final static boolean __ALLOW_PHYLOGENETIC_INFERENCE = true;
public final static String PRG_NAME = "Archaeopteryx";
- final static String VERSION = "0.9913 beta";
- final static String PRG_DATE = "160701";
+ final static String VERSION = "0.9914 beta";
+ final static String PRG_DATE = "160712";
final static String DEFAULT_CONFIGURATION_FILE_NAME = "_aptx_configuration_file";
final static String[] DEFAULT_FONT_CHOICES = {
"Arial Unicode MS", "Dialog", "SansSerif", "Sans", "Arial", "Helvetica" };
import org.forester.phylogeny.PhylogenyMethods;
import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
import org.forester.phylogeny.PhylogenyNode;
+import org.forester.phylogeny.data.BranchWidth;
import org.forester.phylogeny.data.Confidence;
import org.forester.phylogeny.data.Taxonomy;
import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
atv_control.setDrawPhylogram( false );
atv_control.setDrawPhylogramEnabled( false );
}
+
+ if ( t.getFirstExternalNode().getBranchData().getBranchColor() != null
+ && atv_control.getUseVisualStylesCb() != null ) {
+ atv_control.getUseVisualStylesCb().setSelected( true );
+ }
+ if ( t.getFirstExternalNode().getBranchData().getBranchWidth() != null
+ && t.getFirstExternalNode().getBranchData().getBranchWidth().getValue()
+ != BranchWidth.BRANCH_WIDTH_DEFAULT_VALUE
+ && atv_control.getUseBranchWidthsCb() != null ) {
+ atv_control.getUseBranchWidthsCb().setSelected( true );
+ }
+
+
if ( configuration.doGuessCheckOption( Configuration.display_as_phylogram ) ) {
if ( atv_control.getDisplayAsPhylogramCb() != null ) {
if ( has_bl ) {
}
return label;
}
+
+ public JCheckBox getUseBranchWidthsCb() {
+ return _width_branches;
+ }
}
-// $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.JFileChooser;\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
-import javax.swing.filechooser.FileFilter;\r
-\r
-import org.forester.archaeopteryx.AptxUtil.GraphicsExportType;\r
-import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;\r
-import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;\r
-import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;\r
-import org.forester.archaeopteryx.tools.AncestralTaxonomyInferrer;\r
-import org.forester.archaeopteryx.tools.InferenceManager;\r
-import org.forester.archaeopteryx.tools.ProcessPool;\r
-import org.forester.archaeopteryx.tools.ProcessRunning;\r
-import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;\r
-import org.forester.io.writers.PhylogenyWriter;\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.NodeDataField;\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
-import org.forester.util.WindowsUtils;\r
-\r
-public abstract class MainFrame extends JFrame implements ActionListener {\r
-\r
- final static NHFilter nhfilter = new NHFilter();\r
- final static NHXFilter nhxfilter = new NHXFilter();\r
- final static XMLFilter xmlfilter = new XMLFilter();\r
- final static TolFilter tolfilter = new TolFilter();\r
- final static NexusFilter nexusfilter = new NexusFilter();\r
- final static PdfFilter pdffilter = new PdfFilter();\r
- final static GraphicsFileFilter graphicsfilefilter = new GraphicsFileFilter();\r
- final static MsaFileFilter msafilter = new MsaFileFilter();\r
- final static SequencesFileFilter seqsfilter = new SequencesFileFilter();\r
- final static DefaultFilter defaultfilter = new DefaultFilter();\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 = AptxConstants.PHYLOXML_REFERENCE; //TODO //FIXME\r
- static final String APTX_REF_TOOL_TIP = AptxConstants.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
- static final String INFER_ANCESTOR_TAXONOMIES = "Infer Ancestor Taxonomies";\r
- static final String OBTAIN_DETAILED_TAXONOMIC_INFORMATION = "Obtain Detailed Taxonomic Information";\r
- JMenuBar _jmenubar;\r
- JMenu _file_jmenu;\r
- JMenu _tools_menu;\r
- JMenu _view_jmenu;\r
- JMenu _options_jmenu;\r
- JMenu _font_size_menu;\r
- JMenu _help_jmenu;\r
- JMenuItem[] _load_phylogeny_from_webservice_menu_items;\r
- // Analysis menu\r
- JMenu _analysis_menu;\r
- JMenuItem _load_species_tree_item;\r
- JMenuItem _gsdi_item;\r
- JMenuItem _gsdir_item;\r
- JMenuItem _lineage_inference;\r
- // file menu:\r
- JMenuItem _open_item;\r
- JMenuItem _open_url_item;\r
- JMenuItem _save_item;\r
- JMenuItem _save_all_item;\r
- JMenuItem _close_item;\r
- JMenuItem _exit_item;\r
- JMenuItem _new_item;\r
- JMenuItem _print_item;\r
- JMenuItem _write_to_pdf_item;\r
- JMenuItem _write_to_jpg_item;\r
- JMenuItem _write_to_gif_item;\r
- JMenuItem _write_to_tif_item;\r
- JMenuItem _write_to_png_item;\r
- JMenuItem _write_to_bmp_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
- //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
- JCheckBoxMenuItem _color_all_found_nodes_when_coloring_subtree_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
- //\r
- File _current_dir;\r
- JFileChooser _writetopdf_filechooser;\r
- JFileChooser _save_filechooser;\r
- JFileChooser _writetographics_filechooser;\r
- // process menu:\r
- JMenu _process_menu;\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
- _writetopdf_filechooser = new JFileChooser();\r
- _writetopdf_filechooser.setMultiSelectionEnabled( false );\r
- _writetopdf_filechooser.addChoosableFileFilter( pdffilter );\r
- _writetographics_filechooser = new JFileChooser();\r
- _writetographics_filechooser.setMultiSelectionEnabled( false );\r
- _writetographics_filechooser.addChoosableFileFilter( graphicsfilefilter );\r
- _save_filechooser = new JFileChooser();\r
- _save_filechooser.setMultiSelectionEnabled( false );\r
- _save_filechooser.setFileFilter( xmlfilter );\r
- _save_filechooser.addChoosableFileFilter( nhfilter );\r
- _save_filechooser.addChoosableFileFilter( nexusfilter );\r
- _save_filechooser.addChoosableFileFilter( _save_filechooser.getAcceptAllFileFilter() );\r
- try {\r
- final String home_dir = System.getProperty( "user.home" );\r
- _save_filechooser.setCurrentDirectory( new File( home_dir ) );\r
- _writetopdf_filechooser.setCurrentDirectory( new File( home_dir ) );\r
