_filechooser.getFileFilter() == MainFrame.nhxfilter ) ) { - try { - final NHXParser nhx = new NHXParser(); - setSpecialOptionsForNhxParser( nhx ); - phys = PhylogenyMethods.readPhylogenies( nhx, file ); - nhx_or_nexus = true; - } - catch ( final Exception e ) { - exception = true; - exceptionOccuredDuringOpenFile( e ); - } - } - else if ( _open_filechooser.getFileFilter() == MainFrame.xmlfilter ) { - warnIfNotPhyloXmlValidation( getConfiguration() ); - try { - final PhyloXmlParser xml_parser = createPhyloXmlParser(); - phys = PhylogenyMethods.readPhylogenies( xml_parser, file ); - } - catch ( final Exception e ) { - exception = true; - exceptionOccuredDuringOpenFile( e ); - } - } - else if ( _open_filechooser.getFileFilter() == MainFrame.tolfilter ) { - try { - phys = PhylogenyMethods.readPhylogenies( new TolParser(), file ); - } - catch ( final Exception e ) { - exception = true; - exceptionOccuredDuringOpenFile( e ); - } - } - else if ( _open_filechooser.getFileFilter() == MainFrame.nexusfilter ) { - try { - final NexusPhylogeniesParser nex = new NexusPhylogeniesParser(); - setSpecialOptionsForNexParser( nex ); - phys = PhylogenyMethods.readPhylogenies( nex, file ); - nhx_or_nexus = true; - } - catch ( final Exception e ) { - exception = true; - exceptionOccuredDuringOpenFile( e ); - } - } - // "*.*": - else { - try { - final PhylogenyParser parser = ParserUtils - .createParserDependingOnFileType( file, getConfiguration() - .isValidatePhyloXmlAgainstSchema() ); - if ( parser instanceof NexusPhylogeniesParser ) { - final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) parser; - setSpecialOptionsForNexParser( nex ); - nhx_or_nexus = true; - } - else if ( parser instanceof NHXParser ) { - final NHXParser nhx = ( NHXParser ) parser; - setSpecialOptionsForNhxParser( nhx ); - nhx_or_nexus = true; - } - else if ( parser instanceof PhyloXmlParser ) { - warnIfNotPhyloXmlValidation( getConfiguration() ); - } - phys = PhylogenyMethods.readPhylogenies( parser, file ); - } - catch ( final Exception e ) { - exception = true; - exceptionOccuredDuringOpenFile( e ); - } - } - if ( _mainpanel.getCurrentTreePanel() != null ) { - _mainpanel.getCurrentTreePanel().setArrowCursor(); - } - else { - _mainpanel.setArrowCursor(); - } - if ( !exception && ( phys != null ) && ( phys.length > 0 ) ) { - boolean one_desc = false; - if ( nhx_or_nexus ) { - for( final Phylogeny phy : phys ) { - if ( getOptions().isInternalNumberAreConfidenceForNhParsing() ) { - PhylogenyMethods.transferInternalNodeNamesToConfidence( phy, "" ); - } - if ( PhylogenyMethods.getMinimumDescendentsPerInternalNodes( phy ) == 1 ) { - one_desc = true; - break; - } - } - } - if ( PREPROCESS_TREES ) { - preProcessTreesUponReading( phys ); - } - AptxUtil.addPhylogeniesToTabs( phys, - file.getName(), - file.getAbsolutePath(), - getConfiguration(), - getMainPanel() ); - _mainpanel.getControlPanel().showWhole(); - if ( nhx_or_nexus && one_desc ) { - JOptionPane - .showMessageDialog( this, - "One or more trees contain (a) node(s) with one descendant, " - + ForesterUtil.LINE_SEPARATOR - + "possibly indicating illegal parentheses within node names.", - "Warning: Possible Error in New Hampshire Formatted Data", - JOptionPane.WARNING_MESSAGE ); - } - } - } - } - } - activateSaveAllIfNeeded(); - System.gc(); - } - - private void readSpeciesTreeFromFile() { - Phylogeny t = null; - boolean exception = false; - final File my_dir = getCurrentDir(); - _open_filechooser_for_species_tree.setSelectedFile( new File( "" ) ); - if ( my_dir != null ) { - _open_filechooser_for_species_tree.setCurrentDirectory( my_dir ); - } - final int result = _open_filechooser_for_species_tree.showOpenDialog( _contentpane ); - final File file = _open_filechooser_for_species_tree.getSelectedFile(); - if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) { - if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrame.xmlfilter ) { - try { - final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( PhyloXmlParser - .createPhyloXmlParserXsdValidating(), file ); - t = trees[ 0 ]; - } - catch ( final Exception e ) { - exception = true; - exceptionOccuredDuringOpenFile( e ); - } - } - else if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrame.tolfilter ) { - try { - final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new TolParser(), file ); - t = trees[ 0 ]; - } - catch ( final Exception e ) { - exception = true; - exceptionOccuredDuringOpenFile( e ); - } - } - // "*.*": - else { - try { - final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( PhyloXmlParser - .createPhyloXmlParserXsdValidating(), file ); - t = trees[ 0 ]; - } - catch ( final Exception e ) { - exception = true; - exceptionOccuredDuringOpenFile( e ); - } - } - if ( !exception && ( t != null ) && !t.isRooted() ) { - exception = true; - t = null; - JOptionPane.showMessageDialog( this, - "Species tree is not rooted", - "Species tree not loaded", - JOptionPane.ERROR_MESSAGE ); - } - if ( !exception && ( t != null ) ) { - final Set tax_set = new HashSet(); - for( final PhylogenyNodeIterator it = t.iteratorExternalForward(); it.hasNext(); ) { - final PhylogenyNode node = it.next(); - if ( !node.getNodeData().isHasTaxonomy() ) { - exception = true; - t = null; - JOptionPane - .showMessageDialog( this, - "Species tree contains external node(s) without taxonomy information", - "Species tree not loaded", - JOptionPane.ERROR_MESSAGE ); - break; - } - else { - if ( tax_set.contains( node.getNodeData().getTaxonomy() ) ) { - exception = true; - t = null; - JOptionPane.showMessageDialog( this, - "Taxonomy [" - + node.getNodeData().getTaxonomy().asSimpleText() - + "] is not unique in species tree", - "Species tree not loaded", - JOptionPane.ERROR_MESSAGE ); - break; - } - else { - tax_set.add( node.getNodeData().getTaxonomy() ); - } - } - } - } - if ( !exception && ( t != null ) ) { - setSpeciesTree( t ); - JOptionPane.showMessageDialog( this, - "Species tree successfully loaded", - "Species tree loaded", - JOptionPane.INFORMATION_MESSAGE ); - } - _contentpane.repaint(); - System.gc(); - } - } - - private void setArrowCursor() { - try { - _mainpanel.getCurrentTreePanel().setArrowCursor(); - } - catch ( final Exception ex ) { - // Do nothing. - } - } - - private void setMinNotCollapseBlValue( final double min_not_collapse_bl ) { - _min_not_collapse_bl = min_not_collapse_bl; - } - - private void setMinNotCollapseConfidenceValue( final double min_not_collapse ) { - _min_not_collapse = min_not_collapse; - } - - private void setPhylogeneticInferenceOptions( final PhylogeneticInferenceOptions phylogenetic_inference_options ) { - _phylogenetic_inference_options = phylogenetic_inference_options; - } - - private void setSpecialOptionsForNexParser( final NexusPhylogeniesParser nex ) { - nex.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() ); - nex.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() ); - } - - private void setSpecialOptionsForNhxParser( final NHXParser nhx ) { - nhx.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() ); - nhx.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() ); - nhx.setAllowErrorsInDistanceToParent( getOptions().isAllowErrorsInDistanceToParent() ); - } - - void buildAnalysisMenu() { - _analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() ); - _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) ); - _analysis_menu.add( _gsdir_item = new JMenuItem( "GSDIR (GSDI with re-rooting)" ) ); - _analysis_menu.add( _load_species_tree_item = new JMenuItem( "Load Species Tree..." ) ); - customizeJMenuItem( _gsdi_item ); - customizeJMenuItem( _gsdir_item ); - customizeJMenuItem( _load_species_tree_item ); - _analysis_menu.addSeparator(); - _analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) ); - customizeJMenuItem( _lineage_inference ); - _lineage_inference.setToolTipText( "Inference of ancestor taxonomies/lineages" ); - _jmenubar.add( _analysis_menu ); - } - - @Override - void buildFileMenu() { - _file_jmenu = MainFrame.createMenu( "File", getConfiguration() ); - _file_jmenu.add( _open_item = new JMenuItem( "Read Tree from File..." ) ); - _file_jmenu.addSeparator(); - _file_jmenu.add( _open_url_item = new JMenuItem( "Read Tree from URL/Webservice..." ) ); - _file_jmenu.addSeparator(); - final WebservicesManager webservices_manager = WebservicesManager.getInstance(); - _load_phylogeny_from_webservice_menu_items = new JMenuItem[ webservices_manager - .getAvailablePhylogeniesWebserviceClients().size() ]; - for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) { - final PhylogeniesWebserviceClient client = webservices_manager.getAvailablePhylogeniesWebserviceClient( i ); - _load_phylogeny_from_webservice_menu_items[ i ] = new JMenuItem( client.getMenuName() ); - _file_jmenu.add( _load_phylogeny_from_webservice_menu_items[ i ] ); - } - if ( getConfiguration().isEditable() ) { - _file_jmenu.addSeparator(); - _file_jmenu.add( _new_item = new JMenuItem( "New" ) ); - _new_item.setToolTipText( "to create a new tree with one node, as source for manual tree construction" ); - } - _file_jmenu.addSeparator(); - _file_jmenu.add( _save_item = new JMenuItem( "Save Tree As..." ) ); - _file_jmenu.add( _save_all_item = new JMenuItem( "Save All Trees As..." ) ); - _save_all_item.setToolTipText( "Write all phylogenies to one file." ); - _save_all_item.setEnabled( false ); - _file_jmenu.addSeparator(); - _file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) ); - if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" ) || AptxUtil.canWriteFormat( "TIF" ) ) { - _file_jmenu.add( _write_to_tif_item = new JMenuItem( "Export to TIFF file..." ) ); - } - _file_jmenu.add( _write_to_png_item = new JMenuItem( "Export to PNG file..." ) ); - _file_jmenu.add( _write_to_jpg_item = new JMenuItem( "Export to JPG file..." ) ); - if ( AptxUtil.canWriteFormat( "gif" ) ) { - _file_jmenu.add( _write_to_gif_item = new JMenuItem( "Export to GIF file..." ) ); - } - if ( AptxUtil.canWriteFormat( "bmp" ) ) { - _file_jmenu.add( _write_to_bmp_item = new JMenuItem( "Export to BMP file..." ) ); - } - _file_jmenu.addSeparator(); - _file_jmenu.add( _print_item = new JMenuItem( "Print..." ) ); - _file_jmenu.addSeparator(); - _file_jmenu.add( _close_item = new JMenuItem( "Close Tab" ) ); - _close_item.setToolTipText( "To close the current pane." ); - _close_item.setEnabled( true ); - _file_jmenu.addSeparator(); - _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) ); - customizeJMenuItem( _open_item ); - _open_item - .setFont( new Font( _open_item.getFont().getFontName(), Font.BOLD, _open_item.getFont().getSize() + 4 ) ); - customizeJMenuItem( _open_url_item ); - for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) { - customizeJMenuItem( _load_phylogeny_from_webservice_menu_items[ i ] ); - } - customizeJMenuItem( _save_item ); - if ( getConfiguration().isEditable() ) { - customizeJMenuItem( _new_item ); - } - customizeJMenuItem( _close_item ); - customizeJMenuItem( _save_all_item ); - customizeJMenuItem( _write_to_pdf_item ); - customizeJMenuItem( _write_to_png_item ); - customizeJMenuItem( _write_to_jpg_item ); - customizeJMenuItem( _write_to_gif_item ); - customizeJMenuItem( _write_to_tif_item ); - customizeJMenuItem( _write_to_bmp_item ); - customizeJMenuItem( _print_item ); - customizeJMenuItem( _exit_item ); - _jmenubar.add( _file_jmenu ); - } - - void buildOptionsMenu() { - _options_jmenu = MainFrame.createMenu( OPTIONS_HEADER, getConfiguration() ); - _options_jmenu.addChangeListener( new ChangeListener() { - - @Override - public void stateChanged( final ChangeEvent e ) { - MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() ); - MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() ); - MainFrame - .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() ); - MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame - .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) ); - // MainFrame.setTextForGraphicsSizeChooserMenuItem( _print_size_mi, getOptions() ); - MainFrame.setTextForPdfLineWidthChooserMenuItem( _choose_pdf_width_mi, getOptions() ); - MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() ); - MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() ); - MainFrame.setCycleDataReturnMenuItem( _cycle_data_return, getOptions() ); - MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() ); - try { - getMainPanel().getControlPanel().setVisibilityOfDomainStrucureCB(); - getMainPanel().getControlPanel().setVisibilityOfX(); - } - catch ( final Exception ignore ) { - // do nothing, not important. - } - } - } ); - _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( DISPLAY_SUBHEADER ), getConfiguration() ) ); - _options_jmenu - .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) ); - _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) ); - _options_jmenu.add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( NON_LINED_UP_CLADOGRAMS_LABEL ) ); - _radio_group_1 = new ButtonGroup(); - _radio_group_1.add( _ext_node_dependent_cladogram_rbmi ); - _radio_group_1.add( _uniform_cladograms_rbmi ); - _radio_group_1.add( _non_lined_up_cladograms_rbmi ); - _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( SHOW_OVERVIEW_LABEL ) ); - _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( DISPLAY_SCALE_LABEL ) ); - _options_jmenu - .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_INT ) ); - _options_jmenu - .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_EXT ) ); - _options_jmenu - .add( _show_default_node_shapes_for_marked_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_MARKED ) ); - _options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) ); - if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) { - _options_jmenu.add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) ); - _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) ); - } - _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( SHOW_ANN_REF_SOURCE_LABEL ) ); - _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( SHOW_CONF_STDDEV_LABEL ) ); - _options_jmenu.add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( COLOR_BY_TAXONOMIC_GROUP ) ); - _options_jmenu.add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( COLOR_LABELS_LABEL ) ); - _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP ); - _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( ABBREV_SN_LABEL ) ); - _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( LABEL_DIRECTION_LABEL ) ); - _label_direction_cbmi.setToolTipText( LABEL_DIRECTION_TIP ); - _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( SCREEN_ANTIALIAS_LABEL ) ); - _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( BG_GRAD_LABEL ) ); - _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) ); - _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) ); - _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) ); - _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) ); - _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) ); - _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) ); - _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) ); - _options_jmenu.addSeparator(); - _options_jmenu.add( _cycle_data_return = new JMenuItem( "Cycle Data Return" ) ); - _options_jmenu.addSeparator(); - _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( SEARCH_SUBHEADER ), getConfiguration() ) ); - _options_jmenu.add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( SEARCH_CASE_SENSITIVE_LABEL ) ); - _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( SEARCH_TERMS_ONLY_LABEL ) ); - _options_jmenu.add( _search_with_regex_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_REGEX_LABEL ) ); - _search_with_regex_cbmi.setToolTipText( MainFrame.SEARCH_WITH_REGEX_TIP ); - _options_jmenu.add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( INVERSE_SEARCH_RESULT_LABEL ) ); - _options_jmenu.add( _color_all_found_nodes_when_coloring_subtree_cbmi = new JCheckBoxMenuItem( "Colorize All Found Nodes When Colorizing Subtree(s)" ) ); - _options_jmenu.addSeparator(); - _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Graphics Export & Printing:" ), - getConfiguration() ) ); - _options_jmenu.add( _antialias_print_cbmi = new JCheckBoxMenuItem( "Antialias" ) ); - _options_jmenu.add( _print_black_and_white_cbmi = new JCheckBoxMenuItem( "Export in Black and White" ) ); - //_options_jmenu - //.add( _print_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PDF export and Printing" ) ); - //_options_jmenu - //.add( _graphics_export_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PNG, JPG, and GIF export" ) ); - _options_jmenu - .add( _graphics_export_visible_only_cbmi = new JCheckBoxMenuItem( "Limit to Visible ('Screenshot') for PNG, JPG, and GIF export" ) ); - // _options_jmenu.add( _print_size_mi = new JMenuItem( "" ) ); - _options_jmenu.add( _choose_pdf_width_mi = new JMenuItem( "" ) ); - _options_jmenu.addSeparator(); - _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/NHX/Nexus Read:" ), getConfiguration() ) ); - _options_jmenu - .add( _internal_number_are_confidence_for_nh_parsing_cbmi = new JCheckBoxMenuItem( "Internal Node Names are Confidence Values" ) ); - _options_jmenu.add( _replace_underscores_cbmi = new JCheckBoxMenuItem( "Replace Underscores with Spaces" ) ); - _options_jmenu - .add( _allow_errors_in_distance_to_parent_cbmi = new JCheckBoxMenuItem( "Ignore Distance Values Format Errors" ) ); - _options_jmenu.add( _extract_taxonomy_no_rbmi = new JRadioButtonMenuItem( "No Taxonomy Extraction" ) ); - _options_jmenu - .add( _extract_taxonomy_pfam_strict_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style Node Names" ) ); - _options_jmenu - .add( _extract_taxonomy_pfam_relaxed_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style like Node Names" ) ); - _options_jmenu - .add( _extract_taxonomy_agressive_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids/Scientific Names from Node Names" ) ); - _extract_taxonomy_pfam_strict_rbmi - .setToolTipText( "To extract taxonomy codes/ids from node names in the form of e.g. \"BCL2_MOUSE/123-304\" or \"BCL2_10090/123-304\"" ); - _extract_taxonomy_pfam_relaxed_rbmi - .setToolTipText( "To extract taxonomy codes/ids from node names in the form of e.g. \"bax_MOUSE\" or \"bax_10090\"" ); - _extract_taxonomy_agressive_rbmi - .setToolTipText( "To extract taxonomy codes/ids or scientific names from node names in the form of e.g. \"MOUSE\" or \"10090\" or \"xyz_Nematostella_vectensis\"" ); - _radio_group_2 = new ButtonGroup(); - _radio_group_2.add( _extract_taxonomy_no_rbmi ); - _radio_group_2.add( _extract_taxonomy_pfam_strict_rbmi ); - _radio_group_2.add( _extract_taxonomy_pfam_relaxed_rbmi ); - _radio_group_2.add( _extract_taxonomy_agressive_rbmi ); - _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/Nexus Save:" ), getConfiguration() ) ); - _options_jmenu - .add( _use_brackets_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_BRACKETS_FOR_CONF_IN_NH_LABEL ) ); - _use_brackets_for_conf_in_nh_export_cbmi - .setToolTipText( "e.g. \"0.1[90]\" for a branch with support 90 and a length of 0.1" ); - _options_jmenu - .add( _use_internal_names_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL ) ); - customizeJMenuItem( _choose_font_mi ); - customizeJMenuItem( _choose_minimal_confidence_mi ); - customizeJMenuItem( _switch_colors_mi ); - // customizeJMenuItem( _print_size_mi ); - customizeJMenuItem( _choose_pdf_width_mi ); - customizeJMenuItem( _overview_placment_mi ); - customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions() - .isShowDefaultNodeShapesExternal() ); - customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions() - .isShowDefaultNodeShapesInternal() ); - customizeCheckBoxMenuItem( _show_default_node_shapes_for_marked_cbmi, getOptions() - .isShowDefaultNodeShapesForMarkedNodes() ); - customizeJMenuItem( _cycle_node_shape_mi ); - customizeJMenuItem( _cycle_node_fill_mi ); - customizeJMenuItem( _choose_node_size_mi ); - customizeJMenuItem( _cycle_data_return ); - customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() ); - customizeCheckBoxMenuItem( _color_by_taxonomic_group_cbmi, getOptions().isColorByTaxonomicGroup() ); - customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() ); - customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() ); - customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() ); - customizeCheckBoxMenuItem( _show_annotation_ref_source, getOptions().isShowAnnotationRefSource() ); - customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() ); - customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() ); - customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() ); - customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi, - getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP ); - customizeRadioButtonMenuItem( _uniform_cladograms_rbmi, - getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP ); - customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi, - getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP ); - customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() ); - customizeCheckBoxMenuItem( _label_direction_cbmi, - getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL ); - customizeCheckBoxMenuItem( _antialias_print_cbmi, getOptions().isAntialiasPrint() ); - customizeCheckBoxMenuItem( _print_black_and_white_cbmi, getOptions().isPrintBlackAndWhite() ); - customizeCheckBoxMenuItem( _internal_number_are_confidence_for_nh_parsing_cbmi, getOptions() - .isInternalNumberAreConfidenceForNhParsing() ); - customizeRadioButtonMenuItem( _extract_taxonomy_no_rbmi, - getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.NO ); - customizeRadioButtonMenuItem( _extract_taxonomy_pfam_strict_rbmi, - getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); - customizeRadioButtonMenuItem( _extract_taxonomy_pfam_relaxed_rbmi, - getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); - customizeRadioButtonMenuItem( _extract_taxonomy_agressive_rbmi, - getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.AGGRESSIVE ); - customizeCheckBoxMenuItem( _replace_underscores_cbmi, getOptions().isReplaceUnderscoresInNhParsing() ); - customizeCheckBoxMenuItem( _allow_errors_in_distance_to_parent_cbmi, getOptions() - .isReplaceUnderscoresInNhParsing() ); - customizeCheckBoxMenuItem( _search_with_regex_cbmi, getOptions().isSearchWithRegex() ); - customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() ); - customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() ); - customizeCheckBoxMenuItem( _color_all_found_nodes_when_coloring_subtree_cbmi, getOptions().isColorAllFoundNodesWhenColoringSubtree() ); - customizeCheckBoxMenuItem( _graphics_export_visible_only_cbmi, getOptions().isGraphicsExportVisibleOnly() ); - customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() ); - customizeCheckBoxMenuItem( _use_brackets_for_conf_in_nh_export_cbmi, getOptions() - .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS ); - customizeCheckBoxMenuItem( _use_internal_names_for_conf_in_nh_export_cbmi, getOptions() - .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES ); - customizeCheckBoxMenuItem( _line_up_renderable_data_cbmi, getOptions().isLineUpRendarableNodeData() ); - customizeCheckBoxMenuItem( _right_line_up_domains_cbmi, getOptions().isRightLineUpDomains() ); - _jmenubar.add( _options_jmenu ); - } - - void buildPhylogeneticInferenceMenu() { - final InferenceManager im = getInferenceManager(); - _inference_menu = MainFrame.createMenu( "Inference", getConfiguration() ); - _inference_menu.add( _inference_from_msa_item = new JMenuItem( "From Multiple Sequence Alignment..." ) ); - customizeJMenuItem( _inference_from_msa_item ); - _inference_from_msa_item.setToolTipText( "Basic phylogenetic inference from MSA" ); - if ( im.canDoMsa() ) { - _inference_menu.add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences..." ) ); - customizeJMenuItem( _inference_from_seqs_item ); - _inference_from_seqs_item - .setToolTipText( "Basic phylogenetic inference including multiple sequence alignment" ); - } - else { - _inference_menu - .add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences (no program found)" ) ); - customizeJMenuItem( _inference_from_seqs_item ); - _inference_from_seqs_item.setEnabled( false ); - } - _jmenubar.add( _inference_menu ); - } - - void buildToolsMenu() { - _tools_menu = createMenu( "Tools", getConfiguration() ); - _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) ); - customizeJMenuItem( _confcolor_item ); - _tools_menu.add( _color_rank_jmi = new JMenuItem( "Colorize Subtrees via Taxonomic Rank" ) ); - customizeJMenuItem( _color_rank_jmi ); - _color_rank_jmi.setToolTipText( "for example, at \"Class\" level, colorize mammal specific subtree red" ); - _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) ); - customizeJMenuItem( _taxcolor_item ); - _tools_menu.addSeparator(); - _tools_menu.add( _remove_visual_styles_item = new JMenuItem( "Delete All Visual Styles From Nodes" ) ); - _remove_visual_styles_item - .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny" ); - customizeJMenuItem( _remove_visual_styles_item ); - _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete All Colors From Branches" ) ); - _remove_branch_color_item.setToolTipText( "To remove all branch color values from the current phylogeny" ); - customizeJMenuItem( _remove_branch_color_item ); - _tools_menu.addSeparator(); - _tools_menu.add( _annotate_item = new JMenuItem( "Annotate Sequences of Selected Nodes" ) ); - customizeJMenuItem( _annotate_item ); - _tools_menu.addSeparator(); - _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) ); - customizeJMenuItem( _midpoint_root_item ); - _tools_menu.addSeparator(); - _tools_menu.add( _delete_selected_nodes_item = new JMenuItem( "Delete Selected Nodes" ) ); - _delete_selected_nodes_item.setToolTipText( "To delete all selected external nodes" ); - customizeJMenuItem( _delete_selected_nodes_item ); - _tools_menu.add( _delete_not_selected_nodes_item = new JMenuItem( "Retain Selected Nodes" ) ); - _delete_not_selected_nodes_item.setToolTipText( "To delete all not selected external nodes" ); - customizeJMenuItem( _delete_not_selected_nodes_item ); - _tools_menu.addSeparator(); - _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) ); - customizeJMenuItem( _collapse_species_specific_subtrees ); - _collapse_species_specific_subtrees.setToolTipText( "To (reversibly) collapse species-specific subtrees" ); - _tools_menu - .add( _collapse_below_threshold = new JMenuItem( "Collapse Branches with Confidence Below Threshold into Multifurcations" ) ); - customizeJMenuItem( _collapse_below_threshold ); - _collapse_below_threshold - .setToolTipText( "To (permanently) collapse branches with confidence values below a threshold into multifurcations (in the case of multiple confidences per branch: without at least one confidence value above a threshold)" ); - // - _tools_menu - .add( _collapse_below_branch_length = new JMenuItem( "Collapse Branches with Branch Lengths Below Threshold into Multifurcations" ) ); - customizeJMenuItem( _collapse_below_branch_length ); - _collapse_below_branch_length - .setToolTipText( "To (permanently) collapse branches with branches with branch lengths below a threshold into multifurcations" ); - // - _tools_menu.addSeparator(); - _tools_menu - .add( _extract_tax_code_from_node_names_jmi = new JMenuItem( "Extract Taxonomic Data from Node Names" ) ); - customizeJMenuItem( _extract_tax_code_from_node_names_jmi ); - _extract_tax_code_from_node_names_jmi - .setToolTipText( "To extract SwissProt/Uniprot taxonomic codes (mnemonics) from nodes names in the form of 'xyz_CAEEL', Uniprot/NCBI identifiers form of 'xyz_6239', or scientific names form of 'xyz_Caenorhabditis_elegans'" ); - _tools_menu - .add( _move_node_names_to_tax_sn_jmi = new JMenuItem( "Transfer Node Names to Taxonomic Scientific Names" ) ); - customizeJMenuItem( _move_node_names_to_tax_sn_jmi ); - _move_node_names_to_tax_sn_jmi.setToolTipText( "To interpret node names as taxonomic scientific names" ); - _tools_menu.add( _move_node_names_to_seq_names_jmi = new JMenuItem( "Transfer Node Names to Sequence Names" ) ); - customizeJMenuItem( _move_node_names_to_seq_names_jmi ); - _move_node_names_to_seq_names_jmi.setToolTipText( "To interpret node names as sequence (protein, gene) names" ); - _tools_menu.addSeparator(); - _tools_menu.add( _obtain_seq_information_jmi = new JMenuItem( "Obtain Sequence Information" ) ); - customizeJMenuItem( _obtain_seq_information_jmi ); - _obtain_seq_information_jmi.setToolTipText( "To add additional sequence information" ); - _tools_menu - .add( _obtain_detailed_taxonomic_information_jmi = new JMenuItem( OBTAIN_DETAILED_TAXONOMIC_INFORMATION ) ); - customizeJMenuItem( _obtain_detailed_taxonomic_information_jmi ); - _obtain_detailed_taxonomic_information_jmi - .setToolTipText( "To add additional taxonomic information (from UniProt Taxonomy)" ); - _tools_menu - .add( _obtain_detailed_taxonomic_information_deleting_jmi = new JMenuItem( "Obtain Detailed Taxonomic Information (deletes nodes!)" ) ); - customizeJMenuItem( _obtain_detailed_taxonomic_information_deleting_jmi ); - _obtain_detailed_taxonomic_information_deleting_jmi - .setToolTipText( "To add additional taxonomic information, deletes nodes for which taxonomy cannot found (from UniProt Taxonomy)" ); - _tools_menu.addSeparator(); - _tools_menu.add( _read_values_jmi = new JMenuItem( "Attach Vector/Expression Values" ) ); - customizeJMenuItem( _read_values_jmi ); - _read_values_jmi.setToolTipText( "To attach vector (e.g. gene expression) values to tree nodes (beta)" ); - _jmenubar.add( _tools_menu ); - _tools_menu.add( _read_seqs_jmi = new JMenuItem( "Attach Molecular Sequences" ) ); - customizeJMenuItem( _read_seqs_jmi ); - _read_seqs_jmi - .setToolTipText( "To attach molecular sequences to tree nodes (from Fasta-formatted file) (beta)" ); - _jmenubar.add( _tools_menu ); - } - - @Override - void close() { - if ( isUnsavedDataPresent() ) { - final int r = JOptionPane.showConfirmDialog( this, - "Exit despite potentially unsaved changes?", - "Exit?", - JOptionPane.YES_NO_OPTION ); - if ( r != JOptionPane.YES_OPTION ) { - return; - } - } - exit(); - } - - void exit() { - removeAllTextFrames(); - _mainpanel.terminate(); - _contentpane.removeAll(); - setVisible( false ); - dispose(); - // System.exit( 0 ); //TODO reconfirm that this is OK, then remove. - } - - void readPhylogeniesFromURL() { - URL url = null; - Phylogeny[] phys = null; - final String message = "Please enter a complete URL, for example \"http://purl.org/phylo/treebase/phylows/study/TB2:S15480?format=nexus\""; - final String url_string = JOptionPane.showInputDialog( this, - message, - "Use URL/webservice to obtain a phylogeny", - JOptionPane.QUESTION_MESSAGE ); - boolean nhx_or_nexus = false; - if ( ( url_string != null ) && ( url_string.length() > 0 ) ) { - try { - url = new URL( url_string ); - PhylogenyParser parser = null; - if ( url.getHost().toLowerCase().indexOf( "tolweb" ) >= 0 ) { - parser = new TolParser(); - } - else { - parser = ParserUtils.createParserDependingOnUrlContents( url, getConfiguration() - .isValidatePhyloXmlAgainstSchema() ); - } - if ( parser instanceof NexusPhylogeniesParser ) { - nhx_or_nexus = true; - } - else if ( parser instanceof NHXParser ) { - nhx_or_nexus = true; - } - if ( _mainpanel.getCurrentTreePanel() != null ) { - _mainpanel.getCurrentTreePanel().setWaitCursor(); - } - else { - _mainpanel.setWaitCursor(); - } - final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - phys = factory.create( url.openStream(), parser ); - } - catch ( final MalformedURLException e ) { - JOptionPane.showMessageDialog( this, - "Malformed URL: " + url + "\n" + e.getLocalizedMessage(), - "Malformed URL", - JOptionPane.ERROR_MESSAGE ); - } - catch ( final IOException e ) { - JOptionPane.showMessageDialog( this, - "Could not read from " + url + "\n" - + ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ), - "Failed to read URL", - JOptionPane.ERROR_MESSAGE ); - } - catch ( final Exception e ) { - JOptionPane.showMessageDialog( this, - ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ), - "Unexpected Exception", - JOptionPane.ERROR_MESSAGE ); - } - finally { - if ( _mainpanel.getCurrentTreePanel() != null ) { - _mainpanel.getCurrentTreePanel().setArrowCursor(); - } - else { - _mainpanel.setArrowCursor(); - } - } - if ( ( phys != null ) && ( phys.length > 0 ) ) { - if ( nhx_or_nexus && getOptions().isInternalNumberAreConfidenceForNhParsing() ) { - for( final Phylogeny phy : phys ) { - PhylogenyMethods.transferInternalNodeNamesToConfidence( phy, "" ); - } - } - AptxUtil.addPhylogeniesToTabs( phys, - new File( url.getFile() ).getName(), - new File( url.getFile() ).toString(), - getConfiguration(), - getMainPanel() ); - _mainpanel.getControlPanel().showWhole(); - } - } - activateSaveAllIfNeeded(); - System.gc(); - } - - void setMsa( final Msa msa ) { - _msa = msa; - } - - void setMsaFile( final File msa_file ) { - _msa_file = msa_file; - } - - void setSeqs( final List seqs ) { - _seqs = seqs; - } - - void setSeqsFile( final File seqs_file ) { - _seqs_file = seqs_file; - } - - public static MainFrameApplication createInstance( final Phylogeny[] phys, final Configuration config ) { - return new MainFrameApplication( phys, config ); - } - - public static MainFrame createInstance( final Phylogeny[] phys, - final Configuration config, - final String title, - final File current_dir ) { - return new MainFrameApplication( phys, config, title, current_dir ); - } - - static MainFrame createInstance( final Phylogeny[] phys, final Configuration config, final String title ) { - return new MainFrameApplication( phys, config, title ); - } - - static MainFrame createInstance( final Phylogeny[] phys, final String config_file_name, final String title ) { - return new MainFrameApplication( phys, config_file_name, title ); - } - - static void warnIfNotPhyloXmlValidation( final Configuration c ) { - if ( !c.isValidatePhyloXmlAgainstSchema() ) { - JOptionPane - .showMessageDialog( null, - ForesterUtil - .wordWrap( "phyloXML XSD-based validation is turned off [enable with line 'validate_against_phyloxml_xsd_schem: true' in configuration file]", - 80 ), - "Warning", - JOptionPane.WARNING_MESSAGE ); - } - } -} // MainFrameApplication. +// $Id: +// FORESTER -- software libraries and applications +// for evolutionary biology research and applications. +// +// Copyright (C) 2008-2009 Christian M. Zmasek +// Copyright (C) 2008-2009 Burnham Institute for Medical Research +// Copyright (C) 2003-2007 Ethalinda K.S. Cannon +// All rights reserved +// +// This library is free software; you can redistribute it and/or +// modify it under the terms of the GNU Lesser General Public +// License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// +// This library is distributed in the hope that it will be useful, +// but WITHOUT ANY WARRANTY; without even the implied warranty of +// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +// Lesser General Public License for more details. +// +// You should have received a copy of the GNU Lesser General Public +// License along with this library; if not, write to the Free Software +// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +// +// Contact: phylosoft @ gmail . com +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester + +package org.forester.archaeopteryx; + +import java.awt.BorderLayout; +import java.awt.Font; +import java.awt.event.ActionEvent; +import java.awt.event.ComponentAdapter; +import java.awt.event.ComponentEvent; +import java.awt.event.WindowAdapter; +import java.awt.event.WindowEvent; +import java.io.File; +import java.io.FileInputStream; +import java.io.IOException; +import java.io.InputStream; +import java.net.MalformedURLException; +import java.net.URL; +import java.util.ArrayList; +import java.util.HashSet; +import java.util.List; +import java.util.Set; + +import javax.swing.ButtonGroup; +import javax.swing.JCheckBoxMenuItem; +import javax.swing.JFileChooser; +import javax.swing.JMenu; +import javax.swing.JMenuBar; +import javax.swing.JMenuItem; +import javax.swing.JOptionPane; +import javax.swing.JRadioButtonMenuItem; +import javax.swing.UIManager; +import javax.swing.UnsupportedLookAndFeelException; +import javax.swing.WindowConstants; +import javax.swing.event.ChangeEvent; +import javax.swing.event.ChangeListener; + +import org.forester.analysis.TaxonomyDataManager; +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.PhyloInferenceDialog; +import org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions; +import org.forester.archaeopteryx.tools.PhylogeneticInferrer; +import org.forester.archaeopteryx.tools.SequenceDataRetriver; +import org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient; +import org.forester.archaeopteryx.webservices.WebservicesManager; +import org.forester.io.parsers.FastaParser; +import org.forester.io.parsers.GeneralMsaParser; +import org.forester.io.parsers.PhylogenyParser; +import org.forester.io.parsers.nexus.NexusPhylogeniesParser; +import org.forester.io.parsers.nhx.NHXParser; +import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION; +import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException; +import org.forester.io.parsers.phyloxml.PhyloXmlParser; +import org.forester.io.parsers.phyloxml.PhyloXmlUtil; +import org.forester.io.parsers.tol.TolParser; +import org.forester.io.parsers.util.ParserUtils; +import org.forester.io.writers.SequenceWriter; +import org.forester.msa.Msa; +import org.forester.msa.MsaFormatException; +import org.forester.phylogeny.Phylogeny; +import org.forester.phylogeny.PhylogenyMethods; +import org.forester.phylogeny.PhylogenyNode; +import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE; +import org.forester.phylogeny.data.Confidence; +import org.forester.phylogeny.data.PhylogenyDataUtil; +import org.forester.phylogeny.data.Sequence; +import org.forester.phylogeny.data.Taxonomy; +import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory; +import org.forester.phylogeny.factories.PhylogenyFactory; +import org.forester.phylogeny.iterators.PhylogenyNodeIterator; +import org.forester.sequence.MolecularSequence; +import org.forester.util.BasicDescriptiveStatistics; +import org.forester.util.BasicTable; +import