-// $Id:\r
-// FORESTER -- software libraries and applications\r
-// for evolutionary biology research and applications.\r
-//\r
-// Copyright (C) 2008-2010 Christian M. Zmasek\r
-// All rights reserved\r
-//\r
-// This library is free software; you can redistribute it and/or\r
-// modify it under the terms of the GNU Lesser General Public\r
-// License as published by the Free Software Foundation; either\r
-// version 2.1 of the License, or (at your option) any later version.\r
-//\r
-// This library is distributed in the hope that it will be useful,\r
-// but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU\r
-// Lesser General Public License for more details.\r
-//\r
-// You should have received a copy of the GNU Lesser General Public\r
-// License along with this library; if not, write to the Free Software\r
-// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-//\r
-// Contact: phylosoft @ gmail . com\r
-// WWW: https://sites.google.com/site/cmzmasek/home/software/forester\r
-\r
-package org.forester.archaeopteryx;\r
-\r
-import java.awt.Color;\r
-import java.awt.Component;\r
-import java.awt.Container;\r
-import java.awt.Font;\r
-import java.awt.event.ActionEvent;\r
-import java.awt.event.ActionListener;\r
-import java.io.File;\r
-import java.io.IOException;\r
-import java.util.ArrayList;\r
-import java.util.LinkedList;\r
-import java.util.List;\r
-import java.util.Locale;\r
-import java.util.NoSuchElementException;\r
-\r
-import javax.swing.Box;\r
-import javax.swing.JApplet;\r
-import javax.swing.JCheckBoxMenuItem;\r
-import javax.swing.JFrame;\r
-import javax.swing.JLabel;\r
-import javax.swing.JMenu;\r
-import javax.swing.JMenuBar;\r
-import javax.swing.JMenuItem;\r
-import javax.swing.JOptionPane;\r
-import javax.swing.JPanel;\r
-import javax.swing.JRadioButtonMenuItem;\r
-import javax.swing.JTextField;\r
-import javax.swing.SwingUtilities;\r
-\r
-import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;\r
-import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;\r
-import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;\r
-import org.forester.archaeopteryx.tools.InferenceManager;\r
-import org.forester.archaeopteryx.tools.ProcessPool;\r
-import org.forester.archaeopteryx.tools.ProcessRunning;\r
-import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;\r
-import org.forester.phylogeny.Phylogeny;\r
-import org.forester.phylogeny.PhylogenyMethods;\r
-import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;\r
-import org.forester.phylogeny.PhylogenyNode;\r
-import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;\r
-import org.forester.phylogeny.data.Annotation;\r
-import org.forester.phylogeny.data.NodeData;\r
-import org.forester.phylogeny.data.NodeVisualData.NodeFill;\r
-import org.forester.phylogeny.data.NodeVisualData.NodeShape;\r
-import org.forester.phylogeny.iterators.PhylogenyNodeIterator;\r
-import org.forester.sdi.GSDI;\r
-import org.forester.sdi.GSDIR;\r
-import org.forester.sdi.SDIException;\r
-import org.forester.util.ForesterConstants;\r
-import org.forester.util.ForesterUtil;\r
-\r
-public abstract class MainFrame extends JFrame implements ActionListener {\r
-\r
- static final String USE_MOUSEWHEEL_SHIFT_TO_ROTATE = "In this display type, use mousewheel + Shift to rotate [or A and S]";\r
- static final String PHYLOXML_REF_TOOL_TIP = Constants.PHYLOXML_REFERENCE; //TODO //FIXME\r
- static final String APTX_REF_TOOL_TIP = Constants.APTX_REFERENCE;\r
- private static final long serialVersionUID = 3655000897845508358L;\r
- final static Font menu_font = new Font( Configuration.getDefaultFontFamilyName(),\r
- Font.PLAIN,\r
- 10 );\r
- static final String TYPE_MENU_HEADER = "Type";\r
- static final String RECTANGULAR_TYPE_CBMI_LABEL = "Rectangular";\r
- static final String EURO_TYPE_CBMI_LABEL = "Euro Type";\r
- static final String CURVED_TYPE_CBMI_LABEL = "Curved";\r
- static final String TRIANGULAR_TYPE_CBMI_LABEL = "Triangular";\r
- static final String CONVEX_TYPE_CBMI_LABEL = "Convex";\r
- static final String ROUNDED_TYPE_CBMI_LABEL = "Rounded";\r
- static final String UNROOTED_TYPE_CBMI_LABEL = "Unrooted (alpha)"; //TODO\r
- static final String CIRCULAR_TYPE_CBMI_LABEL = "Circular (alpha)"; //TODO\r
- static final String OPTIONS_HEADER = "Options";\r
- static final String SEARCH_SUBHEADER = "Search:";\r
- static final String DISPLAY_SUBHEADER = "Display:";\r
- static final String SEARCH_TERMS_ONLY_LABEL = "Match Complete Terms Only";\r
- static final String SEARCH_REGEX_LABEL = "Search with Regular Expressions";\r
- static final String SEARCH_CASE_SENSITIVE_LABEL = "Case Sensitive";\r
- static final String INVERSE_SEARCH_RESULT_LABEL = "Negate Result";\r
- static final String COLOR_BY_TAXONOMIC_GROUP = "Colorize by Taxonomic Group";\r
- static final String DISPLAY_SCALE_LABEL = "Scale";\r
- static final String NON_LINED_UP_CLADOGRAMS_LABEL = "Non-Lined Up Cladograms";\r
- static final String UNIFORM_CLADOGRAMS_LABEL = "Total Node Sum Dependent Cladograms";\r
- static final String LABEL_DIRECTION_LABEL = "Radial Labels";\r
- static final String LABEL_DIRECTION_TIP = "To use radial node labels in radial and unrooted display types";\r
- static final String 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.";\r
- static final String SCREEN_ANTIALIAS_LABEL = "Antialias";\r
- static final String COLOR_LABELS_LABEL = "Colorize Labels Same as Parent Branch";\r
- static final String BG_GRAD_LABEL = "Background Color Gradient";\r
- static final String DISPLAY_NODE_BOXES_LABEL_EXT = "Shapes for External Nodes";\r
- static final String DISPLAY_NODE_BOXES_LABEL_INT = "Shapes for Internal Nodes";\r
- static final String DISPLAY_NODE_BOXES_LABEL_MARKED = "Shapes for Nodes with Visual Data";\r
- static final String SHOW_OVERVIEW_LABEL = "Overview";\r
- static final String FONT_SIZE_MENU_LABEL = "Font Size";\r
- static final String NONUNIFORM_CLADOGRAMS_LABEL = "External Node Sum Dependent Cladograms";\r
- static final String SHOW_DOMAIN_LABELS_LABEL = "Domain Labels";\r
- static final String SHOW_ANN_REF_SOURCE_LABEL = "Seq Annotation Ref Sources";\r
- static final String COLOR_LABELS_TIP = "To use parent branch colors for node labels as well, need to turn off taxonomy dependent colorization and turn on branch colorization for this to become apparent";\r
- static final String ABBREV_SN_LABEL = "Abbreviate Scientific Taxonomic Names";\r
- static final String TAXONOMY_COLORIZE_NODE_SHAPES_LABEL = "Colorize Node Shapes According to Taxonomy";\r
- static final String CYCLE_NODE_SHAPE_LABEL = "Cycle Node Shapes";\r
- static final String CYCLE_NODE_FILL_LABEL = "Cycle Node Fill Type";\r
- static final String CHOOSE_NODE_SIZE_LABEL = "Choose Node Shape Size";\r
- static final String SHOW_CONF_STDDEV_LABEL = "Confidence Standard Deviations";\r
- static final String USE_BRACKETS_FOR_CONF_IN_NH_LABEL = "Use Brackets for Confidence Values";\r
- static final String USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL = "Use Internal Node Names for Confidence Values";\r
- static final String SHOW_BASIC_TREE_INFORMATION_LABEL = "Basic Tree Information";\r
- static final String RIGHT_LINE_UP_DOMAINS = "Right-align Domain Architectures";\r
- static final String LINE_UP_RENDERABLE_DATA = "Line Up Diagrams (such as Domain Architectures)";\r
- JMenuBar _jmenubar;\r
- JMenu _file_jmenu;\r
- JMenu _tools_menu;\r
- JMenu _view_jmenu;\r
- JMenu _options_jmenu;\r
- JMenu _font_size_menu;\r
- JMenu _help_jmenu;\r
- JMenuItem[] _load_phylogeny_from_webservice_menu_items;\r
- // Analysis menu\r
- JMenu _analysis_menu;\r
- JMenuItem _load_species_tree_item;\r
- JMenuItem _gsdi_item;\r
- JMenuItem _gsdir_item;\r
- JMenuItem _lineage_inference;\r
- // file menu:\r
- JMenuItem _open_item;\r
- JMenuItem _open_url_item;\r
- JMenuItem _save_item;\r
- JMenuItem _save_all_item;\r
- JMenuItem _close_item;\r
- JMenuItem _exit_item;\r
- JMenuItem _new_item;\r
- // tools menu:\r
- JMenuItem _midpoint_root_item;\r
- JMenuItem _taxcolor_item;\r
- JMenuItem _confcolor_item;\r
- JMenuItem _color_rank_jmi;\r
- JMenuItem _collapse_species_specific_subtrees;\r
- JMenuItem _obtain_detailed_taxonomic_information_jmi;\r
- JMenuItem _obtain_detailed_taxonomic_information_deleting_jmi;\r
- JMenuItem _obtain_seq_information_jmi;\r
- JMenuItem _move_node_names_to_tax_sn_jmi;\r
- JMenuItem _move_node_names_to_seq_names_jmi;\r
- JMenuItem _extract_tax_code_from_node_names_jmi;\r
- JMenuItem _annotate_item;\r
- JMenuItem _remove_branch_color_item;\r
- JMenuItem _remove_visual_styles_item;\r
- JMenuItem _delete_selected_nodes_item;\r
- JMenuItem _delete_not_selected_nodes_item;\r
- // font size menu:\r
- JMenuItem _super_tiny_fonts_item;\r
- JMenuItem _tiny_fonts_item;\r
- JMenuItem _small_fonts_item;\r
- JMenuItem _medium_fonts_item;\r
- JMenuItem _large_fonts_item;\r
- // options menu:\r
- // _ screen and print\r
- JMenuItem _choose_font_mi;\r
- JMenuItem _switch_colors_mi;\r
- JCheckBoxMenuItem _label_direction_cbmi;\r
- // _ screen display\r
- JCheckBoxMenuItem _screen_antialias_cbmi;\r
- JCheckBoxMenuItem _background_gradient_cbmi;\r
- JRadioButtonMenuItem _non_lined_up_cladograms_rbmi;\r
- JRadioButtonMenuItem _uniform_cladograms_rbmi;\r
- JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi;\r
- JCheckBoxMenuItem _color_by_taxonomic_group_cbmi;\r
- JCheckBoxMenuItem _show_scale_cbmi; //TODO fix me\r
- JCheckBoxMenuItem _show_overview_cbmi;\r
- JCheckBoxMenuItem _show_domain_labels;\r
- JCheckBoxMenuItem _show_annotation_ref_source;\r
- JCheckBoxMenuItem _abbreviate_scientific_names;\r
- JCheckBoxMenuItem _color_labels_same_as_parent_branch;\r
- JMenuItem _overview_placment_mi;\r
- JMenuItem _choose_minimal_confidence_mi;\r
- JCheckBoxMenuItem _show_default_node_shapes_internal_cbmi;\r
- JCheckBoxMenuItem _show_default_node_shapes_external_cbmi;\r
- JCheckBoxMenuItem _show_default_node_shapes_for_marked_cbmi;\r
- JMenuItem _cycle_node_shape_mi;\r
- JMenuItem _cycle_node_fill_mi;\r
- JMenuItem _choose_node_size_mi;\r
- JMenuItem _cycle_data_return;\r
- JCheckBoxMenuItem _show_confidence_stddev_cbmi;\r
- JCheckBoxMenuItem _right_line_up_domains_cbmi;\r
- JCheckBoxMenuItem _line_up_renderable_data_cbmi;\r
- // _ print\r
- JCheckBoxMenuItem _graphics_export_visible_only_cbmi;\r
- JCheckBoxMenuItem _antialias_print_cbmi;\r
- JCheckBoxMenuItem _print_black_and_white_cbmi;\r
- JCheckBoxMenuItem _print_using_actual_size_cbmi;\r
- JCheckBoxMenuItem _graphics_export_using_actual_size_cbmi;\r
- JMenuItem _print_size_mi;\r
- JMenuItem _choose_pdf_width_mi;\r
- // _ parsing\r
- JCheckBoxMenuItem _internal_number_are_confidence_for_nh_parsing_cbmi;\r
- JRadioButtonMenuItem _extract_taxonomy_no_rbmi;\r
- JRadioButtonMenuItem _extract_taxonomy_agressive_rbmi;\r
- JRadioButtonMenuItem _extract_taxonomy_pfam_strict_rbmi;\r
- JRadioButtonMenuItem _extract_taxonomy_pfam_relaxed_rbmi;\r
- JCheckBoxMenuItem _replace_underscores_cbmi;\r
- JCheckBoxMenuItem _allow_errors_in_distance_to_parent_cbmi;\r
- JCheckBoxMenuItem _use_brackets_for_conf_in_nh_export_cbmi;\r
- JCheckBoxMenuItem _use_internal_names_for_conf_in_nh_export_cbmi;\r
- // _ search\r
- JCheckBoxMenuItem _search_case_senstive_cbmi;\r
- JCheckBoxMenuItem _search_whole_words_only_cbmi;\r
- JCheckBoxMenuItem _inverse_search_result_cbmi;\r
- JCheckBoxMenuItem _search_with_regex_cbmi;\r
- // type menu:\r
- JMenu _type_menu;\r
- JCheckBoxMenuItem _rectangular_type_cbmi;\r
- JCheckBoxMenuItem _triangular_type_cbmi;\r
- JCheckBoxMenuItem _curved_type_cbmi;\r
- JCheckBoxMenuItem _convex_type_cbmi;\r
- JCheckBoxMenuItem _euro_type_cbmi;\r
- JCheckBoxMenuItem _rounded_type_cbmi;\r
- JCheckBoxMenuItem _unrooted_type_cbmi;\r
- JCheckBoxMenuItem _circular_type_cbmi;\r
- // view as text menu:\r
- JMenuItem _view_as_NH_item;\r
- JMenuItem _view_as_XML_item;\r
- JMenuItem _view_as_nexus_item;\r
- JMenuItem _display_basic_information_item;\r
- // help menu:\r
- JMenuItem _about_item;\r
- JMenuItem _help_item;\r
- JMenuItem _website_item;\r
- JMenuItem _phyloxml_website_item;\r
- JMenuItem _phyloxml_ref_item;\r
- JMenuItem _aptx_ref_item;\r
- // process menu:\r
- JMenu _process_menu;\r
- // Handy pointers to child components:\r
- MainPanel _mainpanel;\r
- Container _contentpane;\r
- final LinkedList<TextFrame> _textframes = new LinkedList<TextFrame>(); ;\r
- Configuration _configuration;\r
- Options _options;\r
- private Phylogeny _species_tree;\r
- InferenceManager _inference_manager;\r
- final ProcessPool _process_pool;\r
- private String _previous_node_annotation_ref;\r
-\r
- MainFrame() {\r
- _process_pool = ProcessPool.createInstance();\r
- }\r
-\r
- /**\r
- * Action performed.\r
- */\r
- @Override\r
- public void actionPerformed( final ActionEvent e ) {\r
- final Object o = e.getSource();\r
- boolean is_applet = false;\r
- JApplet applet = null;\r
- if ( getCurrentTreePanel() != null ) {\r
- is_applet = getCurrentTreePanel().isApplet();\r
- if ( is_applet ) {\r
- applet = getCurrentTreePanel().obtainApplet();\r
- }\r
- }\r
- if ( o == _exit_item ) {\r
- close();\r
- }\r
- else if ( o == _gsdi_item ) {\r
- if ( isSubtreeDisplayed() ) {\r
- return;\r
- }\r
- executeGSDI();\r
- }\r
- else if ( o == _gsdir_item ) {\r
- if ( isSubtreeDisplayed() ) {\r
- return;\r
- }\r
- executeGSDIR();\r
- }\r
- else if ( o == _taxcolor_item ) {\r
- taxColor();\r
- }\r
- else if ( o == _confcolor_item ) {\r
- confColor();\r
- }\r
- else if ( o == _color_rank_jmi ) {\r
- colorRank();\r
- }\r
- else if ( o == _collapse_species_specific_subtrees ) {\r
- if ( isSubtreeDisplayed() ) {\r
- return;\r
- }\r
- if ( getCurrentTreePanel() != null ) {\r
- getCurrentTreePanel().collapseSpeciesSpecificSubtrees();\r
- }\r
- }\r
- else if ( o == _remove_branch_color_item ) {\r
- if ( isSubtreeDisplayed() ) {\r
- return;\r
- }\r
- removeBranchColors();\r
- }\r
- else if ( o == _remove_visual_styles_item ) {\r
- if ( isSubtreeDisplayed() ) {\r
- return;\r
- }\r
- removeVisualStyles();\r
- }\r
- else if ( o == _midpoint_root_item ) {\r
- if ( isSubtreeDisplayed() ) {\r
- return;\r
- }\r
- midpointRoot();\r
- }\r
- else if ( o == _delete_selected_nodes_item ) {\r
- if ( isSubtreeDisplayed() ) {\r
- return;\r
- }\r
- deleteSelectedNodes( true );\r
- }\r
- else if ( o == _delete_not_selected_nodes_item ) {\r
- if ( isSubtreeDisplayed() ) {\r
- return;\r
- }\r
- deleteSelectedNodes( false );\r
- }\r
- else if ( o == _annotate_item ) {\r
- annotateSequences();\r
- }\r
- else if ( o == _switch_colors_mi ) {\r
- switchColors();\r
- }\r
- else if ( o == _display_basic_information_item ) {\r
- if ( getCurrentTreePanel() != null ) {\r
- displayBasicInformation( getCurrentTreePanel().getTreeFile() );\r
- }\r
- }\r
- else if ( o == _view_as_NH_item ) {\r
- viewAsNH();\r
- }\r
- else if ( o == _view_as_XML_item ) {\r
- viewAsXML();\r
- }\r
- else if ( o == _view_as_nexus_item ) {\r
- viewAsNexus();\r
- }\r
- else if ( o == _super_tiny_fonts_item ) {\r
- if ( getCurrentTreePanel() != null ) {\r
- getCurrentTreePanel().setSuperTinyFonts();\r
- getCurrentTreePanel().repaint();\r
- }\r
- }\r
- else if ( o == _tiny_fonts_item ) {\r
- if ( getCurrentTreePanel() != null ) {\r
- getCurrentTreePanel().setTinyFonts();\r
- getCurrentTreePanel().repaint();\r
- }\r
- }\r
- else if ( o == _small_fonts_item ) {\r
- if ( getCurrentTreePanel() != null ) {\r
- getCurrentTreePanel().setSmallFonts();\r
- getCurrentTreePanel().repaint();\r
- }\r
- }\r
- else if ( o == _medium_fonts_item ) {\r
- if ( getCurrentTreePanel() != null ) {\r
- getCurrentTreePanel().setMediumFonts();\r
- getCurrentTreePanel().repaint();\r
- }\r
- }\r
- else if ( o == _large_fonts_item ) {\r
- if ( getCurrentTreePanel() != null ) {\r
- getCurrentTreePanel().setLargeFonts();\r
- getCurrentTreePanel().repaint();\r
- }\r
- }\r
- else if ( o == _choose_font_mi ) {\r
- chooseFont();\r
- }\r
- else if ( o == _choose_minimal_confidence_mi ) {\r
- chooseMinimalConfidence();\r
- }\r
- else if ( o == _choose_node_size_mi ) {\r
- chooseNodeSize( getOptions(), this );\r
- }\r
- else if ( o == _overview_placment_mi ) {\r
- MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );\r
- }\r
- else if ( o == _cycle_node_fill_mi ) {\r
- MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() );\r
- }\r
- else if ( o == _cycle_node_shape_mi ) {\r
- MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() );\r
- }\r
- else if ( o == _cycle_data_return ) {\r
- MainFrame.cycleNodeDataReturn( getOptions(), getCurrentTreePanel() );\r
- }\r
- else if ( o == _screen_antialias_cbmi ) {\r
- updateOptions( getOptions() );\r
- updateScreenTextAntialias( getMainPanel().getTreePanels() );\r
- }\r
- else if ( o == _background_gradient_cbmi ) {\r
- updateOptions( getOptions() );\r
- }\r
- else if ( o == _show_domain_labels ) {\r
- updateOptions( getOptions() );\r
- }\r
- else if ( o == _show_annotation_ref_source ) {\r
- updateOptions( getOptions() );\r
- }\r
- else if ( o == _abbreviate_scientific_names ) {\r
- updateOptions( getOptions() );\r
- }\r
- else if ( o == _color_labels_same_as_parent_branch ) {\r
- updateOptions( getOptions() );\r
- }\r
- else if ( o == _show_default_node_shapes_internal_cbmi ) {\r
- updateOptions( getOptions() );\r
- }\r
- else if ( o == _show_default_node_shapes_external_cbmi ) {\r
- updateOptions( getOptions() );\r
- }\r
- else if ( o == _show_default_node_shapes_for_marked_cbmi ) {\r
- updateOptions( getOptions() );\r
- }\r
- else if ( o == _non_lined_up_cladograms_rbmi ) {\r
- updateOptions( getOptions() );\r
- showWhole();\r
- }\r
- else if ( o == _uniform_cladograms_rbmi ) {\r
- updateOptions( getOptions() );\r
- showWhole();\r
- }\r
- else if ( o == _ext_node_dependent_cladogram_rbmi ) {\r
- updateOptions( getOptions() );\r
- showWhole();\r
- }\r
- else if ( o == _search_case_senstive_cbmi ) {\r
- updateOptions( getOptions() );\r
- getMainPanel().getControlPanel().search0();\r
- getMainPanel().getControlPanel().search1();\r
- }\r
- else if ( o == _search_whole_words_only_cbmi ) {\r
- if ( ( _search_with_regex_cbmi != null ) && _search_whole_words_only_cbmi.isSelected() ) {\r
- _search_with_regex_cbmi.setSelected( false );\r
- }\r
- updateOptions( getOptions() );\r
- getMainPanel().getControlPanel().search0();\r
- getMainPanel().getControlPanel().search1();\r
- }\r
- else if ( o == _inverse_search_result_cbmi ) {\r
- updateOptions( getOptions() );\r
- getMainPanel().getControlPanel().search0();\r
- getMainPanel().getControlPanel().search1();\r
- }\r
- else if ( o == _search_with_regex_cbmi ) {\r
- if ( ( _search_whole_words_only_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) {\r
- _search_whole_words_only_cbmi.setSelected( false );\r
- }\r
- if ( ( _search_case_senstive_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) {\r
- _search_case_senstive_cbmi.setSelected( true );\r
- }\r
- updateOptions( getOptions() );\r
- getMainPanel().getControlPanel().search0();\r
- getMainPanel().getControlPanel().search1();\r
- }\r
- else if ( o == _show_scale_cbmi ) {\r
- updateOptions( getOptions() );\r
- }\r
- else if ( o == _color_by_taxonomic_group_cbmi ) {\r
- updateOptions( getOptions() );\r
- }\r
- else if ( o == _show_confidence_stddev_cbmi ) {\r
- updateOptions( getOptions() );\r
- }\r
- else if ( o == _use_brackets_for_conf_in_nh_export_cbmi ) {\r
- if ( _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {\r
- _use_internal_names_for_conf_in_nh_export_cbmi.setSelected( false );\r
- }\r
- updateOptions( getOptions() );\r
- }\r
- else if ( o == _use_internal_names_for_conf_in_nh_export_cbmi ) {\r
- if ( _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {\r