- _writetographics_filechooser.setCurrentDirectory( new File( home_dir ) );\r
- }\r
- catch ( final Exception e ) {\r
- e.printStackTrace();\r
- // Do nothing. Not important.\r
- }\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() );\r
- }\r
- else if ( o == _cycle_node_shape_mi ) {\r
- MainFrame.cycleNodeShape( getOptions() );\r
- }\r
- else if ( o == _cycle_data_return ) {\r
- MainFrame.cycleNodeDataReturn( getOptions(), getConfiguration() );\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 == _color_all_found_nodes_when_coloring_subtree_cbmi ) {\r
- updateOptions( getOptions() );\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( AptxConstants.APTX_DOC_SITE, is_applet, applet );\r
- }\r
- catch ( final IOException e1 ) {\r
- ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() );\r
- }\r
- }\r
- else if ( o == _website_item ) {\r
- try {\r
- AptxUtil.openWebsite( AptxConstants.APTX_WEB_SITE, is_applet, applet );\r
- }\r
- catch ( final IOException e1 ) {\r
- ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() );\r
- }\r
- }\r
- else if ( o == _phyloxml_website_item ) {\r
- try {\r
- AptxUtil.openWebsite( AptxConstants.PHYLOXML_WEB_SITE, is_applet, applet );\r
- }\r
- catch ( final IOException e1 ) {\r
- ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() );\r
- }\r
- }\r
- else if ( o == _aptx_ref_item ) {\r
- try {\r
- AptxUtil.openWebsite( AptxConstants.APTX_REFERENCE_URL, is_applet, applet );\r
- }\r
- catch ( final IOException e1 ) {\r
- ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() );\r
- }\r
- }\r
- else if ( o == _phyloxml_ref_item ) {\r
- try {\r
- AptxUtil.openWebsite( AptxConstants.PHYLOXML_REFERENCE_URL, is_applet, applet );\r
- }\r
- catch ( final IOException e1 ) {\r
- ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() );\r
- }\r
- }\r
- else if ( o == _write_to_pdf_item ) {\r
- final File curr_dir = writeToPdf( _mainpanel.getCurrentPhylogeny(),\r
- getMainPanel(),\r
- _writetopdf_filechooser,\r
- _current_dir,\r
- getContentPane(),\r
- this );\r
- if ( curr_dir != null ) {\r
- setCurrentDir( curr_dir );\r
- }\r
- }\r
- else if ( o == _save_all_item ) {\r
- writeAllToFile();\r
- }\r
- else if ( o == _write_to_jpg_item ) {\r
- final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(),\r
- GraphicsExportType.JPG,\r
- _mainpanel,\r
- _writetographics_filechooser,\r
- this,\r
- getContentPane(),\r
- _current_dir );\r
- if ( new_dir != null ) {\r
- setCurrentDir( new_dir );\r
- }\r
- }\r
- else if ( o == _write_to_gif_item ) {\r
- final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(),\r
- GraphicsExportType.GIF,\r
- _mainpanel,\r
- _writetographics_filechooser,\r
- this,\r
- getContentPane(),\r
- _current_dir );\r
- if ( new_dir != null ) {\r
- setCurrentDir( new_dir );\r
- }\r
- }\r
- else if ( o == _write_to_tif_item ) {\r
- final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(),\r
- GraphicsExportType.TIFF,\r
- _mainpanel,\r
- _writetographics_filechooser,\r
- this,\r
- getContentPane(),\r
- _current_dir );\r
- if ( new_dir != null ) {\r
- setCurrentDir( new_dir );\r
- }\r
- }\r
- else if ( o == _write_to_bmp_item ) {\r
- final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(),\r
- GraphicsExportType.BMP,\r
- _mainpanel,\r
- _writetographics_filechooser,\r
- this,\r
- getContentPane(),\r
- _current_dir );\r
- if ( new_dir != null ) {\r
- setCurrentDir( new_dir );\r
- }\r
- }\r
- else if ( o == _write_to_png_item ) {\r
- final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(),\r
- GraphicsExportType.PNG,\r
- _mainpanel,\r
- _writetographics_filechooser,\r
- this,\r
- getContentPane(),\r
- _current_dir );\r
- if ( new_dir != null ) {\r
- setCurrentDir( new_dir );\r
- }\r
- }\r
- else if ( o == _print_item ) {\r
- print( getCurrentTreePanel(), getOptions(), this );\r
- }\r
- else if ( o == _save_item ) {\r
- final File new_dir = writeToFile( _mainpanel.getCurrentPhylogeny(),\r
- getMainPanel(),\r
- _save_filechooser,\r
- _current_dir,\r
- getContentPane(),\r
- this );\r
- if ( new_dir != null ) {\r
- setCurrentDir( new_dir );\r
- }\r
- }\r
- else if ( o == _graphics_export_visible_only_cbmi ) {\r
- updateOptions( getOptions() );\r
- }\r
- else if ( o == _antialias_print_cbmi ) {\r
- updateOptions( getOptions() );\r
- }\r
- else if ( o == _print_black_and_white_cbmi ) {\r
- updateOptions( getOptions() );\r
- }\r
- else if ( o == _choose_pdf_width_mi ) {\r
- choosePdfWidth();\r
- }\r
- else if ( o == _lineage_inference ) {\r
- if ( isSubtreeDisplayed() ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Subtree is shown.",\r
- "Cannot infer ancestral taxonomies",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- executeLineageInference();\r
- }\r
- else {\r
- if ( _load_phylogeny_from_webservice_menu_items != null ) {\r
- for( int i = 0; i < _load_phylogeny_from_webservice_menu_items.length; ++i ) {\r
- if ( o == _load_phylogeny_from_webservice_menu_items[ i ] ) {\r
- readPhylogeniesFromWebservice( i );\r
- }\r
- }\r
- }\r
- }\r
- _contentpane.repaint();\r
- }\r
-\r
- public Configuration getConfiguration() {\r
- return _configuration;\r
- }\r
-\r
- /**\r
- * This method returns the current external node data which\r
- * has been selected by the user by clicking the "Return ..."\r
- * menu item. This method is expected to be called from Javascript or\r
- * something like it.\r
- *\r
- * @return current external node data as String\r
- */\r
- public String getCurrentExternalNodesDataBuffer() {\r
- return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();\r
- }\r
-\r
- public int getCurrentExternalNodesDataBufferChangeCounter() {\r
- return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();\r
- }\r
-\r
- public int getCurrentExternalNodesDataBufferLength() {\r
- return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();\r
- }\r
-\r
- public InferenceManager getInferenceManager() {\r
- return _inference_manager;\r
- }\r
-\r
- public MainPanel getMainPanel() {\r
- return _mainpanel;\r
- }\r
-\r
- public Options getOptions() {\r
- return _options;\r
- }\r
-\r