org.forester.util.BasicTableParser; +import org.forester.util.DescriptiveStatistics; +import org.forester.util.ForesterUtil; + +public final class MainFrameApplication extends MainFrame { + + private final static int FRAME_X_SIZE = 800; + private final static int FRAME_Y_SIZE = 800; + // Filters for the file-open dialog (classes defined in this file) + private static final long serialVersionUID = -799735726778865234L; + private static final boolean PREPROCESS_TREES = false; + private final JFileChooser _values_filechooser; + private final JFileChooser _sequences_filechooser; + private final JFileChooser _open_filechooser; + private final JFileChooser _msa_filechooser; + private final JFileChooser _seqs_pi_filechooser; + private final JFileChooser _open_filechooser_for_species_tree; + // Application-only print menu items + private JMenuItem _collapse_below_threshold; + private JMenuItem _collapse_below_branch_length; + private ButtonGroup _radio_group_1; + private ButtonGroup _radio_group_2; + // Others: + double _min_not_collapse = AptxConstants.MIN_NOT_COLLAPSE_DEFAULT; + double _min_not_collapse_bl = 0.001; + // Phylogeny Inference menu + private JMenu _inference_menu; + private JMenuItem _inference_from_msa_item; + private JMenuItem _inference_from_seqs_item; + // Phylogeny Inference + private PhylogeneticInferenceOptions _phylogenetic_inference_options = null; + private Msa _msa = null; + private File _msa_file = null; + private List _seqs = null; + private File _seqs_file = null; + JMenuItem _read_values_jmi; + JMenuItem _read_seqs_jmi; + + private MainFrameApplication( final Phylogeny[] phys, final Configuration config ) { + _configuration = config; + if ( _configuration == null ) { + throw new IllegalArgumentException( "configuration is null" ); + } + setVisible( false ); + setOptions( Options.createInstance( _configuration ) ); + _mainpanel = new MainPanel( _configuration, this ); + _open_filechooser = null; + _open_filechooser_for_species_tree = null; + _save_filechooser = null; + _writetopdf_filechooser = null; + _writetographics_filechooser = null; + _msa_filechooser = null; + _seqs_pi_filechooser = null; + _values_filechooser = null; + _sequences_filechooser = null; + _jmenubar = new JMenuBar(); + buildFileMenu(); + buildTypeMenu(); + _contentpane = getContentPane(); + _contentpane.setLayout( new BorderLayout() ); + _contentpane.add( _mainpanel, BorderLayout.CENTER ); + // App is this big + setSize( MainFrameApplication.FRAME_X_SIZE, MainFrameApplication.FRAME_Y_SIZE ); + // The window listener + setDefaultCloseOperation( WindowConstants.DO_NOTHING_ON_CLOSE ); + addWindowListener( new WindowAdapter() { + + @Override + public void windowClosing( final WindowEvent e ) { + exit(); + } + } ); + // setVisible( true ); + if ( ( phys != null ) && ( phys.length > 0 ) ) { + AptxUtil.addPhylogeniesToTabs( phys, "", null, _configuration, _mainpanel ); + validate(); + getMainPanel().getControlPanel().showWholeAll(); + getMainPanel().getControlPanel().showWhole(); + } + //activateSaveAllIfNeeded(); + // ...and its children + _contentpane.repaint(); + } + + private MainFrameApplication( final Phylogeny[] phys, final Configuration config, final String title ) { + this( phys, config, title, null ); + } + + private MainFrameApplication( final Phylogeny[] phys, + final Configuration config, + final String title, + final File current_dir ) { + super(); + _configuration = config; + if ( _configuration == null ) { + throw new IllegalArgumentException( "configuration is null" ); + } + try { + if ( _configuration.isUseNativeUI() ) { + UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() ); + } + else { + UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() ); + } + } + catch ( final UnsupportedLookAndFeelException e ) { + AptxUtil.dieWithSystemError( "unsupported look and feel: " + e.toString() ); + } + catch ( final ClassNotFoundException e ) { + AptxUtil.dieWithSystemError( "class not found exception: " + e.toString() ); + } + catch ( final InstantiationException e ) { + AptxUtil.dieWithSystemError( "instantiation exception: " + e.toString() ); + } + catch ( final IllegalAccessException e ) { + AptxUtil.dieWithSystemError( "illegal access exception: " + e.toString() ); + } + if ( ( current_dir != null ) && current_dir.canRead() && current_dir.isDirectory() ) { + setCurrentDir( current_dir ); + } + // hide until everything is ready + setVisible( false ); + setOptions( Options.createInstance( _configuration ) ); + setInferenceManager( InferenceManager.createInstance( _configuration ) ); + setPhylogeneticInferenceOptions( PhylogeneticInferenceOptions.createInstance( _configuration ) ); + // set title + setTitle( AptxConstants.PRG_NAME + " " + AptxConstants.VERSION + " (" + AptxConstants.PRG_DATE + ")" ); + _mainpanel = new MainPanel( _configuration, this ); + // The file dialogs + _open_filechooser = new JFileChooser(); + _open_filechooser.setMultiSelectionEnabled( true ); + _open_filechooser.addChoosableFileFilter( MainFrame.xmlfilter ); + _open_filechooser.addChoosableFileFilter( MainFrame.nhxfilter ); + _open_filechooser.addChoosableFileFilter( MainFrame.nhfilter ); + _open_filechooser.addChoosableFileFilter( MainFrame.nexusfilter ); + _open_filechooser.addChoosableFileFilter( MainFrame.tolfilter ); + _open_filechooser.addChoosableFileFilter( _open_filechooser.getAcceptAllFileFilter() ); + _open_filechooser.setFileFilter( MainFrame.defaultfilter ); + _open_filechooser_for_species_tree = new JFileChooser(); + _open_filechooser_for_species_tree.setMultiSelectionEnabled( false ); + _open_filechooser_for_species_tree.addChoosableFileFilter( MainFrame.xmlfilter ); + _open_filechooser_for_species_tree.addChoosableFileFilter( MainFrame.tolfilter ); + _open_filechooser_for_species_tree.setFileFilter( MainFrame.xmlfilter ); + // Msa: + _msa_filechooser = new JFileChooser(); + _msa_filechooser.setName( "Read Multiple Sequence Alignment File" ); + _msa_filechooser.setMultiSelectionEnabled( false ); + _msa_filechooser.addChoosableFileFilter( _msa_filechooser.getAcceptAllFileFilter() ); + _msa_filechooser.addChoosableFileFilter( MainFrame.msafilter ); + // Seqs: + _seqs_pi_filechooser = new JFileChooser(); + _seqs_pi_filechooser.setName( "Read Sequences File" ); + _seqs_pi_filechooser.setMultiSelectionEnabled( false ); + _seqs_pi_filechooser.addChoosableFileFilter( _seqs_pi_filechooser.getAcceptAllFileFilter() ); + _seqs_pi_filechooser.addChoosableFileFilter( MainFrame.seqsfilter ); + // Expression + _values_filechooser = new JFileChooser(); + _values_filechooser.setMultiSelectionEnabled( false ); + // Sequences + _sequences_filechooser = new JFileChooser(); + _sequences_filechooser.setMultiSelectionEnabled( false ); + try { + final String home_dir = System.getProperty( "user.home" ); + _open_filechooser.setCurrentDirectory( new File( home_dir ) ); + _open_filechooser_for_species_tree.setCurrentDirectory( new File( home_dir ) ); + _msa_filechooser.setCurrentDirectory( new File( home_dir ) ); + _seqs_pi_filechooser.setCurrentDirectory( new File( home_dir ) ); + _values_filechooser.setCurrentDirectory( new File( home_dir ) ); + _sequences_filechooser.setCurrentDirectory( new File( home_dir ) ); + } + catch ( final Exception e ) { + e.printStackTrace(); + // Do nothing. Not important. + } + // build the menu bar + _jmenubar = new JMenuBar(); + if ( !_configuration.isUseNativeUI() ) { + _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() ); + } + buildFileMenu(); + if ( AptxConstants.__ALLOW_PHYLOGENETIC_INFERENCE ) { + buildPhylogeneticInferenceMenu(); + } + buildAnalysisMenu(); + buildToolsMenu(); + buildViewMenu(); + buildFontSizeMenu(); + buildOptionsMenu(); + buildTypeMenu(); + buildHelpMenu(); + setJMenuBar( _jmenubar ); + _jmenubar.add( _help_jmenu ); + _contentpane = getContentPane(); + _contentpane.setLayout( new BorderLayout() ); + _contentpane.add( _mainpanel, BorderLayout.CENTER ); + // App is this big + setSize( MainFrameApplication.FRAME_X_SIZE, MainFrameApplication.FRAME_Y_SIZE ); + // addWindowFocusListener( new WindowAdapter() { + // + // @Override + // public void windowGainedFocus( WindowEvent e ) { + // requestFocusInWindow(); + // } + // } ); + // The window listener + setDefaultCloseOperation( WindowConstants.DO_NOTHING_ON_CLOSE ); + addWindowListener( new WindowAdapter() { + + @Override + public void windowClosing( final WindowEvent e ) { + if ( isUnsavedDataPresent() ) { + final int r = JOptionPane.showConfirmDialog( null, + "Exit despite potentially unsaved changes?", + "Exit?", + JOptionPane.YES_NO_OPTION ); + if ( r != JOptionPane.YES_OPTION ) { + return; + } + } + else { + final int r = JOptionPane.showConfirmDialog( null, + "Exit Archaeopteryx?", + "Exit?", + JOptionPane.YES_NO_OPTION ); + if ( r != JOptionPane.YES_OPTION ) { + return; + } + } + exit(); + } + } ); + // The component listener + addComponentListener( new ComponentAdapter() { + + @Override + public void componentResized( final ComponentEvent e ) { + if ( _mainpanel.getCurrentTreePanel() != null ) { + _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel() + .getWidth(), + _mainpanel.getCurrentTreePanel() + .getHeight() ); + } + } + } ); + requestFocusInWindow(); + // addKeyListener( this ); + setVisible( true ); + if ( ( phys != null ) && ( phys.length > 0 ) ) { + AptxUtil.addPhylogeniesToTabs( phys, title, null, _configuration, _mainpanel ); + validate(); + getMainPanel().getControlPanel().showWholeAll(); + getMainPanel().getControlPanel().showWhole(); + } + activateSaveAllIfNeeded(); + // ...and its children + _contentpane.repaint(); + System.gc(); + } + + private MainFrameApplication( final Phylogeny[] phys, final String config_file, final String title ) { + // Reads the config file (false, false => not url, not applet): + this( phys, new Configuration( config_file, false, false, true ), title ); + } + + @Override + public void actionPerformed( final ActionEvent e ) { + try { + super.actionPerformed( e ); + final Object o = e.getSource(); + // Handle app-specific actions here: + if ( o == _open_item ) { + readPhylogeniesFromFile(); + } + if ( o == _open_url_item ) { + readPhylogeniesFromURL(); + } + else if ( o == _new_item ) { + newTree(); + } + else if ( o == _close_item ) { + closeCurrentPane(); + } + else if ( o == _load_species_tree_item ) { + readSpeciesTreeFromFile(); + } + else if ( o == _obtain_detailed_taxonomic_information_jmi ) { + if ( isSubtreeDisplayed() ) { + return; + } + obtainDetailedTaxonomicInformation(); + } + else if ( o == _obtain_detailed_taxonomic_information_deleting_jmi ) { + if ( isSubtreeDisplayed() ) { + return; + } + obtainDetailedTaxonomicInformationDelete(); + } + else if ( o == _obtain_seq_information_jmi ) { + obtainSequenceInformation(); + } + else if ( o == _read_values_jmi ) { + if ( isSubtreeDisplayed() ) { + return; + } + addExpressionValuesFromFile(); + } + else if ( o == _read_seqs_jmi ) { + if ( isSubtreeDisplayed() ) { + return; + } + addSequencesFromFile(); + } + else if ( o == _move_node_names_to_tax_sn_jmi ) { + moveNodeNamesToTaxSn(); + } + else if ( o == _move_node_names_to_seq_names_jmi ) { + moveNodeNamesToSeqNames(); + } + else if ( o == _extract_tax_code_from_node_names_jmi ) { + extractTaxDataFromNodeNames(); + } + else if ( o == _internal_number_are_confidence_for_nh_parsing_cbmi ) { + updateOptions( getOptions() ); + } + else if ( o == _replace_underscores_cbmi ) { + if ( ( _extract_taxonomy_no_rbmi != null ) && !_extract_taxonomy_no_rbmi.isSelected() ) { + _extract_taxonomy_no_rbmi.setSelected( true ); + } + updateOptions( getOptions() ); + } + else if ( o == _allow_errors_in_distance_to_parent_cbmi ) { + updateOptions( getOptions() ); + } + else if ( o == _collapse_below_threshold ) { + if ( isSubtreeDisplayed() ) { + return; + } + collapseBelowThreshold(); + } + else if ( o == _collapse_below_branch_length ) { + if ( isSubtreeDisplayed() ) { + return; + } + collapseBelowBranchLengthThreshold(); + } + else if ( ( o == _extract_taxonomy_pfam_strict_rbmi ) || ( o == _extract_taxonomy_pfam_relaxed_rbmi ) + || ( o == _extract_taxonomy_agressive_rbmi ) ) { + if ( _replace_underscores_cbmi != null ) { + _replace_underscores_cbmi.setSelected( false ); + } + updateOptions( getOptions() ); + } + else if ( o == _extract_taxonomy_no_rbmi ) { + updateOptions( getOptions() ); + } + else if ( o == _inference_from_msa_item ) { + executePhyleneticInference( false ); + } + else if ( o == _inference_from_seqs_item ) { + executePhyleneticInference( true ); + } + _contentpane.repaint(); + } + catch ( final Exception ex ) { + AptxUtil.unexpectedException( ex ); + } + catch ( final Error err ) { + AptxUtil.unexpectedError( err ); + } + } + + public void end() { + _mainpanel.terminate(); + _contentpane.removeAll(); + setVisible( false ); + dispose(); + } + + @Override + public MainPanel getMainPanel() { + return _mainpanel; + } + + public Msa getMsa() { + return _msa; + } + + public File getMsaFile() { + return _msa_file; + } + + public List getSeqs() { + return _seqs; + } + + public File getSeqsFile() { + return _seqs_file; + } + + public void readMsaFromFile() { + // Set an initial directory if none set yet + final File my_dir = getCurrentDir(); + _msa_filechooser.setMultiSelectionEnabled( false ); + // Open file-open dialog and set current directory + if ( my_dir != null ) { + _msa_filechooser.setCurrentDirectory( my_dir ); + } + final int result = _msa_filechooser.showOpenDialog( _contentpane ); + // All done: get the msa + final File file = _msa_filechooser.getSelectedFile(); + setCurrentDir( _msa_filechooser.getCurrentDirectory() ); + if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) { + setMsaFile( null ); + setMsa( null ); + Msa msa = null; + try { + final InputStream is = new FileInputStream( file ); + if ( FastaParser.isLikelyFasta( file ) ) { + msa = FastaParser.parseMsa( is ); + } + else { + msa = GeneralMsaParser.parse( is ); + } + } + catch ( final MsaFormatException e ) { + setArrowCursor(); + JOptionPane.showMessageDialog( this, + e.getLocalizedMessage(), + "Multiple sequence alignment format error", + JOptionPane.ERROR_MESSAGE ); + return; + } + catch ( final IOException e ) { + setArrowCursor(); + JOptionPane.showMessageDialog( this, + e.getLocalizedMessage(), + "Failed to read multiple sequence alignment", + JOptionPane.ERROR_MESSAGE ); + return; + } + catch ( final IllegalArgumentException e ) { + setArrowCursor(); + JOptionPane.showMessageDialog( this, + e.getLocalizedMessage(), + "Unexpected error during reading of multiple sequence alignment", + JOptionPane.ERROR_MESSAGE ); + return; + } + catch ( final Exception e ) { + setArrowCursor(); + e.printStackTrace(); + JOptionPane.showMessageDialog( this, + e.getLocalizedMessage(), + "Unexpected error during reading of multiple sequence alignment", + JOptionPane.ERROR_MESSAGE ); + return; + } + if ( ( msa == null ) || ( msa.getNumberOfSequences() < 1 ) ) { + JOptionPane.showMessageDialog( this, + "Multiple sequence alignment is empty", + "Illegal Multiple Sequence Alignment", + JOptionPane.ERROR_MESSAGE ); + return; + } + if ( msa.getNumberOfSequences() < 4 ) { + JOptionPane.showMessageDialog( this, + "Multiple sequence alignment needs to contain at least 3 sequences", + "Illegal multiple sequence alignment", + JOptionPane.ERROR_MESSAGE ); + return; + } + if ( msa.getLength() < 2 ) { + JOptionPane.showMessageDialog( this, + "Multiple sequence alignment needs to contain at least 2 residues", + "Illegal multiple sequence alignment", + JOptionPane.ERROR_MESSAGE ); + return; + } + System.gc(); + setMsaFile( _msa_filechooser.getSelectedFile() ); + setMsa( msa ); + } + } + + public void readSeqsFromFileforPI() { + // Set an initial directory if none set yet + final File my_dir = getCurrentDir(); + _seqs_pi_filechooser.setMultiSelectionEnabled( false ); + // Open file-open dialog and set current directory + if ( my_dir != null ) { + _seqs_pi_filechooser.setCurrentDirectory( my_dir ); + } + final int result = _seqs_pi_filechooser.showOpenDialog( _contentpane ); + // All done: get the seqs + final File file = _seqs_pi_filechooser.getSelectedFile(); + setCurrentDir( _seqs_pi_filechooser.getCurrentDirectory() ); + if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) { + setSeqsFile( null ); + setSeqs( null ); + List seqs = null; + try { + if ( FastaParser.isLikelyFasta( new FileInputStream( file ) ) ) { + seqs = FastaParser.parse( new FileInputStream( file ) ); + for( final MolecularSequence seq : seqs ) { + System.out.println( SequenceWriter.toFasta( seq, 60 ) ); + } + } + else { + //TODO error + } + } + catch ( final MsaFormatException e ) { + setArrowCursor(); + JOptionPane.showMessageDialog( this, + e.getLocalizedMessage(), + "Multiple sequence file format error", + JOptionPane.ERROR_MESSAGE ); + return; + } + catch ( final IOException e ) { + setArrowCursor(); + JOptionPane.showMessageDialog( this, + e.getLocalizedMessage(), + "Failed to read multiple sequence file", + JOptionPane.ERROR_MESSAGE ); + return; + } + catch ( final IllegalArgumentException e ) { + setArrowCursor(); + JOptionPane.showMessageDialog( this, + e.getLocalizedMessage(), + "Unexpected error during reading of multiple sequence file", + JOptionPane.ERROR_MESSAGE ); + return; + } + catch ( final Exception e ) { + setArrowCursor(); + e.printStackTrace(); + JOptionPane.showMessageDialog( this, + e.getLocalizedMessage(), + "Unexpected error during reading of multiple sequence file", + JOptionPane.ERROR_MESSAGE ); + return; + } + if ( ( seqs == null ) || ( seqs.size() < 1 ) ) { + JOptionPane.showMessageDialog( this, + "Multiple sequence file is empty", + "Illegal multiple sequence file", + JOptionPane.ERROR_MESSAGE ); + return; + } + if ( seqs.size() < 4 ) { + JOptionPane.showMessageDialog( this, + "Multiple sequence file needs to contain at least 3 sequences", + "Illegal multiple sequence file", + JOptionPane.ERROR_MESSAGE ); + return; + } + // if ( msa.getLength() < 2 ) { + // JOptionPane.showMessageDialog( this, + // "Multiple sequence alignment needs to contain at least 2 residues", + // "Illegal multiple sequence file", + // JOptionPane.ERROR_MESSAGE ); + // return; + // } + System.gc(); + setSeqsFile( _seqs_pi_filechooser.getSelectedFile() ); + setSeqs( seqs ); + } + } + + private void addExpressionValuesFromFile() { + if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) { + JOptionPane.showMessageDialog( this, + "Need to load evolutionary tree first", + "Can Not Read Expression Values", + JOptionPane.WARNING_MESSAGE ); + return; + } + final File my_dir = getCurrentDir(); + if ( my_dir != null ) { + _values_filechooser.setCurrentDirectory( my_dir ); + } + final int result = _values_filechooser.showOpenDialog( _contentpane ); + final File file = _values_filechooser.getSelectedFile(); + if ( ( file != null ) && ( file.length() > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) { + BasicTable t = null; + try { + t = BasicTableParser.parse( file, '\t' ); + if ( t.getNumberOfColumns() < 2 ) { + t = BasicTableParser.parse( file, ',' ); + } + if ( t.getNumberOfColumns() < 2 ) { + t = BasicTableParser.parse( file, ' ' ); + } + } + catch ( final IOException