- _use_brackets_for_conf_in_nh_export_cbmi.setSelected( false );\r
- }\r
- updateOptions( getOptions() );\r
- }\r
- else if ( o == _label_direction_cbmi ) {\r
- updateOptions( getOptions() );\r
- }\r
- else if ( o == _show_overview_cbmi ) {\r
- updateOptions( getOptions() );\r
- if ( getCurrentTreePanel() != null ) {\r
- getCurrentTreePanel().updateOvSizes();\r
- }\r
- }\r
- else if ( o == _line_up_renderable_data_cbmi ) {\r
- if ( !_line_up_renderable_data_cbmi.isSelected() ) {\r
- _right_line_up_domains_cbmi.setSelected( false );\r
- }\r
- updateOptions( getOptions() );\r
- }\r
- else if ( o == _right_line_up_domains_cbmi ) {\r
- if ( _right_line_up_domains_cbmi.isSelected() ) {\r
- _line_up_renderable_data_cbmi.setSelected( true );\r
- }\r
- updateOptions( getOptions() );\r
- }\r
- else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )\r
- || ( o == _convex_type_cbmi ) || ( o == _euro_type_cbmi ) || ( o == _rounded_type_cbmi )\r
- || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {\r
- typeChanged( o );\r
- }\r
- else if ( o == _about_item ) {\r
- about();\r
- }\r
- else if ( o == _help_item ) {\r
- try {\r
- AptxUtil.openWebsite( Constants.APTX_DOC_SITE, is_applet, applet );\r
- }\r
- catch ( final IOException e1 ) {\r
- ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
- }\r
- }\r
- else if ( o == _website_item ) {\r
- try {\r
- AptxUtil.openWebsite( Constants.APTX_WEB_SITE, is_applet, applet );\r
- }\r
- catch ( final IOException e1 ) {\r
- ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
- }\r
- }\r
- else if ( o == _phyloxml_website_item ) {\r
- try {\r
- AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, is_applet, applet );\r
- }\r
- catch ( final IOException e1 ) {\r
- ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
- }\r
- }\r
- else if ( o == _aptx_ref_item ) {\r
- try {\r
- AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, is_applet, applet );\r
- }\r
- catch ( final IOException e1 ) {\r
- ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
- }\r
- }\r
- else if ( o == _phyloxml_ref_item ) {\r
- try {\r
- AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, is_applet, applet );\r
- }\r
- catch ( final IOException e1 ) {\r
- ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
- }\r
- }\r
- else {\r
- if ( _load_phylogeny_from_webservice_menu_items != null ) {\r
- for( int i = 0; i < _load_phylogeny_from_webservice_menu_items.length; ++i ) {\r
- if ( o == _load_phylogeny_from_webservice_menu_items[ i ] ) {\r
- readPhylogeniesFromWebservice( i );\r
- }\r
- }\r
- }\r
- }\r
- _contentpane.repaint();\r
- }\r
-\r
- private void deleteSelectedNodes( final boolean delete ) {\r
- final Phylogeny phy = getMainPanel().getCurrentPhylogeny();\r
- if ( ( phy == null ) || ( phy.getNumberOfExternalNodes() < 2 ) ) {\r
- return;\r
- }\r
- final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();\r
- if ( ( getCurrentTreePanel().getFoundNodes0() != null ) || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {\r
- final List<PhylogenyNode> all_selected_nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();\r
- for( final PhylogenyNode n : all_selected_nodes ) {\r
- if ( n.isExternal() ) {\r
- nodes.add( n );\r
- }\r
- }\r
- }\r
- String function = "Retain";\r
- if ( delete ) {\r
- function = "Delete";\r
- }\r
- if ( ( nodes == null ) || nodes.isEmpty() ) {\r
- JOptionPane\r
- .showMessageDialog( this,\r
- "Need to select external nodes, either via direct selection or via the \"Search\" function",\r
- "No external nodes selected to " + function.toLowerCase(),\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- final int todo = nodes.size();\r
- final int ext = phy.getNumberOfExternalNodes();\r
- int res = todo;\r
- if ( delete ) {\r
- res = ext - todo;\r
- }\r
- if ( res < 1 ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Cannot delete all nodes",\r
- "Attempt to delete all nodes ",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- final int result = JOptionPane.showConfirmDialog( null, function + " " + todo\r
- + " external node(s), from a total of " + ext + " external nodes," + "\nresulting in tree with " + res\r
- + " nodes?", function + " external nodes", JOptionPane.OK_CANCEL_OPTION );\r
- if ( result == JOptionPane.OK_OPTION ) {\r
- if ( !delete ) {\r
- final List<PhylogenyNode> to_delete = new ArrayList<PhylogenyNode>();\r
- for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {\r
- final PhylogenyNode n = it.next();\r
- if ( !nodes.contains( n ) ) {\r
- to_delete.add( n );\r
- }\r
- }\r
- for( final PhylogenyNode n : to_delete ) {\r
- phy.deleteSubtree( n, true );\r
- }\r
- }\r
- else {\r
- for( final PhylogenyNode n : nodes ) {\r
- phy.deleteSubtree( n, true );\r
- }\r
- }\r
- resetSearch();\r
- getCurrentTreePanel().setNodeInPreorderToNull();\r
- phy.externalNodesHaveChanged();\r
- phy.clearHashIdToNodeMap();\r
- phy.recalculateNumberOfExternalDescendants( true );\r
- getCurrentTreePanel().resetNodeIdToDistToLeafMap();\r
- getCurrentTreePanel().setEdited( true );\r
- repaint();\r
- }\r
- }\r
-\r
- void resetSearch() {\r
- getMainPanel().getCurrentTreePanel().setFoundNodes0( null );\r
- getMainPanel().getCurrentTreePanel().setFoundNodes1( null );\r
- getMainPanel().getControlPanel().setSearchFoundCountsOnLabel0( 0 );\r
- getMainPanel().getControlPanel().getSearchFoundCountsLabel0().setVisible( false );\r
- getMainPanel().getControlPanel().getSearchTextField0().setText( "" );\r
- getMainPanel().getControlPanel().getSearchResetButton0().setEnabled( false );\r
- getMainPanel().getControlPanel().getSearchResetButton0().setVisible( false );\r
- getMainPanel().getControlPanel().setSearchFoundCountsOnLabel1( 0 );\r
- getMainPanel().getControlPanel().getSearchFoundCountsLabel1().setVisible( false );\r
- getMainPanel().getControlPanel().getSearchTextField1().setText( "" );\r
- getMainPanel().getControlPanel().getSearchResetButton1().setEnabled( false );\r
- getMainPanel().getControlPanel().getSearchResetButton1().setVisible( false );\r
- }\r
-\r
- public Configuration getConfiguration() {\r
- return _configuration;\r
- }\r
-\r
- /**\r
- * This method returns the current external node data which\r
- * has been selected by the user by clicking the "Return ..."\r
- * menu item. This method is expected to be called from Javascript or\r
- * something like it.\r
- *\r
- * @return current external node data as String\r
- */\r
- public String getCurrentExternalNodesDataBuffer() {\r
- return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();\r
- }\r
-\r
- public int getCurrentExternalNodesDataBufferChangeCounter() {\r
- return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();\r
- }\r
-\r
- public int getCurrentExternalNodesDataBufferLength() {\r
- return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();\r
- }\r
-\r
- public InferenceManager getInferenceManager() {\r
- return _inference_manager;\r
- }\r
-\r
- public MainPanel getMainPanel() {\r
- return _mainpanel;\r
- }\r
-\r
- public Options getOptions() {\r
- return _options;\r
- }\r
-\r
- public ProcessPool getProcessPool() {\r
- return _process_pool;\r
- }\r
-\r
- public void showTextFrame( final String s, final String title ) {\r
- checkTextFrames();\r
- _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );\r
- }\r
-\r
- public void showWhole() {\r
- _mainpanel.getControlPanel().showWhole();\r
- }\r
-\r
- public void updateProcessMenu() {\r
- // In general Swing is not thread safe.\r
- // See "Swing's Threading Policy".\r
- SwingUtilities.invokeLater( new Runnable() {\r
-\r
- @Override\r
- public void run() {\r
- doUpdateProcessMenu();\r
- }\r
- } );\r
- }\r
-\r
- void activateSaveAllIfNeeded() {\r
- if ( ( getMainPanel().getTabbedPane() != null ) && ( getMainPanel().getTabbedPane().getTabCount() > 1 ) ) {\r
- _save_all_item.setEnabled( true );\r
- }\r
- else {\r
- _save_all_item.setEnabled( false );\r
- }\r
- }\r
-\r
- void buildFileMenu() {\r
- _file_jmenu = createMenu( "File", getConfiguration() );\r
- _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );\r
- customizeJMenuItem( _exit_item );\r
- _jmenubar.add( _file_jmenu );\r
- }\r
-\r
- void buildFontSizeMenu() {\r
- _font_size_menu = createMenu( FONT_SIZE_MENU_LABEL, getConfiguration() );\r
- _font_size_menu.add( _super_tiny_fonts_item = new JMenuItem( "Super Tiny Fonts" ) );\r
- _font_size_menu.add( _tiny_fonts_item = new JMenuItem( "Tiny Fonts" ) );\r
- _font_size_menu.add( _small_fonts_item = new JMenuItem( "Small Fonts" ) );\r
- _font_size_menu.add( _medium_fonts_item = new JMenuItem( "Medium Fonts" ) );\r
- _font_size_menu.add( _large_fonts_item = new JMenuItem( "Large Fonts" ) );\r
- customizeJMenuItem( _super_tiny_fonts_item );\r
- customizeJMenuItem( _tiny_fonts_item );\r
- customizeJMenuItem( _small_fonts_item );\r
- customizeJMenuItem( _medium_fonts_item );\r
- customizeJMenuItem( _large_fonts_item );\r
- _jmenubar.add( _font_size_menu );\r
- }\r
-\r
- void buildHelpMenu() {\r
- _help_jmenu = createMenu( "Help", getConfiguration() );\r
- _help_jmenu.add( _help_item = new JMenuItem( "Documentation" ) );\r
- _help_jmenu.addSeparator();\r
- _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );\r
- _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" ); //TODO need to add this...\r
- _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );\r
- _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );\r
- _help_jmenu.addSeparator();\r
- _help_jmenu.add( _about_item = new JMenuItem( "About" ) );\r
- customizeJMenuItem( _help_item );\r
- customizeJMenuItem( _website_item );\r
- customizeJMenuItem( _phyloxml_website_item );\r
- customizeJMenuItem( _aptx_ref_item );\r
- customizeJMenuItem( _phyloxml_ref_item );\r
- customizeJMenuItem( _about_item );\r
- _phyloxml_ref_item.setToolTipText( PHYLOXML_REF_TOOL_TIP );\r
- _aptx_ref_item.setToolTipText( APTX_REF_TOOL_TIP );\r
- _jmenubar.add( _help_jmenu );\r
- }\r
-\r
- void buildTypeMenu() {\r
- _type_menu = createMenu( TYPE_MENU_HEADER, getConfiguration() );\r
- _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );\r
- _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );\r
- _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );\r
- _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );\r
- _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );\r
- _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );\r
- _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );\r
- _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );\r
- customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );\r
- customizeCheckBoxMenuItem( _triangular_type_cbmi, false );\r
- customizeCheckBoxMenuItem( _euro_type_cbmi, false );\r
- customizeCheckBoxMenuItem( _rounded_type_cbmi, false );\r
- customizeCheckBoxMenuItem( _curved_type_cbmi, false );\r
- customizeCheckBoxMenuItem( _convex_type_cbmi, false );\r
- customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );\r
- customizeCheckBoxMenuItem( _circular_type_cbmi, false );\r
- _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );\r
- _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );\r
- initializeTypeMenu( getOptions() );\r
- _jmenubar.add( _type_menu );\r
- }\r
-\r
- void buildViewMenu() {\r
- _view_jmenu = createMenu( "View", getConfiguration() );\r
- _view_jmenu.add( _display_basic_information_item = new JMenuItem( SHOW_BASIC_TREE_INFORMATION_LABEL ) );\r
- _view_jmenu.addSeparator();\r
- _view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) );\r
- _view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) );\r
- _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "as Nexus" ) );\r
- customizeJMenuItem( _display_basic_information_item );\r
- customizeJMenuItem( _view_as_NH_item );\r
- customizeJMenuItem( _view_as_XML_item );\r
- customizeJMenuItem( _view_as_nexus_item );\r
- _jmenubar.add( _view_jmenu );\r
- }\r
-\r
- void checkTextFrames() {\r
- if ( _textframes.size() > 5 ) {\r
- try {\r
- if ( _textframes.getFirst() != null ) {\r
- _textframes.getFirst().removeMe();\r
- }\r
- else {\r
- _textframes.removeFirst();\r
- }\r
- }\r
- catch ( final NoSuchElementException e ) {\r
- // Ignore.\r
- }\r
- }\r
- }\r
-\r
- void close() {\r
- removeAllTextFrames();\r
- if ( _mainpanel != null ) {\r
- _mainpanel.terminate();\r
- }\r
- if ( _contentpane != null ) {\r
- _contentpane.removeAll();\r
- }\r
- setVisible( false );\r
- dispose();\r
- }\r
-\r
- void colorRank() {\r
- if ( _mainpanel.getCurrentTreePanel() != null ) {\r
- final String[] ranks = AptxUtil.getAllPossibleRanks();\r
- final String rank = ( String ) JOptionPane\r
- .showInputDialog( this,\r
- "What rank should the colorization be based on",\r
- "Rank Selection",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null,\r
- ranks,\r
- null );\r
- if ( !ForesterUtil.isEmpty( rank ) ) {\r
- _mainpanel.getCurrentTreePanel().colorRank( rank );\r
- }\r
- }\r
- }\r
-\r
- void confColor() {\r
- if ( _mainpanel.getCurrentTreePanel() != null ) {\r
- _mainpanel.getCurrentTreePanel().confColor();\r
- }\r
- }\r
-\r
- void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {\r
- if ( item != null ) {\r
- item.setFont( MainFrame.menu_font );\r
- if ( !getConfiguration().isUseNativeUI() ) {\r
- item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
- item.setForeground( getConfiguration().getGuiMenuTextColor() );\r
- }\r
- item.setSelected( is_selected );\r
- item.addActionListener( this );\r
- }\r
- }\r
-\r
- JMenuItem customizeJMenuItem( final JMenuItem jmi ) {\r
- if ( jmi != null ) {\r
- jmi.setFont( MainFrame.menu_font );\r
- if ( !getConfiguration().isUseNativeUI() ) {\r
- jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
- jmi.setForeground( getConfiguration().getGuiMenuTextColor() );\r
- }\r
- jmi.addActionListener( this );\r
- }\r
- return jmi;\r
- }\r
-\r
- void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {\r
- if ( item != null ) {\r
- item.setFont( MainFrame.menu_font );\r
- if ( !getConfiguration().isUseNativeUI() ) {\r
- item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
- item.setForeground( getConfiguration().getGuiMenuTextColor() );\r
- }\r
- item.setSelected( is_selected );\r
- item.addActionListener( this );\r
- }\r
- }\r
-\r
- void displayBasicInformation( final File treefile ) {\r
- if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
- String title = "Basic Information";\r
- if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
- title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\"";\r
- }\r
- showTextFrame( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny(), treefile ), title );\r
- }\r
- }\r
-\r
- void exceptionOccuredDuringOpenFile( final Exception e ) {\r
- try {\r
- _mainpanel.getCurrentTreePanel().setArrowCursor();\r
- }\r
- catch ( final Exception ex ) {\r
- // Do nothing.\r
- }\r
- JOptionPane.showMessageDialog( this,\r
- ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),\r
- "Error during File|Open",\r
- JOptionPane.ERROR_MESSAGE );\r
- }\r
-\r
- void exceptionOccuredDuringSaveAs( final Exception e ) {\r
- try {\r
- _mainpanel.getCurrentTreePanel().setArrowCursor();\r
- }\r
- catch ( final Exception ex ) {\r
- // Do nothing.\r
- }\r
- JOptionPane.showMessageDialog( this, "Exception" + e, "Error during File|SaveAs", JOptionPane.ERROR_MESSAGE );\r
- }\r
-\r
- void executeGSDI() {\r
- if ( !isOKforSDI( false, true ) ) {\r
- return;\r
- }\r
- if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Gene tree is not rooted.",\r
- "Cannot execute GSDI",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();\r
- gene_tree.setAllNodesToNotCollapse();\r
- gene_tree.recalculateNumberOfExternalDescendants( false );\r
- GSDI gsdi = null;\r
- final Phylogeny species_tree = getSpeciesTree().copy();\r
- try {\r
- gsdi = new GSDI( gene_tree, species_tree, false, true, true, true );\r
- }\r
- catch ( final SDIException e ) {\r
- JOptionPane.showMessageDialog( this,\r
- e.getLocalizedMessage(),\r
- "Error during GSDI",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- catch ( final Exception e ) {\r
- AptxUtil.unexpectedException( e );\r
- return;\r
- }\r
- gene_tree.setRerootable( false );\r
- gene_tree.clearHashIdToNodeMap();\r
- gene_tree.recalculateNumberOfExternalDescendants( true );\r
- _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null );\r
- getMainPanel().getControlPanel().setShowEvents( true );\r
- showWhole();\r
- final int selected = _mainpanel.getTabbedPane().getSelectedIndex();\r
- _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );\r
- showWhole();\r
- _mainpanel.getTabbedPane().setSelectedIndex( selected );\r
- showWhole();\r
- _mainpanel.getCurrentTreePanel().setEdited( true );\r
- final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );\r
- if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Duplications: " + gsdi.getDuplicationsSum() + "\n"\r
- + "Potential duplications: "\r
- + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"\r
- + "Speciations: " + gsdi.getSpeciationsSum() + "\n"\r
- + "Stripped gene tree nodes: "\r
- + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"\r
- + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"\r
- + "Number of polytomies in species tree used: " + poly + "\n",\r
- "GSDI successfully completed",\r
- JOptionPane.WARNING_MESSAGE );\r
- }\r
- else {\r
- JOptionPane.showMessageDialog( this,\r
- "Duplications: " + gsdi.getDuplicationsSum() + "\n"\r
- + "Potential duplications: "\r
- + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"\r
- + "Speciations: " + gsdi.getSpeciationsSum() + "\n"\r
- + "Stripped gene tree nodes: "\r
- + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"\r
- + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"\r
- + "Number of polytomies in species tree used: " + poly + "\n",\r
- "GSDI successfully completed",\r
- JOptionPane.INFORMATION_MESSAGE );\r
- }\r
- }\r
-\r
- void executeGSDIR() {\r
- if ( !isOKforSDI( false, false ) ) {\r
- return;\r
- }\r
- final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() );\r
- if ( ( p > 0 )\r
- && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Gene tree is not completely binary",\r
- "Cannot execute GSDI",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();\r
- gene_tree.setAllNodesToNotCollapse();\r
- gene_tree.recalculateNumberOfExternalDescendants( false );\r
- GSDIR gsdir = null;\r
- final Phylogeny species_tree = getSpeciesTree().copy();\r
- try {\r
- gsdir = new GSDIR( gene_tree, species_tree, true, true, true );\r
- }\r
- catch ( final SDIException e ) {\r
- JOptionPane.showMessageDialog( this,\r
- e.getLocalizedMessage(),\r
- "Error during GSDIR",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- catch ( final Exception e ) {\r
- AptxUtil.unexpectedException( e );\r
- return;\r
- }\r
- final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree();\r
- result_gene_tree.setRerootable( false );\r
- result_gene_tree.clearHashIdToNodeMap();\r
- result_gene_tree.recalculateNumberOfExternalDescendants( true );\r
- PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );\r
- _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );\r
- getMainPanel().getControlPanel().setShowEvents( true );\r
- showWhole();\r
- final int selected = _mainpanel.getTabbedPane().getSelectedIndex();\r
- _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );\r
- showWhole();\r
- _mainpanel.getTabbedPane().setSelectedIndex( selected );\r
- showWhole();\r
- _mainpanel.getCurrentTreePanel().setEdited( true );\r
- final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );\r
- if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"\r