- public ProcessPool getProcessPool() {\r
- return _process_pool;\r
- }\r
-\r
- public void showTextFrame( final String s, final String title ) {\r
- checkTextFrames();\r
- _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );\r
- }\r
-\r
- public void showWhole() {\r
- _mainpanel.getControlPanel().showWhole();\r
- }\r
-\r
- public void updateProcessMenu() {\r
- // In general Swing is not thread safe.\r
- // See "Swing's Threading Policy".\r
- SwingUtilities.invokeLater( new Runnable() {\r
-\r
- @Override\r
- public void run() {\r
- doUpdateProcessMenu();\r
- }\r
- } );\r
- }\r
-\r
- 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
- getControlPanel().displayedPhylogenyMightHaveChanged( true );\r
- getMainPanel().getCurrentTreePanel().resetPreferredSize();\r
- getMainPanel().getCurrentTreePanel().updateOvSizes();\r
- \r
- repaint();\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 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
- 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
- private void writeAllToFile() {\r
- if ( ( getMainPanel().getTabbedPane() == null ) || ( getMainPanel().getTabbedPane().getTabCount() < 1 ) ) {\r
- return;\r
- }\r
- final File my_dir = getCurrentDir();\r
- if ( my_dir != null ) {\r
- _save_filechooser.setCurrentDirectory( my_dir );\r
- }\r
- _save_filechooser.setSelectedFile( new File( "" ) );\r
- final int result = _save_filechooser.showSaveDialog( _contentpane );\r
- final File file = _save_filechooser.getSelectedFile();\r
- setCurrentDir( _save_filechooser.getCurrentDirectory() );\r
- if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
- if ( file.exists() ) {\r
- final int i = JOptionPane.showConfirmDialog( this,\r
- file + " already exists. Overwrite?",\r
- "Warning",\r
- JOptionPane.OK_CANCEL_OPTION,\r
- JOptionPane.WARNING_MESSAGE );\r
- if ( i != JOptionPane.OK_OPTION ) {\r
- return;\r
- }\r
- else {\r
- try {\r
- file.delete();\r
- }\r
- catch ( final Exception e ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Failed to delete: " + file,\r
- "Error",\r
- JOptionPane.WARNING_MESSAGE );\r
- }\r
- }\r
- }\r
- final int count = getMainPanel().getTabbedPane().getTabCount();\r
- final List<Phylogeny> trees = new ArrayList<Phylogeny>();\r
- for( int i = 0; i < count; ++i ) {\r
- final Phylogeny phy = getMainPanel().getPhylogeny( i );\r
- if ( ForesterUtil.isEmpty( phy.getName() )\r
- && !ForesterUtil.isEmpty( getMainPanel().getTabbedPane().getTitleAt( i ) ) ) {\r
- phy.setName( getMainPanel().getTabbedPane().getTitleAt( i ) );\r
- }\r
- trees.add( phy );\r
- getMainPanel().getTreePanels().get( i ).setEdited( false );\r
- }\r
- final PhylogenyWriter writer = new PhylogenyWriter();\r
- try {\r
- writer.toPhyloXML( file, trees, 0, ForesterUtil.LINE_SEPARATOR );\r
- }\r
- catch ( final IOException e ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Failed to write to: " + file,\r
- "Error",\r
- JOptionPane.WARNING_MESSAGE );\r
- }\r
- }\r
- }\r
-\r
- 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 = MainFrame.createMenu( "File", getConfiguration() );\r
- _file_jmenu.add( _save_item = new JMenuItem( "Save Tree As..." ) );\r
- _file_jmenu.addSeparator();\r
- _file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) );\r
- if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" ) || AptxUtil.canWriteFormat( "TIF" ) ) {\r
- _file_jmenu.add( _write_to_tif_item = new JMenuItem( "Export to TIFF file..." ) );\r
- }\r
- _file_jmenu.add( _write_to_png_item = new JMenuItem( "Export to PNG file..." ) );\r
- _file_jmenu.add( _write_to_jpg_item = new JMenuItem( "Export to JPG file..." ) );\r
- if ( AptxUtil.canWriteFormat( "gif" ) ) {\r
- _file_jmenu.add( _write_to_gif_item = new JMenuItem( "Export to GIF file..." ) );\r
- }\r
- if ( AptxUtil.canWriteFormat( "bmp" ) ) {\r
- _file_jmenu.add( _write_to_bmp_item = new JMenuItem( "Export to BMP file..." ) );\r
- }\r
- _file_jmenu.addSeparator();\r
- _file_jmenu.add( _print_item = new JMenuItem( "Print..." ) );\r
- _file_jmenu.addSeparator();\r
- _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );\r
- customizeJMenuItem( _save_item );\r
- customizeJMenuItem( _write_to_pdf_item );\r
- customizeJMenuItem( _write_to_png_item );\r
- customizeJMenuItem( _write_to_jpg_item );\r
- customizeJMenuItem( _write_to_gif_item );\r
- customizeJMenuItem( _write_to_tif_item );\r
- customizeJMenuItem( _write_to_bmp_item );\r
- customizeJMenuItem( _print_item );\r
- customizeJMenuItem( _exit_item );\r
- _jmenubar.add( _file_jmenu );\r
- }\r
-\r
- void 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 choosePdfWidth() {\r
- final String s = ( String ) JOptionPane.showInputDialog( this,\r
- "Please enter the default line width for PDF export.\n"\r
- + "[current value: "\r
- + getOptions().getPrintLineWidth() + "]\n",\r
- "Line Width for PDF Export",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null,\r
- null,\r
- getOptions().getPrintLineWidth() );\r
- if ( !ForesterUtil.isEmpty( s ) ) {\r
- boolean success = true;\r
- float f = 0.0f;\r
- final String m_str = s.trim();\r
- if ( !ForesterUtil.isEmpty( m_str ) ) {\r
- try {\r
- f = Float.parseFloat( m_str );\r
- }\r
- catch ( final Exception ex ) {\r
- success = false;\r
- }\r
- }\r
- else {\r
- success = false;\r
- }\r
- if ( success && ( f > 0.0 ) ) {\r
- getOptions().setPrintLineWidth( f );\r
- }\r
- }\r
- }\r
-\r
- 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 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
- void executeLineageInference() {\r
- if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) {\r
- return;\r
- }\r
- if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Phylogeny is not rooted.",\r
- "Cannot infer ancestral taxonomies",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- final AncestralTaxonomyInferrer inferrer = new AncestralTaxonomyInferrer( this,\r
- _mainpanel.getCurrentTreePanel(),\r
- _mainpanel.getCurrentPhylogeny()\r
- .copy() );\r
- new Thread( inferrer ).start();\r
- }\r
-\r
- 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