e ) { + JOptionPane.showMessageDialog( this, + e.getMessage(), + "Could Not Read Expression Value Table", + JOptionPane.ERROR_MESSAGE ); + return; + } + if ( t.getNumberOfColumns() < 2 ) { + JOptionPane.showMessageDialog( this, + "Table contains " + t.getNumberOfColumns() + " column(s)", + "Problem with Expression Value Table", + JOptionPane.ERROR_MESSAGE ); + return; + } + if ( t.getNumberOfRows() < 1 ) { + JOptionPane.showMessageDialog( this, + "Table contains zero rows", + "Problem with Expression Value Table", + JOptionPane.ERROR_MESSAGE ); + return; + } + final Phylogeny phy = getCurrentTreePanel().getPhylogeny(); + if ( t.getNumberOfRows() != phy.getNumberOfExternalNodes() ) { + JOptionPane.showMessageDialog( this, + "Table contains " + t.getNumberOfRows() + " rows, but tree contains " + + phy.getNumberOfExternalNodes() + " external nodes", + "Warning", + JOptionPane.WARNING_MESSAGE ); + } + final DescriptiveStatistics stats = new BasicDescriptiveStatistics(); + int not_found = 0; + for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) { + final PhylogenyNode node = iter.next(); + final String node_name = node.getName(); + if ( !ForesterUtil.isEmpty( node_name ) ) { + int row = -1; + try { + row = t.findRow( node_name ); + } + catch ( final IllegalArgumentException e ) { + JOptionPane + .showMessageDialog( this, + e.getMessage(), + "Error Mapping Node Identifiers to Expression Value Identifiers", + JOptionPane.ERROR_MESSAGE ); + return; + } + if ( row < 0 ) { + if ( node.isExternal() ) { + not_found++; + } + continue; + } + final List l = new ArrayList(); + for( int col = 1; col < t.getNumberOfColumns(); ++col ) { + double d = -100; + try { + d = Double.parseDouble( t.getValueAsString( col, row ) ); + } + catch ( final NumberFormatException e ) { + JOptionPane.showMessageDialog( this, + "Could not parse \"" + t.getValueAsString( col, row ) + + "\" into a decimal value", + "Issue with Expression Value Table", + JOptionPane.ERROR_MESSAGE ); + return; + } + stats.addValue( d ); + l.add( d ); + } + if ( !l.isEmpty() ) { + if ( node.getNodeData().getProperties() != null ) { + node.getNodeData().getProperties() + .removePropertiesWithGivenReferencePrefix( PhyloXmlUtil.VECTOR_PROPERTY_REF ); + } + node.getNodeData().setVector( l ); + } + } + } + if ( not_found > 0 ) { + JOptionPane.showMessageDialog( this, "Could not fine expression values for " + not_found + + " external node(s)", "Warning", JOptionPane.WARNING_MESSAGE ); + } + getCurrentTreePanel().setStatisticsForExpressionValues( stats ); + } + } + + private void addSequencesFromFile() { + if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) { + JOptionPane.showMessageDialog( this, + "Need to load evolutionary tree first", + "Can Not Read Sequences", + JOptionPane.WARNING_MESSAGE ); + return; + } + final File my_dir = getCurrentDir(); + if ( my_dir != null ) { + _sequences_filechooser.setCurrentDirectory( my_dir ); + } + final int result = _sequences_filechooser.showOpenDialog( _contentpane ); + final File file = _sequences_filechooser.getSelectedFile(); + List seqs = null; + if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) { + try { + final FileInputStream fis1 = new FileInputStream( file ); + if ( FastaParser.isLikelyFasta( fis1 ) ) { + final FileInputStream fis2 = new FileInputStream( file ); + seqs = FastaParser.parse( fis2 ); + try { + fis2.close(); + } + catch ( final Exception e ) { + // Ignore. + } + } + else { + JOptionPane.showMessageDialog( this, + "Format does not appear to be Fasta", + "Multiple sequence file format error", + JOptionPane.ERROR_MESSAGE ); + return; + } + try { + fis1.close(); + } + catch ( final Exception e ) { + // Ignore. + } + } + catch ( final MsaFormatException e ) { + setArrowCursor(); + JOptionPane.showMessageDialog( this, + e.getLocalizedMessage(), + "Multiple sequence file format error", + JOptionPane.ERROR_MESSAGE ); + return; + } + catch ( final IOException e ) { + setArrowCursor(); + JOptionPane.showMessageDialog( this, + e.getLocalizedMessage(), + "Failed to read multiple sequence file", + JOptionPane.ERROR_MESSAGE ); + return; + } + catch ( final Exception e ) { + setArrowCursor(); + e.printStackTrace(); + JOptionPane.showMessageDialog( this, + e.getLocalizedMessage(), + "Unexpected error during reading of multiple sequence file", + JOptionPane.ERROR_MESSAGE ); + return; + } + if ( ( seqs == null ) || ( seqs.size() < 1 ) ) { + JOptionPane.showMessageDialog( this, + "Multiple sequence file is empty", + "Empty multiple sequence file", + JOptionPane.ERROR_MESSAGE ); + setArrowCursor(); + return; + } + } + if ( seqs != null ) { + for( final MolecularSequence seq : seqs ) { + System.out.println( seq.getIdentifier() ); + } + final Phylogeny phy = getCurrentTreePanel().getPhylogeny(); + int total_counter = 0; + int attached_counter = 0; + for( final MolecularSequence seq : seqs ) { + ++total_counter; + final String seq_name = seq.getIdentifier(); + if ( !ForesterUtil.isEmpty( seq_name ) ) { + List nodes = phy.getNodesViaSequenceName( seq_name ); + if ( nodes.isEmpty() ) { + nodes = phy.getNodesViaSequenceSymbol( seq_name ); + } + if ( nodes.isEmpty() ) { + nodes = phy.getNodesViaGeneName( seq_name ); + } + if ( nodes.isEmpty() ) { + nodes = phy.getNodes( seq_name ); + } + if ( nodes.size() > 1 ) { + JOptionPane.showMessageDialog( this, + "Sequence name \"" + seq_name + "\" is not unique", + "Sequence name not unique", + JOptionPane.ERROR_MESSAGE ); + setArrowCursor(); + return; + } + final String[] a = seq_name.split( "\\s" ); + if ( nodes.isEmpty() && ( a.length > 1 ) ) { + final String seq_name_split = a[ 0 ]; + nodes = phy.getNodesViaSequenceName( seq_name_split ); + if ( nodes.isEmpty() ) { + nodes = phy.getNodesViaSequenceSymbol( seq_name_split ); + } + if ( nodes.isEmpty() ) { + nodes = phy.getNodes( seq_name_split ); + } + if ( nodes.size() > 1 ) { + JOptionPane.showMessageDialog( this, "Split sequence name \"" + seq_name_split + + "\" is not unique", "Sequence name not unique", JOptionPane.ERROR_MESSAGE ); + setArrowCursor(); + return; + } + } + if ( nodes.size() == 1 ) { + ++attached_counter; + final PhylogenyNode n = nodes.get( 0 ); + if ( !n.getNodeData().isHasSequence() ) { + n.getNodeData().addSequence( new org.forester.phylogeny.data.Sequence() ); + } + n.getNodeData().getSequence().setMolecularSequence( seq.getMolecularSequenceAsString() ); + if ( ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) { + n.getNodeData().getSequence().setName( seq_name ); + } + } + } + } + if ( attached_counter > 0 ) { + int ext_nodes = 0; + int ext_nodes_with_seq = 0; + for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) { + ++ext_nodes; + final PhylogenyNode n = iter.next(); + if ( n.getNodeData().isHasSequence() + && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getMolecularSequence() ) ) { + ++ext_nodes_with_seq; + } + } + final String s; + if ( ext_nodes == ext_nodes_with_seq ) { + s = "All " + ext_nodes_with_seq + " external nodes now have a molecular sequence attached to them."; + } + else { + s = ext_nodes_with_seq + " out of " + ext_nodes + + " external nodes now have a molecular sequence attached to them."; + } + if ( ( attached_counter == total_counter ) && ( ext_nodes == ext_nodes_with_seq ) ) { + JOptionPane.showMessageDialog( this, + "Attached all " + total_counter + " sequences to tree nodes.\n" + s, + "All sequences attached", + JOptionPane.INFORMATION_MESSAGE ); + } + else { + JOptionPane.showMessageDialog( this, "Attached " + attached_counter + + " sequences out of a total of " + total_counter + " sequences.\n" + s, attached_counter + + " sequences attached", JOptionPane.WARNING_MESSAGE ); + } + } + else { + JOptionPane.showMessageDialog( this, "No maching tree node for any of the " + total_counter + + " sequences", "Could not attach any sequences", JOptionPane.ERROR_MESSAGE ); + } + } + } + + private void closeCurrentPane() { + if ( getMainPanel().getCurrentTreePanel() != null ) { + if ( getMainPanel().getCurrentTreePanel().isEdited() ) { + final int r = JOptionPane.showConfirmDialog( this, + "Close tab despite potentially unsaved changes?", + "Close Tab?", + JOptionPane.YES_NO_OPTION ); + if ( r != JOptionPane.YES_OPTION ) { + return; + } + } + getMainPanel().closeCurrentPane(); + activateSaveAllIfNeeded(); + } + } + + private void collapse( final Phylogeny phy ) { + final PhylogenyNodeIterator it = phy.iteratorPostorder(); + final List to_be_removed = new ArrayList(); + double min_support = Double.MAX_VALUE; + boolean conf_present = false; + while ( it.hasNext() ) { + final PhylogenyNode n = it.next(); + if ( !n.isExternal() && !n.isRoot() ) { + final List c = n.getBranchData().getConfidences(); + if ( ( c != null ) && ( c.size() > 0 ) ) { + conf_present = true; + double max = 0; + for( final Confidence confidence : c ) { + if ( confidence.getValue() > max ) { + max = confidence.getValue(); + } + } + if ( max < getMinNotCollapseConfidenceValue() ) { + to_be_removed.add( n ); + } + if ( max < min_support ) { + min_support = max; + } + } + } + } + if ( conf_present ) { + for( final PhylogenyNode node : to_be_removed ) { + PhylogenyMethods.removeNode( node, phy ); + } + if ( to_be_removed.size() > 0 ) { + phy.externalNodesHaveChanged(); + phy.clearHashIdToNodeMap(); + phy.recalculateNumberOfExternalDescendants( true ); + getCurrentTreePanel().resetNodeIdToDistToLeafMap(); + getCurrentTreePanel().updateSetOfCollapsedExternalNodes(); + getCurrentTreePanel().calculateLongestExtNodeInfo(); + getCurrentTreePanel().setNodeInPreorderToNull(); + getCurrentTreePanel().recalculateMaxDistanceToRoot(); + getCurrentTreePanel().resetPreferredSize(); + getCurrentTreePanel().setEdited( true ); + getCurrentTreePanel().repaint(); + repaint(); + } + if ( to_be_removed.size() > 0 ) { + JOptionPane.showMessageDialog( this, "Collapsed " + to_be_removed.size() + + " branches with\nconfidence values below " + getMinNotCollapseConfidenceValue(), "Collapsed " + + to_be_removed.size() + " branches", JOptionPane.INFORMATION_MESSAGE ); + } + else { + JOptionPane.showMessageDialog( this, "No branch collapsed,\nminimum confidence value per branch is " + + min_support, "No branch collapsed", JOptionPane.INFORMATION_MESSAGE ); + } + } + else { + JOptionPane.showMessageDialog( this, + "No branch collapsed because no confidence values present", + "No confidence values present", + JOptionPane.INFORMATION_MESSAGE ); + } + } + + private void collapseBelowBranchLengthThreshold() { + if ( getCurrentTreePanel() != null ) { + final Phylogeny phy = getCurrentTreePanel().getPhylogeny(); + if ( ( phy != null ) && !phy.isEmpty() ) { + final String s = ( String ) JOptionPane + .showInputDialog( this, + "Please enter the minimum branch length value\n", + "Minimal Branch Length Value", + JOptionPane.QUESTION_MESSAGE, + null, + null, + getMinNotCollapseBlValue() ); + 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 ) ) { + setMinNotCollapseBlValue( m ); + collapseBl( phy ); + } + } + } + } + } + + private void collapseBelowThreshold() { + if ( getCurrentTreePanel() != null ) { + final Phylogeny phy = getCurrentTreePanel().getPhylogeny(); + if ( ( phy != null ) && !phy.isEmpty() ) { + final String s = ( String ) JOptionPane.showInputDialog( this, + "Please enter the minimum confidence value\n", + "Minimal Confidence Value", + JOptionPane.QUESTION_MESSAGE, + null, + null, + getMinNotCollapseConfidenceValue() ); + if ( !ForesterUtil.isEmpty( s ) ) { + boolean success = true; + double m = 0.0; + final String m_str = s.trim(); + if ( !ForesterUtil.isEmpty( m_str ) ) { + try { + m = Double.parseDouble( m_str ); + } + catch ( final Exception ex ) { + success = false; + } + } + else { + success = false; + } + if ( success && ( m >= 0.0 ) ) { + setMinNotCollapseConfidenceValue( m ); + collapse( phy ); + } + } + } + } + } + + private void collapseBl( final Phylogeny phy ) { + final PhylogenyNodeIterator it = phy.iteratorPostorder(); + final List to_be_removed = new ArrayList(); + double min_bl = Double.MAX_VALUE; + boolean bl_present = false; + while ( it.hasNext() ) { + final PhylogenyNode n = it.next(); + if ( !n.isExternal() && !n.isRoot() ) { + final double bl = n.getDistanceToParent(); + if ( bl != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) { + bl_present = true; + if ( bl < getMinNotCollapseBlValue() ) { + to_be_removed.add( n ); + } + if ( bl < min_bl ) { + min_bl = bl; + } + } + } + } + if ( bl_present ) { + for( final PhylogenyNode node : to_be_removed ) { + PhylogenyMethods.removeNode( node, phy ); + } + if ( to_be_removed.size() > 0 ) { + phy.externalNodesHaveChanged(); + phy.clearHashIdToNodeMap(); + phy.recalculateNumberOfExternalDescendants( true ); + getCurrentTreePanel().resetNodeIdToDistToLeafMap(); + getCurrentTreePanel().updateSetOfCollapsedExternalNodes(); + getCurrentTreePanel().calculateLongestExtNodeInfo(); + getCurrentTreePanel().setNodeInPreorderToNull(); + getCurrentTreePanel().recalculateMaxDistanceToRoot(); + getCurrentTreePanel().resetPreferredSize(); + getCurrentTreePanel().setEdited( true ); + getCurrentTreePanel().repaint(); + repaint(); + } + if ( to_be_removed.size() > 0 ) { + JOptionPane.showMessageDialog( this, "Collapsed " + to_be_removed.size() + + " branches with\nbranch length values below " + getMinNotCollapseBlValue(), "Collapsed " + + to_be_removed.size() + " branches", JOptionPane.INFORMATION_MESSAGE ); + } + else { + JOptionPane.showMessageDialog( this, + "No branch collapsed,\nminimum branch length is " + min_bl, + "No branch collapsed", + JOptionPane.INFORMATION_MESSAGE ); + } + } + else { + JOptionPane.showMessageDialog( this, + "No branch collapsed because no branch length values present", + "No branch length values present", + JOptionPane.INFORMATION_MESSAGE ); + } + } + + private PhyloXmlParser createPhyloXmlParser() { + PhyloXmlParser xml_parser = null; + if ( getConfiguration().isValidatePhyloXmlAgainstSchema() ) { + try { + xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating(); + } + catch ( final Exception e ) { + JOptionPane.showMessageDialog( this, + e.getLocalizedMessage(), + "failed to create validating XML parser", + JOptionPane.WARNING_MESSAGE ); + } + } + if ( xml_parser == null ) { + xml_parser = PhyloXmlParser.createPhyloXmlParser(); + } + return xml_parser; + } + + private void executePhyleneticInference( final boolean from_unaligned_seqs ) { + final PhyloInferenceDialog dialog = new PhyloInferenceDialog( this, + getPhylogeneticInferenceOptions(), + from_unaligned_seqs ); + dialog.activate(); + if ( dialog.getValue() == JOptionPane.OK_OPTION ) { + if ( !from_unaligned_seqs ) { + if ( getMsa() != null ) { + final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getMsa(), + getPhylogeneticInferenceOptions() + .copy(), this ); + new Thread( inferrer ).start(); + } + else { + JOptionPane.showMessageDialog( this, + "No multiple sequence alignment selected", + "Phylogenetic Inference Not Launched", + JOptionPane.WARNING_MESSAGE ); + } + } + else { + if ( getSeqs() != null ) { + final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getSeqs(), + getPhylogeneticInferenceOptions() + .copy(), this ); + new Thread( inferrer ).start(); + } + else { + JOptionPane.showMessageDialog( this, + "No input sequences selected", + "Phylogenetic Inference Not Launched", + JOptionPane.WARNING_MESSAGE ); + } + } + } + } + + private void extractTaxDataFromNodeNames() throws PhyloXmlDataFormatException { + final StringBuilder sb = new StringBuilder(); + final StringBuilder sb_failed = new StringBuilder(); + int counter = 0; + int counter_failed = 0; + if ( getCurrentTreePanel() != null ) { + final Phylogeny phy = getCurrentTreePanel().getPhylogeny(); + if ( ( phy != null ) && !phy.isEmpty() ) { + final PhylogenyNodeIterator it = phy.iteratorExternalForward(); + while ( it.hasNext() ) { + final PhylogenyNode n = it.next(); + final String name = n.getName().trim(); + if ( !ForesterUtil.isEmpty( name ) ) { + final String nt = ParserUtils.extractTaxonomyDataFromNodeName( n, + TAXONOMY_EXTRACTION.AGGRESSIVE ); + if ( !ForesterUtil.isEmpty( nt ) ) { + if ( counter < 15 ) { + sb.append( name + ": " + nt + "\n" ); + } + else if ( counter == 15 ) { + sb.append( "...\n" ); + } + counter++; + } + else { + if ( counter_failed < 15 ) { + sb_failed.append( name + "\n" ); + } + else if ( counter_failed == 15 ) { + sb_failed.append( "...\n" ); + } + counter_failed++; + } + } + } + if ( counter > 0 ) { + String failed = ""; + String all = "all "; + if ( counter_failed > 0 ) { + all = ""; + failed = "\nCould not extract taxonomic data for " + counter_failed + + " named external nodes:\n" + sb_failed; + } + JOptionPane.showMessageDialog( this, + "Extracted taxonomic data from " + all + counter + + " named external nodes:\n" + sb.toString() + failed, + "Taxonomic Data Extraction Completed", + counter_failed > 0 ? JOptionPane.WARNING_MESSAGE + : JOptionPane.INFORMATION_MESSAGE ); + } + else { + JOptionPane + .showMessageDialog( this, + "Could not extract any taxonomic data.\nMaybe node names are empty\n" + + "or not in the forms \"XYZ_CAEEL\", \"XYZ_6239\", or \"XYZ_Caenorhabditis_elegans\"\n" + + "or nodes already have taxonomic data?\n", + "No Taxonomic Data Extracted", + JOptionPane.ERROR_MESSAGE ); + } + } + } + } + + private double getMinNotCollapseBlValue() { + return _min_not_collapse_bl; + } + + private double getMinNotCollapseConfidenceValue() { + return _min_not_collapse; + } + + private PhylogeneticInferenceOptions getPhylogeneticInferenceOptions() { + if ( _phylogenetic_inference_options == null ) { + _phylogenetic_inference_options = new PhylogeneticInferenceOptions(); + } + return _phylogenetic_inference_options; + } + + private boolean isUnsavedDataPresent() { + final List tps = getMainPanel().getTreePanels(); + for( final TreePanel tp : tps ) { + if ( tp.isEdited() ) { + return true; + } + } + return false; + } + + private void moveNodeNamesToSeqNames() throws PhyloXmlDataFormatException { + if ( getCurrentTreePanel() != null ) { + final Phylogeny phy = getCurrentTreePanel().getPhylogeny(); + if ( ( phy != null ) && !phy.isEmpty() ) { + PhylogenyMethods + .transferNodeNameToField( phy, PhylogenyMethods.PhylogenyNodeField.SEQUENCE_NAME, false ); + } + } + } + + private void moveNodeNamesToTaxSn() throws PhyloXmlDataFormatException { + if ( getCurrentTreePanel() != null ) { + final Phylogeny phy = getCurrentTreePanel().getPhylogeny(); + if ( ( phy != null ) && !phy.isEmpty() ) { + PhylogenyMethods.transferNodeNameToField( phy, + PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME, + false ); + } + } + } + + private void newTree() { + final Phylogeny[] phys = new Phylogeny[ 1 ]; + final Phylogeny phy = new Phylogeny(); + final PhylogenyNode node = new PhylogenyNode(); + phy.setRoot( node ); + phy.setRooted( true ); + phys[ 0 ] = phy; + AptxUtil.addPhylogeniesToTabs( phys, "", "", getConfiguration(), getMainPanel() ); + _mainpanel.getControlPanel().showWhole(); + _mainpanel.getCurrentTreePanel().