- + "Speciations: " + gsdir.getSpeciationsSum() + "\n"\r
- + "Stripped gene tree nodes: "\r
- + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"\r
- + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"\r
- + "Number of polytomies in species tree used: " + poly + "\n",\r
- "GSDIR successfully completed",\r
- JOptionPane.WARNING_MESSAGE );\r
- }\r
- else {\r
- JOptionPane.showMessageDialog( this,\r
- "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"\r
- + "Speciations: " + gsdir.getSpeciationsSum() + "\n"\r
- + "Stripped gene tree nodes: "\r
- + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"\r
- + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"\r
- + "Number of polytomies in species tree used: " + poly + "\n",\r
- "GSDIR successfully completed",\r
- JOptionPane.INFORMATION_MESSAGE );\r
- }\r
- }\r
-\r
- boolean GAndSDoHaveMoreThanOneSpeciesInComman( final Phylogeny gene_tree ) {\r
- if ( ( gene_tree == null ) || gene_tree.isEmpty() ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Gene tree and species tree have no species in common.",\r
- "Error during SDI",\r
- JOptionPane.ERROR_MESSAGE );\r
- return false;\r
- }\r
- else if ( gene_tree.getNumberOfExternalNodes() < 2 ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Gene tree and species tree have only one species in common.",\r
- "Error during SDI",\r
- JOptionPane.ERROR_MESSAGE );\r
- return false;\r
- }\r
- else {\r
- return true;\r
- }\r
- }\r
-\r
- TreePanel getCurrentTreePanel() {\r
- return getMainPanel().getCurrentTreePanel();\r
- }\r
-\r
- JMenu getHelpMenu() {\r
- return _help_jmenu;\r
- }\r
-\r
- JCheckBoxMenuItem getlabelDirectionCbmi() {\r
- return _label_direction_cbmi;\r
- }\r
-\r
- JMenuBar getMenuBarOfMainFrame() {\r
- return _jmenubar;\r
- }\r
-\r
- final Phylogeny getSpeciesTree() {\r
- return _species_tree;\r
- }\r
-\r
- void initializeTypeMenu( final Options options ) {\r
- setTypeMenuToAllUnselected();\r
- switch ( options.getPhylogenyGraphicsType() ) {\r
- case CONVEX:\r
- _convex_type_cbmi.setSelected( true );\r
- break;\r
- case CURVED:\r
- _curved_type_cbmi.setSelected( true );\r
- break;\r
- case EURO_STYLE:\r
- _euro_type_cbmi.setSelected( true );\r
- break;\r
- case ROUNDED:\r
- _rounded_type_cbmi.setSelected( true );\r
- break;\r
- case TRIANGULAR:\r
- _triangular_type_cbmi.setSelected( true );\r
- break;\r
- case UNROOTED:\r
- _unrooted_type_cbmi.setSelected( true );\r
- break;\r
- case CIRCULAR:\r
- _circular_type_cbmi.setSelected( true );\r
- break;\r
- default:\r
- _rectangular_type_cbmi.setSelected( true );\r
- break;\r
- }\r
- }\r
-\r
- boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {\r
- if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
- return false;\r
- }\r
- else if ( ( getSpeciesTree() == null ) || getSpeciesTree().isEmpty() ) {\r
- JOptionPane.showMessageDialog( this,\r
- "No species tree loaded",\r
- "Cannot execute GSDI",\r
- JOptionPane.ERROR_MESSAGE );\r
- return false;\r
- }\r
- else if ( species_tree_has_to_binary && !getSpeciesTree().isCompletelyBinary() ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Species tree is not completely binary",\r
- "Cannot execute GSDI",\r
- JOptionPane.ERROR_MESSAGE );\r
- return false;\r
- }\r
- else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Gene tree is not completely binary",\r
- "Cannot execute GSDI",\r
- JOptionPane.ERROR_MESSAGE );\r
- return false;\r
- }\r
- else {\r
- return true;\r
- }\r
- }\r
-\r
- boolean isSubtreeDisplayed() {\r
- if ( getCurrentTreePanel() != null ) {\r
- if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {\r
- JOptionPane\r
- .showMessageDialog( this,\r
- "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",\r
- "Operation can not be exectuted on a sub-tree",\r
- JOptionPane.WARNING_MESSAGE );\r
- return true;\r
- }\r
- }\r
- return false;\r
- }\r
-\r
- void midpointRoot() {\r
- if ( _mainpanel.getCurrentTreePanel() != null ) {\r
- _mainpanel.getCurrentTreePanel().midpointRoot();\r
- }\r
- }\r
-\r
- void readPhylogeniesFromWebservice( final int i ) {\r
- final UrlTreeReader reader = new UrlTreeReader( this, i );\r
- new Thread( reader ).start();\r
- }\r
-\r
- void removeAllTextFrames() {\r
- for( final TextFrame tf : _textframes ) {\r
- if ( tf != null ) {\r
- tf.close();\r
- }\r
- }\r
- _textframes.clear();\r
- }\r
-\r
- void setConfiguration( final Configuration configuration ) {\r
- _configuration = configuration;\r
- }\r
-\r
- void setInferenceManager( final InferenceManager i ) {\r
- _inference_manager = i;\r
- }\r
-\r
- void setOptions( final Options options ) {\r
- _options = options;\r
- }\r
-\r
- void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {\r
- setTypeMenuToAllUnselected();\r
- switch ( type ) {\r
- case CIRCULAR:\r
- _circular_type_cbmi.setSelected( true );\r
- break;\r
- case CONVEX:\r
- _convex_type_cbmi.setSelected( true );\r
- break;\r
- case CURVED:\r
- _curved_type_cbmi.setSelected( true );\r
- break;\r
- case EURO_STYLE:\r
- _euro_type_cbmi.setSelected( true );\r
- break;\r
- case ROUNDED:\r
- _rounded_type_cbmi.setSelected( true );\r
- break;\r
- case RECTANGULAR:\r
- _rectangular_type_cbmi.setSelected( true );\r
- break;\r
- case TRIANGULAR:\r
- _triangular_type_cbmi.setSelected( true );\r
- break;\r
- case UNROOTED:\r
- _unrooted_type_cbmi.setSelected( true );\r
- break;\r
- default:\r
- throw new IllegalArgumentException( "unknown type: " + type );\r
- }\r
- }\r
-\r
- final void setSpeciesTree( final Phylogeny species_tree ) {\r
- _species_tree = species_tree;\r
- }\r
-\r
- void setTypeMenuToAllUnselected() {\r
- _convex_type_cbmi.setSelected( false );\r
- _curved_type_cbmi.setSelected( false );\r
- _euro_type_cbmi.setSelected( false );\r
- _rounded_type_cbmi.setSelected( false );\r
- _triangular_type_cbmi.setSelected( false );\r
- _rectangular_type_cbmi.setSelected( false );\r
- _unrooted_type_cbmi.setSelected( false );\r
- _circular_type_cbmi.setSelected( false );\r
- }\r
-\r
- void switchColors() {\r
- final TreeColorSet colorset = _mainpanel.getTreeColorSet();\r
- final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );\r
- csc.setVisible( true );\r
- }\r
-\r
- void taxColor() {\r
- if ( _mainpanel.getCurrentTreePanel() != null ) {\r
- _mainpanel.getCurrentTreePanel().taxColor();\r
- }\r
- }\r
-\r
- void typeChanged( final Object o ) {\r
- updateTypeCheckboxes( getOptions(), o );\r
- updateOptions( getOptions() );\r
- if ( getCurrentTreePanel() != null ) {\r
- final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();\r
- final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();\r
- if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )\r
- || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )\r
- || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )\r
- || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {\r
- getCurrentTreePanel().getControlPanel().showWhole();\r
- }\r
- if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {\r
- getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );\r
- }\r
- else {\r
- getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );\r
- }\r
- getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );\r
- updateScreenTextAntialias( getMainPanel().getTreePanels() );\r
- if ( getCurrentTreePanel().getControlPanel().getDynamicallyHideData() != null ) {\r
- if ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {\r
- getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( false );\r
- }\r
- else {\r
- getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( true );\r
- }\r
- }\r
- }\r
- }\r
-\r
- void updateOptions( final Options options ) {\r
- options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );\r
- options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )\r
- && _background_gradient_cbmi.isSelected() );\r
- options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );\r
- options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null )\r
- && _show_annotation_ref_source.isSelected() );\r
- options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )\r
- && _abbreviate_scientific_names.isSelected() );\r
- options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )\r
- && _color_labels_same_as_parent_branch.isSelected() );\r
- options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )\r
- && _show_default_node_shapes_internal_cbmi.isSelected() );\r
- options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )\r
- && _show_default_node_shapes_external_cbmi.isSelected() );\r
- options.setShowDefaultNodeShapesForMarkedNodes( ( _show_default_node_shapes_for_marked_cbmi != null )\r
- && _show_default_node_shapes_for_marked_cbmi.isSelected() );\r
- if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {\r
- options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );\r
- }\r
- else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {\r
- options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );\r
- }\r
- else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {\r
- options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );\r
- }\r
- options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )\r
- && _search_case_senstive_cbmi.isSelected() );\r
- if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {\r
- options.setShowScale( _show_scale_cbmi.isSelected() );\r
- }\r
- if ( _label_direction_cbmi != null ) {\r
- if ( _label_direction_cbmi.isSelected() ) {\r
- options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );\r
- }\r
- else {\r
- options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );\r
- }\r
- }\r
- options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );\r
- options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )\r
- && _show_confidence_stddev_cbmi.isSelected() );\r
- if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) {\r
- options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() );\r
- }\r
- options.setPrintUsingActualSize( ( _print_using_actual_size_cbmi != null )\r
- && ( _print_using_actual_size_cbmi.isSelected() ) );\r
- options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null )\r
- && ( _graphics_export_using_actual_size_cbmi.isSelected() ) );\r
- options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() );\r
- if ( ( _use_brackets_for_conf_in_nh_export_cbmi != null )\r
- && _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {\r
- options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );\r
- }\r
- else if ( ( _use_internal_names_for_conf_in_nh_export_cbmi != null )\r
- && _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {\r
- options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );\r
- }\r
- else {\r
- options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );\r
- }\r
- options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null )\r
- && _print_black_and_white_cbmi.isSelected() );\r
- options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null )\r
- && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );\r
- if ( ( _extract_taxonomy_pfam_strict_rbmi != null ) && _extract_taxonomy_pfam_strict_rbmi.isSelected() ) {\r
- options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );\r
- }\r
- else if ( ( _extract_taxonomy_pfam_relaxed_rbmi != null ) && _extract_taxonomy_pfam_relaxed_rbmi.isSelected() ) {\r
- options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );\r
- }\r
- else if ( ( _extract_taxonomy_agressive_rbmi != null ) && _extract_taxonomy_agressive_rbmi.isSelected() ) {\r
- options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );\r
- }\r
- else if ( ( _extract_taxonomy_no_rbmi != null ) && _extract_taxonomy_no_rbmi.isSelected() ) {\r
- options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );\r
- }\r
- options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )\r
- && _replace_underscores_cbmi.isSelected() );\r
- options.setAllowErrorsInDistanceToParent( ( _allow_errors_in_distance_to_parent_cbmi != null )\r
- && _allow_errors_in_distance_to_parent_cbmi.isSelected() );\r
- options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )\r
- && _search_whole_words_only_cbmi.isSelected() );\r
- options.setSearchWithRegex( ( _search_with_regex_cbmi != null ) && _search_with_regex_cbmi.isSelected() );\r
- options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )\r
- && _inverse_search_result_cbmi.isSelected() );\r
- if ( _graphics_export_visible_only_cbmi != null ) {\r
- options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_cbmi.isSelected() );\r
- if ( _graphics_export_visible_only_cbmi.isSelected() && ( _graphics_export_using_actual_size_cbmi != null ) ) {\r
- _graphics_export_using_actual_size_cbmi.setSelected( true );\r
- _graphics_export_using_actual_size_cbmi.setEnabled( false );\r
- }\r
- else {\r
- _graphics_export_using_actual_size_cbmi.setEnabled( true );\r
- }\r
- }\r
- if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {\r
- options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );\r
- }\r
- else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {\r
- options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );\r
- }\r
- else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {\r
- options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );\r
- }\r
- else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {\r
- options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );\r
- }\r
- else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {\r
- options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );\r
- }\r
- else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {\r
- options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );\r
- }\r
- else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {\r
- options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );\r
- }\r
- else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {\r
- options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );\r
- }\r
- if ( ( _right_line_up_domains_cbmi != null ) && _right_line_up_domains_cbmi.isEnabled() ) {\r
- options.setRightLineUpDomains( _right_line_up_domains_cbmi.isSelected() );\r
- }\r
- if ( ( _line_up_renderable_data_cbmi != null ) && _line_up_renderable_data_cbmi.isEnabled() ) {\r
- options.setLineUpRendarableNodeData( _line_up_renderable_data_cbmi.isSelected() );\r
- }\r
- }\r
-\r
- void updateTypeCheckboxes( final Options options, final Object o ) {\r
- setTypeMenuToAllUnselected();\r
- ( ( JCheckBoxMenuItem ) o ).setSelected( true );\r
- }\r
-\r
- void viewAsNexus() {\r
- if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
- String title = "Nexus";\r
- if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
- title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
- }\r
- showTextFrame( _mainpanel.getCurrentPhylogeny().toNexus( getOptions().getNhConversionSupportValueStyle() ),\r
- title );\r
- }\r
- }\r
-\r
- void viewAsNH() {\r
- if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
- String title = "New Hampshire";\r
- if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
- title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
- }\r
- showTextFrame( _mainpanel.getCurrentPhylogeny().toNewHampshire( getOptions()\r
- .getNhConversionSupportValueStyle() ),\r
- title );\r
- }\r
- }\r
-\r
- void viewAsXML() {\r
- if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
- String title = "phyloXML";\r
- if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
- title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
- }\r
- showTextFrame( _mainpanel.getCurrentPhylogeny().toPhyloXML( 0 ), title );\r
- }\r
- }\r
-\r
- private void annotateSequences() {\r
- if ( getCurrentTreePanel() != null ) {\r
- List<PhylogenyNode> nodes = null;\r
- if ( ( getCurrentTreePanel().getFoundNodes0() != null )\r
- || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {\r
- nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();\r
- }\r
- if ( ( nodes == null ) || nodes.isEmpty() ) {\r
- JOptionPane\r
- .showMessageDialog( this,\r
- "Need to select nodes, either via direct selection or via the \"Search\" function",\r
- "No nodes selected for annotation",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- final Phylogeny phy = getMainPanel().getCurrentPhylogeny();\r
- if ( ( phy != null ) && !phy.isEmpty() ) {\r
- final JTextField ref_field = new JTextField( 10 );\r
- final JTextField desc_filed = new JTextField( 20 );\r
- ref_field.setText( ForesterUtil.isEmpty( getPreviousNodeAnnotationReference() ) ? ""\r
- : getPreviousNodeAnnotationReference() );\r
- final JPanel my_panel = new JPanel();\r
- my_panel.add( new JLabel( "Reference " ) );\r
- my_panel.add( ref_field );\r
- my_panel.add( Box.createHorizontalStrut( 15 ) );\r
- my_panel.add( new JLabel( "Description " ) );\r
- my_panel.add( desc_filed );\r
- final int result = JOptionPane.showConfirmDialog( null,\r
- my_panel,\r
- "Enter the sequence annotation(s) for the "\r
- + nodes.size() + " selected nodes",\r
- JOptionPane.OK_CANCEL_OPTION );\r
- if ( result == JOptionPane.OK_OPTION ) {\r
- String ref = ref_field.getText();\r
- String desc = desc_filed.getText();\r
- if ( !ForesterUtil.isEmpty( ref ) ) {\r
- ref = ref.trim();\r
- ref = ref.replaceAll( "\\s+", " " );\r
- if ( ( ref.indexOf( ':' ) < 1 ) || ( ref.indexOf( ':' ) > ( ref.length() - 2 ) )\r
- || ( ref.length() < 3 ) ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Reference needs to be in the form of \"GO:1234567\"",\r
- "Illegal Format for Annotation Reference",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- }\r
- if ( ref != null ) {\r
- setPreviousNodeAnnotationReference( ref );\r
- }\r
- if ( desc != null ) {\r
- desc = desc.trim();\r
- desc = desc.replaceAll( "\\s+", " " );\r
- }\r
- if ( !ForesterUtil.isEmpty( ref ) || !ForesterUtil.isEmpty( desc ) ) {\r
- for( final PhylogenyNode n : nodes ) {\r
- ForesterUtil.ensurePresenceOfSequence( n );\r
- final Annotation ann = ForesterUtil.isEmpty( ref ) ? new Annotation()\r
- : new Annotation( ref );\r
- if ( !ForesterUtil.isEmpty( desc ) ) {\r
- ann.setDesc( desc );\r
- }\r
- n.getNodeData().getSequence().addAnnotation( ann );\r
- }\r
- }\r
- getMainPanel().getControlPanel().showAnnotations();\r
- }\r
- }\r
- }\r
- }\r
-\r
- private void chooseFont() {\r
- final FontChooser fc = new FontChooser();\r
- fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );\r
- fc.showDialog( this, "Select the Base Font" );\r
- getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );\r
- }\r
-\r
- private void chooseMinimalConfidence() {\r
- final String s = ( String ) JOptionPane\r
- .showInputDialog( this,\r
- "Please enter the minimum for confidence values to be displayed.\n"\r
- + "[current value: " + getOptions().getMinConfidenceValue() + "]\n",\r
- "Minimal Confidence Value",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null,\r
- null,\r
- getOptions().getMinConfidenceValue() );\r
- if ( !ForesterUtil.isEmpty( s ) ) {\r
- boolean success = true;\r
- double m = 0.0;\r
- final String m_str = s.trim();\r
- if ( !ForesterUtil.isEmpty( m_str ) ) {\r
- try {\r
- m = Double.parseDouble( m_str );\r
- }\r
- catch ( final Exception ex ) {\r
- success = false;\r
- }\r
- }\r
- else {\r
- success = false;\r
- }\r
- if ( success && ( m >= 0.0 ) ) {\r
- getOptions().setMinConfidenceValue( m );\r
- }\r
- }\r
- }\r
-\r
- private void doUpdateProcessMenu() {\r
- if ( _process_pool.size() > 0 ) {\r
- if ( _process_menu == null ) {\r
- _process_menu = createMenu( "", getConfiguration() );\r
- _process_menu.setForeground( Color.RED );\r
- }\r
- _process_menu.removeAll();\r