- ControlPanel getControlPanel() {\r
- return getMainPanel().getControlPanel();\r
- }\r
-\r
- File getCurrentDir() {\r
- if ( ( _current_dir == null ) || !_current_dir.canRead() ) {\r
- if ( ForesterUtil.isWindows() ) {\r
- try {\r
- _current_dir = new File( WindowsUtils.getCurrentUserDesktopPath() );\r
- }\r
- catch ( final Exception e ) {\r
- _current_dir = null;\r
- }\r
- }\r
- }\r
- if ( ( _current_dir == null ) || !_current_dir.canRead() ) {\r
- if ( System.getProperty( "user.home" ) != null ) {\r
- _current_dir = new File( System.getProperty( "user.home" ) );\r
- }\r
- else if ( System.getProperty( "user.dir" ) != null ) {\r
- _current_dir = new File( System.getProperty( "user.dir" ) );\r
- }\r
- }\r
- return _current_dir;\r
- }\r
-\r
- 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 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
- void setConfiguration( final Configuration configuration ) {\r
- _configuration = configuration;\r
- }\r
-\r
- void setCurrentDir( final File current_dir ) {\r
- _current_dir = current_dir;\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.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
- }\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
- if ( ( _color_all_found_nodes_when_coloring_subtree_cbmi != null ) && _color_all_found_nodes_when_coloring_subtree_cbmi.isEnabled() ) {\r
- options.setColorAllFoundNodesWhenColoringSubtree( _color_all_found_nodes_when_coloring_subtree_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 static void cycleNodeDataReturn( final Options op, final Configuration conf ) {\r
- switch ( op.getExtDescNodeDataToReturn() ) {\r
- case UNKNOWN:\r
- op.setExtDescNodeDataToReturn( NodeDataField.DOMAINS_ALL );\r
- break;\r
- case DOMAINS_ALL:\r
- op.setExtDescNodeDataToReturn( NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN );\r
- break;\r
- case DOMAINS_COLLAPSED_PER_PROTEIN:\r
- op.setExtDescNodeDataToReturn( NodeDataField.SEQ_ANNOTATIONS );\r
- break;\r
- case SEQ_ANNOTATIONS:\r
- op.setExtDescNodeDataToReturn( NodeDataField.GO_TERM_IDS );\r
- break;\r
- case GO_TERM_IDS:\r
- op.setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_MOL_SEQ_FASTA );\r
- break;\r
- case SEQUENCE_MOL_SEQ_FASTA:\r
- if ( ( conf != null ) && ( conf.getExtDescNodeDataToReturn() != null )\r
- && ( conf.getExtDescNodeDataToReturn() != NodeDataField.DOMAINS_ALL )\r
- && ( conf.getExtDescNodeDataToReturn() != NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN )\r
- && ( conf.getExtDescNodeDataToReturn() != NodeDataField.SEQ_ANNOTATIONS )\r
- && ( conf.getExtDescNodeDataToReturn() != NodeDataField.GO_TERM_IDS )\r
- && ( conf.getExtDescNodeDataToReturn() != NodeDataField.SEQUENCE_MOL_SEQ_FASTA ) ) {\r
- op.setExtDescNodeDataToReturn( conf.getExtDescNodeDataToReturn() );\r
- }\r
- else {\r
- op.setExtDescNodeDataToReturn( NodeDataField.UNKNOWN );\r
- }\r
- break;\r
- default:\r
- op.setExtDescNodeDataToReturn( NodeDataField.UNKNOWN );\r
- }\r
- }\r
-\r
- /**\r
- * Display the about box.\r
- */\r
- static void about() {\r
- final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + AptxConstants.VERSION + "\n" );\r
- about.append( "Copyright (C) 2016 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: " + AptxConstants.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( AptxConstants.PHYLOXML_REFERENCE_SHORT + "\n" );\r
- about.append( "For more information & download:\n" );\r
- about.append( AptxConstants.APTX_WEB_SITE + "\n" );\r
- about.append( "Documentation:\n" );\r
- about.append( AptxConstants.APTX_DOC_SITE + "\n" );\r
- about.append( "Comments: " + AptxConstants.AUTHOR_EMAIL );\r
- JOptionPane.showMessageDialog( null, about, AptxConstants.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 ) {\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 ) {\r
- switch ( op.getDefaultNodeShape() ) {\r
- case CIRCLE:\r
- op.setDefaultNodeShape( NodeShape.RECTANGLE );\r
- break;\r
- case RECTANGLE:\r
- op.setDefaultNodeShape( NodeShape.CIRCLE );\r
- break;\r
- default:\r
- throw new RuntimeException( "unknown shape: " + op.getDefaultNodeShape() );\r
- }\r
- }\r
-\r
- static void cycleOverview( final Options op, final TreePanel tree_panel ) {\r
- switch ( op.getOvPlacement() ) {\r
- case LOWER_LEFT:\r
- op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );\r
- break;\r
- case LOWER_RIGHT:\r
- op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );\r
- break;\r
- case UPPER_LEFT:\r
- op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );\r
- break;\r
- case UPPER_RIGHT:\r
- op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );\r
- break;\r
- default:\r
- throw new RuntimeException( "unknown placement: " + op.getOvPlacement() );\r
- }\r
- if ( tree_panel != null ) {\r
- tree_panel.updateOvSettings();\r
- }\r
- }\r
-\r
- static void exceptionOccuredDuringSaveAs( final Exception e, final TreePanel tp, final Component comp ) {\r
- try {\r
- tp.setArrowCursor();\r
- }\r
- catch ( final Exception ex ) {\r
- // Do nothing.\r
- }\r
- JOptionPane.showMessageDialog( comp, "Exception" + e, "Error during File|SaveAs", JOptionPane.ERROR_MESSAGE );\r
- }\r
-\r
- static void print( final TreePanel tp, final Options op, final Component c ) {\r
- if ( ( tp == null ) || ( tp.getPhylogeny() == null ) || tp.getPhylogeny().isEmpty() ) {\r
- return;\r
- }\r
- final String job_name = AptxConstants.PRG_NAME;\r
- boolean error = false;\r
- String printer_name = null;\r
- try {\r
- printer_name = Printer.print( tp, job_name );\r
- }\r
- catch ( final Exception e ) {\r
- error = true;\r
- JOptionPane.showMessageDialog( c, e.getMessage(), "Printing Error", JOptionPane.ERROR_MESSAGE );\r
- }\r
- if ( !error && ( printer_name != null ) ) {\r
- String msg = "Printing data sent to printer";\r
- if ( printer_name.length() > 1 ) {\r
- msg += " [" + printer_name + "]";\r
- }\r
- JOptionPane.showMessageDialog( c, msg, "Printing...", JOptionPane.INFORMATION_MESSAGE );\r
- }\r
- if ( !op.isPrintUsingActualSize() ) {\r
- tp.getControlPanel().showWhole();\r
- }\r
- }\r
-\r
- static void printPhylogenyToPdf( final String file_name,\r