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ); + _mainpanel.getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ); + if ( getMainPanel().getMainFrame() == null ) { + // Must be "E" applet version. + ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() ) + .setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ); + } + else { + getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ); + } + activateSaveAllIfNeeded(); + System.gc(); + } + + private void obtainDetailedTaxonomicInformation() { + if ( getCurrentTreePanel() != null ) { + final Phylogeny phy = getCurrentTreePanel().getPhylogeny(); + if ( ( phy != null ) && !phy.isEmpty() ) { + final TaxonomyDataManager t = new TaxonomyDataManager( this, + _mainpanel.getCurrentTreePanel(), + phy.copy(), + false, + true ); + new Thread( t ).start(); + } + } + } + + private void obtainDetailedTaxonomicInformationDelete() { + if ( getCurrentTreePanel() != null ) { + final Phylogeny phy = getCurrentTreePanel().getPhylogeny(); + if ( ( phy != null ) && !phy.isEmpty() ) { + final TaxonomyDataManager t = new TaxonomyDataManager( this, + _mainpanel.getCurrentTreePanel(), + phy.copy(), + true, + true ); + new Thread( t ).start(); + } + } + } + + private void obtainSequenceInformation() { + if ( getCurrentTreePanel() != null ) { + final Phylogeny phy = getCurrentTreePanel().getPhylogeny(); + if ( ( phy != null ) && !phy.isEmpty() ) { + final SequenceDataRetriver u = new SequenceDataRetriver( this, + _mainpanel.getCurrentTreePanel(), + phy.copy() ); + new Thread( u ).start(); + } + } + } + + private void preProcessTreesUponReading( final Phylogeny[] phys ) { + for( final Phylogeny phy : phys ) { + if ( ( phy != null ) && !phy.isEmpty() ) { + for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) { + final PhylogenyNode n = it.next(); + if ( n.isExternal() ) { + if ( n.getNodeData().isHasSequence() ) { + final Sequence s = n.getNodeData().getSequence(); + if ( ForesterUtil.isEmpty( s.getGeneName() ) || s.getGeneName().startsWith( "LOC" ) ) { + if ( ( s.getAccession() != null ) + && !ForesterUtil.isEmpty( s.getAccession().getValue() ) ) { + s.setGeneName( s.getAccession().getValue() ); + } + else if ( !ForesterUtil.isEmpty( n.getName() ) ) { + s.setGeneName( n.getName() ); + } + } + } + } + } + } + } + } + + private void readPhylogeniesFromFile() { + boolean exception = false; + Phylogeny[] phys = null; + // Set an initial directory if none set yet + final File my_dir = getCurrentDir(); + // Open file-open dialog and set current directory + if ( my_dir != null ) { + _open_filechooser.setCurrentDirectory( my_dir ); + } + final int result = _open_filechooser.showOpenDialog( _contentpane ); + // All done: get the file + final File[] files = _open_filechooser.getSelectedFiles(); + setCurrentDir( _open_filechooser.getCurrentDirectory() ); + boolean nhx_or_nexus = false; + if ( ( files != null ) && ( files.length > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) { + for( final File file : files ) { + if ( ( file != null ) && !file.isDirectory() ) { + if ( _mainpanel.getCurrentTreePanel() != null ) { + _mainpanel.getCurrentTreePanel().setWaitCursor(); + } + else { + _mainpanel.setWaitCursor(); + } + if ( ( _open_filechooser.getFileFilter() == MainFrame.nhfilter ) + || ( _open_filechooser.getFileFilter() == MainFrame.nhxfilter ) ) { + try { + final NHXParser nhx = new NHXParser(); + setSpecialOptionsForNhxParser( nhx ); + phys = PhylogenyMethods.readPhylogenies( nhx, file ); + nhx_or_nexus = true; + } + catch ( final Exception e ) { + exception = true; + exceptionOccuredDuringOpenFile( e ); + } + } + else if ( _open_filechooser.getFileFilter() == MainFrame.xmlfilter ) { + warnIfNotPhyloXmlValidation( getConfiguration() ); + try { + final PhyloXmlParser xml_parser = createPhyloXmlParser(); + phys = PhylogenyMethods.readPhylogenies( xml_parser, file ); + } + catch ( final Exception e ) { + exception = true; + exceptionOccuredDuringOpenFile( e ); + } + } + else if ( _open_filechooser.getFileFilter() == MainFrame.tolfilter ) { + try { + phys = PhylogenyMethods.readPhylogenies( new TolParser(), file ); + } + catch ( final Exception e ) { + exception = true; + exceptionOccuredDuringOpenFile( e ); + } + } + else if ( _open_filechooser.getFileFilter() == MainFrame.nexusfilter ) { + try { + final NexusPhylogeniesParser nex = new NexusPhylogeniesParser(); + setSpecialOptionsForNexParser( nex ); + phys = PhylogenyMethods.readPhylogenies( nex, file ); + nhx_or_nexus = true; + } + catch ( final Exception e ) { + exception = true; + exceptionOccuredDuringOpenFile( e ); + } + } + // "*.*": + else { + try { + final PhylogenyParser parser = ParserUtils + .createParserDependingOnFileType( file, getConfiguration() + .isValidatePhyloXmlAgainstSchema() ); + if ( parser instanceof NexusPhylogeniesParser ) { + final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) parser; + setSpecialOptionsForNexParser( nex ); + nhx_or_nexus = true; + } + else if ( parser instanceof NHXParser ) { + final NHXParser nhx = ( NHXParser ) parser; + setSpecialOptionsForNhxParser( nhx ); + nhx_or_nexus = true; + } + else if ( parser instanceof PhyloXmlParser ) { + warnIfNotPhyloXmlValidation( getConfiguration() ); + } + phys = PhylogenyMethods.readPhylogenies( parser, file ); + } + catch ( final Exception e ) { + exception = true; + exceptionOccuredDuringOpenFile( e ); + } + } + if ( _mainpanel.getCurrentTreePanel() != null ) { + _mainpanel.getCurrentTreePanel().setArrowCursor(); + } + else { + _mainpanel.setArrowCursor(); + } + if ( !exception && ( phys != null ) && ( phys.length > 0 ) ) { + boolean one_desc = false; + if ( nhx_or_nexus ) { + for( final Phylogeny phy : phys ) { + if ( getOptions().isInternalNumberAreConfidenceForNhParsing() ) { + PhylogenyMethods.transferInternalNodeNamesToConfidence( phy, "" ); + } + if ( PhylogenyMethods.getMinimumDescendentsPerInternalNodes( phy ) == 1 ) { + one_desc = true; + break; + } + } + } + if ( PREPROCESS_TREES ) { + preProcessTreesUponReading( phys ); + } + AptxUtil.addPhylogeniesToTabs( phys, + file.getName(), + file.getAbsolutePath(), + getConfiguration(), + getMainPanel() ); + _mainpanel.getControlPanel().showWhole(); + if ( nhx_or_nexus && one_desc ) { + JOptionPane + .showMessageDialog( this, + "One or more trees contain (a) node(s) with one descendant, " + + ForesterUtil.LINE_SEPARATOR + + "possibly indicating illegal parentheses within node names.", + "Warning: Possible Error in New Hampshire Formatted Data", + JOptionPane.WARNING_MESSAGE ); + } + } + } + } + } + activateSaveAllIfNeeded(); + System.gc(); + } + + private void readSpeciesTreeFromFile() { + Phylogeny t = null; + boolean exception = false; + final File my_dir = getCurrentDir(); + _open_filechooser_for_species_tree.setSelectedFile( new File( "" ) ); + if ( my_dir != null ) { + _open_filechooser_for_species_tree.setCurrentDirectory( my_dir ); + } + final int result = _open_filechooser_for_species_tree.showOpenDialog( _contentpane ); + final File file = _open_filechooser_for_species_tree.getSelectedFile(); + if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) { + if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrame.xmlfilter ) { + try { + final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( PhyloXmlParser + .createPhyloXmlParserXsdValidating(), file ); + t = trees[ 0 ]; + } + catch ( final Exception e ) { + exception = true; + exceptionOccuredDuringOpenFile( e ); + } + } + else if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrame.tolfilter ) { + try { + final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new TolParser(), file ); + t = trees[ 0 ]; + } + catch ( final Exception e ) { + exception = true; + exceptionOccuredDuringOpenFile( e ); + } + } + // "*.*": + else { + try { + final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( PhyloXmlParser + .createPhyloXmlParserXsdValidating(), file ); + t = trees[ 0 ]; + } + catch ( final Exception e ) { + exception = true; + exceptionOccuredDuringOpenFile( e ); + } + } + if ( !exception && ( t != null ) && !t.isRooted() ) { + exception = true; + t = null; + JOptionPane.showMessageDialog( this, + "Species tree is not rooted", + "Species tree not loaded", + JOptionPane.ERROR_MESSAGE ); + } + if ( !exception && ( t != null ) ) { + final Set tax_set = new HashSet(); + for( final PhylogenyNodeIterator it = t.iteratorExternalForward(); it.hasNext(); ) { + final PhylogenyNode node = it.next(); + if ( !node.getNodeData().isHasTaxonomy() ) { + exception = true; + t = null; + JOptionPane + .showMessageDialog( this, + "Species tree contains external node(s) without taxonomy information", + "Species tree not loaded", + JOptionPane.ERROR_MESSAGE ); + break; + } + else { + if ( tax_set.contains( node.getNodeData().getTaxonomy() ) ) { + exception = true; + t = null; + JOptionPane.showMessageDialog( this, + "Taxonomy [" + + node.getNodeData().getTaxonomy().asSimpleText() + + "] is not unique in species tree", + "Species tree not loaded", + JOptionPane.ERROR_MESSAGE ); + break; + } + else { + tax_set.add( node.getNodeData().getTaxonomy() ); + } + } + } + } + if ( !exception && ( t != null ) ) { + setSpeciesTree( t ); + JOptionPane.showMessageDialog( this, + "Species tree successfully loaded", + "Species tree loaded", + JOptionPane.INFORMATION_MESSAGE ); + } + _contentpane.repaint(); + System.gc(); + } + } + + private void setArrowCursor() { + try { + _mainpanel.getCurrentTreePanel().setArrowCursor(); + } + catch ( final Exception ex ) { + // Do nothing. + } + } + + private void setMinNotCollapseBlValue( final double min_not_collapse_bl ) { + _min_not_collapse_bl = min_not_collapse_bl; + } + + private void setMinNotCollapseConfidenceValue( final double min_not_collapse ) { + _min_not_collapse = min_not_collapse; + } + + private void setPhylogeneticInferenceOptions( final PhylogeneticInferenceOptions phylogenetic_inference_options ) { + _phylogenetic_inference_options = phylogenetic_inference_options; + } + + private void setSpecialOptionsForNexParser( final NexusPhylogeniesParser nex ) { + nex.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() ); + nex.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() ); + nex.setParseBeastStyleExtendedTags( getOptions().isParseBeastStyleExtendedNexusTags() ); + } + + private void setSpecialOptionsForNhxParser( final NHXParser nhx ) { + nhx.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() ); + nhx.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() ); + nhx.setAllowErrorsInDistanceToParent( getOptions().isAllowErrorsInDistanceToParent() ); + nhx.setParseBeastStyleExtendedTags( getOptions().isParseBeastStyleExtendedNexusTags() ); + } + + void buildAnalysisMenu() { + _analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() ); + _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) ); + _analysis_menu.add( _gsdir_item = new JMenuItem( "GSDIR (GSDI with re-rooting)" ) ); + _analysis_menu.add( _load_species_tree_item = new JMenuItem( "Load Species Tree..." ) ); + customizeJMenuItem( _gsdi_item ); + customizeJMenuItem( _gsdir_item ); + customizeJMenuItem( _load_species_tree_item ); + _analysis_menu.addSeparator(); + _analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) ); + customizeJMenuItem( _lineage_inference ); + _lineage_inference.setToolTipText( "Inference of ancestor taxonomies/lineages" ); + _jmenubar.add( _analysis_menu ); + } + + @Override + void buildFileMenu() { + _file_jmenu = MainFrame.createMenu( "File", getConfiguration() ); + _file_jmenu.add( _open_item = new JMenuItem( "Read Tree from File..." ) ); + _file_jmenu.addSeparator(); + _file_jmenu.add( _open_url_item = new JMenuItem( "Read Tree from URL/Webservice..." ) ); + _file_jmenu.addSeparator(); + final WebservicesManager webservices_manager = WebservicesManager.getInstance(); + _load_phylogeny_from_webservice_menu_items = new JMenuItem[ webservices_manager + .getAvailablePhylogeniesWebserviceClients().size() ]; + for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) { + final PhylogeniesWebserviceClient client = webservices_manager.getAvailablePhylogeniesWebserviceClient( i ); + _load_phylogeny_from_webservice_menu_items[ i ] = new JMenuItem( client.getMenuName() ); + _file_jmenu.add( _load_phylogeny_from_webservice_menu_items[ i ] ); + } + if ( getConfiguration().isEditable() ) { + _file_jmenu.addSeparator(); + _file_jmenu.add( _new_item = new JMenuItem( "New" ) ); + _new_item.setToolTipText( "to create a new tree with one node, as source for manual tree construction" ); + } + _file_jmenu.addSeparator(); + _file_jmenu.add( _save_item = new JMenuItem( "Save Tree As..." ) ); + _file_jmenu.add( _save_all_item = new JMenuItem( "Save All Trees As..." ) ); + _save_all_item.setToolTipText( "Write all phylogenies to one file." ); + _save_all_item.setEnabled( false ); + _file_jmenu.addSeparator(); + _file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) ); + if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" ) || AptxUtil.canWriteFormat( "TIF" ) ) { + _file_jmenu.add( _write_to_tif_item = new JMenuItem( "Export to TIFF file..." ) ); + } + _file_jmenu.add( _write_to_png_item = new JMenuItem( "Export to PNG file..." ) ); + _file_jmenu.add( _write_to_jpg_item = new JMenuItem( "Export to JPG file..." ) ); + if ( AptxUtil.canWriteFormat( "gif" ) ) { + _file_jmenu.add( _write_to_gif_item = new JMenuItem( "Export to GIF file..." ) ); + } + if ( AptxUtil.canWriteFormat( "bmp" ) ) { + _file_jmenu.add( _write_to_bmp_item = new JMenuItem( "Export to BMP file..." ) ); + } + _file_jmenu.addSeparator(); + _file_jmenu.add( _print_item = new JMenuItem( "Print..." ) ); + _file_jmenu.addSeparator(); + _file_jmenu.add( _close_item = new JMenuItem( "Close Tab" ) ); + _close_item.setToolTipText( "To close the current pane." ); + _close_item.setEnabled( true ); + _file_jmenu.addSeparator(); + _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) ); + customizeJMenuItem( _open_item ); + _open_item + .setFont( new Font( _open_item.getFont().getFontName(), Font.BOLD, _open_item.getFont().getSize() + 4 ) ); + customizeJMenuItem( _open_url_item ); + for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) { + customizeJMenuItem( _load_phylogeny_from_webservice_menu_items[ i ] ); + } + customizeJMenuItem( _save_item ); + if ( getConfiguration().isEditable() ) { + customizeJMenuItem( _new_item ); + } + customizeJMenuItem( _close_item ); + customizeJMenuItem( _save_all_item ); + customizeJMenuItem( _write_to_pdf_item ); + customizeJMenuItem( _write_to_png_item ); + customizeJMenuItem( _write_to_jpg_item ); + customizeJMenuItem( _write_to_gif_item ); + customizeJMenuItem( _write_to_tif_item ); + customizeJMenuItem( _write_to_bmp_item ); + customizeJMenuItem( _print_item ); + customizeJMenuItem( _exit_item ); + _jmenubar.add( _file_jmenu ); + } + + void buildOptionsMenu() { + _options_jmenu = MainFrame.createMenu( OPTIONS_HEADER, getConfiguration() ); + _options_jmenu.addChangeListener( new ChangeListener() { + + @Override + public void stateChanged( final ChangeEvent e ) { + MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() ); + MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() ); + MainFrame + .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() ); + MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame + .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) ); + // MainFrame.setTextForGraphicsSizeChooserMenuItem( _print_size_mi, getOptions() ); + MainFrame.setTextForPdfLineWidthChooserMenuItem( _choose_pdf_width_mi, getOptions() ); + MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() ); + MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() ); + MainFrame.setCycleDataReturnMenuItem( _cycle_data_return, getOptions() ); + MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() ); + try { + getMainPanel().getControlPanel().setVisibilityOfDomainStrucureCB(); + getMainPanel().getControlPanel().setVisibilityOfX(); + } + catch ( final Exception ignore ) { + // do nothing, not important. + } + } + } ); + _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( DISPLAY_SUBHEADER ), getConfiguration() ) ); + _options_jmenu + .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) ); + _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) ); + _options_jmenu.add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( NON_LINED_UP_CLADOGRAMS_LABEL ) ); + _radio_group_1 = new ButtonGroup(); + _radio_group_1.add( _ext_node_dependent_cladogram_rbmi ); + _radio_group_1.add( _uniform_cladograms_rbmi ); + _radio_group_1.add( _non_lined_up_cladograms_rbmi ); + _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( SHOW_OVERVIEW_LABEL ) ); + _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( DISPLAY_SCALE_LABEL ) ); + _options_jmenu + .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_INT ) ); + _options_jmenu + .