- final String text = "processes running: " + _process_pool.size();\r
- _process_menu.setText( text );\r
- _jmenubar.add( _process_menu );\r
- for( int i = 0; i < _process_pool.size(); ++i ) {\r
- final ProcessRunning p = _process_pool.getProcessByIndex( i );\r
- _process_menu.add( customizeJMenuItem( new JMenuItem( p.getName() + " [" + p.getStart() + "]" ) ) );\r
- }\r
- }\r
- else {\r
- if ( _process_menu != null ) {\r
- _process_menu.removeAll();\r
- _jmenubar.remove( _process_menu );\r
- }\r
- }\r
- _jmenubar.validate();\r
- _jmenubar.repaint();\r
- repaint();\r
- }\r
-\r
- private String getPreviousNodeAnnotationReference() {\r
- return _previous_node_annotation_ref;\r
- }\r
-\r
- private void removeBranchColors() {\r
- if ( getMainPanel().getCurrentPhylogeny() != null ) {\r
- AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );\r
- }\r
- }\r
-\r
- private void removeVisualStyles() {\r
- if ( getMainPanel().getCurrentPhylogeny() != null ) {\r
- AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() );\r
- }\r
- }\r
-\r
- private void setPreviousNodeAnnotationReference( final String previous_node_annotation_ref ) {\r
- _previous_node_annotation_ref = previous_node_annotation_ref;\r
- }\r
-\r
- /**\r
- * Display the about box.\r
- */\r
- static void about() {\r
- final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + Constants.VERSION + "\n" );\r
- about.append( "Copyright (C) 2014 Christian M Zmasek\n" );\r
- about.append( "All Rights Reserved\n" );\r
- about.append( "License: GNU Lesser General Public License (LGPL)\n" );\r
- about.append( "Last modified: " + Constants.PRG_DATE + "\n" );\r
- about.append( "Based on: " + ForesterUtil.getForesterLibraryInformation() + "\n" );\r
- about.append( "phyloXML version : " + ForesterConstants.PHYLO_XML_VERSION + "\n" );\r
- about.append( "phyloXML location: " + ForesterConstants.PHYLO_XML_LOCATION + "\n" );\r
- if ( !ForesterUtil.isEmpty( ForesterUtil.JAVA_VERSION ) && !ForesterUtil.isEmpty( ForesterUtil.JAVA_VENDOR ) ) {\r
- about.append( "[your Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]\n" );\r
- }\r
- if ( !ForesterUtil.isEmpty( ForesterUtil.OS_NAME ) && !ForesterUtil.isEmpty( ForesterUtil.OS_ARCH )\r
- && !ForesterUtil.isEmpty( ForesterUtil.OS_VERSION ) ) {\r
- about.append( "[your OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " "\r
- + ForesterUtil.OS_VERSION + "]\n" );\r
- }\r
- final Runtime rt = java.lang.Runtime.getRuntime();\r
- final long free_memory = rt.freeMemory() / 1000000;\r
- final long total_memory = rt.totalMemory() / 1000000;\r
- about.append( "[free memory: " + free_memory + "MB, total memory: " + total_memory + "MB]\n" );\r
- about.append( "[locale: " + Locale.getDefault() + "]\n" );\r
- about.append( "References:\n" );\r
- about.append( Constants.PHYLOXML_REFERENCE_SHORT + "\n" );\r
- about.append( "For more information & download:\n" );\r
- about.append( Constants.APTX_WEB_SITE + "\n" );\r
- about.append( "Documentation:\n" );\r
- about.append( Constants.APTX_DOC_SITE + "\n" );\r
- about.append( "Comments: " + Constants.AUTHOR_EMAIL );\r
- JOptionPane.showMessageDialog( null, about, Constants.PRG_NAME, JOptionPane.PLAIN_MESSAGE );\r
- }\r
-\r
- static void chooseNodeSize( final Options options, final Component parent ) {\r
- final String s = ( String ) JOptionPane.showInputDialog( parent,\r
- "Please enter the default size for node shapes.\n"\r
- + "[current value: "\r
- + options.getDefaultNodeShapeSize() + "]\n",\r
- "Node Shape Size",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null,\r
- null,\r
- options.getDefaultNodeShapeSize() );\r
- if ( !ForesterUtil.isEmpty( s ) ) {\r
- boolean success = true;\r
- double m = 0.0;\r
- final String m_str = s.trim();\r
- if ( !ForesterUtil.isEmpty( m_str ) ) {\r
- try {\r
- m = Double.parseDouble( m_str );\r
- }\r
- catch ( final Exception ex ) {\r
- success = false;\r
- }\r
- }\r
- else {\r
- success = false;\r
- }\r
- if ( success && ( m >= 0.0 ) ) {\r
- final short size = ForesterUtil.roundToShort( m );\r
- if ( size >= 0.0 ) {\r
- options.setDefaultNodeShapeSize( size );\r
- }\r
- }\r
- }\r
- }\r
-\r
- static String createCurrentFontDesc( final TreeFontSet tree_font_set ) {\r
- return tree_font_set.getLargeFont().getFamily() + " " + tree_font_set.getLargeFont().getSize();\r
- }\r
-\r
- static JMenu createMenu( final String title, final Configuration conf ) {\r
- final JMenu jmenu = new JMenu( title );\r
- if ( !conf.isUseNativeUI() ) {\r
- jmenu.setFont( MainFrame.menu_font );\r
- jmenu.setBackground( conf.getGuiMenuBackgroundColor() );\r
- jmenu.setForeground( conf.getGuiMenuTextColor() );\r
- }\r
- return jmenu;\r
- }\r
-\r
- static JMenuItem customizeMenuItemAsLabel( final JMenuItem label, final Configuration configuration ) {\r
- label.setFont( MainFrame.menu_font.deriveFont( Font.BOLD ) );\r
- if ( !configuration.isUseNativeUI() ) {\r
- label.setBackground( configuration.getGuiMenuBackgroundColor() );\r
- label.setForeground( configuration.getGuiMenuTextColor() );\r
- label.setOpaque( true );\r
- }\r
- label.setSelected( false );\r
- label.setEnabled( false );\r
- return label;\r
- }\r
-\r
- static void cycleNodeFill( final Options op, final TreePanel tree_panel ) {\r
- switch ( op.getDefaultNodeFill() ) {\r
- case GRADIENT:\r
- op.setDefaultNodeFill( NodeFill.SOLID );\r
- break;\r
- case NONE:\r
- op.setDefaultNodeFill( NodeFill.GRADIENT );\r
- break;\r
- case SOLID:\r
- op.setDefaultNodeFill( NodeFill.NONE );\r
- break;\r
- default:\r
- throw new RuntimeException( "unknown fill: " + op.getDefaultNodeFill() );\r
- }\r
- }\r
-\r
- static void cycleNodeShape( final Options op, final TreePanel tree_panel ) {\r
- switch ( op.getDefaultNodeShape() ) {\r
- case CIRCLE:\r
- op.setDefaultNodeShape( NodeShape.RECTANGLE );\r
- break;\r
- case RECTANGLE:\r
- op.setDefaultNodeShape( NodeShape.CIRCLE );\r
- break;\r
- default:\r
- throw new RuntimeException( "unknown shape: " + op.getDefaultNodeShape() );\r
- }\r
- }\r
-\r
- static void cycleNodeDataReturn( final Options op, final TreePanel tree_panel ) {\r
- switch ( op.getExtDescNodeDataToReturn() ) {\r
- case UNKNOWN:\r
- op.setExtDescNodeDataToReturn( NodeData.NODE_DATA.DOMAINS_ALL );\r
- break;\r
- case DOMAINS_ALL:\r
- op.setExtDescNodeDataToReturn( NodeData.NODE_DATA.DOMAINS_COLLAPSED_PER_PROTEIN );\r
- break;\r
- case DOMAINS_COLLAPSED_PER_PROTEIN:\r
- op.setExtDescNodeDataToReturn( NodeData.NODE_DATA.GO_TERM_IDS );\r
- break;\r
- case GO_TERM_IDS:\r
- op.setExtDescNodeDataToReturn( NodeData.NODE_DATA.SEQUENCE_MOL_SEQ );\r
- break;\r
- case SEQUENCE_MOL_SEQ:\r
- op.setExtDescNodeDataToReturn( NodeData.NODE_DATA.SEQUENCE_MOL_SEQ_FASTA );\r
- break;\r
- default:\r
- op.setExtDescNodeDataToReturn( NodeData.NODE_DATA.UNKNOWN );\r
- }\r
- }\r
-\r
- static void cycleOverview( final Options op, final TreePanel tree_panel ) {\r
- switch ( op.getOvPlacement() ) {\r
- case LOWER_LEFT:\r
- op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );\r
- break;\r
- case LOWER_RIGHT:\r
- op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );\r
- break;\r
- case UPPER_LEFT:\r
- op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );\r
- break;\r
- case UPPER_RIGHT:\r
- op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );\r
- break;\r
- default:\r
- throw new RuntimeException( "unknown placement: " + op.getOvPlacement() );\r
- }\r
- if ( tree_panel != null ) {\r
- tree_panel.updateOvSettings();\r
- }\r
- }\r
-\r
- static void setCycleNodeFillMenuItem( final JMenuItem mi, final Options options ) {\r
- if ( ( options != null ) && ( options.getDefaultNodeFill() != null ) ) {\r
- mi.setText( "Cycle Node Shape Fill Type... (current: "\r
- + options.getDefaultNodeFill().toString().toLowerCase() + ")" );\r
- }\r
- else {\r
- mi.setText( "Cycle Node Shape Fill Type..." );\r
- }\r
- }\r
-\r
- static void setCycleNodeShapeMenuItem( final JMenuItem mi, final Options options ) {\r
- if ( ( options != null ) && ( options.getDefaultNodeShape() != null ) ) {\r
- mi.setText( "Cycle Node Shape Fill Type... (current: "\r
- + options.getDefaultNodeShape().toString().toLowerCase() + ")" );\r
- }\r
- else {\r
- mi.setText( "Cycle Node Shape Fill Type..." );\r
- }\r
- }\r
-\r
- static void setCycleDataReturnMenuItem( final JMenuItem mi, final Options options ) {\r
- if ( ( options != null ) && ( options.getExtDescNodeDataToReturn() != null ) ) {\r
- mi.setText( "Cycle Node Return Data... (current: "\r
- + options.getExtDescNodeDataToReturn().toString().toLowerCase() + ")" );\r
- }\r
- else {\r
- mi.setText( "Cycle Node Return Data..." );\r
- }\r
- }\r
-\r
- static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) {\r
- if ( ( options != null ) && ( options.getOvPlacement() != null ) ) {\r
- mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" );\r
- }\r
- else {\r
- mi.setText( "Cycle Overview Placement..." );\r
- }\r
- }\r
-\r
- static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) {\r
- if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) {\r
- mi.setText( "Select Color Scheme... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName()\r
- + ")" );\r
- }\r
- else {\r
- mi.setText( "Select Color Scheme..." );\r
- }\r
- }\r
-\r
- static void setTextForFontChooserMenuItem( final JMenuItem mi, final String font_desc ) {\r
- mi.setText( "Select Default Font... (current: " + font_desc + ")" );\r
- }\r
-\r
- static void setTextMinSupportMenuItem( final JMenuItem mi, final Options options, final TreePanel current_tree_panel ) {\r
- if ( ( current_tree_panel == null ) || ( current_tree_panel.getPhylogeny() == null ) ) {\r
- mi.setEnabled( true );\r
- }\r
- else if ( AptxUtil.isHasAtLeastOneBranchWithSupportValues( current_tree_panel.getPhylogeny() ) ) {\r
- mi.setEnabled( true );\r
- }\r
- else {\r
- mi.setEnabled( false );\r
- }\r
- mi.setText( "Enter Min Confidence Value... (current: " + options.getMinConfidenceValue() + ")" );\r
- }\r
-\r
- static void setTextNodeSizeMenuItem( final JMenuItem mi, final Options options ) {\r
- mi.setText( "Enter Default Node Shape Size... (current: " + options.getDefaultNodeShapeSize() + ")" );\r
- }\r
-\r
- static void updateScreenTextAntialias( final List<TreePanel> treepanels ) {\r
- for( final TreePanel tree_panel : treepanels ) {\r
- tree_panel.setTextAntialias();\r
- }\r
- }\r
-}\r
+// $Id:
+// FORESTER -- software libraries and applications
+// for evolutionary biology research and applications.
+//
+// Copyright (C) 2008-2010 Christian M. Zmasek
+// All rights reserved
+//
+// This library is free software; you can redistribute it and/or
+// modify it under the terms of the GNU Lesser General Public
+// License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+//
+// This library is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+// Lesser General Public License for more details.
+//
+// You should have received a copy of the GNU Lesser General Public
+// License along with this library; if not, write to the Free Software
+// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+//
+// Contact: phylosoft @ gmail . com
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
+
+package org.forester.archaeopteryx;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Container;
+import java.awt.Font;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ComponentAdapter;
+import java.awt.event.ComponentListener;
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Locale;
+import java.util.Map;
+import java.util.NoSuchElementException;
+
+import javax.swing.Box;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JFileChooser;
+import javax.swing.JFrame;
+import javax.swing.JInternalFrame;
+import javax.swing.JLabel;
+import javax.swing.JMenu;
+import javax.swing.JMenuBar;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JRadioButtonMenuItem;
+import javax.swing.JTextField;
+import javax.swing.SwingUtilities;
+import javax.swing.filechooser.FileFilter;
+
+import org.forester.archaeopteryx.AptxUtil.GraphicsExportType;
+import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
+import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
+import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
+import org.forester.archaeopteryx.tools.AncestralTaxonomyInferrer;
+import org.forester.archaeopteryx.tools.InferenceManager;
+import org.forester.archaeopteryx.tools.ProcessPool;
+import org.forester.archaeopteryx.tools.ProcessRunning;
+import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
+import org.forester.io.writers.PhylogenyWriter;
+import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyMethods;
+import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
+import org.forester.phylogeny.PhylogenyNode;
+import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
+import org.forester.phylogeny.data.Annotation;
+import org.forester.phylogeny.data.NodeDataField;
+import org.forester.phylogeny.data.NodeVisualData.NodeFill;
+import org.forester.phylogeny.data.NodeVisualData.NodeShape;
+import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
+import org.forester.sdi.GSDI;
+import org.forester.sdi.GSDIR;
+import org.forester.sdi.SDIException;
+import org.forester.util.ForesterConstants;
+import org.forester.util.ForesterUtil;
+import org.forester.util.WindowsUtils;
+
+public abstract class MainFrame implements ActionListener {
+
+ public final static NHFilter nhfilter = new NHFilter();
+ public final static NHXFilter nhxfilter = new NHXFilter();
+ public final static XMLFilter xmlfilter = new XMLFilter();
+ public final static TolFilter tolfilter = new TolFilter();
+ public final static NexusFilter nexusfilter = new NexusFilter();
+ public final static PdfFilter pdffilter = new PdfFilter();
+ public final static GraphicsFileFilter graphicsfilefilter = new GraphicsFileFilter();
+ public final static MsaFileFilter msafilter = new MsaFileFilter();
+ public final static SequencesFileFilter seqsfilter = new SequencesFileFilter();
+ public final static DefaultFilter defaultfilter = new DefaultFilter();
+ static final String USE_MOUSEWHEEL_SHIFT_TO_ROTATE = "rotate with mousewheel + Shift (or A and S), D toggles between horizontal and radial labels";
+ static final String PHYLOXML_REF_TOOL_TIP = AptxConstants.PHYLOXML_REFERENCE; //TODO //FIXME
+ static final String APTX_REF_TOOL_TIP = AptxConstants.APTX_REFERENCE;
+ private static final long serialVersionUID = 3655000897845508358L;
+ final static Font menu_font = new Font( Configuration.getDefaultFontFamilyName(),
+ Font.PLAIN,
+ 10 );
+ static final String TYPE_MENU_HEADER = "Type";
+ static final String RECTANGULAR_TYPE_CBMI_LABEL = "Rectangular";
+ static final String EURO_TYPE_CBMI_LABEL = "Euro Type";
+ static final String CURVED_TYPE_CBMI_LABEL = "Curved";
+ static final String TRIANGULAR_TYPE_CBMI_LABEL = "Triangular";
+ static final String CONVEX_TYPE_CBMI_LABEL = "Convex";
+ static final String ROUNDED_TYPE_CBMI_LABEL = "Rounded";
+ static final String UNROOTED_TYPE_CBMI_LABEL = "Unrooted (alpha)"; //TODO
+ static final String CIRCULAR_TYPE_CBMI_LABEL = "Circular (alpha)"; //TODO
+ static final String OPTIONS_HEADER = "Options";
+ static final String SEARCH_SUBHEADER = "Search:";
+ static final String DISPLAY_SUBHEADER = "Display:";
+ static final String SEARCH_TERMS_ONLY_LABEL = "Words";
+ static final String SEARCH_REGEX_LABEL = "Regex";
+ static final String SEARCH_CASE_SENSITIVE_LABEL = "Match Case";
+ static final String INVERSE_SEARCH_RESULT_LABEL = "Inverse";
+ static final String COLOR_BY_TAXONOMIC_GROUP = "Colorize by Taxonomic Group";
+ static final String DISPLAY_SCALE_LABEL = "Scale";
+ static final String NON_LINED_UP_CLADOGRAMS_LABEL = "Non-Lined Up Cladogram";
+ static final String LABEL_DIRECTION_LABEL = "Radial Labels";
+ static final String LABEL_DIRECTION_TIP = "To use radial node labels in radial and unrooted display types";
+ static final String SEARCH_WITH_REGEX_TIP = "To search using regular expressions (~Java/Perl syntax). For example, use \"^B.+\\d{2,}$\" to search for everything starting with a B and ending with at least two digits.";
+ static final String SCREEN_ANTIALIAS_LABEL = "Antialias";
+ static final String COLOR_LABELS_LABEL = "Colorize Labels Same as Parent Branch";
+ static final String BG_GRAD_LABEL = "Background Color Gradient";
+ static final String DISPLAY_NODE_BOXES_LABEL_EXT = "Shapes for External Nodes";
+ static final String DISPLAY_NODE_BOXES_LABEL_INT = "Shapes for Internal Nodes";
+ static final String DISPLAY_NODE_BOXES_LABEL_MARKED = "Shapes for Nodes with Visual Data";
+ static final String SHOW_OVERVIEW_LABEL = "Overview";
+ static final String FONT_SIZE_MENU_LABEL = "Font Size";
+ static final String NONUNIFORM_CLADOGRAMS_LABEL = "Lined Up Cladogram";
+ static final String SHOW_DOMAIN_LABELS_LABEL = "Domain Labels";
+ static final String SHOW_ANN_REF_SOURCE_LABEL = "Seq Annotation Ref Sources";
+ static final String COLOR_LABELS_TIP = "To use parent branch colors for node labels as well, need to turn off taxonomy dependent colorization and turn on branch colorization for this to become apparent";
+ static final String ABBREV_SN_LABEL = "Abbreviate Scientific Taxonomic Names";
+ static final String TAXONOMY_COLORIZE_NODE_SHAPES_LABEL = "Colorize Node Shapes According to Taxonomy";
+ static final String CYCLE_NODE_SHAPE_LABEL = "Cycle Node Shapes";
+ static final String CYCLE_NODE_FILL_LABEL = "Cycle Node Fill Type";
+ static final String CHOOSE_NODE_SIZE_LABEL = "Choose Node Shape Size";
+ static final String SHOW_CONF_STDDEV_LABEL = "Confidence Standard Deviations";
+ static final String USE_BRACKETS_FOR_CONF_IN_NH_LABEL = "Use Brackets for Confidence Values";
+ static final String USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL = "Use Internal Node Names for Confidence Values";
+ static final String SHOW_BASIC_TREE_INFORMATION_LABEL = "Basic Tree Information";
+ static final String RIGHT_LINE_UP_DOMAINS = "Right-align Domain Architectures";
+ static final String LINE_UP_RENDERABLE_DATA = "Line Up Diagrams (such as Domain Architectures)";
+ static final String INFER_ANCESTOR_TAXONOMIES = "Infer Ancestor Taxonomies";
+ static final String OBTAIN_DETAILED_TAXONOMIC_INFORMATION = "Obtain Detailed Taxonomic Information";
+
+ final AptxFrame _frame;
+ JMenuBar _jmenubar;
+ JMenu _file_jmenu;
+ JMenu _tools_menu;
+ JMenu _view_jmenu;
+ JMenu _options_jmenu;
+ JMenu _font_size_menu;
+ JMenu _help_jmenu;
+ JMenuItem[] _load_phylogeny_from_webservice_menu_items;
+ // Analysis menu
+ JMenu _analysis_menu;
+ JMenuItem _load_species_tree_item;
+ JMenuItem _gsdi_item;
+ JMenuItem _gsdir_item;
+ JMenuItem _lineage_inference;
+ // file menu:
+ JMenuItem _open_item;
+ JMenuItem _open_url_item;
+ JMenuItem _save_item;
+ JMenuItem _save_all_item;
+ JMenuItem _close_item;
+ JMenuItem _exit_item;
+ JMenuItem _new_item;
+ JMenuItem _print_item;
+ JMenuItem _write_to_pdf_item;
+ JMenuItem _write_to_jpg_item;
+ JMenuItem _write_to_gif_item;
+ JMenuItem _write_to_tif_item;
+ JMenuItem _write_to_png_item;
+ JMenuItem _write_to_bmp_item;
+ // tools menu:
+ JMenuItem _midpoint_root_item;
+ JMenuItem _taxcolor_item;
+ JMenuItem _confcolor_item;
+ JMenuItem _color_rank_jmi;
+ JMenuItem _collapse_species_specific_subtrees;
+
+ JMenuItem _obtain_detailed_taxonomic_information_jmi;
+ JMenuItem _obtain_detailed_taxonomic_information_deleting_jmi;
+ JMenuItem _obtain_seq_information_jmi;
+ JMenuItem _move_node_names_to_tax_sn_jmi;
+ JMenuItem _move_node_names_to_seq_names_jmi;
+ JMenuItem _extract_tax_code_from_node_names_jmi;
+ JMenuItem _annotate_item;