- final Options opts,\r
- final TreePanel tp,\r
- final Component comp ) {\r
- \r
- String pdf_written_to = "";\r
- boolean error = false;\r
- try {\r
- if ( opts.isPrintUsingActualSize() ) {\r
- pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name, tp, tp.getWidth() , tp.getHeight() );\r
- }\r
- else {\r
- // Never false.\r
- }\r
- }\r
- catch ( final IOException e ) {\r
- error = true;\r
- JOptionPane.showMessageDialog( comp, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );\r
- }\r
- if ( !error ) {\r
- if ( !ForesterUtil.isEmpty( pdf_written_to ) ) {\r
- JOptionPane.showMessageDialog( comp,\r
- "Wrote PDF to: " + pdf_written_to,\r
- "Information",\r
- JOptionPane.INFORMATION_MESSAGE );\r
- }\r
- else {\r
- JOptionPane.showMessageDialog( comp,\r
- "There was an unknown problem when attempting to write to PDF file: \""\r
- + file_name + "\"",\r
- "Error",\r
- JOptionPane.ERROR_MESSAGE );\r
- }\r
- }\r
- if ( !opts.isPrintUsingActualSize() ) {\r
- tp.getControlPanel().showWhole();\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: " + options.getExtDescNodeDataToReturn().toString() + ")" );\r
- }\r
- else {\r
- mi.setText( "Cycle Node Return Data..." );\r
- }\r
- }\r
-\r
- static void setCycleNodeFillMenuItem( final JMenuItem mi, final Options options ) {\r
- if ( ( options != null ) && ( options.getDefaultNodeFill() != null ) ) {\r
- mi.setText( "Cycle Node Shape Fill Type... (current: "\r
- + options.getDefaultNodeFill().toString().toLowerCase() + ")" );\r
- }\r
- else {\r
- mi.setText( "Cycle Node Shape Fill Type..." );\r
- }\r
- }\r
-\r
- static void setCycleNodeShapeMenuItem( final JMenuItem mi, final Options options ) {\r
- if ( ( options != null ) && ( options.getDefaultNodeShape() != null ) ) {\r
- mi.setText( "Cycle Node Shape Fill Type... (current: "\r
- + options.getDefaultNodeShape().toString().toLowerCase() + ")" );\r
- }\r
- else {\r
- mi.setText( "Cycle Node Shape Fill Type..." );\r
- }\r
- }\r
-\r
- static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) {\r
- if ( ( options != null ) && ( options.getOvPlacement() != null ) ) {\r
- mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" );\r
- }\r
- else {\r
- mi.setText( "Cycle Overview Placement..." );\r
- }\r
- }\r
-\r
- static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) {\r
- if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) {\r
- mi.setText( "Select Color Scheme... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName()\r
- + ")" );\r
- }\r
- else {\r
- mi.setText( "Select Color Scheme..." );\r
- }\r
- }\r
-\r
- static void setTextForFontChooserMenuItem( final JMenuItem mi, final String font_desc ) {\r
- mi.setText( "Select Default Font... (current: " + font_desc + ")" );\r
- }\r
-\r
- static void setTextForPdfLineWidthChooserMenuItem( final JMenuItem mi, final Options o ) {\r
- mi.setText( "Enter Default Line Width for PDF Export... (current: " + o.getPrintLineWidth() + ")" );\r
- }\r
-\r
- static void 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
- static boolean writeAsNewHampshire( final TreePanel tp, final Options op, boolean exception, final File file ) {\r
- try {\r
- final PhylogenyWriter writer = new PhylogenyWriter();\r
- writer.toNewHampshire( tp.getPhylogeny(), true, op.getNhConversionSupportValueStyle(), file );\r
- }\r
- catch ( final Exception e ) {\r
- exception = true;\r
- exceptionOccuredDuringSaveAs( e, tp, tp );\r
- }\r
- return exception;\r
- }\r
-\r
- static boolean writeAsNexus( final TreePanel tp, final Options op, boolean exception, final File file ) {\r
- try {\r
- final PhylogenyWriter writer = new PhylogenyWriter();\r
- writer.toNexus( file, tp.getPhylogeny(), op.getNhConversionSupportValueStyle() );\r
- }\r
- catch ( final Exception e ) {\r
- exception = true;\r
- exceptionOccuredDuringSaveAs( e, tp, tp );\r
- }\r
- return exception;\r
- }\r
-\r
- static boolean writeAsPhyloXml( final TreePanel tp, final Options op, boolean exception, final File file ) {\r
- try {\r
- final PhylogenyWriter writer = new PhylogenyWriter();\r
- writer.toPhyloXML( file, tp.getPhylogeny(), 0 );\r
- }\r
- catch ( final Exception e ) {\r
- exception = true;\r
- exceptionOccuredDuringSaveAs( e, tp, tp );\r
- }\r
- return exception;\r
- }\r
-\r
- static void writePhylogenyToGraphicsFile( final String file_name,\r
- final GraphicsExportType type,\r
- final MainPanel mp,\r
- final Component comp,\r
- final Container contentpane ) {\r
- mp.getCurrentTreePanel().calcParametersForPainting( mp.getCurrentTreePanel().getWidth(),\r
- mp.getCurrentTreePanel().getHeight() );\r
- String file_written_to = "";\r
- boolean error = false;\r
- try {\r
- file_written_to = AptxUtil.writePhylogenyToGraphicsFile( file_name,\r
- mp.getCurrentTreePanel().getWidth(),\r
- mp.getCurrentTreePanel().getHeight(),\r
- mp.getCurrentTreePanel(),\r
- mp.getControlPanel(),\r
- type,\r
- mp.getOptions() );\r
- }\r
- catch ( final IOException e ) {\r
- error = true;\r
- JOptionPane.showMessageDialog( comp, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );\r
- }\r
- if ( !error ) {\r
- if ( ( file_written_to != null ) && ( file_written_to.length() > 0 ) ) {\r
- JOptionPane.showMessageDialog( comp,\r
- "Wrote image to: " + file_written_to,\r
- "Graphics Export",\r
- JOptionPane.INFORMATION_MESSAGE );\r
- }\r
- else {\r
- JOptionPane.showMessageDialog( comp,\r
- "There was an unknown problem when attempting to write to an image file: \""\r
- + file_name + "\"",\r
- "Error",\r
- JOptionPane.ERROR_MESSAGE );\r
- }\r
- }\r
- contentpane.repaint();\r
- }\r
-\r
- static File writeToFile( final Phylogeny t,\r
- final MainPanel mp,\r
- final JFileChooser save_filechooser,\r
- final File current_dir,\r
- final Container contentpane,\r
- final Component comp ) {\r
- File new_file = null;\r
- if ( t == null ) {\r
- return null;\r
- }\r
- String initial_filename = null;\r
- if ( mp.getCurrentTreePanel().getTreeFile() != null ) {\r
- try {\r
- initial_filename = mp.getCurrentTreePanel().getTreeFile().getCanonicalPath();\r
- }\r