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_EXT ) ); + _options_jmenu + .add( _show_default_node_shapes_for_marked_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_MARKED ) ); + _options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) ); + if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) { + _options_jmenu.add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) ); + _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) ); + } + _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( SHOW_ANN_REF_SOURCE_LABEL ) ); + _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( SHOW_CONF_STDDEV_LABEL ) ); + _options_jmenu.add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( COLOR_BY_TAXONOMIC_GROUP ) ); + _options_jmenu.add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( COLOR_LABELS_LABEL ) ); + _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP ); + _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( ABBREV_SN_LABEL ) ); + _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( LABEL_DIRECTION_LABEL ) ); + _label_direction_cbmi.setToolTipText( LABEL_DIRECTION_TIP ); + _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( SCREEN_ANTIALIAS_LABEL ) ); + _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( BG_GRAD_LABEL ) ); + _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) ); + _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) ); + _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) ); + _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) ); + _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) ); + _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) ); + _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) ); + _options_jmenu.addSeparator(); + _options_jmenu.add( _cycle_data_return = new JMenuItem( "Cycle Data Return" ) ); + _options_jmenu.addSeparator(); + _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( SEARCH_SUBHEADER ), getConfiguration() ) ); + _options_jmenu.add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( SEARCH_CASE_SENSITIVE_LABEL ) ); + _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( SEARCH_TERMS_ONLY_LABEL ) ); + _options_jmenu.add( _search_with_regex_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_REGEX_LABEL ) ); + _search_with_regex_cbmi.setToolTipText( MainFrame.SEARCH_WITH_REGEX_TIP ); + _options_jmenu.add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( INVERSE_SEARCH_RESULT_LABEL ) ); + _options_jmenu.add( _color_all_found_nodes_when_coloring_subtree_cbmi = new JCheckBoxMenuItem( "Colorize All Found Nodes When Colorizing Subtree(s)" ) ); + _options_jmenu.addSeparator(); + _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Graphics Export & Printing:" ), + getConfiguration() ) ); + _options_jmenu.add( _antialias_print_cbmi = new JCheckBoxMenuItem( "Antialias" ) ); + _options_jmenu.add( _print_black_and_white_cbmi = new JCheckBoxMenuItem( "Export in Black and White" ) ); + _options_jmenu + .add( _graphics_export_visible_only_cbmi = new JCheckBoxMenuItem( "Limit to Visible ('Screenshot') for PNG, JPG, and GIF export" ) ); + _options_jmenu.add( _choose_pdf_width_mi = new JMenuItem( "" ) ); + _options_jmenu.addSeparator(); + _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/NHX/Nexus Read:" ), getConfiguration() ) ); + _options_jmenu + .add( _internal_number_are_confidence_for_nh_parsing_cbmi = new JCheckBoxMenuItem( "Internal Node Names are Confidence Values" ) ); + _options_jmenu.add( _replace_underscores_cbmi = new JCheckBoxMenuItem( "Replace Underscores with Spaces" ) ); + _options_jmenu.add( _parse_beast_style_extended_nexus_tags_cbmi = new JCheckBoxMenuItem( "Parse BEAST-style extended Newick/Nexus tags" ) ); + + _parse_beast_style_extended_nexus_tags_cbmi.setToolTipText( "to parse elements in the form of \"[&!color=#800080]\" in Newick/Nexus formatted trees" ); + + + _options_jmenu + .add( _allow_errors_in_distance_to_parent_cbmi = new JCheckBoxMenuItem( "Ignore Distance Values Format Errors" ) ); + _options_jmenu.add( _extract_taxonomy_no_rbmi = new JRadioButtonMenuItem( "No Taxonomy Extraction" ) ); + _options_jmenu + .add( _extract_taxonomy_pfam_strict_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style Node Names" ) ); + _options_jmenu + .add( _extract_taxonomy_pfam_relaxed_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style like Node Names" ) ); + _options_jmenu + .add( _extract_taxonomy_agressive_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids/Scientific Names from Node Names" ) ); + _extract_taxonomy_pfam_strict_rbmi + .setToolTipText( "To extract taxonomy codes/ids from node names in the form of e.g. \"BCL2_MOUSE/123-304\" or \"BCL2_10090/123-304\"" ); + _extract_taxonomy_pfam_relaxed_rbmi + .setToolTipText( "To extract taxonomy codes/ids from node names in the form of e.g. \"bax_MOUSE\" or \"bax_10090\"" ); + _extract_taxonomy_agressive_rbmi + .setToolTipText( "To extract taxonomy codes/ids or scientific names from node names in the form of e.g. \"MOUSE\" or \"10090\" or \"xyz_Nematostella_vectensis\"" ); + _radio_group_2 = new ButtonGroup(); + _radio_group_2.add( _extract_taxonomy_no_rbmi ); + _radio_group_2.add( _extract_taxonomy_pfam_strict_rbmi ); + _radio_group_2.add( _extract_taxonomy_pfam_relaxed_rbmi ); + _radio_group_2.add( _extract_taxonomy_agressive_rbmi ); + _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/Nexus Save:" ), getConfiguration() ) ); + _options_jmenu + .add( _use_brackets_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_BRACKETS_FOR_CONF_IN_NH_LABEL ) ); + _use_brackets_for_conf_in_nh_export_cbmi + .setToolTipText( "e.g. \"0.1[90]\" for a branch with support 90 and a length of 0.1" ); + _options_jmenu + .add( _use_internal_names_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL ) ); + customizeJMenuItem( _choose_font_mi ); + customizeJMenuItem( _choose_minimal_confidence_mi ); + customizeJMenuItem( _switch_colors_mi ); + customizeJMenuItem( _choose_pdf_width_mi ); + customizeJMenuItem( _overview_placment_mi ); + customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions() + .isShowDefaultNodeShapesExternal() ); + customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions() + .isShowDefaultNodeShapesInternal() ); + customizeCheckBoxMenuItem( _show_default_node_shapes_for_marked_cbmi, getOptions() + .isShowDefaultNodeShapesForMarkedNodes() ); + customizeJMenuItem( _cycle_node_shape_mi ); + customizeJMenuItem( _cycle_node_fill_mi ); + customizeJMenuItem( _choose_node_size_mi ); + customizeJMenuItem( _cycle_data_return ); + customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() ); + customizeCheckBoxMenuItem( _color_by_taxonomic_group_cbmi, getOptions().isColorByTaxonomicGroup() ); + customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() ); + customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() ); + customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() ); + customizeCheckBoxMenuItem( _show_annotation_ref_source, getOptions().isShowAnnotationRefSource() ); + customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() ); + customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() ); + customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() ); + customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi, + getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP ); + customizeRadioButtonMenuItem( _uniform_cladograms_rbmi, + getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP ); + customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi, + getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP ); + customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() ); + customizeCheckBoxMenuItem( _label_direction_cbmi, + getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL ); + customizeCheckBoxMenuItem( _antialias_print_cbmi, getOptions().isAntialiasPrint() ); + customizeCheckBoxMenuItem( _print_black_and_white_cbmi, getOptions().isPrintBlackAndWhite() ); + customizeCheckBoxMenuItem( _internal_number_are_confidence_for_nh_parsing_cbmi, getOptions() + .isInternalNumberAreConfidenceForNhParsing() ); + customizeRadioButtonMenuItem( _extract_taxonomy_no_rbmi, + getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.NO ); + customizeRadioButtonMenuItem( _extract_taxonomy_pfam_strict_rbmi, + getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); + customizeRadioButtonMenuItem( _extract_taxonomy_pfam_relaxed_rbmi, + getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + customizeRadioButtonMenuItem( _extract_taxonomy_agressive_rbmi, + getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.AGGRESSIVE ); + customizeCheckBoxMenuItem( _replace_underscores_cbmi, getOptions().isReplaceUnderscoresInNhParsing() ); + customizeCheckBoxMenuItem( _allow_errors_in_distance_to_parent_cbmi, getOptions() + .isReplaceUnderscoresInNhParsing() ); + customizeCheckBoxMenuItem( _search_with_regex_cbmi, getOptions().isSearchWithRegex() ); + customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() ); + customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() ); + customizeCheckBoxMenuItem( _color_all_found_nodes_when_coloring_subtree_cbmi, getOptions().isColorAllFoundNodesWhenColoringSubtree() ); + customizeCheckBoxMenuItem( _parse_beast_style_extended_nexus_tags_cbmi, getOptions().isParseBeastStyleExtendedNexusTags() ); + + customizeCheckBoxMenuItem( _graphics_export_visible_only_cbmi, getOptions().isGraphicsExportVisibleOnly() ); + customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() ); + customizeCheckBoxMenuItem( _use_brackets_for_conf_in_nh_export_cbmi, getOptions() + .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS ); + customizeCheckBoxMenuItem( _use_internal_names_for_conf_in_nh_export_cbmi, getOptions() + .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES ); + customizeCheckBoxMenuItem( _line_up_renderable_data_cbmi, getOptions().isLineUpRendarableNodeData() ); + customizeCheckBoxMenuItem( _right_line_up_domains_cbmi, getOptions().isRightLineUpDomains() ); + _jmenubar.add( _options_jmenu ); + } + + void buildPhylogeneticInferenceMenu() { + final InferenceManager im = getInferenceManager(); + _inference_menu = MainFrame.createMenu( "Inference", getConfiguration() ); + _inference_menu.add( _inference_from_msa_item = new JMenuItem( "From Multiple Sequence Alignment..." ) ); + customizeJMenuItem( _inference_from_msa_item ); + _inference_from_msa_item.setToolTipText( "Basic phylogenetic inference from MSA" ); + if ( im.canDoMsa() ) { + _inference_menu.add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences..." ) ); + customizeJMenuItem( _inference_from_seqs_item ); + _inference_from_seqs_item + .setToolTipText( "Basic phylogenetic inference including multiple sequence alignment" ); + } + else { + _inference_menu + .add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences (no program found)" ) ); + customizeJMenuItem( _inference_from_seqs_item ); + _inference_from_seqs_item.setEnabled( false ); + } + _jmenubar.add( _inference_menu ); + } + + void buildToolsMenu() { + _tools_menu = createMenu( "Tools", getConfiguration() ); + _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) ); + customizeJMenuItem( _confcolor_item ); + _tools_menu.add( _color_rank_jmi = new JMenuItem( "Colorize Subtrees via Taxonomic Rank" ) ); + customizeJMenuItem( _color_rank_jmi ); + _color_rank_jmi.setToolTipText( "for example, at \"Class\" level, colorize mammal specific subtree red" ); + _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) ); + customizeJMenuItem( _taxcolor_item ); + _tools_menu.addSeparator(); + _tools_menu.add( _remove_visual_styles_item = new JMenuItem( "Delete All Visual Styles From Nodes" ) ); + _remove_visual_styles_item + .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny" ); + customizeJMenuItem( _remove_visual_styles_item ); + _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete All Colors From Branches" ) ); + _remove_branch_color_item.setToolTipText( "To remove all branch color values from the current phylogeny" ); + customizeJMenuItem( _remove_branch_color_item ); + _tools_menu.addSeparator(); + _tools_menu.add( _annotate_item = new JMenuItem( "Annotate Sequences of Selected Nodes" ) ); + customizeJMenuItem( _annotate_item ); + _tools_menu.addSeparator(); + _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) ); + customizeJMenuItem( _midpoint_root_item ); + _tools_menu.addSeparator(); + _tools_menu.add( _delete_selected_nodes_item = new JMenuItem( "Delete Selected Nodes" ) ); + _delete_selected_nodes_item.setToolTipText( "To delete all selected external nodes" ); + customizeJMenuItem( _delete_selected_nodes_item ); + _tools_menu.add( _delete_not_selected_nodes_item = new JMenuItem( "Retain Selected Nodes" ) ); + _delete_not_selected_nodes_item.setToolTipText( "To delete all not selected external nodes" ); + customizeJMenuItem( _delete_not_selected_nodes_item ); + _tools_menu.addSeparator(); + _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) ); + customizeJMenuItem( _collapse_species_specific_subtrees ); + _collapse_species_specific_subtrees.setToolTipText( "To (reversibly) collapse species-specific subtrees" ); + _tools_menu + .add( _collapse_below_threshold = new JMenuItem( "Collapse Branches with Confidence Below Threshold into Multifurcations" ) ); + customizeJMenuItem( _collapse_below_threshold ); + _collapse_below_threshold + .setToolTipText( "To (permanently) collapse branches with confidence values below a threshold into multifurcations (in the case of multiple confidences per branch: without at least one confidence value above a threshold)" ); + // + _tools_menu + .add( _collapse_below_branch_length = new JMenuItem( "Collapse Branches with Branch Lengths Below Threshold into Multifurcations" ) ); + customizeJMenuItem( _collapse_below_branch_length ); + _collapse_below_branch_length + .setToolTipText( "To (permanently) collapse branches with branches with branch lengths below a threshold into multifurcations" ); + // + _tools_menu.addSeparator(); + _tools_menu + .add( _extract_tax_code_from_node_names_jmi = new JMenuItem( "Extract Taxonomic Data from Node Names" ) ); + customizeJMenuItem( _extract_tax_code_from_node_names_jmi ); + _extract_tax_code_from_node_names_jmi + .setToolTipText( "To extract SwissProt/Uniprot taxonomic codes (mnemonics) from nodes names in the form of 'xyz_CAEEL', Uniprot/NCBI identifiers form of 'xyz_6239', or scientific names form of 'xyz_Caenorhabditis_elegans'" ); + _tools_menu + .add( _move_node_names_to_tax_sn_jmi = new JMenuItem( "Transfer Node Names to Taxonomic Scientific Names" ) ); + customizeJMenuItem( _move_node_names_to_tax_sn_jmi ); + _move_node_names_to_tax_sn_jmi.setToolTipText( "To interpret node names as taxonomic scientific names" ); + _tools_menu.add( _move_node_names_to_seq_names_jmi = new JMenuItem( "Transfer Node Names to Sequence Names" ) ); + customizeJMenuItem( _move_node_names_to_seq_names_jmi ); + _move_node_names_to_seq_names_jmi.setToolTipText( "To interpret node names as sequence (protein, gene) names" ); + _tools_menu.addSeparator(); + _tools_menu.add( _obtain_seq_information_jmi = new JMenuItem( "Obtain Sequence Information" ) ); + customizeJMenuItem( _obtain_seq_information_jmi ); + _obtain_seq_information_jmi.setToolTipText( "To add additional sequence information" ); + _tools_menu + .add( _obtain_detailed_taxonomic_information_jmi = new JMenuItem( OBTAIN_DETAILED_TAXONOMIC_INFORMATION ) ); + customizeJMenuItem( _obtain_detailed_taxonomic_information_jmi ); + _obtain_detailed_taxonomic_information_jmi + .setToolTipText( "To add additional taxonomic information (from UniProt Taxonomy)" ); + _tools_menu + .add( _obtain_detailed_taxonomic_information_deleting_jmi = new JMenuItem( "Obtain Detailed Taxonomic Information (deletes nodes!)" ) ); + customizeJMenuItem( _obtain_detailed_taxonomic_information_deleting_jmi ); + _obtain_detailed_taxonomic_information_deleting_jmi + .setToolTipText( "To add additional taxonomic information, deletes nodes for which taxonomy cannot found (from UniProt Taxonomy)" ); + _tools_menu.addSeparator(); + _tools_menu.add( _read_values_jmi = new JMenuItem( "Attach Vector/Expression Values" ) ); + customizeJMenuItem( _read_values_jmi ); + _read_values_jmi.setToolTipText( "To attach vector (e.g. gene expression) values to tree nodes (beta)" ); + _jmenubar.add( _tools_menu ); + _tools_menu.add( _read_seqs_jmi = new JMenuItem( "Attach Molecular Sequences" ) ); + customizeJMenuItem( _read_seqs_jmi ); + _read_seqs_jmi + .setToolTipText( "To attach molecular sequences to tree nodes (from Fasta-formatted file) (beta)" ); + _jmenubar.add( _tools_menu ); + } + + @Override + void close() { + if ( isUnsavedDataPresent() ) { + final int r = JOptionPane.showConfirmDialog( this, + "Exit despite potentially unsaved changes?", + "Exit?", + JOptionPane.YES_NO_OPTION ); + if ( r != JOptionPane.YES_OPTION ) { + return; + } + } + exit(); + } + + void exit() { + removeAllTextFrames(); + _mainpanel.terminate(); + _contentpane.removeAll(); + setVisible( false ); + dispose(); + // System.exit( 0 ); //TODO reconfirm that this is OK, then remove. + } + + void readPhylogeniesFromURL() { + URL url = null; + Phylogeny[] phys = null; + final String message = "Please enter a complete URL, for example \"http://purl.org/phylo/treebase/phylows/study/TB2:S15480?format=nexus\""; + final String url_string = JOptionPane.showInputDialog( this, + message, + "Use URL/webservice to obtain a phylogeny", + JOptionPane.QUESTION_MESSAGE ); + boolean nhx_or_nexus = false; + if ( ( url_string != null ) && ( url_string.length() > 0 ) ) { + try { + url = new URL( url_string ); + PhylogenyParser parser = null; + if ( url.getHost().toLowerCase().indexOf( "tolweb" ) >= 0 ) { + parser = new TolParser(); + } + else { + parser = ParserUtils.createParserDependingOnUrlContents( url, getConfiguration() + .isValidatePhyloXmlAgainstSchema() ); + } + if ( parser instanceof NexusPhylogeniesParser ) { + nhx_or_nexus = true; + } + else if ( parser instanceof NHXParser ) { + nhx_or_nexus = true; + } + if ( _mainpanel.getCurrentTreePanel() != null ) { + _mainpanel.getCurrentTreePanel().setWaitCursor(); + } + else { + _mainpanel.setWaitCursor(); + } + final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); + phys = factory.create( url.openStream(), parser ); + } + catch ( final MalformedURLException e ) { + JOptionPane.showMessageDialog( this, + "Malformed URL: " + url + "\n" + e.getLocalizedMessage(), + "Malformed URL", + JOptionPane.ERROR_MESSAGE ); + } + catch ( final IOException e ) { + JOptionPane.showMessageDialog( this, + "Could not read from " + url + "\n" + + ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ), + "Failed to read URL", + JOptionPane.ERROR_MESSAGE ); + } + catch ( final Exception e ) { + JOptionPane.showMessageDialog( this, + ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ), + "Unexpected Exception", + JOptionPane.ERROR_MESSAGE ); + } + finally { + if ( _mainpanel.getCurrentTreePanel() != null ) { + _mainpanel.getCurrentTreePanel().setArrowCursor(); + } + else { + _mainpanel.setArrowCursor(); + } + } + if ( ( phys != null ) && ( phys.length > 0 ) ) { + if ( nhx_or_nexus && getOptions().isInternalNumberAreConfidenceForNhParsing() ) { + for( final Phylogeny phy : phys ) { + PhylogenyMethods.transferInternalNodeNamesToConfidence( phy, "" ); + } + } + AptxUtil.addPhylogeniesToTabs( phys, + new File( url.getFile() ).getName(), + new File( url.getFile() ).toString(), + getConfiguration(), + getMainPanel() ); + _mainpanel.getControlPanel().showWhole(); + } + } + activateSaveAllIfNeeded(); + System.gc(); + } + + void setMsa( final Msa msa ) { + _msa = msa; + } + + void setMsaFile( final File msa_file ) { + _msa_file = msa_file; + } + + void setSeqs( final List seqs ) { + _seqs = seqs; + } + + void setSeqsFile( final File seqs_file ) { + _seqs_file = seqs_file; + } + + public static MainFrameApplication createInstance( final Phylogeny[] phys, final Configuration config ) { + return new MainFrameApplication( phys, config ); + } + + public static MainFrame createInstance( final Phylogeny[] phys, + final Configuration config, + final String title, + final File current_dir ) { + return new MainFrameApplication( phys, config, title, current_dir ); + } + + static MainFrame createInstance( final Phylogeny[] phys, final Configuration config, final String title ) { + return new MainFrameApplication( phys, config, title ); + } + + static MainFrame createInstance( final Phylogeny[] phys, final String config_file_name, final String title ) { + return new MainFrameApplication( phys, config_file_name, title ); + } + + static void warnIfNotPhyloXmlValidation( final Configuration c ) { + if ( !c.isValidatePhyloXmlAgainstSchema() ) { + JOptionPane + .showMessageDialog( null, + ForesterUtil + .wordWrap( "phyloXML XSD-based validation is turned off [enable with line 'validate_against_phyloxml_xsd_schem: true' in configuration file]", + 80 ), + "Warning", + JOptionPane.WARNING_MESSAGE ); + } + } +} // MainFrameApplication. diff --git a/forester/java/src/org/forester/archaeopteryx/Options.java b/forester/java/src/org/forester/archaeopteryx/Options.java index 1143288..8494510 100644 --- a/forester/java/src/org/forester/archaeopteryx/Options.java +++ b/forester/java/src/org/forester/archaeopteryx/Options.java @@ -119,6 +119,7 @@ final public class Options { private boolean _line_up_renderable_node_data; private boolean _right_align_domains; private boolean _color_all_found_nodes_when_coloring_subtree; + private boolean _parse_beast_style_extended_nexus_tags; private Options() { init(); @@ -195,6 +196,7 @@ final public class Options { _show_default_node_shapes_external = false; _show_default_node_shapes_for_marked_nodes = false; _color_all_found_nodes_when_coloring_subtree = false; + _parse_beast_style_extended_nexus_tags= true; _min_confidence_value = MIN_CONFIDENCE_DEFAULT; _print_black_and_white = false; _phylogeny_graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR; @@ -591,4 +593,12 @@ final public class Options { final void setColorAllFoundNodesWhenColoringSubtree( final boolean color_all_found_nodes_when_coloring_subtree ) { _color_all_found_nodes_when_coloring_subtree = color_all_found_nodes_when_coloring_subtree; } + + final boolean isParseBeastStyleExtendedNexusTags() { + return _parse_beast_style_extended_nexus_tags; + } + + final void setParseBeastStyleExtendedNexusTags( boolean parse_beast_style_extended_nexus_tags ) { + _parse_beast_style_extended_nexus_tags = parse_beast_style_extended_nexus_tags; + } } diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java index e271b52..a20689d 100644 --- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java +++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java @@ -1996,7 +1996,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee .equalsIgnoreCase( "uniprot" ) ) ) { try { uri_str = "http://www.uniprot.org/taxonomy/" - + URLEncoder.encode( tax.getIdentifier().getValue(), ForesterConstants.UTF8 ); + + URLEncoder.encode( tax.getIdentifier().getValue(), ForesterConstants.UTF_8 ); } catch ( final UnsupportedEncodingException e ) { AptxUtil.showErrorMessage( this, e.toString() ); @@ -2006,7 +2006,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee else if ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) { try { uri_str = "http://www.uniprot.org/taxonomy/?query=" - + URLEncoder.encode( tax.getScientificName(), ForesterConstants.UTF8 ); + + URLEncoder.encode( tax.getScientificName(), ForesterConstants.UTF_8 ); } catch ( final UnsupportedEncodingException e ) { AptxUtil.showErrorMessage( this, e.toString() ); @@ -2016,7 +2016,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee else if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) { try { uri_str = "http://www.uniprot.org/taxonomy/?query=" - + URLEncoder.encode( tax.getTaxonomyCode(), ForesterConstants.UTF8 ); + + URLEncoder.encode( tax.getTaxonomyCode(), ForesterConstants.UTF_8 ); } catch ( final UnsupportedEncodingException e ) { AptxUtil.showErrorMessage( this, e.toString() ); @@ -2026,7 +2026,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee else if ( !ForesterUtil.isEmpty( tax.getCommonName() ) ) { try { uri_str = "http://www.uniprot.org/taxonomy/?query=" - + URLEncoder.encode( tax.getCommonName(), ForesterConstants.UTF8 ); + + URLEncoder.encode( tax.getCommonName(), ForesterConstants.UTF_8 ); } catch ( final UnsupportedEncodingException e ) { AptxUtil.showErrorMessage( this, e.toString() ); diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanelUtil.java b/forester/java/src/org/forester/archaeopteryx/TreePanelUtil.java index a6017d9..ac47498 100644 --- a/forester/java/src/org/forester/archaeopteryx/TreePanelUtil.java +++ b/forester/java/src/org/forester/archaeopteryx/TreePanelUtil.java @@ -46,7 +46,7 @@ public class TreePanelUtil { final String upkb = SequenceAccessionTools.obtainUniProtAccessorFromDataFields( node ); if ( !ForesterUtil.isEmpty( upkb ) ) { try { - uri_str = ForesterUtil.UNIPROT_KB + URLEncoder.encode( upkb, ForesterConstants.UTF8 ); + uri_str = ForesterUtil.UNIPROT_KB + URLEncoder.encode( upkb, ForesterConstants.UTF_8 ); } catch ( final UnsupportedEncodingException e ) { AptxUtil.showErrorMessage( tp, e.toString() ); @@ -58,10 +58,10 @@ public class TreePanelUtil { if ( !ForesterUtil.isEmpty( v ) ) { try { if ( SequenceAccessionTools.isProteinDbQuery( v ) ) { - uri_str = ForesterUtil.NCBI_PROTEIN + URLEncoder.encode( v, ForesterConstants.UTF8 ); + uri_str = ForesterUtil.NCBI_PROTEIN + URLEncoder.encode( v, ForesterConstants.UTF_8 ); } else { - uri_str = ForesterUtil.NCBI_NUCCORE + URLEncoder.encode( v, ForesterConstants.UTF8 ); + uri_str = ForesterUtil.NCBI_NUCCORE + URLEncoder.encode( v, ForesterConstants.UTF_8 ); } } catch ( final UnsupportedEncodingException e ) { @@ -75,10 +75,10 @@ public class TreePanelUtil { if ( !ForesterUtil.isEmpty( v ) ) { try { if ( SequenceAccessionTools.isProteinDbQuery( v ) ) { - uri_str = ForesterUtil.NCBI_PROTEIN + URLEncoder.encode( v, ForesterConstants.UTF8 ); + uri_str = ForesterUtil.NCBI_PROTEIN + URLEncoder.encode( v, ForesterConstants.UTF_8 ); } else { - uri_str = ForesterUtil.NCBI_NUCCORE + URLEncoder.encode( v, ForesterConstants.UTF8 ); + uri_str = ForesterUtil.NCBI_NUCCORE + URLEncoder.encode( v, ForesterConstants.UTF_8 ); } } catch ( final UnsupportedEncodingException e ) { @@ -91,7 +91,7 @@ public class TreePanelUtil { final String v = SequenceAccessionTools.obtainGiNumberFromDataFields( node ); if ( !ForesterUtil.isEmpty( v ) ) { try { - uri_str = ForesterUtil.NCBI_GI + URLEncoder.encode( v, ForesterConstants.UTF8 ); + uri_str = ForesterUtil.NCBI_GI + URLEncoder.encode( v, ForesterConstants.UTF_8 ); } catch ( final UnsupportedEncodingException e ) { AptxUtil.showErrorMessage( tp, e.toString() ); diff --git a/forester/java/src/org/forester/io/parsers/nexus/NexusBinaryStatesMatrixParser.java b/forester/java/src/org/forester/io/parsers/nexus/NexusBinaryStatesMatrixParser.java index e110ec1..b6bea46 100644 --- a/forester/java/src/org/forester/io/parsers/nexus/NexusBinaryStatesMatrixParser.java +++ b/forester/java/src/org/forester/io/parsers/nexus/NexusBinaryStatesMatrixParser.java @@ -35,10 +35,10 @@ import org.forester.evoinference.matrix.character.CharacterStateMatrix; import org.forester.evoinference.matrix.character.CharacterStateMatrix.BinaryStates; import org.forester.io.parsers.util.ParserUtils; import org.forester.io.parsers.util.PhylogenyParserException; +import org.forester.util.ForesterConstants; public class NexusBinaryStatesMatrixParser { - private static final String UTF_8 = "UTF-8"; private Object _nexus_source; private CharacterStateMatrix _matrix; private int _nchar; @@ -62,7 +62,7 @@ public class NexusBinaryStatesMatrixParser { public void parse() throws IOException { reset(); - final BufferedReader reader = ParserUtils.createReader( getNexusSource(), UTF_8 ); + final BufferedReader reader = ParserUtils.createReader( getNexusSource(), ForesterConstants.UTF_8 ); String line; boolean in_matrix = false; int identifier_index = 0; diff --git a/forester/java/src/org/forester/io/parsers/nexus/NexusCharactersParser.java b/forester/java/src/org/forester/io/parsers/nexus/NexusCharactersParser.java index 3407441..0ee589e 100644 --- a/forester/java/src/org/forester/io/parsers/nexus/NexusCharactersParser.java +++ b/forester/java/src/org/forester/io/parsers/nexus/NexusCharactersParser.java @@ -33,12 +33,12 @@ import java.util.List; import org.forester.io.parsers.util.ParserUtils; import org.forester.io.parsers.util.PhylogenyParserException; +import org.forester.util.ForesterConstants; import org.forester.util.ForesterUtil; public class NexusCharactersParser { - private static final String UTF_8 = "UTF-8"; - final private static String charstatelabels = NexusConstants.CHARSTATELABELS.toLowerCase(); + final private static String charstatelabels = NexusConstants.CHARSTATELABELS.toLowerCase(); private Object _nexus_source; private String[] _char_state_labels; @@ -52,7 +52,7 @@ public class NexusCharactersParser { public void parse() throws IOException { reset(); - final BufferedReader reader = ParserUtils.createReader( getNexusSource(), UTF_8 ); + final BufferedReader reader = ParserUtils.createReader( getNexusSource(), ForesterConstants.UTF_8 ); String line; boolean in_charstatelabels = false; final List labels_list = new ArrayList(); diff --git a/forester/java/src/org/forester/io/parsers/nexus/NexusPhylogeniesParser.java b/forester/java/src/org/forester/io/parsers/nexus/NexusPhylogeniesParser.java index d4eabfd..6ff0439 100644 --- a/forester/java/src/org/forester/io/parsers/nexus/NexusPhylogeniesParser.java +++ b/forester/java/src/org/forester/io/parsers/nexus/NexusPhylogeniesParser.java @@ -49,12 +49,12 @@ import org.forester.phylogeny.data.Sequence; import org.forester.phylogeny.iterators.PhylogenyNodeIterator; import org.forester.sequence.BasicSequence; import org.forester.sequence.MolecularSequence; +import org.forester.util.ForesterConstants; import org.forester.util.ForesterUtil; public final class NexusPhylogeniesParser implements IteratingPhylogenyParser, PhylogenyParser { - private static final String UTF_8 = "UTF-8"; - + final private static boolean DEBUG = false; final private static String begin_trees = NexusConstants.BEGIN_TREES.toLowerCase(); @@ -98,6 +98,8 @@ public final class NexusPhylogeniesParser implements IteratingPhylogenyParser, P private StringBuilder _translate_sb; private Map _seqs; private final boolean _add_sequences = true; + private boolean _parse_beast_style_extended_tags = false; + @Override public String getName() { @@ -146,7 +148,7 @@ public final class NexusPhylogeniesParser implements IteratingPhylogenyParser, P _rooted_info_present = false; _is_rooted = false; _seqs = new HashMap(); - _br = ParserUtils.createReader( _nexus_source, UTF_8 ); + _br = ParserUtils.createReader( _nexus_source, ForesterConstants.UTF_8 ); getNext(); } @@ -181,6 +183,7 @@ public final class NexusPhylogeniesParser implements IteratingPhylogenyParser, P pars.setTaxonomyExtraction( _taxonomy_extraction ); pars.setReplaceUnderscores( _replace_underscores ); pars.setIgnoreQuotes( _ignore_quotes_in_nh_data ); + pars.setParseBeastStyleExtendedTags( _parse_beast_style_extended_tags ); if ( rooted_info_present ) { pars.setGuessRootedness( false ); } @@ -475,7 +478,11 @@ public final class NexusPhylogeniesParser implements IteratingPhylogenyParser, P _translate_map.put( key, value ); } } - + + public final void setParseBeastStyleExtendedTags( final boolean parse_beast_style_extended_tags ) { + _parse_beast_style_extended_tags = parse_beast_style_extended_tags; + } + private final static String removeWhiteSpaceBeforeSemicolon( final String s ) { return s.replaceAll( "\\s+;", ";" ); } diff --git a/forester/java/src/org/forester/io/parsers/nhx/NHXParser.java b/forester/java/src/org/forester/io/parsers/nhx/NHXParser.java index 04f5f85..2a5b647 100644 --- a/forester/java/src/org/forester/io/parsers/nhx/NHXParser.java +++ b/forester/java/src/org/forester/io/parsers/nhx/NHXParser.java @@ -23,6 +23,7 @@ package org.forester.io.parsers.nhx; +import java.awt.Color; import java.io.BufferedReader; import java.io.ByteArrayInputStream; import java.io.File; @@ -46,6 +47,7 @@ import org.forester.phylogeny.Phylogeny; import org.forester.phylogeny.PhylogenyMethods; import org.forester.phylogeny.PhylogenyNode; import org.forester.phylogeny.data.Accession; +import org.forester.phylogeny.data.BranchColor; import org.forester.phylogeny.data.Confidence; import org.forester.phylogeny.data.Event; import org.forester.phylogeny.data.Identifier; @@ -53,26 +55,31 @@ import org.forester.phylogeny.data.PhylogenyDataUtil; import org.forester.phylogeny.data.Sequence; import org.forester.phylogeny.data.Taxonomy; import org.forester.phylogeny.iterators.PhylogenyNodeIterator; +import org.forester.util.ForesterConstants; import org.forester.util.ForesterUtil; public final class NHXParser implements PhylogenyParser, IteratingPhylogenyParser { - public final static Pattern MB_BL_PATTERN = Pattern.compile( "length.median=([^,]+)" ); - public final static Pattern MB_PROB_PATTERN = Pattern.compile( "prob=([^,]+)" ); - public final static Pattern MB_PROB_SD_PATTERN = Pattern.compile( "prob.stddev=([^,]+)" ); - public final static Pattern NUMBERS_ONLY_PATTERN = Pattern.compile( "^[0-9\\.]+$" ); - final static public boolean REPLACE_UNDERSCORES_DEFAULT = false; - private static final boolean ALLOW_ERRORS_IN_DISTANCE_TO_PARENT_DEFAULT = false; - final static private byte BUFFERED_READER = 3; - final static private byte CHAR_ARRAY = 2; - final static private boolean GUESS_IF_SUPPORT_VALUES = true; - final static private boolean GUESS_ROOTEDNESS_DEFAULT = true; - final static private boolean IGNORE_QUOTES_DEFAULT = false; + private final static Pattern MB_BL_PATTERN = Pattern.compile( "length.median=([-+eE0-9\\.]+)" ); + private final static Pattern MB_PROB_PATTERN = Pattern.compile( "prob=([-+eE0-9\\.]+)" ); + private final static Pattern MB_PROB_SD_PATTERN = Pattern.compile( "prob.stddev=([-+eE0-9\\.]+)" ); + private final static Pattern NUMBERS_ONLY_PATTERN = Pattern.compile( "^[0-9\\.]+$" ); + + private final static Pattern BEAST_STYLE_EXTENDED_BOOTSTRAP_PATTERN = Pattern.compile( "boot?strap=([\\d\\.]+)" ); + private final static Pattern BEAST_STYLE_EXTENDED_COLOR_PATTERN = Pattern.compile( "colou?r=(#[\\da-fA-F]{6})" ); + private final static Pattern ENDS_WITH_NUMBER_PATTERN = Pattern.compile( "(:[-+eE0-9\\.]+$)" ); + + + public final static boolean REPLACE_UNDERSCORES_DEFAULT = false; + private final static boolean ALLOW_ERRORS_IN_DISTANCE_TO_PARENT_DEFAULT = false; + private final static byte BUFFERED_READER = 3; + private final static byte CHAR_ARRAY = 2; + private final static boolean GUESS_IF_SUPPORT_VALUES = true; + private final static boolean GUESS_ROOTEDNESS_DEFAULT = true; + private final static boolean IGNORE_QUOTES_DEFAULT = false; - final static private char BELL = 7; - public final static String UTF_8 = "UTF-8"; - public final static String ISO_8859_1 = "ISO-8859-1"; - private final static String ENCODING_DEFAULT = UTF_8; + private final static char BELL = 7; + private final static String ENCODING_DEFAULT = ForesterConstants.UTF_8; private boolean _allow_errors_in_distance_to_parent; private int _clade_level; private StringBuilder _current_anotation; @@ -97,6 +104,7 @@ public final class NHXParser implements PhylogenyParser, IteratingPhylogenyParse private Object _source; private int _source_length; private TAXONOMY_EXTRACTION _taxonomy_extraction; + private boolean _parse_beast_style_extended_tags = false; private final String _encoding; public NHXParser() { @@ -282,7 +290,8 @@ public final class NHXParser implements PhylogenyParser, IteratingPhylogenyParse getTaxonomyExtraction(), isReplaceUnderscores(), isAllowErrorsInDistanceToParent(), - true ); + true, + isParseBeastStyleExtendedTags()); if ( GUESS_IF_SUPPORT_VALUES ) { if ( isBranchLengthsLikeBootstrapValues( _current_phylogeny ) ) { moveBranchLengthsToConfidenceValues( _current_phylogeny ); @@ -308,7 +317,8 @@ public final class NHXParser implements PhylogenyParser, IteratingPhylogenyParse getTaxonomyExtraction(), isReplaceUnderscores(), isAllowErrorsInDistanceToParent(), - true ); + true, + isParseBeastStyleExtendedTags()); _current_phylogeny = new Phylogeny(); _current_phylogeny.setRoot( new_node ); return _current_phylogeny; @@ -320,6 +330,7 @@ public final class NHXParser implements PhylogenyParser, IteratingPhylogenyParse setGuessRootedness( GUESS_ROOTEDNESS_DEFAULT ); setIgnoreQuotes( IGNORE_QUOTES_DEFAULT ); setAllowErrorsInDistanceToParent( ALLOW_ERRORS_IN_DISTANCE_TO_PARENT_DEFAULT ); + setParseBeastStyleExtendedTags( false ); } private final boolean isAllowErrorsInDistanceToParent() { @@ -363,7 +374,7 @@ public final class NHXParser implements PhylogenyParser, IteratingPhylogenyParse if ( c == ':' ) { _saw_colon = true; } - else if ( !( ( c < 33 ) || ( c > 126 ) ) && _saw_colon + else if ( !( ( c < 33 ) || ( c == 127 ) ) && _saw_colon && ( ( c != '[' ) && ( c != '.' ) && ( ( c < 48 ) || ( c > 57 ) ) ) ) { _saw_colon = false; } @@ -488,7 +499,8 @@ public final class NHXParser implements PhylogenyParser, IteratingPhylogenyParse getTaxonomyExtraction(), isReplaceUnderscores(), isAllowErrorsInDistanceToParent(), - true ); + true, + isParseBeastStyleExtendedTags()); _current_anotation = new StringBuilder(); _current_node.addAsChild( new_node ); } @@ -498,7 +510,8 @@ public final class NHXParser implements PhylogenyParser, IteratingPhylogenyParse getTaxonomyExtraction(), isReplaceUnderscores(), isAllowErrorsInDistanceToParent(), - true ); + true, + isParseBeastStyleExtendedTags()); _current_anotation = new StringBuilder(); } if ( !_current_node.isRoot() ) { @@ -515,7 +528,8 @@ public final class NHXParser implements PhylogenyParser, IteratingPhylogenyParse getTaxonomyExtraction(), isReplaceUnderscores(), isAllowErrorsInDistanceToParent(), - true ); + true, + isParseBeastStyleExtendedTags()); if ( _current_node == null ) { throw new NHXFormatException( "format might not be NH or NHX" ); } @@ -527,7 +541,8 @@ public final class NHXParser implements PhylogenyParser, IteratingPhylogenyParse getTaxonomyExtraction(), isReplaceUnderscores(), isAllowErrorsInDistanceToParent(), - true ); + true, + isParseBeastStyleExtendedTags()); } _current_anotation = new StringBuilder(); _saw_closing_paren = false; @@ -570,7 +585,8 @@ public final class NHXParser implements PhylogenyParser, IteratingPhylogenyParse final TAXONOMY_EXTRACTION taxonomy_extraction, final boolean replace_underscores, final boolean allow_errors_in_distance_to_parent, - final boolean replace_bell ) throws NHXFormatException, + final boolean replace_bell, + final boolean parse_beast_style_extended_tags ) throws NHXFormatException, PhyloXmlDataFormatException { if ( ( taxonomy_extraction != TAXONOMY_EXTRACTION.NO ) && replace_underscores ) { throw new IllegalArgumentException( "cannot extract taxonomies and replace under scores at the same time" ); @@ -602,6 +618,13 @@ public final class NHXParser implements PhylogenyParser, IteratingPhylogenyParse else if ( s.indexOf( "prob=" ) > -1 ) { processMrBayes3Data( s, node_to_annotate ); } + if ( parse_beast_style_extended_tags ) { + processBeastStyleExtendedData( s, node_to_annotate ); + } + final Matcher ewn_matcher = ENDS_WITH_NUMBER_PATTERN.matcher( s ); + if ( ewn_matcher.find() ) { + b = ewn_matcher.group(1); + } } s = s.substring( 0, ob ) + b; if ( ( s.indexOf( "[" ) > -1 ) || ( s.indexOf( "]" ) > -1 ) ) { @@ -609,6 +632,7 @@ public final class NHXParser implements PhylogenyParser, IteratingPhylogenyParse } } final StringTokenizer t = new StringTokenizer( s, ":" ); + if ( t.countTokens() > 0 ) { if ( !s.startsWith( ":" ) ) { if ( ( s.indexOf( BELL ) <= -1 ) || !replace_bell ) { @@ -718,6 +742,41 @@ public final class NHXParser implements PhylogenyParser, IteratingPhylogenyParse } } + private final static void processBeastStyleExtendedData( final String s, + final PhylogenyNode node_to_annotate ) + throws NHXFormatException { + final Matcher ft_bs_matcher = BEAST_STYLE_EXTENDED_BOOTSTRAP_PATTERN.matcher( s ); + + double bs = -1; + if ( ft_bs_matcher.find() ) { + try { + bs = Double.parseDouble( ft_bs_matcher.group( 1 ) ); + } + catch ( final NumberFormatException e ) { + throw new NHXFormatException( "failed to parse bootstrap support from \"" + + s + "\"" ); + } + if ( bs >= 0.0 ) { + node_to_annotate.getBranchData() + .addConfidence( new Confidence( bs, "bootstrap" ) ); + } + } + final Matcher ft_color_matcher = BEAST_STYLE_EXTENDED_COLOR_PATTERN.matcher( s ); + Color c = null; + if ( ft_color_matcher.find() ) { + try { + c = Color.decode(ft_color_matcher.group( 1 ) ); + } + catch ( final NumberFormatException e ) { + throw new