+ JMenuItem _remove_branch_color_item;
+ JMenuItem _remove_visual_styles_item;
+ JMenuItem _delete_selected_nodes_item;
+ JMenuItem _delete_not_selected_nodes_item;
+ // font size menu:
+ JMenuItem _super_tiny_fonts_item;
+ JMenuItem _tiny_fonts_item;
+ JMenuItem _small_fonts_item;
+ JMenuItem _medium_fonts_item;
+ JMenuItem _large_fonts_item;
+ // options menu:
+ // _ screen and print
+ JMenuItem _choose_font_mi;
+ JMenuItem _switch_colors_mi;
+ JCheckBoxMenuItem _label_direction_cbmi;
+ // _ screen display
+ JCheckBoxMenuItem _screen_antialias_cbmi;
+ JCheckBoxMenuItem _background_gradient_cbmi;
+ JRadioButtonMenuItem _non_lined_up_cladograms_rbmi;
+ JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi;
+ JCheckBoxMenuItem _color_by_taxonomic_group_cbmi;
+ JCheckBoxMenuItem _show_scale_cbmi; //TODO fix me
+ JCheckBoxMenuItem _show_overview_cbmi;
+ JCheckBoxMenuItem _show_domain_labels;
+ JCheckBoxMenuItem _show_annotation_ref_source;
+ JCheckBoxMenuItem _abbreviate_scientific_names;
+ JCheckBoxMenuItem _color_labels_same_as_parent_branch;
+ JMenuItem _overview_placment_mi;
+ JMenuItem _choose_minimal_confidence_mi;
+ JCheckBoxMenuItem _show_default_node_shapes_internal_cbmi;
+ JCheckBoxMenuItem _show_default_node_shapes_external_cbmi;
+ JCheckBoxMenuItem _show_default_node_shapes_for_marked_cbmi;
+ JMenuItem _cycle_node_shape_mi;
+ JMenuItem _cycle_node_fill_mi;
+ JMenuItem _choose_node_size_mi;
+ JMenuItem _cycle_data_return;
+ JCheckBoxMenuItem _show_confidence_stddev_cbmi;
+ JCheckBoxMenuItem _right_line_up_domains_cbmi;
+ JCheckBoxMenuItem _line_up_renderable_data_cbmi;
+ JCheckBoxMenuItem _collapsed_with_average_height_cbmi;
+ JCheckBoxMenuItem _show_abbreviated_labels_for_collapsed_nodes_cbmi;
+ // _ print
+ JCheckBoxMenuItem _graphics_export_visible_only_cbmi;
+ JCheckBoxMenuItem _antialias_print_cbmi;
+ JCheckBoxMenuItem _print_black_and_white_cbmi;
+ //JMenuItem _print_size_mi;
+ JMenuItem _choose_pdf_width_mi;
+ // _ parsing
+ JCheckBoxMenuItem _internal_number_are_confidence_for_nh_parsing_cbmi;
+ JRadioButtonMenuItem _extract_taxonomy_no_rbmi;
+ JRadioButtonMenuItem _extract_taxonomy_agressive_rbmi;
+ JRadioButtonMenuItem _extract_taxonomy_pfam_strict_rbmi;
+ JRadioButtonMenuItem _extract_taxonomy_pfam_relaxed_rbmi;
+ JCheckBoxMenuItem _replace_underscores_cbmi;
+ JCheckBoxMenuItem _allow_errors_in_distance_to_parent_cbmi;
+ JCheckBoxMenuItem _use_brackets_for_conf_in_nh_export_cbmi;
+ JCheckBoxMenuItem _use_internal_names_for_conf_in_nh_export_cbmi;
+ JCheckBoxMenuItem _parse_beast_style_extended_nexus_tags_cbmi;
+ // _ search
+ JCheckBoxMenuItem _search_case_senstive_cbmi;
+ JCheckBoxMenuItem _search_whole_words_only_cbmi;
+ JCheckBoxMenuItem _inverse_search_result_cbmi;
+ JCheckBoxMenuItem _search_with_regex_cbmi;
+ JCheckBoxMenuItem _color_all_found_nodes_when_coloring_subtree_cbmi;
+ // type menu:
+ JMenu _type_menu;
+ JCheckBoxMenuItem _rectangular_type_cbmi;
+ JCheckBoxMenuItem _triangular_type_cbmi;
+ JCheckBoxMenuItem _curved_type_cbmi;
+ JCheckBoxMenuItem _convex_type_cbmi;
+ JCheckBoxMenuItem _euro_type_cbmi;
+ JCheckBoxMenuItem _rounded_type_cbmi;
+ JCheckBoxMenuItem _unrooted_type_cbmi;
+ JCheckBoxMenuItem _circular_type_cbmi;
+ // view as text menu:
+ JMenuItem _view_as_NH_item;
+ JMenuItem _view_as_XML_item;
+ JMenuItem _view_as_nexus_item;
+ JMenuItem _display_basic_information_item;
+ // help menu:
+ JMenuItem _about_item;
+ JMenuItem _help_item;
+ JMenuItem _website_item;
+ JMenuItem _aptxjs_website_item;
+ JMenuItem _mailing_list_item;
+ JMenuItem _phyloxml_website_item;
+ JMenuItem _phyloxml_ref_item;
+ JMenuItem _aptx_ref_item;
+ //
+ File _current_dir;
+ JFileChooser _writetopdf_filechooser;
+ JFileChooser _save_filechooser;
+ JFileChooser _writetographics_filechooser;
+ // process menu:
+ JMenu _process_menu;
+ MainPanel _mainpanel;
+ Container _contentpane;
+ final LinkedList<TextFrame> _textframes = new LinkedList<TextFrame>(); ;
+ Configuration _configuration;
+ Options _options;
+ private Phylogeny _species_tree;
+ InferenceManager _inference_manager;
+ final ProcessPool _process_pool;
+ private String _previous_node_annotation_ref;
+
+ MainFrame() {
+ this(false);
+ }
+ MainFrame(boolean embedded){
+ if (embedded) {
+ _frame = new EmbeddedFrame();
+ }
+ else {
+ _frame = new StandaloneFrame();
+ }
+ _process_pool = ProcessPool.createInstance();
+ _writetopdf_filechooser = new JFileChooser();
+ _writetopdf_filechooser.setMultiSelectionEnabled( false );
+ _writetopdf_filechooser.addChoosableFileFilter( pdffilter );
+ _writetographics_filechooser = new JFileChooser();
+ _writetographics_filechooser.setMultiSelectionEnabled( false );
+ _writetographics_filechooser.addChoosableFileFilter( graphicsfilefilter );
+ _save_filechooser = new JFileChooser();
+ _save_filechooser.setMultiSelectionEnabled( false );
+ _save_filechooser.setFileFilter( xmlfilter );
+ _save_filechooser.addChoosableFileFilter( nhfilter );
+ _save_filechooser.addChoosableFileFilter( nexusfilter );
+ _save_filechooser.addChoosableFileFilter( _save_filechooser.getAcceptAllFileFilter() );
+ try {
+ final String home_dir = System.getProperty( "user.home" );
+ _save_filechooser.setCurrentDirectory( new File( home_dir ) );
+ _writetopdf_filechooser.setCurrentDirectory( new File( home_dir ) );
+ _writetographics_filechooser.setCurrentDirectory( new File( home_dir ) );
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace();
+ // Do nothing. Not important.
+ }
+ }
+ public void addComponentListener( ComponentListener componentListener ) {
+ _frame.addComponentListener( componentListener );
+
+ }
+
+ public void dispose() {
+ _frame.dispose();
+ }
+ public Container getContentPane() {
+ return _frame.getContentPane();
+ }
+
+ public void repaint() {
+ _frame.repaint();
+ }
+
+
+ public void addFrameListener(FrameListener frameListener) {
+ _frame.addFrameListener(frameListener);
+ }
+
+ public void setSize(int x, int y) {
+ _frame.setSize(x,y);
+ }
+ public Container getJMenuBar() {
+ return _frame.getJMenuBar();
+ }
+ public void setDefaultCloseOperation( int doNothingOnClose ) {
+ _frame.setDefaultCloseOperation(doNothingOnClose);
+
+ }
+ public Container getParent() {
+ return _frame.getParent();
+ }
+ public void setVisible(boolean visible) {
+ _frame.setVisible(visible);
+ }
+ public void requestFocusInWindow() {
+ _frame.requestFocusInWindow();
+ }
+ public void setJMenuBar( JMenuBar jmenubar ) {
+ _frame.setJMenuBar(jmenubar);
+ }
+ public void setLocationRelativeTo( Component component ) {
+ _frame.setLocationRelativeTo(component);
+ }
+ public void setTitle(String title) {
+ _frame.setTitle(title);
+ }
+
+ public Container getThisFrame() {
+ return _frame.getThisFrame();
+ }
+
+ public void validate() {
+ _frame.validate();
+ }
+
+
+
+
+
+
+ /**
+ * Action performed.
+ */
+ @Override
+ public void actionPerformed( final ActionEvent e ) {
+ final Object o = e.getSource();
+
+ if ( o == _exit_item ) {
+ close();
+ }
+ else if ( o == _gsdi_item ) {
+ if ( isSubtreeDisplayed() ) {
+ return;
+ }
+ executeGSDI();
+ }
+ else if ( o == _gsdir_item ) {
+ if ( isSubtreeDisplayed() ) {
+ return;
+ }
+ executeGSDIR();
+ }
+ else if ( o == _taxcolor_item ) {
+ taxColor();
+ }
+ else if ( o == _confcolor_item ) {
+ confColor();
+ }
+ else if ( o == _color_rank_jmi ) {
+ colorRank();
+ }
+ else if ( o == _collapse_species_specific_subtrees ) {
+ if ( isSubtreeDisplayed() ) {
+ return;
+ }
+ if ( getCurrentTreePanel() != null ) {
+ getCurrentTreePanel().collapseSpeciesSpecificSubtrees();
+ }
+ }
+ else if ( o == _remove_branch_color_item ) {
+ if ( isSubtreeDisplayed() ) {
+ return;
+ }
+ removeBranchColors();
+ }
+ else if ( o == _remove_visual_styles_item ) {
+ if ( isSubtreeDisplayed() ) {
+ return;
+ }
+ removeVisualStyles();
+ }
+ else if ( o == _midpoint_root_item ) {
+ if ( isSubtreeDisplayed() ) {
+ return;
+ }
+ midpointRoot();
+ }
+ else if ( o == _delete_selected_nodes_item ) {
+ if ( isSubtreeDisplayed() ) {
+ return;
+ }
+ deleteSelectedNodes( true );
+ }
+ else if ( o == _delete_not_selected_nodes_item ) {
+ if ( isSubtreeDisplayed() ) {
+ return;
+ }
+ deleteSelectedNodes( false );
+ }
+ else if ( o == _annotate_item ) {
+ annotateSequences();
+ }
+ else if ( o == _switch_colors_mi ) {
+ switchColors();
+ }
+ else if ( o == _display_basic_information_item ) {
+ if ( getCurrentTreePanel() != null ) {
+ displayBasicInformation( getCurrentTreePanel().getTreeFile() );
+ }
+ }
+ else if ( o == _view_as_NH_item ) {
+ viewAsNH();
+ }
+ else if ( o == _view_as_XML_item ) {
+ viewAsXML();
+ }
+ else if ( o == _view_as_nexus_item ) {
+ viewAsNexus();
+ }
+ else if ( o == _super_tiny_fonts_item ) {
+ if ( getCurrentTreePanel() != null ) {
+ getCurrentTreePanel().setSuperTinyFonts();
+ getCurrentTreePanel().repaint();
+ }
+ }
+ else if ( o == _tiny_fonts_item ) {
+ if ( getCurrentTreePanel() != null ) {
+ getCurrentTreePanel().setTinyFonts();
+ getCurrentTreePanel().repaint();
+ }
+ }
+ else if ( o == _small_fonts_item ) {
+ if ( getCurrentTreePanel() != null ) {
+ getCurrentTreePanel().setSmallFonts();
+ getCurrentTreePanel().repaint();
+ }
+ }
+ else if ( o == _medium_fonts_item ) {
+ if ( getCurrentTreePanel() != null ) {
+ getCurrentTreePanel().setMediumFonts();
+ getCurrentTreePanel().repaint();
+ }
+ }
+ else if ( o == _large_fonts_item ) {
+ if ( getCurrentTreePanel() != null ) {
+ getCurrentTreePanel().setLargeFonts();
+ getCurrentTreePanel().repaint();
+ }
+ }
+ else if ( o == _choose_font_mi ) {
+ chooseFont();
+ }
+ else if ( o == _choose_minimal_confidence_mi ) {
+ chooseMinimalConfidence();
+ }
+ else if ( o == _choose_node_size_mi ) {
+ chooseNodeSize( getOptions(), _frame.getThisFrame() );
+ }
+ else if ( o == _overview_placment_mi ) {
+ MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );
+ }
+ else if ( o == _cycle_node_fill_mi ) {
+ MainFrame.cycleNodeFill( getOptions() );
+ }
+ else if ( o == _cycle_node_shape_mi ) {
+ MainFrame.cycleNodeShape( getOptions() );
+ }
+ else if ( o == _cycle_data_return ) {
+ MainFrame.cycleNodeDataReturn( getOptions(), getConfiguration() );
+ }
+ else if ( o == _screen_antialias_cbmi ) {
+ updateOptions( getOptions() );
+ updateScreenTextAntialias( getMainPanel().getTreePanels() );
+ }
+ else if ( o == _background_gradient_cbmi ) {
+ updateOptions( getOptions() );
+ }
+ else if ( o == _show_domain_labels ) {
+ updateOptions( getOptions() );
+ }
+ else if ( o == _show_annotation_ref_source ) {
+ updateOptions( getOptions() );
+ }
+ else if ( o == _abbreviate_scientific_names ) {
+ updateOptions( getOptions() );
+ }
+ else if ( o == _color_labels_same_as_parent_branch ) {
+ updateOptions( getOptions() );
+ }
+ else if ( o == _show_default_node_shapes_internal_cbmi ) {
+ updateOptions( getOptions() );
+ }
+ else if ( o == _show_default_node_shapes_external_cbmi ) {
+ updateOptions( getOptions() );
+ }
+ else if ( o == _show_default_node_shapes_for_marked_cbmi ) {
+ updateOptions( getOptions() );
+ }
+ else if ( o == _non_lined_up_cladograms_rbmi ) {
+ updateOptions( getOptions() );
+ showWhole();
+ }
+ else if ( o == _ext_node_dependent_cladogram_rbmi ) {
+ updateOptions( getOptions() );
+ showWhole();
+ }
+ else if ( o == _search_case_senstive_cbmi ) {
+ if ( ( _search_with_regex_cbmi != null ) && _search_case_senstive_cbmi.isSelected() ) {
+ _search_with_regex_cbmi.setSelected( false );
+ }
+ updateOptions( getOptions() );
+ getMainPanel().getControlPanel().search0();
+ getMainPanel().getControlPanel().search1();
+ }
+ else if ( o == _search_whole_words_only_cbmi ) {
+ if ( ( _search_with_regex_cbmi != null ) && _search_whole_words_only_cbmi.isSelected() ) {
+ _search_with_regex_cbmi.setSelected( false );
+ }
+ updateOptions( getOptions() );
+ getMainPanel().getControlPanel().search0();
+ getMainPanel().getControlPanel().search1();
+ }
+ else if ( o == _inverse_search_result_cbmi ) {
+ updateOptions( getOptions() );
+ getMainPanel().getControlPanel().search0();
+ getMainPanel().getControlPanel().search1();
+ }
+ else if ( o == _search_with_regex_cbmi ) {
+ if ( ( _search_whole_words_only_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) {
+ _search_whole_words_only_cbmi.setSelected( false );
+ }
+ if ( ( _search_case_senstive_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) {
+ _search_case_senstive_cbmi.setSelected( false );
+ }
+ updateOptions( getOptions() );
+ getMainPanel().getControlPanel().search0();
+ getMainPanel().getControlPanel().search1();
+ }
+ else if ( o == _color_all_found_nodes_when_coloring_subtree_cbmi ) {
+ updateOptions( getOptions() );
+ }
+ else if ( o == _parse_beast_style_extended_nexus_tags_cbmi ) {
+ updateOptions( getOptions() );
+ }
+ else if ( o == _show_scale_cbmi ) {
+ updateOptions( getOptions() );
+ }
+ else if ( o == _color_by_taxonomic_group_cbmi ) {
+ updateOptions( getOptions() );
+ }
+ else if ( o == _show_confidence_stddev_cbmi ) {
+ updateOptions( getOptions() );
+ }
+ else if ( o == _use_brackets_for_conf_in_nh_export_cbmi ) {
+ if ( _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {
+ _use_internal_names_for_conf_in_nh_export_cbmi.setSelected( false );
+ }
+ updateOptions( getOptions() );
+ }
+ else if ( o == _use_internal_names_for_conf_in_nh_export_cbmi ) {
+ if ( _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {
+ _use_brackets_for_conf_in_nh_export_cbmi.setSelected( false );
+ }
+ updateOptions( getOptions() );
+ }
+ else if ( o == _label_direction_cbmi ) {
+ updateOptions( getOptions() );
+ }
+ else if ( o == _show_overview_cbmi ) {
+ updateOptions( getOptions() );
+ if ( getCurrentTreePanel() != null ) {
+ getCurrentTreePanel().updateOvSizes();
+ }
+ }
+ else if ( o == _line_up_renderable_data_cbmi ) {
+ if ( !_line_up_renderable_data_cbmi.isSelected() ) {
+ _right_line_up_domains_cbmi.setSelected( false );
+ }
+ updateOptions( getOptions() );
+ }
+
+ else if ( o == _collapsed_with_average_height_cbmi ) {
+ if ( _collapsed_with_average_height_cbmi.isSelected() ) {
+ _collapsed_with_average_height_cbmi.setSelected( true );
+ }
+ updateOptions( getOptions() );
+ }
+ else if ( o == _show_abbreviated_labels_for_collapsed_nodes_cbmi ) {
+ if ( _show_abbreviated_labels_for_collapsed_nodes_cbmi.isSelected() ) {
+ _show_abbreviated_labels_for_collapsed_nodes_cbmi.setSelected( true );
+ }
+ updateOptions( getOptions() );
+ }
+ else if ( o == _right_line_up_domains_cbmi ) {
+ if ( _right_line_up_domains_cbmi.isSelected() ) {
+ _line_up_renderable_data_cbmi.setSelected( true );
+ }
+ updateOptions( getOptions() );
+ }
+ else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )
+ || ( o == _convex_type_cbmi ) || ( o == _euro_type_cbmi ) || ( o == _rounded_type_cbmi )
+ || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {
+ typeChanged( o );
+ }
+ else if ( o == _about_item ) {
+ about();
+ }
+ else if ( o == _help_item ) {
+ try {
+ AptxUtil.openWebsite( AptxConstants.APTX_DOC_SITE );
+ }
+ catch ( final IOException e1 ) {
+ ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() );
+ }
+ }
+ else if ( o == _website_item ) {
+ try {
+ AptxUtil.openWebsite( AptxConstants.APTX_WEB_SITE);
+ }
+ catch ( final IOException e1 ) {
+ ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() );
+ }
+ }
+ else if ( o == _aptxjs_website_item ) {
+ try {
+ AptxUtil.openWebsite( AptxConstants.APTX_JS_WEB_SITE);;
+ }
+ catch ( final IOException e1 ) {
+ ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() );
+ }
+ }
+ else if ( o == _mailing_list_item ) {
+ try {
+ AptxUtil.openWebsite( AptxConstants.APTX_MAILING_LIST );
+ }
+ catch ( final IOException e1 ) {
+ ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() );
+ }
+ }
+ else if ( o == _phyloxml_website_item ) {
+ try {
+ AptxUtil.openWebsite( AptxConstants.PHYLOXML_WEB_SITE );
+ }
+ catch ( final IOException e1 ) {
+ ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() );
+ }
+ }
+ else if ( o == _aptx_ref_item ) {
+ try {
+ AptxUtil.openWebsite( AptxConstants.APTX_REFERENCE_URL );
+ }
+ catch ( final IOException e1 ) {
+ ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() );
+ }
+ }
+ else if ( o == _phyloxml_ref_item ) {
+ try {
+ AptxUtil.openWebsite( AptxConstants.PHYLOXML_REFERENCE_URL );
+ }
+ catch ( final IOException e1 ) {
+ ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() );
+ }
+ }
+ else if ( o == _write_to_pdf_item ) {
+ final File curr_dir = writeToPdf( _mainpanel.getCurrentPhylogeny(),
+ getMainPanel(),
+ _writetopdf_filechooser,
+ _current_dir,
+ getContentPane(),
+ getThisFrame() );
+ if ( curr_dir != null ) {
+ setCurrentDir( curr_dir );
+ }
+ }
+ else if ( o == _save_all_item ) {
+ writeAllToFile();
+ }
+ else if ( o == _write_to_jpg_item ) {
+ final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(),
+ GraphicsExportType.JPG,
+ _mainpanel,
+ _writetographics_filechooser,
+ getThisFrame(),
+ getContentPane(),
+ _current_dir );
+ if ( new_dir != null ) {
+ setCurrentDir( new_dir );
+ }
+ }
+ else if ( o == _write_to_gif_item ) {
+ final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(),
+ GraphicsExportType.GIF,
+ _mainpanel,
+ _writetographics_filechooser,
+ getThisFrame(),
+ getContentPane(),
+ _current_dir );
+ if ( new_dir != null ) {
+ setCurrentDir( new_dir );
+ }
+ }
+ else if ( o == _write_to_tif_item ) {
+ final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(),
+ GraphicsExportType.TIFF,
+ _mainpanel,
+ _writetographics_filechooser,
+ getThisFrame(),
+ getContentPane(),
+ _current_dir );
+ if ( new_dir != null ) {
+ setCurrentDir( new_dir );
+ }
+ }
+ else if ( o == _write_to_bmp_item ) {
+ final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(),
+ GraphicsExportType.BMP,
+ _mainpanel,
+ _writetographics_filechooser,
+ getThisFrame(),
+ getContentPane(),
+ _current_dir );
+ if ( new_dir != null ) {
+ setCurrentDir( new_dir );
+ }
+ }
+ else if ( o == _write_to_png_item ) {
+ final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(),
+ GraphicsExportType.PNG,
+ _mainpanel,
+ _writetographics_filechooser,
+ getThisFrame(),
+ getContentPane(),
+ _current_dir );
+ if ( new_dir != null ) {
+ setCurrentDir( new_dir );
+ }
+ }
+ else if ( o == _print_item ) {
+ print( getCurrentTreePanel(), getOptions(), _frame.getThisFrame() );
+ }
+ else if ( o == _save_item ) {
+ final File new_dir = writeToFile( _mainpanel.getCurrentPhylogeny(),
+ getMainPanel(),
+ _save_filechooser,
+ _current_dir,
+ getContentPane(),
+ _frame.getThisFrame() );
+ if ( new_dir != null ) {
+ setCurrentDir( new_dir );
+ }
+ }
+ else if ( o == _graphics_export_visible_only_cbmi ) {
+ updateOptions( getOptions() );
+ }
+ else if ( o == _antialias_print_cbmi ) {
+ updateOptions( getOptions() );
+ }
+ else if ( o == _print_black_and_white_cbmi ) {
+ updateOptions( getOptions() );
+ }
+ else if ( o == _choose_pdf_width_mi ) {
+ choosePdfWidth();
+ }
+ else if ( o == _lineage_inference ) {
+ if ( isSubtreeDisplayed() ) {
+ JOptionPane.showMessageDialog( getThisFrame(),
+ "Subtree is shown.",
+ "Cannot infer ancestral taxonomies",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ executeLineageInference();
+ }
+ else {
+ if ( _load_phylogeny_from_webservice_menu_items != null ) {
+ for( int i = 0; i < _load_phylogeny_from_webservice_menu_items.length; ++i ) {
+ if ( o == _load_phylogeny_from_webservice_menu_items[ i ] ) {
+ readPhylogeniesFromWebservice( i );
+ }
+ }
+ }
+ }
+ _contentpane.repaint();
+ }
+
+
+ public Configuration getConfiguration() {
+ return _configuration;
+ }
+
+ /**
+ * This method returns the current external node data which
+ * has been selected by the user by clicking the "Return ..."