- catch ( final IOException e ) {\r
- initial_filename = null;\r
- }\r
- }\r
- if ( !ForesterUtil.isEmpty( initial_filename ) ) {\r
- save_filechooser.setSelectedFile( new File( initial_filename ) );\r
- }\r
- else {\r
- save_filechooser.setSelectedFile( new File( "" ) );\r
- }\r
- final File my_dir = current_dir;\r
- if ( my_dir != null ) {\r
- save_filechooser.setCurrentDirectory( my_dir );\r
- }\r
- final int result = save_filechooser.showSaveDialog( contentpane );\r
- final File file = save_filechooser.getSelectedFile();\r
- new_file = save_filechooser.getCurrentDirectory();\r
- boolean exception = false;\r
- if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
- if ( file.exists() ) {\r
- final int i = JOptionPane.showConfirmDialog( comp,\r
- file + " already exists.\nOverwrite?",\r
- "Overwrite?",\r
- JOptionPane.OK_CANCEL_OPTION,\r
- JOptionPane.QUESTION_MESSAGE );\r
- if ( i != JOptionPane.OK_OPTION ) {\r
- return null;\r
- }\r
- else {\r
- final File to = new File( file.getAbsoluteFile().toString() + AptxConstants.BACKUP_FILE_SUFFIX );\r
- try {\r
- ForesterUtil.copyFile( file, to );\r
- }\r
- catch ( final Exception e ) {\r
- JOptionPane.showMessageDialog( comp,\r
- "Failed to create backup copy " + to,\r
- "Failed to Create Backup Copy",\r
- JOptionPane.WARNING_MESSAGE );\r
- }\r
- try {\r
- file.delete();\r
- }\r
- catch ( final Exception e ) {\r
- JOptionPane.showMessageDialog( comp,\r
- "Failed to delete: " + file,\r
- "Failed to Delete",\r
- JOptionPane.WARNING_MESSAGE );\r
- }\r
- }\r
- }\r
- if ( save_filechooser.getFileFilter() == MainFrame.nhfilter ) {\r
- exception = writeAsNewHampshire( mp.getCurrentTreePanel(), mp.getOptions(), exception, file );\r
- }\r
- else if ( save_filechooser.getFileFilter() == MainFrame.xmlfilter ) {\r
- exception = writeAsPhyloXml( mp.getCurrentTreePanel(), mp.getOptions(), exception, file );\r
- }\r
- else if ( save_filechooser.getFileFilter() == MainFrame.nexusfilter ) {\r
- exception = writeAsNexus( mp.getCurrentTreePanel(), mp.getOptions(), exception, file );\r
- }\r
- // "*.*":\r
- else {\r
- final String file_name = file.getName().trim().toLowerCase();\r
- if ( file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )\r
- || file_name.endsWith( ".tree" ) ) {\r
- exception = writeAsNewHampshire( mp.getCurrentTreePanel(), mp.getOptions(), exception, file );\r
- }\r
- else if ( file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) ) {\r
- exception = writeAsNexus( mp.getCurrentTreePanel(), mp.getOptions(), exception, file );\r
- }\r
- // XML is default:\r
- else {\r
- exception = writeAsPhyloXml( mp.getCurrentTreePanel(), mp.getOptions(), exception, file );\r
- }\r
- }\r
- if ( !exception ) {\r
- mp.setTitleOfSelectedTab( file.getName() );\r
- mp.getCurrentTreePanel().setTreeFile( file );\r
- mp.getCurrentTreePanel().setEdited( false );\r
- }\r
- }\r
- return new_file;\r
- }\r
-\r
- static File writeToGraphicsFile( final Phylogeny t,\r
- final GraphicsExportType type,\r
- final MainPanel mp,\r
- final JFileChooser writetographics_filechooser,\r
- final Component component,\r
- final Container contentpane,\r
- final File current_dir ) {\r
- File new_dir = null;\r
- if ( ( t == null ) || t.isEmpty() ) {\r
- return null;\r
- }\r
- String initial_filename = "";\r
- if ( mp.getCurrentTreePanel().getTreeFile() != null ) {\r
- initial_filename = mp.getCurrentTreePanel().getTreeFile().toString();\r
- }\r
- if ( initial_filename.indexOf( '.' ) > 0 ) {\r
- initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );\r
- }\r
- initial_filename = initial_filename + "." + type;\r
- writetographics_filechooser.setSelectedFile( new File( initial_filename ) );\r
- final File my_dir = current_dir;\r
- if ( my_dir != null ) {\r
- writetographics_filechooser.setCurrentDirectory( my_dir );\r
- }\r
- final int result = writetographics_filechooser.showSaveDialog( contentpane );\r
- File file = writetographics_filechooser.getSelectedFile();\r
- //setCurrentDir( writetographics_filechooser.getCurrentDirectory() );\r
- new_dir = writetographics_filechooser.getCurrentDirectory();\r
- if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
- if ( !file.toString().toLowerCase().endsWith( type.toString() ) ) {\r
- file = new File( file.toString() + "." + type );\r
- }\r
- if ( file.exists() ) {\r
- final int i = JOptionPane.showConfirmDialog( component,\r
- file + " already exists. Overwrite?",\r
- "Warning",\r
- JOptionPane.OK_CANCEL_OPTION,\r
- JOptionPane.WARNING_MESSAGE );\r
- if ( i != JOptionPane.OK_OPTION ) {\r
- return null;\r
- }\r
- else {\r
- try {\r
- file.delete();\r
- }\r
- catch ( final Exception e ) {\r
- JOptionPane.showMessageDialog( component,\r
- "Failed to delete: " + file,\r
- "Error",\r
- JOptionPane.WARNING_MESSAGE );\r
- }\r
- }\r
- }\r
- writePhylogenyToGraphicsFile( file.toString(), type, mp, component, contentpane );\r
- }\r
- return new_dir;\r
- }\r
-\r
- static File writeToPdf( final Phylogeny t,\r
- final MainPanel mp,\r
- final JFileChooser writetopdf_filechooser,\r
- final File curr_dir,\r
- final Container contentpane,\r
- final Component component ) {\r
- if ( ( t == null ) || t.isEmpty() ) {\r
- return null;\r
- }\r
- String initial_filename = "";\r
- if ( mp.getCurrentTreePanel().getTreeFile() != null ) {\r
- initial_filename = mp.getCurrentTreePanel().getTreeFile().toString();\r
- }\r
- if ( initial_filename.indexOf( '.' ) > 0 ) {\r
- initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );\r
- }\r
- initial_filename = initial_filename + ".pdf";\r
- writetopdf_filechooser.setSelectedFile( new File( initial_filename ) );\r
- final File my_dir = curr_dir;\r
- if ( my_dir != null ) {\r
- writetopdf_filechooser.setCurrentDirectory( my_dir );\r
- }\r
- final int result = writetopdf_filechooser.showSaveDialog( contentpane );\r
- File file = writetopdf_filechooser.getSelectedFile();\r
- // setCurrentDir( writetopdf_filechooser.getCurrentDirectory() );\r
- final File new_current_dir = writetopdf_filechooser.getCurrentDirectory();\r
- if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