NHXFormatException( "failed to parse color from \"" + + s + "\"" ); + } + } + if ( c != null ) { + node_to_annotate.getBranchData().setBranchColor( new BranchColor( c ) ); + } + } + private final static void processMrBayes3Data( final String s, final PhylogenyNode node_to_annotate ) throws NHXFormatException { double sd = -1; @@ -770,6 +829,14 @@ public final class NHXParser implements PhylogenyParser, IteratingPhylogenyParse return _encoding; } + private final boolean isParseBeastStyleExtendedTags() { + return _parse_beast_style_extended_tags; + } + + public final void setParseBeastStyleExtendedTags( final boolean parse_beast_style_extended_tags ) { + _parse_beast_style_extended_tags = parse_beast_style_extended_tags; + } + public static enum TAXONOMY_EXTRACTION { AGGRESSIVE, NO, PFAM_STYLE_RELAXED, PFAM_STYLE_STRICT; } diff --git a/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlMapping.java b/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlMapping.java index ab19a1c..1db3384 100644 --- a/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlMapping.java +++ b/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlMapping.java @@ -59,6 +59,7 @@ public final class PhyloXmlMapping { public static final String COLOR_BLUE = "blue"; public static final String COLOR_GREEN = "green"; public static final String COLOR_RED = "red"; + public static final String COLOR_ALPHA = "alpha"; public static final String CONFIDENCE = "confidence"; public static final String CONFIDENCE_SD_ATTR = "stddev"; public static final String CONFIDENCE_TYPE_ATTR = "type"; diff --git a/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlParser.java b/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlParser.java index 2b46c0f..f85968d 100644 --- a/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlParser.java +++ b/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlParser.java @@ -59,7 +59,6 @@ import org.xml.sax.helpers.DefaultHandler; public class PhyloXmlParser implements PhylogenyParser { - private static final String UTF_8 = "UTF-8"; final public static String JAXP_SCHEMA_LANGUAGE = "http://java.sun.com/xml/jaxp/properties/schemaLanguage"; final public static String W3C_XML_SCHEMA = "http://www.w3.org/2001/XMLSchema"; final public static String JAXP_SCHEMA_SOURCE = "http://java.sun.com/xml/jaxp/properties/schemaSource"; @@ -98,7 +97,7 @@ public class PhyloXmlParser implements PhylogenyParser { final ZipEntry zip_file_entry = ( ZipEntry ) zip_file_entries.nextElement(); if ( !zip_file_entry.isDirectory() && ( zip_file_entry.getSize() > 0 ) ) { final InputStream is = zip_file.getInputStream( zip_file_entry ); - reader = new InputStreamReader( is, UTF_8 ); + reader = new InputStreamReader( is, ForesterConstants.UTF_8 ); break; } } @@ -185,7 +184,7 @@ public class PhyloXmlParser implements PhylogenyParser { if ( getSource() instanceof File ) { if ( !getSource().toString().toLowerCase().endsWith( ".zip" ) ) { final InputStream is = new FileInputStream( (File) getSource() ); - final InputStreamReader isr = new InputStreamReader( is, UTF_8 ); + final InputStreamReader isr = new InputStreamReader( is, ForesterConstants.UTF_8 ); xml_reader.parse( new InputSource( new BufferedReader( isr ) ) ); } else { @@ -199,18 +198,18 @@ public class PhyloXmlParser implements PhylogenyParser { } else if ( getSource() instanceof InputSource ) { final InputSource is = ( InputSource ) getSource(); - is.setEncoding( UTF_8 ); + is.setEncoding( ForesterConstants.UTF_8 ); xml_reader.parse( is ); } else if ( getSource() instanceof InputStream ) { if ( !isZippedInputstream() ) { final InputStream is = ( InputStream ) getSource(); - xml_reader.parse( new InputSource( new BufferedReader( new InputStreamReader( is, UTF_8 ) ) ) ); + xml_reader.parse( new InputSource( new BufferedReader( new InputStreamReader( is, ForesterConstants.UTF_8 ) ) ) ); } else { final ZipInputStream zip_is = new ZipInputStream( ( InputStream ) getSource() ); zip_is.getNextEntry(); - xml_reader.parse( new InputSource( new BufferedReader( new InputStreamReader( zip_is, UTF_8 ) ) ) ); + xml_reader.parse( new InputSource( new BufferedReader( new InputStreamReader( zip_is, ForesterConstants.UTF_8 ) ) ) ); } } else if ( getSource() instanceof StringBuffer ) { diff --git a/forester/java/src/org/forester/io/parsers/phyloxml/data/ColorParser.java b/forester/java/src/org/forester/io/parsers/phyloxml/data/ColorParser.java index 65e6658..88f1d0c 100644 --- a/forester/java/src/org/forester/io/parsers/phyloxml/data/ColorParser.java +++ b/forester/java/src/org/forester/io/parsers/phyloxml/data/ColorParser.java @@ -53,6 +53,7 @@ public class ColorParser implements PhylogenyDataPhyloXmlParser { int red = 0; int green = 0; int blue = 0; + int alpha = -1; for( int j = 0; j < element.getNumberOfChildElements(); ++j ) { final XmlElement c = element.getChildElement( j ); if ( c.getQualifiedName().equals( PhyloXmlMapping.COLOR_RED ) ) { @@ -64,9 +65,17 @@ public class ColorParser implements PhylogenyDataPhyloXmlParser { else if ( c.getQualifiedName().equals( PhyloXmlMapping.COLOR_BLUE ) ) { blue = c.getValueAsInt(); } + else if ( c.getQualifiedName().equals( PhyloXmlMapping.COLOR_ALPHA ) ) { + alpha = c.getValueAsInt(); + } } final BranchColor color = new BranchColor(); - color.setValue( new Color( red, green, blue ) ); + if ( alpha < 0 ) { + color.setValue( new Color( red, green, blue ) ); + } + else { + color.setValue( new Color( red, green, blue ) ); + } return color; } diff --git a/forester/java/src/org/forester/io/writers/PhylogenyWriter.java b/forester/java/src/org/forester/io/writers/PhylogenyWriter.java index 6d3c836..911ebb5 100644 --- a/forester/java/src/org/forester/io/writers/PhylogenyWriter.java +++ b/forester/java/src/org/forester/io/writers/PhylogenyWriter.java @@ -49,7 +49,6 @@ import org.forester.util.ForesterUtil; public final class PhylogenyWriter { - private static final String UTF_8 = "UTF-8"; public final static boolean INDENT_PHYLOXML_DEAFULT = true; public final static String PHYLO_XML_INTENDATION_BASE = " "; public final static String PHYLO_XML_VERSION_ENCODING_LINE = ""; @@ -399,7 +398,7 @@ public final class PhylogenyWriter { public void toNexus( final File out_file, final Phylogeny tree, final NH_CONVERSION_SUPPORT_VALUE_STYLE svs ) throws IOException { - final Writer writer = new BufferedWriter( new PrintWriter( out_file, UTF_8 ) ); + final Writer writer = new BufferedWriter( new PrintWriter( out_file, ForesterConstants.UTF_8 ) ); final List trees = new ArrayList( 1 ); trees.add( tree ); writeNexusStart( writer ); @@ -426,14 +425,14 @@ public final class PhylogenyWriter { final List trees, final int phyloxml_level, final String separator ) throws IOException { - final Writer writer = new BufferedWriter( new PrintWriter( out_file, UTF_8 ) ); + final Writer writer = new BufferedWriter( new PrintWriter( out_file, ForesterConstants.UTF_8 ) ); toPhyloXML( writer, trees, phyloxml_level, separator ); writer.flush(); writer.close(); } public void toPhyloXML( final File out_file, final Phylogeny tree, final int phyloxml_level ) throws IOException { - final Writer writer = new BufferedWriter( new PrintWriter( out_file, UTF_8 ) ); + final Writer writer = new BufferedWriter( new PrintWriter( out_file, ForesterConstants.UTF_8 ) ); writePhyloXmlStart( writer ); toPhyloXMLNoPhyloXmlSource( writer, tree, phyloxml_level ); writePhyloXmlEnd( writer ); @@ -633,7 +632,7 @@ public final class PhylogenyWriter { if ( out_file.exists() ) { throw new IOException( "attempt to overwrite existing file \"" + out_file.getAbsolutePath() + "\"" ); } - final PrintWriter out = new PrintWriter( out_file, UTF_8 ); + final PrintWriter out = new PrintWriter( out_file, ForesterConstants.UTF_8 ); out.print( sb ); out.flush(); out.close(); diff --git a/forester/java/src/org/forester/phylogeny/PhylogenyNode.java b/forester/java/src/org/forester/phylogeny/PhylogenyNode.java index da0ab5d..d37cc3b 100644 --- a/forester/java/src/org/forester/phylogeny/PhylogenyNode.java +++ b/forester/java/src/org/forester/phylogeny/PhylogenyNode.java @@ -86,7 +86,23 @@ public final class PhylogenyNode implements Comparable { private PhylogenyNode( final String nhx, final NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction, final boolean replace_underscores ) throws NHXFormatException, PhyloXmlDataFormatException { - NHXParser.parseNHX( nhx, this, taxonomy_extraction, replace_underscores, false, false ); + NHXParser.parseNHX( nhx, this, taxonomy_extraction, replace_underscores, false, false, false ); + setId( PhylogenyNode.getNodeCount() ); + PhylogenyNode.increaseNodeCount(); + setSumExtNodes( 1 ); // For ext node, this number is 1 (not 0!!). + } + + private PhylogenyNode( final String nhx, + final NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction, + final boolean replace_underscores, + final boolean parse_extended_tags ) throws NHXFormatException, PhyloXmlDataFormatException { + NHXParser.parseNHX( nhx, + this, + taxonomy_extraction, + replace_underscores, + false, + false, + parse_extended_tags ); setId( PhylogenyNode.getNodeCount() ); PhylogenyNode.increaseNodeCount(); setSumExtNodes( 1 ); // For ext node, this number is 1 (not 0!!). @@ -1086,6 +1102,14 @@ public final class PhylogenyNode implements Comparable { throws NHXFormatException, PhyloXmlDataFormatException { return new PhylogenyNode( nhx, taxonomy_extraction, replace_underscores ); } + + public static PhylogenyNode createInstanceFromNhxString( final String nhx, + final NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction, + final boolean replace_underscores, + final boolean parse_extended_tags ) + throws NHXFormatException, PhyloXmlDataFormatException { + return new PhylogenyNode( nhx, taxonomy_extraction, replace_underscores, parse_extended_tags ); + } /** * Returns the total number of all Nodes created so far. diff --git a/forester/java/src/org/forester/phylogeny/data/BranchColor.java b/forester/java/src/org/forester/phylogeny/data/BranchColor.java index 7d47e24..5b5ff65 100644 --- a/forester/java/src/org/forester/phylogeny/data/BranchColor.java +++ b/forester/java/src/org/forester/phylogeny/data/BranchColor.java @@ -91,6 +91,9 @@ public class BranchColor implements PhylogenyData { PhylogenyDataUtil.appendElement( writer, PhyloXmlMapping.COLOR_RED, getValue().getRed() + "", indentation ); PhylogenyDataUtil.appendElement( writer, PhyloXmlMapping.COLOR_GREEN, getValue().getGreen() + "", indentation ); PhylogenyDataUtil.appendElement( writer, PhyloXmlMapping.COLOR_BLUE, getValue().getBlue() + "", indentation ); + if ( getValue().getAlpha() != 255 ) { + PhylogenyDataUtil.appendElement( writer, PhyloXmlMapping.COLOR_ALPHA, getValue().getAlpha() + "", indentation ); + } writer.write( ForesterUtil.LINE_SEPARATOR ); writer.write( indentation ); PhylogenyDataUtil.appendClose( writer, PhyloXmlMapping.COLOR ); diff --git a/forester/java/src/org/forester/phylogeny/data/SequenceRelation.java b/forester/java/src/org/forester/phylogeny/data/SequenceRelation.java index 45134e4..ee18746 100644 --- a/forester/java/src/org/forester/phylogeny/data/SequenceRelation.java +++ b/forester/java/src/org/forester/phylogeny/data/SequenceRelation.java @@ -60,13 +60,11 @@ public class SequenceRelation implements PhylogenyData { @Override public StringBuffer asSimpleText() { - // TODO Auto-generated method stub return null; } @Override public StringBuffer asText() { - // TODO Auto-generated method stub return null; } diff --git a/forester/java/src/org/forester/test/Test.java b/forester/java/src/org/forester/test/Test.java index f714686..1c76c8d 100644 --- a/forester/java/src/org/forester/test/Test.java +++ b/forester/java/src/org/forester/test/Test.java @@ -344,6 +344,15 @@ public final class Test { System.out.println( "failed." ); failed++; } + System.out.print( "Node construction and parsing of NHX (node level): " ); + if ( Test.testNHXNodeParsing2() ) { + System.out.println( "OK." ); + succeeded++; + } + else { + System.out.println( "failed." ); + failed++; + } System.out.print( "NHX parsing iterating: " ); if ( Test.testNHParsingIter() ) { System.out.println( "OK." ); @@ -9805,6 +9814,151 @@ public final class Test { return true; } + + private static boolean testNHXNodeParsing2() { + try { + + final PhylogenyNode n0_0 = PhylogenyNode + .createInstanceFromNhxString( "n0:[ignore me 123]:1E-3", NHXParser.TAXONOMY_EXTRACTION.NO, true, true ); + if ( !n0_0.getName().equals( "n0" ) ) { + return false; + } + if ( !isEqual( n0_0.getDistanceToParent(), 0.001 ) ) { + return false; + } + final PhylogenyNode n0_1 = PhylogenyNode + .createInstanceFromNhxString( "n0[ignore me 123]:1E-3", NHXParser.TAXONOMY_EXTRACTION.NO, true, true ); + if ( !n0_1.getName().equals( "n0" ) ) { + return false; + } + if ( !isEqual( n0_1.getDistanceToParent(), 0.001 ) ) { + return false; + } + final PhylogenyNode n0_2 = PhylogenyNode + .createInstanceFromNhxString( "n0:1E-3[ignore me 123]", NHXParser.TAXONOMY_EXTRACTION.NO, true, true ); + if ( !n0_2.getName().equals( "n0" ) ) { + return false; + } + if ( !isEqual( n0_2.getDistanceToParent(), 0.001 ) ) { + return false; + } + final PhylogenyNode n0_3 = PhylogenyNode + .createInstanceFromNhxString( "n0:1E-3:[ignore me 123]", NHXParser.TAXONOMY_EXTRACTION.NO, true, true ); + if ( !n0_3.getName().equals( "n0" ) ) { + return false; + } + if ( !isEqual( n0_3.getDistanceToParent(), 0.001 ) ) { + return false; + } + final PhylogenyNode n0_4 = PhylogenyNode + .createInstanceFromNhxString( "n0:0.001:[ignore me 123]", NHXParser.TAXONOMY_EXTRACTION.NO, true, true ); + if ( !n0_4.getName().equals( "n0" ) ) { + return false; + } + if ( !isEqual( n0_4.getDistanceToParent(), 0.001 ) ) { + return false; + } + final PhylogenyNode n1_0 = PhylogenyNode + .createInstanceFromNhxString( "xyz|A/American_duck/NH/00321/|Duck|Canada[&!color=#FFFFFF]", NHXParser.TAXONOMY_EXTRACTION.NO, true, true ); + if ( !n1_0.getName().equals( "xyz|A/American duck/NH/00321/|Duck|Canada" ) ) { + return false; + } + if ( n1_0.getBranchData().getBranchColor().getValue().getGreen()!=255 ) { + return false; + } + final PhylogenyNode n1_1 = PhylogenyNode + .createInstanceFromNhxString( "xyz|A/American_duck/NH/00321/|Duck|Canada[&!color=#FFFFFF]:0.001", NHXParser.TAXONOMY_EXTRACTION.NO, true, true ); + if ( !n1_1.getName().equals( "xyz|A/American duck/NH/00321/|Duck|Canada" ) ) { + return false; + } + if ( n1_1.getBranchData().getBranchColor().getValue().getGreen()!=255 ) { + return false; + } + if ( !isEqual( n1_1.getDistanceToParent(), 0.001 ) ) { + return false; + } + final PhylogenyNode n1_2 = PhylogenyNode + .createInstanceFromNhxString( "xyz|A/American_duck/NH/00321/|Duck|Canada:0.001[&!color=#FFFFFF]", NHXParser.TAXONOMY_EXTRACTION.NO, true, true ); + if ( !n1_2.getName().equals( "xyz|A/American duck/NH/00321/|Duck|Canada" ) ) { + return false; + } + if ( n1_2.getBranchData().getBranchColor().getValue().getGreen()!=255 ) { + return false; + } + if ( !isEqual( n1_2.getDistanceToParent(), 0.001 ) ) { + return false; + } + final PhylogenyNode n1_3 = PhylogenyNode + .createInstanceFromNhxString( "xyz|A/American_duck/NH/00321/|Duck|Canada:1e-3[&boostrap=69,&!color=#FFFFFF]", NHXParser.TAXONOMY_EXTRACTION.NO, true, true ); + if ( !n1_3.getName().equals( "xyz|A/American duck/NH/00321/|Duck|Canada" ) ) { + return false; + } + if ( n1_3.getBranchData().getBranchColor().getValue().getGreen()!=255 ) { + return false; + } + if ( !isEqual( n1_3.getDistanceToParent(), 0.001 ) ) { + return false; + } + if ( !isEqual( n1_3.getBranchData().getConfidence( 0 ).getValue(), 69 ) ) { + return false; + } + if ( !n1_3.getBranchData().getConfidence( 0 ).getType().equals( "bootstrap" ) ) { + return false; + } + final PhylogenyNode n1_4 = PhylogenyNode + .createInstanceFromNhxString( "xyz|A/American_duck/NH/00321/|Duck|Canada[&bootstrap=69,&!colour=#FFFFFF]:1e-3", NHXParser.TAXONOMY_EXTRACTION.NO, true, true ); + if ( !n1_4.getName().equals( "xyz|A/American duck/NH/00321/|Duck|Canada" ) ) { + return false; + } + if ( n1_4.getBranchData().getBranchColor().getValue().getGreen()!=255 ) { + return false; + } + if ( !isEqual( n1_4.getDistanceToParent(), 0.001 ) ) { + return false; + } + if ( !isEqual( n1_4.getBranchData().getConfidence( 0 ).getValue(), 69 ) ) { + return false; + } + if ( !n1_4.getBranchData().getConfidence( 0 ).getType().equals( "bootstrap" ) ) { + return false; + } + final PhylogenyNode n1_5 = PhylogenyNode + .createInstanceFromNhxString( "xyz|A/American_duck/NH/00321/|Duck|Canada:1e-3[69.0]", NHXParser.TAXONOMY_EXTRACTION.NO, true, true ); + if ( !n1_5.getName().equals( "xyz|A/American duck/NH/00321/|Duck|Canada" ) ) { + return false; + } + if ( !isEqual( n1_5.getDistanceToParent(), 0.001 ) ) { + return false; + } + if ( !isEqual( n1_5.getBranchData().getConfidence( 0 ).getValue(), 69 ) ) { + return false; + } + final PhylogenyNode n1_6 = PhylogenyNode + .createInstanceFromNhxString( "xyz|A/American_duck/NH/00321/|Duck|Canada[&prob=0.9500000000000000e+00,prob_stddev=0.1100000000000000e+00]:1e-3", NHXParser.TAXONOMY_EXTRACTION.NO, true, true ); + if ( !n1_6.getName().equals( "xyz|A/American duck/NH/00321/|Duck|Canada" ) ) { + return false; + } + + if ( !isEqual( n1_6.getDistanceToParent(), 0.001 ) ) { + return false; + } + if ( !isEqual( n1_6.getBranchData().getConfidence( 0 ).getStandardDeviation(), 0.11 ) ) { + return false; + } + if ( !isEqual( n1_6.getBranchData().getConfidence( 0 ).getValue(), 0.95 ) ) { + return false; + } + if ( !n1_6.getBranchData().getConfidence( 0 ).getType().equals( "posterior probability" ) ) { + return false; + } + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + private static boolean testNHXParsing() { try { final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); diff --git a/forester/java/src/org/forester/util/ForesterConstants.java b/forester/java/src/org/forester/util/ForesterConstants.java index 9c2749b..3444b64 100644 --- a/forester/java/src/org/forester/util/ForesterConstants.java +++ b/forester/java/src/org/forester/util/ForesterConstants.java @@ -27,19 +27,22 @@ package org.forester.util; public final class ForesterConstants { - public final static String FORESTER_VERSION = "1.041"; - public final static String FORESTER_DATE = "160701"; + public final static String FORESTER_VERSION = "1.042"; + public final static String FORESTER_DATE = "160712"; public final static String PHYLO_XML_VERSION = "1.10"; public final static String PHYLO_XML_LOCATION = "http://www.phyloxml.org"; public final static String PHYLO_XML_XSD = "phyloxml.xsd"; public final static String XML_SCHEMA_INSTANCE = "http://www.w3.org/2001/XMLSchema-instance"; public final static String LOCAL_PHYLOXML_XSD_RESOURCE = "resources/phyloxml.xsd"; public final static String PHYLO_XML_SUFFIX = ".xml"; - public final static String UTF8 = "UTF-8"; + public final static String UTF_8 = "UTF-8"; + public final static String ISO_8859_1 = "ISO-8859-1"; public final static String PHYLO_XML_REFERENCE = "Han MV and Zmasek CM (2009): \"phyloXML: XML for evolutionary biology and comparative genomics\", BMC Bioinformatics 10:356"; public final static boolean RELEASE = false; public enum PhylogeneticTreeFormats { NH, NHX, NEXUS, PHYLOXML } + + }