+ * menu item. This method is expected to be called from Javascript or
+ * something like it.
+ *
+ * @return current external node data as String
+ */
+ public String getCurrentExternalNodesDataBuffer() {
+ return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();
+ }
+
+ public int getCurrentExternalNodesDataBufferChangeCounter() {
+ return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();
+ }
+
+ public int getCurrentExternalNodesDataBufferLength() {
+ return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();
+ }
+
+ public InferenceManager getInferenceManager() {
+ return _inference_manager;
+ }
+
+ public MainPanel getMainPanel() {
+ return _mainpanel;
+ }
+
+ public Options getOptions() {
+ return _options;
+ }
+
+ public ProcessPool getProcessPool() {
+ return _process_pool;
+ }
+
+ public void showTextFrame( final String s, final String title ) {
+ checkTextFrames();
+ _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );
+ }
+
+ public void showWhole() {
+ _mainpanel.getControlPanel().showWhole();
+ }
+
+ public void updateProcessMenu() {
+ // In general Swing is not thread safe.
+ // See "Swing's Threading Policy".
+ SwingUtilities.invokeLater( new Runnable() {
+
+ @Override
+ public void run() {
+ doUpdateProcessMenu();
+ }
+ } );
+ }
+
+ private void annotateSequences() {
+ if ( getCurrentTreePanel() != null ) {
+ List<PhylogenyNode> nodes = null;
+ if ( ( getCurrentTreePanel().getFoundNodes0() != null )
+ || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {
+ nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();
+ }
+ if ( ( nodes == null ) || nodes.isEmpty() ) {
+ JOptionPane
+ .showMessageDialog( getThisFrame(),
+ "Need to select nodes, either via direct selection or via the \"Search\" function",
+ "No nodes selected for annotation",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ final Phylogeny phy = getMainPanel().getCurrentPhylogeny();
+ if ( ( phy != null ) && !phy.isEmpty() ) {
+ final JTextField ref_field = new JTextField( 10 );
+ final JTextField desc_filed = new JTextField( 20 );
+ ref_field.setText( ForesterUtil.isEmpty( getPreviousNodeAnnotationReference() ) ? ""
+ : getPreviousNodeAnnotationReference() );
+ final JPanel my_panel = new JPanel();
+ my_panel.add( new JLabel( "Reference " ) );
+ my_panel.add( ref_field );
+ my_panel.add( Box.createHorizontalStrut( 15 ) );
+ my_panel.add( new JLabel( "Description " ) );
+ my_panel.add( desc_filed );
+ final int result = JOptionPane.showConfirmDialog( null,
+ my_panel,
+ "Enter the sequence annotation(s) for the "
+ + nodes.size() + " selected nodes",
+ JOptionPane.OK_CANCEL_OPTION );
+ if ( result == JOptionPane.OK_OPTION ) {
+ String ref = ref_field.getText();
+ String desc = desc_filed.getText();
+ if ( !ForesterUtil.isEmpty( ref ) ) {
+ ref = ref.trim();
+ ref = ref.replaceAll( "\\s+", " " );
+ if ( ( ref.indexOf( ':' ) < 1 ) || ( ref.indexOf( ':' ) > ( ref.length() - 2 ) )
+ || ( ref.length() < 3 ) ) {
+ JOptionPane.showMessageDialog( getThisFrame(),
+ "Reference needs to be in the form of \"GO:1234567\"",
+ "Illegal Format for Annotation Reference",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ }
+ if ( ref != null ) {
+ setPreviousNodeAnnotationReference( ref );
+ }
+ if ( desc != null ) {
+ desc = desc.trim();
+ desc = desc.replaceAll( "\\s+", " " );
+ }
+ if ( !ForesterUtil.isEmpty( ref ) || !ForesterUtil.isEmpty( desc ) ) {
+ for( final PhylogenyNode n : nodes ) {
+ ForesterUtil.ensurePresenceOfSequence( n );
+ final Annotation ann = ForesterUtil.isEmpty( ref ) ? new Annotation()
+ : new Annotation( ref );
+ if ( !ForesterUtil.isEmpty( desc ) ) {
+ ann.setDesc( desc );
+ }
+ n.getNodeData().getSequence().addAnnotation( ann );
+ }
+ }
+ getMainPanel().getControlPanel().showAnnotations();
+ }
+ }
+ }
+ }
+
+ private void chooseFont() {
+ final FontChooser fc = new FontChooser();
+ fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
+ fc.showDialog( getThisFrame(), "Select the Base Font" );
+ getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );
+ getControlPanel().displayedPhylogenyMightHaveChanged( true );
+ if ( getMainPanel().getCurrentTreePanel() != null ) {
+ getMainPanel().getCurrentTreePanel().resetPreferredSize();
+ getMainPanel().getCurrentTreePanel().updateOvSizes();
+ }
+
+ repaint();
+ }
+
+ private void chooseMinimalConfidence() {
+ final String s = ( String ) JOptionPane
+ .showInputDialog( getThisFrame(),
+ "Please enter the minimum for confidence values to be displayed.\n"
+ + "[current value: " + getOptions().getMinConfidenceValue() + "]\n",
+ "Minimal Confidence Value",
+ JOptionPane.QUESTION_MESSAGE,
+ null,
+ null,
+ getOptions().getMinConfidenceValue() );
+ if ( !ForesterUtil.isEmpty( s ) ) {
+ boolean success = true;
+ double m = 0.0;
+ final String m_str = s.trim();
+ if ( !ForesterUtil.isEmpty( m_str ) ) {
+ try {
+ m = Double.parseDouble( m_str );
+ }
+ catch ( final Exception ex ) {
+ success = false;
+ }
+ }
+ else {
+ success = false;
+ }
+ if ( success && ( m >= 0.0 ) ) {
+ getOptions().setMinConfidenceValue( m );
+ }
+ }
+ }
+
+ private void deleteSelectedNodes( final boolean delete ) {
+ final Phylogeny phy = getMainPanel().getCurrentPhylogeny();
+ if ( ( phy == null ) || ( phy.getNumberOfExternalNodes() < 2 ) ) {
+ return;
+ }
+ final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
+ if ( ( getCurrentTreePanel().getFoundNodes0() != null ) || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {
+ final List<PhylogenyNode> all_selected_nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();
+ for( final PhylogenyNode n : all_selected_nodes ) {
+ if ( n.isExternal() ) {
+ nodes.add( n );
+ }
+ }
+ }
+ String function = "Retain";
+ if ( delete ) {
+ function = "Delete";
+ }
+ if ( ( nodes == null ) || nodes.isEmpty() ) {
+ JOptionPane
+ .showMessageDialog( getThisFrame(),
+ "Need to select external nodes, either via direct selection or via the \"Search\" function",
+ "No external nodes selected to " + function.toLowerCase(),
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ final int todo = nodes.size();
+ final int ext = phy.getNumberOfExternalNodes();
+ int res = todo;
+ if ( delete ) {
+ res = ext - todo;
+ }
+ if ( res < 1 ) {
+ JOptionPane.showMessageDialog( getThisFrame(),
+ "Cannot delete all nodes",
+ "Attempt to delete all nodes ",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ final int result = JOptionPane.showConfirmDialog( null, function + " " + todo
+ + " external node(s), from a total of " + ext + " external nodes," + "\nresulting in tree with " + res
+ + " nodes?", function + " external nodes", JOptionPane.OK_CANCEL_OPTION );
+ if ( result == JOptionPane.OK_OPTION ) {
+ if ( !delete ) {
+ final List<PhylogenyNode> to_delete = new ArrayList<PhylogenyNode>();
+ for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
+ final PhylogenyNode n = it.next();
+ if ( !nodes.contains( n ) ) {
+ to_delete.add( n );
+ }
+ }
+ for( final PhylogenyNode n : to_delete ) {
+ phy.deleteSubtree( n, true );
+ }
+ }
+ else {
+ for( final PhylogenyNode n : nodes ) {
+ phy.deleteSubtree( n, true );
+ }
+ }
+ resetSearch();
+ getCurrentTreePanel().setNodeInPreorderToNull();
+ phy.externalNodesHaveChanged();
+ phy.clearHashIdToNodeMap();
+ phy.recalculateNumberOfExternalDescendants( true );
+ getCurrentTreePanel().resetNodeIdToDistToLeafMap();
+ getCurrentTreePanel().setEdited( true );
+ repaint();
+ }
+ }
+
+ private void doUpdateProcessMenu() {
+ if ( _process_pool.size() > 0 ) {
+ if ( _process_menu == null ) {
+ _process_menu = createMenu( "", getConfiguration() );
+ _process_menu.setForeground( Color.RED );
+ }
+ _process_menu.removeAll();
+ final String text = "Processes Running: " + _process_pool.size();
+ _process_menu.setText( text );
+ _jmenubar.add( _process_menu );
+ for( int i = 0; i < _process_pool.size(); ++i ) {
+ final ProcessRunning p = _process_pool.getProcessByIndex( i );
+ _process_menu.add( customizeJMenuItem( new JMenuItem( p.getName() + " [" + p.getStart() + "]" ) ) );
+ }
+ }
+ else {
+ if ( _process_menu != null ) {
+ _process_menu.removeAll();
+ _jmenubar.remove( _process_menu );
+ }
+ }
+ _jmenubar.validate();
+ _jmenubar.repaint();
+ repaint();
+ }
+
+ private String getPreviousNodeAnnotationReference() {
+ return _previous_node_annotation_ref;
+ }
+
+ private void removeBranchColors() {
+ if ( getMainPanel().getCurrentPhylogeny() != null ) {
+ AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
+ }
+ }
+
+ private void removeVisualStyles() {
+ if ( getMainPanel().getCurrentPhylogeny() != null ) {
+ AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() );
+ }
+ }
+
+ private void setPreviousNodeAnnotationReference( final String previous_node_annotation_ref ) {
+ _previous_node_annotation_ref = previous_node_annotation_ref;
+ }
+
+ private void writeAllToFile() {
+ if ( ( getMainPanel().getTabbedPane() == null ) || ( getMainPanel().getTabbedPane().getTabCount() < 1 ) ) {
+ return;
+ }
+ final File my_dir = getCurrentDir();
+ if ( my_dir != null ) {
+ _save_filechooser.setCurrentDirectory( my_dir );
+ }
+ _save_filechooser.setSelectedFile( new File( "" ) );
+ final int result = _save_filechooser.showSaveDialog( _contentpane );
+ final File file = _save_filechooser.getSelectedFile();
+ setCurrentDir( _save_filechooser.getCurrentDirectory() );
+ if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
+ if ( file.exists() ) {
+ final int i = JOptionPane.showConfirmDialog( getThisFrame(),
+ file + " already exists. Overwrite?",
+ "Warning",
+ JOptionPane.OK_CANCEL_OPTION,
+ JOptionPane.WARNING_MESSAGE );
+ if ( i != JOptionPane.OK_OPTION ) {
+ return;
+ }
+ else {
+ try {
+ file.delete();
+ }
+ catch ( final Exception e ) {
+ JOptionPane.showMessageDialog( getThisFrame(),
+ "Failed to delete: " + file,
+ "Error",
+ JOptionPane.WARNING_MESSAGE );
+ }
+ }
+ }
+ final int count = getMainPanel().getTabbedPane().getTabCount();
+ final List<Phylogeny> trees = new ArrayList<Phylogeny>();
+ for( int i = 0; i < count; ++i ) {
+ final Phylogeny phy = getMainPanel().getPhylogeny( i );
+ if ( ForesterUtil.isEmpty( phy.getName() )
+ && !ForesterUtil.isEmpty( getMainPanel().getTabbedPane().getTitleAt( i ) ) ) {
+ phy.setName( getMainPanel().getTabbedPane().getTitleAt( i ) );
+ }
+ trees.add( phy );
+ getMainPanel().getTreePanels().get( i ).setEdited( false );
+ }
+ final PhylogenyWriter writer = new PhylogenyWriter();
+ try {
+ writer.toPhyloXML( file, trees, 0, ForesterUtil.LINE_SEPARATOR );
+ }
+ catch ( final IOException e ) {
+ JOptionPane.showMessageDialog( getThisFrame(),
+ "Failed to write to: " + file,
+ "Error",
+ JOptionPane.WARNING_MESSAGE );
+ }
+ }
+ }
+
+ public void activateSaveAllIfNeeded() {
+ if ( ( getMainPanel().getTabbedPane() != null ) && ( getMainPanel().getTabbedPane().getTabCount() > 1 ) ) {
+ _save_all_item.setEnabled( true );
+ }
+ else {
+ _save_all_item.setEnabled( false );
+ }
+ }
+
+ void buildFileMenu() {
+ _file_jmenu = MainFrame.createMenu( "File", getConfiguration() );
+ _file_jmenu.add( _save_item = new JMenuItem( "Save Tree As..." ) );
+ _file_jmenu.addSeparator();
+ _file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) );
+ if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" ) || AptxUtil.canWriteFormat( "TIF" ) ) {
+ _file_jmenu.add( _write_to_tif_item = new JMenuItem( "Export to TIFF file..." ) );
+ }
+ _file_jmenu.add( _write_to_png_item = new JMenuItem( "Export to PNG file..." ) );
+ _file_jmenu.add( _write_to_jpg_item = new JMenuItem( "Export to JPG file..." ) );
+ if ( AptxUtil.canWriteFormat( "gif" ) ) {
+ _file_jmenu.add( _write_to_gif_item = new JMenuItem( "Export to GIF file..." ) );
+ }
+ if ( AptxUtil.canWriteFormat( "bmp" ) ) {
+ _file_jmenu.add( _write_to_bmp_item = new JMenuItem( "Export to BMP file..." ) );
+ }
+ _file_jmenu.addSeparator();
+ _file_jmenu.add( _print_item = new JMenuItem( "Print..." ) );
+ _file_jmenu.addSeparator();
+ _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );
+ customizeJMenuItem( _save_item );
+ customizeJMenuItem( _write_to_pdf_item );
+ customizeJMenuItem( _write_to_png_item );
+ customizeJMenuItem( _write_to_jpg_item );
+ customizeJMenuItem( _write_to_gif_item );
+ customizeJMenuItem( _write_to_tif_item );
+ customizeJMenuItem( _write_to_bmp_item );
+ customizeJMenuItem( _print_item );
+ customizeJMenuItem( _exit_item );
+ _jmenubar.add( _file_jmenu );
+ }
+
+ void buildFontSizeMenu() {
+ _font_size_menu = createMenu( FONT_SIZE_MENU_LABEL, getConfiguration() );
+ _font_size_menu.add( _super_tiny_fonts_item = new JMenuItem( "Super Tiny Fonts" ) );
+ _font_size_menu.add( _tiny_fonts_item = new JMenuItem( "Tiny Fonts" ) );
+ _font_size_menu.add( _small_fonts_item = new JMenuItem( "Small Fonts" ) );
+ _font_size_menu.add( _medium_fonts_item = new JMenuItem( "Medium Fonts" ) );
+ _font_size_menu.add( _large_fonts_item = new JMenuItem( "Large Fonts" ) );
+ customizeJMenuItem( _super_tiny_fonts_item );
+ customizeJMenuItem( _tiny_fonts_item );
+ customizeJMenuItem( _small_fonts_item );
+ customizeJMenuItem( _medium_fonts_item );
+ customizeJMenuItem( _large_fonts_item );
+ _jmenubar.add( _font_size_menu );
+ }
+
+ void buildHelpMenu() {
+ _help_jmenu = createMenu( "Help", getConfiguration() );
+ _help_jmenu.add( _help_item = new JMenuItem( "Documentation" ) );
+ _help_jmenu.addSeparator();
+ _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );
+ _help_jmenu.add( _aptxjs_website_item = new JMenuItem( "NEW! Archaeopteryx online version: Archaeopteryx.js" ) );
+ _help_jmenu.add( _mailing_list_item = new JMenuItem( "Mailing List" ) );
+ _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" ); //TODO need to add this...