- if ( !file.toString().toLowerCase().endsWith( ".pdf" ) ) {\r
- file = new File( file.toString() + ".pdf" );\r
- }\r
- if ( file.exists() ) {\r
- final int i = JOptionPane.showConfirmDialog( component,\r
- file + " already exists. Overwrite?",\r
- "WARNING",\r
- JOptionPane.OK_CANCEL_OPTION,\r
- JOptionPane.WARNING_MESSAGE );\r
- if ( i != JOptionPane.OK_OPTION ) {\r
- return null;\r
- }\r
- }\r
- printPhylogenyToPdf( file.toString(), mp.getOptions(), mp.getCurrentTreePanel(), component );\r
- }\r
- return new_current_dir;\r
- }\r
-}\r
-\r
-class DefaultFilter extends FileFilter {\r
-\r
- @Override\r
- public boolean accept( final File f ) {\r
- final String file_name = f.getName().trim().toLowerCase();\r
- return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )\r
- || file_name.endsWith( ".nwk" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".ph" )\r
- || file_name.endsWith( ".tr" ) || file_name.endsWith( ".dnd" ) || file_name.endsWith( ".tree" )\r
- || file_name.endsWith( ".nhx" ) || file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" )\r
- || file_name.endsWith( "phylo.xml" ) || file_name.endsWith( ".pxml" ) || file_name.endsWith( ".nexus" )\r
- || file_name.endsWith( ".nx" ) || file_name.endsWith( ".nex" ) || file_name.endsWith( ".tre" )\r
- || file_name.endsWith( ".zip" ) || file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" )\r
- || file_name.endsWith( ".con" ) || f.isDirectory();\r
- }\r
-\r
- @Override\r
- public String getDescription() {\r
- return "All supported files (*.xml, *.phyloxml, *phylo.xml, *.nhx, *.nh, *.newick, *.nex, *.nexus, *.phy, *.tre, *.tree, *.tol, ...)";\r
- }\r
-}\r
-\r
-class GraphicsFileFilter extends FileFilter {\r
-\r
- @Override\r
- public boolean accept( final File f ) {\r
- final String file_name = f.getName().trim().toLowerCase();\r
- return file_name.endsWith( ".jpg" ) || file_name.endsWith( ".jpeg" ) || file_name.endsWith( ".png" )\r
- || file_name.endsWith( ".gif" ) || file_name.endsWith( ".bmp" ) || f.isDirectory();\r
- }\r
-\r
- @Override\r
- public String getDescription() {\r
- return "Image files (*.jpg, *.jpeg, *.png, *.gif, *.bmp)";\r
- }\r
-}\r
-\r
-class MsaFileFilter extends FileFilter {\r
-\r
- @Override\r
- public boolean accept( final File f ) {\r
- final String file_name = f.getName().trim().toLowerCase();\r
- return file_name.endsWith( ".msa" ) || file_name.endsWith( ".aln" ) || file_name.endsWith( ".fasta" )\r
- || file_name.endsWith( ".fas" ) || file_name.endsWith( ".fa" ) || f.isDirectory();\r
- }\r
-\r
- @Override\r
- public String getDescription() {\r
- return "Multiple sequence alignment files (*.msa, *.aln, *.fasta, *.fa, *.fas)";\r
- }\r
-}\r
-\r
-class NexusFilter extends FileFilter {\r
-\r
- @Override\r
- public boolean accept( final File f ) {\r
- final String file_name = f.getName().trim().toLowerCase();\r
- return file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) || file_name.endsWith( ".nx" )\r
- || file_name.endsWith( ".tre" ) || f.isDirectory();\r
- }\r
-\r
- @Override\r
- public String getDescription() {\r
- return "Nexus files (*.nex, *.nexus, *.nx, *.tre)";\r
- }\r
-} // NexusFilter\r
-\r
-class NHFilter extends FileFilter {\r
-\r
- @Override\r
- public boolean accept( final File f ) {\r
- final String file_name = f.getName().trim().toLowerCase();\r
- return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )\r
- || file_name.endsWith( ".tr" ) || file_name.endsWith( ".tree" ) || file_name.endsWith( ".dnd" )\r
- || file_name.endsWith( ".ph" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".nwk" )\r
- || f.isDirectory();\r
- }\r
-\r
- @Override\r
- public String getDescription() {\r
- return "New Hampshire - Newick files (*.nh, *.newick, *.phy, *.tree, *.dnd, *.tr, *.ph, *.phb, *.nwk)";\r
- }\r
-} // NHFilter\r
-\r
-class NHXFilter extends FileFilter {\r
-\r
- @Override\r
- public boolean accept( final File f ) {\r
- final String file_name = f.getName().trim().toLowerCase();\r
- return file_name.endsWith( ".nhx" ) || f.isDirectory();\r
- }\r
-\r
- @Override\r
- public String getDescription() {\r
- return "NHX files (*.nhx) [deprecated]";\r
- }\r
-}\r
-\r
-class PdfFilter extends FileFilter {\r
-\r
- @Override\r
- public boolean accept( final File f ) {\r
- return f.getName().trim().toLowerCase().endsWith( ".pdf" ) || f.isDirectory();\r
- }\r
-\r
- @Override\r
- public String getDescription() {\r
- return "PDF files (*.pdf)";\r
- }\r
-} // PdfFilter\r
-\r
-class SequencesFileFilter extends FileFilter {\r
-\r
- @Override\r
- public boolean accept( final File f ) {\r
- final String file_name = f.getName().trim().toLowerCase();\r
- return file_name.endsWith( ".fasta" ) || file_name.endsWith( ".fa" ) || file_name.endsWith( ".fas" )\r
- || file_name.endsWith( ".seqs" ) || f.isDirectory();\r
- }\r
-\r
- @Override\r
- public String getDescription() {\r
- return "Sequences files (*.fasta, *.fa, *.fas, *.seqs )";\r
- }\r
-}\r
-\r
-class TolFilter extends FileFilter {\r
-\r
- @Override\r
- public boolean accept( final File f ) {\r
- final String file_name = f.getName().trim().toLowerCase();\r
- return ( file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" ) || file_name.endsWith( ".zip" ) || f\r
- .isDirectory() ) && ( !file_name.endsWith( ".xml.zip" ) );\r
- }\r
-\r
- @Override\r
- public String getDescription() {\r
- return "Tree of Life files (*.tol, *.tolxml)";\r
- }\r
-} // TolFilter\r
-\r
-class XMLFilter extends FileFilter {\r
-\r
- @Override\r
- public boolean accept( final File f ) {\r
- final String file_name = f.getName().trim().toLowerCase();\r
- return file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" ) || file_name.endsWith( "phylo.xml" )\r
- || file_name.endsWith( ".pxml" ) || file_name.endsWith( ".zip" ) || f.isDirectory();\r
- }\r
-\r
- @Override\r
- public String getDescription() {\r
- return "phyloXML files (*.xml, *.phyloxml, *phylo.xml, *.pxml, *.zip)";\r
- }\r
-} // XMLFilter\r
+// $Id:
+// FORESTER -- software libraries and applications
+// for evolutionary biology research and applications.