+ _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );
+ _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );
+ _help_jmenu.addSeparator();
+ _help_jmenu.add( _about_item = new JMenuItem( "About" ) );
+ customizeJMenuItem( _help_item );
+ customizeJMenuItem( _website_item );
+ customizeJMenuItem( _aptxjs_website_item );
+ customizeJMenuItem( _mailing_list_item );
+ customizeJMenuItem( _phyloxml_website_item );
+ customizeJMenuItem( _aptx_ref_item );
+ customizeJMenuItem( _phyloxml_ref_item );
+ customizeJMenuItem( _about_item );
+ _phyloxml_ref_item.setToolTipText( PHYLOXML_REF_TOOL_TIP );
+ _aptx_ref_item.setToolTipText( APTX_REF_TOOL_TIP );
+ _jmenubar.add( _help_jmenu );
+ }
+
+ void buildTypeMenu() {
+ _type_menu = createMenu( TYPE_MENU_HEADER, getConfiguration() );
+ _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );
+ _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );
+ _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );
+ _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );
+ _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );
+ _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );
+ _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );
+ _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );
+ customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );
+ customizeCheckBoxMenuItem( _triangular_type_cbmi, false );
+ customizeCheckBoxMenuItem( _euro_type_cbmi, false );
+ customizeCheckBoxMenuItem( _rounded_type_cbmi, false );
+ customizeCheckBoxMenuItem( _curved_type_cbmi, false );
+ customizeCheckBoxMenuItem( _convex_type_cbmi, false );
+ customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );
+ customizeCheckBoxMenuItem( _circular_type_cbmi, false );
+ _triangular_type_cbmi.setToolTipText( "not suitable for phylograms" );
+ _curved_type_cbmi.setToolTipText( "not suitable for phylograms" );
+ _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
+ _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
+ initializeTypeMenu( getOptions() );
+ _jmenubar.add( _type_menu );
+ }
+
+ void buildViewMenu() {
+ _view_jmenu = createMenu( "View", getConfiguration() );
+ _view_jmenu.add( _display_basic_information_item = new JMenuItem( SHOW_BASIC_TREE_INFORMATION_LABEL ) );
+ _view_jmenu.addSeparator();
+ _view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) );
+ _view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) );
+ _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "as Nexus" ) );
+ customizeJMenuItem( _display_basic_information_item );
+ customizeJMenuItem( _view_as_NH_item );
+ customizeJMenuItem( _view_as_XML_item );
+ customizeJMenuItem( _view_as_nexus_item );
+ _jmenubar.add( _view_jmenu );
+ }
+
+ void checkTextFrames() {
+ if ( _textframes.size() > 5 ) {
+ try {
+ if ( _textframes.getFirst() != null ) {
+ _textframes.getFirst().removeMe();
+ }
+ else {
+ _textframes.removeFirst();
+ }
+ }
+ catch ( final NoSuchElementException e ) {
+ // Ignore.
+ }
+ }
+ }
+
+ void choosePdfWidth() {
+ final String s = ( String ) JOptionPane.showInputDialog( getThisFrame(),
+ "Please enter the default line width for PDF export.\n"
+ + "[current value: "
+ + getOptions().getPrintLineWidth() + "]\n",
+ "Line Width for PDF Export",
+ JOptionPane.QUESTION_MESSAGE,
+ null,
+ null,
+ getOptions().getPrintLineWidth() );
+ if ( !ForesterUtil.isEmpty( s ) ) {
+ boolean success = true;
+ float f = 0.0f;
+ final String m_str = s.trim();
+ if ( !ForesterUtil.isEmpty( m_str ) ) {
+ try {
+ f = Float.parseFloat( m_str );
+ }
+ catch ( final Exception ex ) {
+ success = false;
+ }
+ }
+ else {
+ success = false;
+ }
+ if ( success && ( f > 0.0 ) ) {
+ getOptions().setPrintLineWidth( f );
+ }
+ }
+ }
+
+ void close() {
+ removeAllTextFrames();
+ if ( _mainpanel != null ) {
+ _mainpanel.terminate();
+ }
+ if ( _contentpane != null ) {
+ _contentpane.removeAll();
+ }
+ setVisible( false );
+ dispose();
+ }
+
+ void colorRank() {
+ if ( _mainpanel.getCurrentTreePanel() != null ) {
+ final Map<String, Integer> present_ranks = AptxUtil.getRankCounts( _mainpanel.getCurrentTreePanel().getPhylogeny());
+ final String[] ranks = AptxUtil.getAllPossibleRanks(present_ranks);
+ String rank = ( String ) JOptionPane
+ .showInputDialog( getThisFrame(),
+ "What rank should the colorization be based on",
+ "Rank Selection",
+ JOptionPane.QUESTION_MESSAGE,
+ null,
+ ranks,
+ null );
+ if ( !ForesterUtil.isEmpty( rank ) ) {
+ if ( rank.indexOf( '(' ) > 0 ) {
+ rank = rank.substring( 0, rank.indexOf( '(' ) ).trim();
+ }
+ _mainpanel.getCurrentTreePanel().colorRank( rank );
+ }
+ }
+ }
+
+ void confColor() {
+ if ( _mainpanel.getCurrentTreePanel() != null ) {
+ _mainpanel.getCurrentTreePanel().confColor();
+ }
+ }
+
+ void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {
+ if ( item != null ) {
+ item.setFont( MainFrame.menu_font );
+ if ( !getConfiguration().isUseNativeUI() ) {
+ item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
+ item.setForeground( getConfiguration().getGuiMenuTextColor() );
+ }
+ item.setSelected( is_selected );
+ item.addActionListener( this );
+ }
+ }
+
+ JMenuItem customizeJMenuItem( final JMenuItem jmi ) {
+ if ( jmi != null ) {
+ jmi.setFont( MainFrame.menu_font );
+ if ( !getConfiguration().isUseNativeUI() ) {
+ jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
+ jmi.setForeground( getConfiguration().getGuiMenuTextColor() );
+ }
+ jmi.addActionListener( this );
+ }
+ return jmi;
+ }
+
+ void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {
+ if ( item != null ) {
+ item.setFont( MainFrame.menu_font );
+ if ( !getConfiguration().isUseNativeUI() ) {
+ item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
+ item.setForeground( getConfiguration().getGuiMenuTextColor() );
+ }
+ item.setSelected( is_selected );
+ item.addActionListener( this );
+ }
+ }
+
+ void displayBasicInformation( final File treefile ) {
+ if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
+ String title = "Basic Information";
+ if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
+ title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\"";
+ }
+ showTextFrame( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny(), treefile ), title );
+ }
+ }
+
+ void exceptionOccuredDuringOpenFile( final Exception e ) {
+ try {
+ _mainpanel.getCurrentTreePanel().setArrowCursor();
+ }
+ catch ( final Exception ex ) {
+ // Do nothing.
+ }
+ JOptionPane.showMessageDialog( getThisFrame(),
+ ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
+ "Error during File|Open",
+ JOptionPane.ERROR_MESSAGE );
+ }
+
+ void executeGSDI() {
+ if ( !isOKforSDI( false, true ) ) {
+ return;
+ }
+ if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
+ JOptionPane.showMessageDialog( getThisFrame(),
+ "Gene tree is not rooted.",
+ "Cannot execute GSDI",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
+ gene_tree.setAllNodesToNotCollapse();
+ gene_tree.recalculateNumberOfExternalDescendants( false );
+ GSDI gsdi = null;
+ final Phylogeny species_tree = getSpeciesTree().copy();
+ try {
+ gsdi = new GSDI( gene_tree, species_tree, false, true, true, true );
+ }
+ catch ( final SDIException e ) {
+ JOptionPane.showMessageDialog( getThisFrame(),
+ e.getLocalizedMessage(),
+ "Error during GSDI",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ catch ( final Exception e ) {
+ AptxUtil.unexpectedException( e );
+ return;
+ }
+ gene_tree.setRerootable( false );
+ gene_tree.clearHashIdToNodeMap();
+ gene_tree.recalculateNumberOfExternalDescendants( true );
+ _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null );
+ getMainPanel().getControlPanel().setShowEvents( true );
+ showWhole();
+ final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
+ _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
+ showWhole();
+ _mainpanel.getTabbedPane().setSelectedIndex( selected );
+ showWhole();
+ _mainpanel.getCurrentTreePanel().setEdited( true );
+ final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
+ if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) {
+ JOptionPane.showMessageDialog( getThisFrame(),
+ "Duplications: " + gsdi.getDuplicationsSum() + "\n"
+ + "Potential duplications: "
+ + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
+ + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
+ + "Stripped gene tree nodes: "
+ + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
+ + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
+ + "Number of polytomies in species tree used: " + poly + "\n",
+ "GSDI successfully completed",
+ JOptionPane.WARNING_MESSAGE );
+ }
+ else {
+ JOptionPane.showMessageDialog( getThisFrame(),
+ "Duplications: " + gsdi.getDuplicationsSum() + "\n"
+ + "Potential duplications: "
+ + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
+ + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
+ + "Stripped gene tree nodes: "
+ + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
+ + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
+ + "Number of polytomies in species tree used: " + poly + "\n",
+ "GSDI successfully completed",
+ JOptionPane.INFORMATION_MESSAGE );
+ }
+ }
+
+ void executeGSDIR() {
+ if ( !isOKforSDI( false, false ) ) {
+ return;
+ }
+ final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() );
+ if ( ( p > 0 )
+ && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) {
+ JOptionPane.showMessageDialog( getThisFrame(),
+ "Gene tree is not completely binary",
+ "Cannot execute GSDI",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
+ gene_tree.setAllNodesToNotCollapse();
+ gene_tree.recalculateNumberOfExternalDescendants( false );
+ GSDIR gsdir = null;
+ final Phylogeny species_tree = getSpeciesTree().copy();
+ try {
+ gsdir = new GSDIR( gene_tree, species_tree, true, true, true );
+ }
+ catch ( final SDIException e ) {
+ JOptionPane.showMessageDialog( getThisFrame(),
+ e.getLocalizedMessage(),
+ "Error during GSDIR",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ catch ( final Exception e ) {
+ AptxUtil.unexpectedException( e );
+ return;
+ }
+ final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree();
+ result_gene_tree.setRerootable( false );
+ result_gene_tree.clearHashIdToNodeMap();
+ result_gene_tree.recalculateNumberOfExternalDescendants( true );
+ PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );
+ _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );
+ getMainPanel().getControlPanel().setShowEvents( true );
+ showWhole();
+ final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
+ _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
+ showWhole();
+ _mainpanel.getTabbedPane().setSelectedIndex( selected );
+ showWhole();
+ _mainpanel.getCurrentTreePanel().setEdited( true );
+ final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
+ if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) {
+ JOptionPane.showMessageDialog( getThisFrame(),
+ "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
+ + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
+ + "Stripped gene tree nodes: "
+ + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
+ + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
+ + "Number of polytomies in species tree used: " + poly + "\n",
+ "GSDIR successfully completed",
+ JOptionPane.WARNING_MESSAGE );
+ }
+ else {
+ JOptionPane.showMessageDialog( getThisFrame(),
+ "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
+ + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
+ + "Stripped gene tree nodes: "
+ + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
+ + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
+ + "Number of polytomies in species tree used: " + poly + "\n",
+ "GSDIR successfully completed",
+ JOptionPane.INFORMATION_MESSAGE );
+ }
+ }
+
+ void executeLineageInference() {
+ if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) {
+ return;
+ }
+ if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
+ JOptionPane.showMessageDialog( getThisFrame(),
+ "Phylogeny is not rooted.",
+ "Cannot infer ancestral taxonomies",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ final AncestralTaxonomyInferrer inferrer = new AncestralTaxonomyInferrer( this,
+ _mainpanel.getCurrentTreePanel(),
+ _mainpanel.getCurrentPhylogeny()
+ .copy() );
+ new Thread( inferrer ).start();
+ }
+
+ boolean GAndSDoHaveMoreThanOneSpeciesInComman( final Phylogeny gene_tree ) {
+ if ( ( gene_tree == null ) || gene_tree.isEmpty() ) {
+ JOptionPane.showMessageDialog( getThisFrame(),
+ "Gene tree and species tree have no species in common.",
+ "Error during SDI",
+ JOptionPane.ERROR_MESSAGE );
+ return false;
+ }
+ else if ( gene_tree.getNumberOfExternalNodes() < 2 ) {
+ JOptionPane.showMessageDialog( getThisFrame(),
+ "Gene tree and species tree have only one species in common.",
+ "Error during SDI",
+ JOptionPane.ERROR_MESSAGE );
+ return false;
+ }
+ else {
+ return true;
+ }
+ }
+
+ ControlPanel getControlPanel() {
+ return getMainPanel().getControlPanel();
+ }
+
+ File getCurrentDir() {
+ if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
+ if ( ForesterUtil.isWindows() ) {
+ try {
+ _current_dir = new File( WindowsUtils.getCurrentUserDesktopPath() );
+ }
+ catch ( final Exception e ) {
+ _current_dir = null;
+ }
+ }
+ }
+ if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
+ if ( System.getProperty( "user.home" ) != null ) {
+ _current_dir = new File( System.getProperty( "user.home" ) );
+ }
+ else if ( System.getProperty( "user.dir" ) != null ) {
+ _current_dir = new File( System.getProperty( "user.dir" ) );
+ }
+ }
+ return _current_dir;
+ }
+
+ TreePanel getCurrentTreePanel() {
+ return getMainPanel().getCurrentTreePanel();
+ }
+
+ JMenu getHelpMenu() {
+ return _help_jmenu;
+ }
+
+ JCheckBoxMenuItem getlabelDirectionCbmi() {
+ return _label_direction_cbmi;
+ }
+
+ JMenuBar getMenuBarOfMainFrame() {
+ return _jmenubar;
+ }
+
+ final Phylogeny getSpeciesTree() {
+ return _species_tree;
+ }
+
+ void initializeTypeMenu( final Options options ) {
+ setTypeMenuToAllUnselected();
+ switch ( options.getPhylogenyGraphicsType() ) {
+ case CONVEX:
+ _convex_type_cbmi.setSelected( true );
+ break;
+ case CURVED:
+ _curved_type_cbmi.setSelected( true );
+ break;
+ case EURO_STYLE:
+ _euro_type_cbmi.setSelected( true );
+ break;
+ case ROUNDED:
+ _rounded_type_cbmi.setSelected( true );
+ break;
+ case TRIANGULAR:
+ _triangular_type_cbmi.setSelected( true );
+ break;
+ case UNROOTED:
+ _unrooted_type_cbmi.setSelected( true );
+ break;
+ case CIRCULAR:
+ _circular_type_cbmi.setSelected( true );
+ break;
+ default:
+ _rectangular_type_cbmi.setSelected( true );
+ break;
+ }
+ }
+
+ boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {
+ if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {
+ return false;
+ }
+ else if ( ( getSpeciesTree() == null ) || getSpeciesTree().isEmpty() ) {
+ JOptionPane.showMessageDialog( getThisFrame(),
+ "No species tree loaded",
+ "Cannot execute GSDI",
+ JOptionPane.ERROR_MESSAGE );
+ return false;
+ }
+ else if ( species_tree_has_to_binary && !getSpeciesTree().isCompletelyBinary() ) {
+ JOptionPane.showMessageDialog( getThisFrame(),
+ "Species tree is not completely binary",
+ "Cannot execute GSDI",
+ JOptionPane.ERROR_MESSAGE );
+ return false;
+ }
+ else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {
+ JOptionPane.showMessageDialog( getThisFrame(),
+ "Gene tree is not completely binary",
+ "Cannot execute GSDI",
+ JOptionPane.ERROR_MESSAGE );
+ return false;
+ }
+ else {
+ return true;
+ }
+ }
+
+ boolean isSubtreeDisplayed() {
+ if ( getCurrentTreePanel() != null ) {
+ if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {
+ JOptionPane
+ .showMessageDialog( getThisFrame(),
+ "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",
+ "Operation can not be exectuted on a sub-tree",
+ JOptionPane.WARNING_MESSAGE );
+ return true;
+ }
+ }
+ return false;
+ }
+
+ void midpointRoot() {
+ if ( _mainpanel.getCurrentTreePanel() != null ) {
+ _mainpanel.getCurrentTreePanel().midpointRoot();
+ }
+ }
+
+ void readPhylogeniesFromWebservice( final int i ) {
+ final UrlTreeReader reader = new UrlTreeReader( this, i );
+ new Thread( reader ).start();
+ }
+
+ void removeAllTextFrames() {
+ for( final TextFrame tf : _textframes ) {
+ if ( tf != null ) {
+ tf.close();
+ }
+ }
+ _textframes.clear();
+ }
+
+ void resetSearch() {
+ getMainPanel().getCurrentTreePanel().setFoundNodes0( null );
+ getMainPanel().getCurrentTreePanel().setFoundNodes1( null );
+ getMainPanel().getControlPanel().setSearchFoundCountsOnLabel0( 0 );
+ getMainPanel().getControlPanel().getSearchFoundCountsLabel0().setVisible( false );
+ getMainPanel().getControlPanel().getSearchTextField0().setText( "" );
+ getMainPanel().getControlPanel().getSearchResetButton0().setEnabled( false );
+ getMainPanel().getControlPanel().getSearchResetButton0().setVisible( false );
+ getMainPanel().getControlPanel().setSearchFoundCountsOnLabel1( 0 );
+ getMainPanel().getControlPanel().getSearchFoundCountsLabel1().setVisible( false );
+ getMainPanel().getControlPanel().getSearchTextField1().setText( "" );
+ getMainPanel().getControlPanel().getSearchResetButton1().setEnabled( false );
+ getMainPanel().getControlPanel().getSearchResetButton1().setVisible( false );
+ }
+
+ void setConfiguration( final Configuration configuration ) {
+ _configuration = configuration;
+ }
+
+ void setCurrentDir( final File current_dir ) {
+ _current_dir = current_dir;
+ }
+
+ void setInferenceManager( final InferenceManager i ) {
+ _inference_manager = i;
+ }
+
+ void setOptions( final Options options ) {
+ _options = options;
+ }
+
+ void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {
+ setTypeMenuToAllUnselected();
+ switch ( type ) {
+ case CIRCULAR:
+ _circular_type_cbmi.setSelected( true );
+ break;
+ case CONVEX:
+ _convex_type_cbmi.setSelected( true );
+ break;
+ case CURVED:
+ _curved_type_cbmi.setSelected( true );
+ break;
+ case EURO_STYLE:
+ _euro_type_cbmi.setSelected( true );
+ break;
+ case ROUNDED:
+ _rounded_type_cbmi.setSelected( true );
+ break;
+ case RECTANGULAR:
+ _rectangular_type_cbmi.setSelected( true );
+ break;
+ case TRIANGULAR:
+ _triangular_type_cbmi.setSelected( true );
+ break;
+ case UNROOTED:
+ _unrooted_type_cbmi.setSelected( true );
+ break;
+ default:
+ throw new IllegalArgumentException( "unknown type: " + type );
+ }
+ }
+
+ final void setSpeciesTree( final Phylogeny species_tree ) {
+ _species_tree = species_tree;
+ }
+
+ void setTypeMenuToAllUnselected() {
+ _convex_type_cbmi.setSelected( false );
+ _curved_type_cbmi.setSelected( false );
+ _euro_type_cbmi.setSelected( false );
+ _rounded_type_cbmi.setSelected( false );
+ _triangular_type_cbmi.setSelected( false );
+ _rectangular_type_cbmi.setSelected( false );
+ _unrooted_type_cbmi.setSelected( false );
+ _circular_type_cbmi.setSelected( false );
+ }
+
+ void switchColors() {
+ final TreeColorSet colorset = _mainpanel.getTreeColorSet();
+ final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );
+ csc.setVisible( true );
+ }
+
+ void taxColor() {
+ if ( _mainpanel.getCurrentTreePanel() != null ) {
+ _mainpanel.getCurrentTreePanel().taxColor();
+ }
+ }
+
+ void typeChanged( final Object o ) {
+ updateTypeCheckboxes( getOptions(), o );
+ updateOptions( getOptions() );
+ if ( getCurrentTreePanel() != null ) {
+ final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();
+ final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();
+ if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
+ || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )
+ || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
+ || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {
+ getCurrentTreePanel().getControlPanel().showWhole();
+ }
+ if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
+ getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );
+ }
+ else {
+ getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );
+ }
+ getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );
+ updateScreenTextAntialias( getMainPanel().getTreePanels() );
+ if ( getCurrentTreePanel().getControlPanel().getDynamicallyHideData() != null ) {
+ if ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
+ getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( false );
+ }
+ else {
+ getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( true );
+ }
+ }
+ }
+ }
+
+ void updateOptions( final Options options ) {
+ options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );
+ options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
+ && _background_gradient_cbmi.isSelected() );
+ options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
+ options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null )
+ && _show_annotation_ref_source.isSelected() );
+ options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
+ && _abbreviate_scientific_names.isSelected() );
+ options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
+ && _color_labels_same_as_parent_branch.isSelected() );
+ options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )
+ && _show_default_node_shapes_internal_cbmi.isSelected() );
+ options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )
+ && _show_default_node_shapes_external_cbmi.isSelected() );
+ options.setShowDefaultNodeShapesForMarkedNodes( ( _show_default_node_shapes_for_marked_cbmi != null )
+ && _show_default_node_shapes_for_marked_cbmi.isSelected() );
+ if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
+ options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
+ }
+ else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {
+ options.setCladogramType( CLADOGRAM_TYPE.LINED_UP );
+ }
+ options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )
+ && _search_case_senstive_cbmi.isSelected() );
+ if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {
+ options.setShowScale( _show_scale_cbmi.isSelected() );
+ }
+ if ( _label_direction_cbmi != null ) {
+ if ( _label_direction_cbmi.isSelected() ) {
+ options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
+ }
+ else {
+ options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
+ }
+ }
+ options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
+ options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )
+ && _show_confidence_stddev_cbmi.isSelected() );
+ if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) {
+ options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() );
+ }
+ options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() );
+ if ( ( _use_brackets_for_conf_in_nh_export_cbmi != null )
+ && _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {
+ options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );
+ }
+ else if ( ( _use_internal_names_for_conf_in_nh_export_cbmi != null )
+ && _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {
+ options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );
+ }
+ else {
+ options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );
+ }
+ options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null )
+ && _print_black_and_white_cbmi.isSelected() );
+ options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null )
+ && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );
+ if ( ( _extract_taxonomy_pfam_strict_rbmi != null ) && _extract_taxonomy_pfam_strict_rbmi.isSelected() ) {
+ options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ }
+ else if ( ( _extract_taxonomy_pfam_relaxed_rbmi != null ) && _extract_taxonomy_pfam_relaxed_rbmi.isSelected() ) {
+ options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ }
+ else if ( ( _extract_taxonomy_agressive_rbmi != null ) && _extract_taxonomy_agressive_rbmi.isSelected() ) {
+ options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );
+ }
+ else if ( ( _extract_taxonomy_no_rbmi != null ) && _extract_taxonomy_no_rbmi.isSelected() ) {
+ options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );
+ }
+ options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )
+ && _replace_underscores_cbmi.isSelected() );
+ options.setAllowErrorsInDistanceToParent( ( _allow_errors_in_distance_to_parent_cbmi != null )
+ && _allow_errors_in_distance_to_parent_cbmi.isSelected() );
+ options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
+ && _search_whole_words_only_cbmi.isSelected() );
+ options.setSearchWithRegex( ( _search_with_regex_cbmi != null ) && _search_with_regex_cbmi.isSelected() );
+ options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
+ && _inverse_search_result_cbmi.isSelected() );
+ if ( _graphics_export_visible_only_cbmi != null ) {
+ options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_cbmi.isSelected() );
+ }
+ if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
+ }
+ else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
+ }
+ else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
+ }
+ else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
+ }
+ else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
+ }
+ else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
+ }
+ else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
+ }
+ else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
+ }
+ if ( ( _right_line_up_domains_cbmi != null ) && _right_line_up_domains_cbmi.isEnabled() ) {
+ options.setRightLineUpDomains( _right_line_up_domains_cbmi.isSelected() );
+ }
+ if ( ( _line_up_renderable_data_cbmi != null ) && _line_up_renderable_data_cbmi.isEnabled() ) {
+ options.setLineUpRendarableNodeData( _line_up_renderable_data_cbmi.isSelected() );
+ }
+ if ( ( _color_all_found_nodes_when_coloring_subtree_cbmi != null ) && _color_all_found_nodes_when_coloring_subtree_cbmi.isEnabled() ) {
+ options.setColorAllFoundNodesWhenColoringSubtree( _color_all_found_nodes_when_coloring_subtree_cbmi.isSelected() );
+ }
+ if ( ( _parse_beast_style_extended_nexus_tags_cbmi != null ) && _parse_beast_style_extended_nexus_tags_cbmi.isEnabled() ) {
+ options.setParseBeastStyleExtendedNexusTags(_parse_beast_style_extended_nexus_tags_cbmi.isSelected() );
+ }
+ if ( ( _collapsed_with_average_height_cbmi != null ) && _collapsed_with_average_height_cbmi.isEnabled() ) {
+ options.setCollapsedWithAverageHeigh(_collapsed_with_average_height_cbmi.isSelected() );
+ }
+ if ( ( _show_abbreviated_labels_for_collapsed_nodes_cbmi != null ) && _show_abbreviated_labels_for_collapsed_nodes_cbmi.isEnabled() ) {
+ options.setShowAbbreviatedLabelsForCollapsedNodes(_show_abbreviated_labels_for_collapsed_nodes_cbmi.isSelected() );
+ }
+
+ }
+
+ void updateTypeCheckboxes( final Options options, final Object o ) {
+ setTypeMenuToAllUnselected();
+ ( ( JCheckBoxMenuItem ) o ).setSelected( true );
+ }
+
+ void viewAsNexus() {
+ if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
+ String title = "Nexus";
+ if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
+ title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
+ }
+ showTextFrame( _mainpanel.getCurrentPhylogeny().toNexus( getOptions().getNhConversionSupportValueStyle() ),
+ title );
+ }
+ }
+
+ void viewAsNH() {
+ if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
+ String title = "New Hampshire";
+ if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
+ title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
+ }
+ showTextFrame( _mainpanel.getCurrentPhylogeny().toNewHampshire( getOptions()
+ .getNhConversionSupportValueStyle() ),
+ title );
+ }
+ }
+
+ void viewAsXML() {
+ if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
+ String title = "phyloXML";
+ if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
+ title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
+ }
+ showTextFrame( _mainpanel.getCurrentPhylogeny().toPhyloXML( 0 ), title );
+ }
+ }
+
+ private static void cycleNodeDataReturn( final Options op, final Configuration conf ) {
+ switch ( op.getExtDescNodeDataToReturn() ) {
+ case UNKNOWN:
+ op.setExtDescNodeDataToReturn( NodeDataField.DOMAINS_ALL );
+ break;
+ case DOMAINS_ALL:
+ op.setExtDescNodeDataToReturn( NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN );
+ break;
+ case DOMAINS_COLLAPSED_PER_PROTEIN:
+ op.setExtDescNodeDataToReturn( NodeDataField.SEQ_ANNOTATIONS );
+ break;
+ case SEQ_ANNOTATIONS:
+ op.setExtDescNodeDataToReturn( NodeDataField.GO_TERM_IDS );
+ break;
+ case GO_TERM_IDS:
+ op.setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_MOL_SEQ_FASTA );
+ break;
+ case SEQUENCE_MOL_SEQ_FASTA:
+ if ( ( conf != null ) && ( conf.getExtDescNodeDataToReturn() != null )
+ && ( conf.getExtDescNodeDataToReturn() != NodeDataField.DOMAINS_ALL )
+ && ( conf.getExtDescNodeDataToReturn() != NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN )
+ && ( conf.getExtDescNodeDataToReturn() != NodeDataField.SEQ_ANNOTATIONS )
+ && ( conf.getExtDescNodeDataToReturn() != NodeDataField.GO_TERM_IDS )
+ && ( conf.getExtDescNodeDataToReturn() != NodeDataField.SEQUENCE_MOL_SEQ_FASTA ) ) {
+ op.setExtDescNodeDataToReturn( conf.getExtDescNodeDataToReturn() );
+ }
+ else {
+ op.setExtDescNodeDataToReturn( NodeDataField.UNKNOWN );
+ }
+ break;
+ default:
+ op.setExtDescNodeDataToReturn( NodeDataField.UNKNOWN );
+ }
+ }
+
+ /**
+ * Display the about box.
+ */
+ void about() {
+ final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + AptxConstants.VERSION + "\n" );
+ about.append( "Copyright (C) 2016 Christian M Zmasek\n" );
+ about.append( "All Rights Reserved\n" );
+ about.append( "License: GNU Lesser General Public License (LGPL)\n" );
+ about.append( "Last modified: " + AptxConstants.PRG_DATE + "\n" );
+ about.append( "Based on: " + ForesterUtil.getForesterLibraryInformation() + "\n" );
+
+ if ( _configuration.isCouldReadConfigFile() ) {
+ about.append( "Using configuration file: " + _configuration.config_filename + "\n" );
+ }
+ else {
+ about.append( "Not using a configuration file\n" );
+ }
+
+ about.append( "phyloXML version : " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
+ about.append( "phyloXML location: " + ForesterConstants.PHYLO_XML_LOCATION + "\n" );
+ if ( !ForesterUtil.isEmpty( ForesterUtil.JAVA_VERSION ) && !ForesterUtil.isEmpty( ForesterUtil.JAVA_VENDOR ) ) {
+ about.append( "[your Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]\n" );
+ }
+ if ( !ForesterUtil.isEmpty( ForesterUtil.OS_NAME ) && !ForesterUtil.isEmpty( ForesterUtil.OS_ARCH )
+ && !ForesterUtil.isEmpty( ForesterUtil.OS_VERSION ) ) {
+ about.append( "[your OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " "
+ + ForesterUtil.OS_VERSION + "]\n" );
+ }
+ final Runtime rt = java.lang.Runtime.getRuntime();
+ final long free_memory = rt.freeMemory() / 1000000;
+ final long total_memory = rt.totalMemory() / 1000000;
+ about.append( "[free memory: " + free_memory + "MB, total memory: " + total_memory + "MB]\n" );
+ about.append( "[locale: " + Locale.getDefault() + "]\n" );
+ about.append( "References:\n" );
+ about.append( AptxConstants.PHYLOXML_REFERENCE_SHORT + "\n" );
+ about.append( "For more information & download:\n" );
+ about.append( AptxConstants.APTX_WEB_SITE + "\n" );
+ about.append( "Documentation:\n" );
+ about.append( AptxConstants.APTX_DOC_SITE + "\n" );
+ about.append( "Comments: " + AptxConstants.AUTHOR_EMAIL );
+ JOptionPane.showMessageDialog( null, about, AptxConstants.PRG_NAME, JOptionPane.PLAIN_MESSAGE );
+ }
+
+ static void chooseNodeSize( final Options options, final Component parent ) {
+ final String s = ( String ) JOptionPane.showInputDialog( parent,
+ "Please enter the default size for node shapes.\n"
+ + "[current value: "
+ + options.getDefaultNodeShapeSize() + "]\n",
+ "Node Shape Size",
+ JOptionPane.QUESTION_MESSAGE,
+ null,
+ null,
+ options.getDefaultNodeShapeSize() );
+ if ( !ForesterUtil.isEmpty( s ) ) {
+ boolean success = true;
+ double m = 0.0;
+ final String m_str = s.trim();
+ if ( !ForesterUtil.isEmpty( m_str ) ) {
+ try {
+ m = Double.parseDouble( m_str );
+ }
+ catch ( final Exception ex ) {
+ success = false;
+ }
+ }
+ else {
+ success = false;
+ }
+ if ( success && ( m >= 0.0 ) ) {
+ final short size = ForesterUtil.roundToShort( m );
+ if ( size >= 0.0 ) {
+ options.setDefaultNodeShapeSize( size );
+ }
+ }
+ }
+ }
+
+ static String createCurrentFontDesc( final TreeFontSet tree_font_set ) {
+ return tree_font_set.getLargeFont().getFamily() + " " + tree_font_set.getLargeFont().getSize();
+ }
+
+ static JMenu createMenu( final String title, final Configuration conf ) {
+ final JMenu jmenu = new JMenu( title );
+ if ( !conf.isUseNativeUI() ) {
+ jmenu.setFont( MainFrame.menu_font );
+ jmenu.setBackground( conf.getGuiMenuBackgroundColor() );
+ jmenu.setForeground( conf.getGuiMenuTextColor() );
+ }
+ return jmenu;
+ }
+
+ static JMenuItem customizeMenuItemAsLabel( final JMenuItem label, final Configuration configuration ) {
+ label.setFont( MainFrame.menu_font.deriveFont( Font.BOLD ) );
+ if ( !configuration.isUseNativeUI() ) {
+ label.setBackground( configuration.getGuiMenuBackgroundColor() );
+ label.setForeground( configuration.getGuiMenuTextColor() );
+ label.setOpaque( true );
+ }
+ label.setSelected( false );
+ label.setEnabled( false );
+ return label;
+ }
+
+ static void cycleNodeFill( final Options op ) {
+ switch ( op.getDefaultNodeFill() ) {
+ case GRADIENT:
+ op.setDefaultNodeFill( NodeFill.SOLID );
+ break;
+ case NONE:
+ op.setDefaultNodeFill( NodeFill.GRADIENT );
+ break;
+ case SOLID:
+ op.setDefaultNodeFill( NodeFill.NONE );
+ break;
+ default:
+ throw new RuntimeException( "unknown fill: " + op.getDefaultNodeFill() );
+ }
+ }
+
+ static void cycleNodeShape( final Options op ) {
+ switch ( op.getDefaultNodeShape() ) {
+ case CIRCLE:
+ op.setDefaultNodeShape( NodeShape.RECTANGLE );
+ break;
+ case RECTANGLE:
+ op.setDefaultNodeShape( NodeShape.CIRCLE );
+ break;
+ default:
+ throw new RuntimeException( "unknown shape: " + op.getDefaultNodeShape() );
+ }
+ }
+
+ static void cycleOverview( final Options op, final TreePanel tree_panel ) {
+ switch ( op.getOvPlacement() ) {
+ case LOWER_LEFT:
+ op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
+ break;
+ case LOWER_RIGHT:
+ op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );
+ break;
+ case UPPER_LEFT:
+ op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );
+ break;
+ case UPPER_RIGHT:
+ op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );
+ break;
+ default:
+ throw new RuntimeException( "unknown placement: " + op.getOvPlacement() );
+ }
+ if ( tree_panel != null ) {
+ tree_panel.updateOvSettings();
+ }
+ }
+
+ static void exceptionOccuredDuringSaveAs( final Exception e, final TreePanel tp, final Component comp ) {
+ try {
+ tp.setArrowCursor();
+ }
+ catch ( final Exception ex ) {
+ // Do nothing.
+ }
+ JOptionPane.showMessageDialog( comp, "Exception" + e, "Error during File|SaveAs", JOptionPane.ERROR_MESSAGE );
+ }
+
+ static void print( final TreePanel tp, final Options op, final Component c ) {
+ if ( ( tp == null ) || ( tp.getPhylogeny() == null ) || tp.getPhylogeny().isEmpty() ) {
+ return;
+ }
+ final String job_name = AptxConstants.PRG_NAME;
+ boolean error = false;
+ String printer_name = null;
+ try {
+ printer_name = Printer.print( tp, job_name );
+ }
+ catch ( final Exception e ) {
+ error = true;
+ JOptionPane.showMessageDialog( c, e.getMessage(), "Printing Error", JOptionPane.ERROR_MESSAGE );
+ }
+ if ( !error && ( printer_name != null ) ) {
+ String msg = "Printing data sent to printer";
+ if ( printer_name.length() > 1 ) {
+ msg += " [" + printer_name + "]";
+ }
+ JOptionPane.showMessageDialog( c, msg, "Printing...", JOptionPane.INFORMATION_MESSAGE );
+ }
+ if ( !op.isPrintUsingActualSize() ) {
+ tp.getControlPanel().showWhole();
+ }
+ }
+
+ static void printPhylogenyToPdf( final String file_name,
+ final Options opts,
+ final TreePanel tp,
+ final Component comp ) {
+
+ String pdf_written_to = "";
+ boolean error = false;
+ try {
+ if ( opts.isPrintUsingActualSize() ) {
+ pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name, tp, tp.getWidth() , tp.getHeight() );
+ }
+ else {
+ // Never false.
+ }
+ }
+ catch ( final IOException e ) {
+ error = true;
+ JOptionPane.showMessageDialog( comp, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );
+ }
+ if ( !error ) {
+ if ( !ForesterUtil.isEmpty( pdf_written_to ) ) {
+ JOptionPane.showMessageDialog( comp,
+ "Wrote PDF to: " + pdf_written_to,
+ "Information",
+ JOptionPane.INFORMATION_MESSAGE );
+ }
+ else {
+ JOptionPane.showMessageDialog( comp,
+ "There was an unknown problem when attempting to write to PDF file: \""
+ + file_name + "\"",
+ "Error",
+ JOptionPane.ERROR_MESSAGE );
+ }
+ }
+ if ( !opts.isPrintUsingActualSize() ) {
+ tp.getControlPanel().showWhole();
+ }
+ }
+
+ static void setCycleDataReturnMenuItem( final JMenuItem mi, final Options options ) {
+ if ( ( options != null ) && ( options.getExtDescNodeDataToReturn() != null ) ) {
+ mi.setText( "Cycle Node Return Data... (current: " + options.getExtDescNodeDataToReturn().toString() + ")" );
+ }
+ else {
+ mi.setText( "Cycle Node Return Data..." );
+ }
+ }
+
+ static void setCycleNodeFillMenuItem( final JMenuItem mi, final Options options ) {
+ if ( ( options != null ) && ( options.getDefaultNodeFill() != null ) ) {
+ mi.setText( "Cycle Node Shape Fill Type... (current: "
+ + options.getDefaultNodeFill().toString().toLowerCase() + ")" );
+ }
+ else {
+ mi.setText( "Cycle Node Shape Fill Type..." );
+ }
+ }
+
+ static void setCycleNodeShapeMenuItem( final JMenuItem mi, final Options options ) {
+ if ( ( options != null ) && ( options.getDefaultNodeShape() != null ) ) {
+ mi.setText( "Cycle Node Shape Fill Type... (current: "
+ + options.getDefaultNodeShape().toString().toLowerCase() + ")" );
+ }
+ else {
+ mi.setText( "Cycle Node Shape Fill Type..." );
+ }
+ }
+
+ static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) {
+ if ( ( options != null ) && ( options.getOvPlacement() != null ) ) {
+ mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" );
+ }
+ else {
+ mi.setText( "Cycle Overview Placement..." );
+ }
+ }
+
+ static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) {
+ if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) {
+ mi.setText( "Select Color Scheme... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName()
+ + ")" );
+ }
+ else {
+ mi.setText( "Select Color Scheme..." );
+ }
+ }
+
+ static void setTextForFontChooserMenuItem( final JMenuItem mi, final String font_desc ) {
+ mi.setText( "Select Default Font... (current: " + font_desc + ")" );
+ }
+
+ static void setTextForPdfLineWidthChooserMenuItem( final JMenuItem mi, final Options o ) {
+ mi.setText( "Enter Default Line Width for PDF Export... (current: " + o.getPrintLineWidth() + ")" );
+ }
+
+ static void setTextMinSupportMenuItem( final JMenuItem mi, final Options options, final TreePanel current_tree_panel ) {
+ if ( ( current_tree_panel == null ) || ( current_tree_panel.getPhylogeny() == null ) ) {
+ mi.setEnabled( true );
+ }
+ else if ( AptxUtil.isHasAtLeastOneBranchWithSupportValues( current_tree_panel.getPhylogeny() ) ) {
+ mi.setEnabled( true );
+ }
+ else {
+ mi.setEnabled( false );
+ }
+ mi.setText( "Enter Min Confidence Value... (current: " + options.getMinConfidenceValue() + ")" );
+ }
+
+ static void setTextNodeSizeMenuItem( final JMenuItem mi, final Options options ) {
+ mi.setText( "Enter Default Node Shape Size... (current: " + options.getDefaultNodeShapeSize() + ")" );
+ }
+
+ static void updateScreenTextAntialias( final List<TreePanel> 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
git://source.jalview.org / jalview.git / blobdiff