+//
+// Copyright (C) 2008-2010 Christian M. Zmasek
+// All rights reserved
+//
+// This library is free software; you can redistribute it and/or
+// modify it under the terms of the GNU Lesser General Public
+// License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+//
+// This library is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+// Lesser General Public License for more details.
+//
+// You should have received a copy of the GNU Lesser General Public
+// License along with this library; if not, write to the Free Software
+// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+//
+// Contact: phylosoft @ gmail . com
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
+
+package org.forester.archaeopteryx;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Container;
+import java.awt.Font;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Locale;
+import java.util.NoSuchElementException;
+
+import javax.swing.Box;
+import javax.swing.JApplet;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JFileChooser;
+import javax.swing.JFrame;
+import javax.swing.JLabel;
+import javax.swing.JMenu;
+import javax.swing.JMenuBar;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JRadioButtonMenuItem;
+import javax.swing.JTextField;
+import javax.swing.SwingUtilities;
+import javax.swing.filechooser.FileFilter;
+
+import org.forester.archaeopteryx.AptxUtil.GraphicsExportType;
+import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
+import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
+import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
+import org.forester.archaeopteryx.tools.AncestralTaxonomyInferrer;
+import org.forester.archaeopteryx.tools.InferenceManager;
+import org.forester.archaeopteryx.tools.ProcessPool;
+import org.forester.archaeopteryx.tools.ProcessRunning;
+import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
+import org.forester.io.writers.PhylogenyWriter;
+import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyMethods;
+import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
+import org.forester.phylogeny.PhylogenyNode;
+import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
+import org.forester.phylogeny.data.Annotation;
+import org.forester.phylogeny.data.NodeDataField;
+import org.forester.phylogeny.data.NodeVisualData.NodeFill;
+import org.forester.phylogeny.data.NodeVisualData.NodeShape;
+import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
+import org.forester.sdi.GSDI;
+import org.forester.sdi.GSDIR;
+import org.forester.sdi.SDIException;
+import org.forester.util.ForesterConstants;
+import org.forester.util.ForesterUtil;
+import org.forester.util.WindowsUtils;
+
+public abstract class MainFrame extends JFrame implements ActionListener {
+
+ final static NHFilter nhfilter = new NHFilter();
+ final static NHXFilter nhxfilter = new NHXFilter();
+ final static XMLFilter xmlfilter = new XMLFilter();
+ final static TolFilter tolfilter = new TolFilter();
+ final static NexusFilter nexusfilter = new NexusFilter();
+ final static PdfFilter pdffilter = new PdfFilter();
+ final static GraphicsFileFilter graphicsfilefilter = new GraphicsFileFilter();
+ final static MsaFileFilter msafilter = new MsaFileFilter();
+ final static SequencesFileFilter seqsfilter = new SequencesFileFilter();
+ final static DefaultFilter defaultfilter = new DefaultFilter();
+ static final String USE_MOUSEWHEEL_SHIFT_TO_ROTATE = "In this display type, use mousewheel + Shift to rotate [or A and S]";
+ static final String PHYLOXML_REF_TOOL_TIP = AptxConstants.PHYLOXML_REFERENCE; //TODO //FIXME
+ static final String APTX_REF_TOOL_TIP = AptxConstants.APTX_REFERENCE;
+ private static final long serialVersionUID = 3655000897845508358L;
+ final static Font menu_font = new Font( Configuration.getDefaultFontFamilyName(),
+ Font.PLAIN,
+ 10 );
+ static final String TYPE_MENU_HEADER = "Type";
+ static final String RECTANGULAR_TYPE_CBMI_LABEL = "Rectangular";
+ static final String EURO_TYPE_CBMI_LABEL = "Euro Type";
+ static final String CURVED_TYPE_CBMI_LABEL = "Curved";
+ static final String TRIANGULAR_TYPE_CBMI_LABEL = "Triangular";
+ static final String CONVEX_TYPE_CBMI_LABEL = "Convex";
+ static final String ROUNDED_TYPE_CBMI_LABEL = "Rounded";
+ static final String UNROOTED_TYPE_CBMI_LABEL = "Unrooted (alpha)"; //TODO
+ static final String CIRCULAR_TYPE_CBMI_LABEL = "Circular (alpha)"; //TODO
+ static final String OPTIONS_HEADER = "Options";
+ static final String SEARCH_SUBHEADER = "Search:";
+ static final String DISPLAY_SUBHEADER = "Display:";
+ static final String SEARCH_TERMS_ONLY_LABEL = "Match Complete Terms Only";
+ static final String SEARCH_REGEX_LABEL = "Search with Regular Expressions";
+ static final String SEARCH_CASE_SENSITIVE_LABEL = "Case Sensitive";
+ static final String INVERSE_SEARCH_RESULT_LABEL = "Negate Result";
+ static final String COLOR_BY_TAXONOMIC_GROUP = "Colorize by Taxonomic Group";
+ static final String DISPLAY_SCALE_LABEL = "Scale";
+ static final String NON_LINED_UP_CLADOGRAMS_LABEL = "Non-Lined Up Cladograms";
+ static final String UNIFORM_CLADOGRAMS_LABEL = "Total Node Sum Dependent Cladograms";
+ static final String LABEL_DIRECTION_LABEL = "Radial Labels";
+ static final String LABEL_DIRECTION_TIP = "To use radial node labels in radial and unrooted display types";
+ static final String SEARCH_WITH_REGEX_TIP = "To search using regular expressions (~Java/Perl syntax). For example, use \"^B.+\\d{2,}$\" to search for everything starting with a B and ending with at least two digits.";
+ static final String SCREEN_ANTIALIAS_LABEL = "Antialias";
+ static final String COLOR_LABELS_LABEL = "Colorize Labels Same as Parent Branch";
+ static final String BG_GRAD_LABEL = "Background Color Gradient";
+ static final String DISPLAY_NODE_BOXES_LABEL_EXT = "Shapes for External Nodes";
+ static final String DISPLAY_NODE_BOXES_LABEL_INT = "Shapes for Internal Nodes";
+ static final String DISPLAY_NODE_BOXES_LABEL_MARKED = "Shapes for Nodes with Visual Data";
+ static final String SHOW_OVERVIEW_LABEL = "Overview";
+ static final String FONT_SIZE_MENU_LABEL = "Font Size";
+ static final String NONUNIFORM_CLADOGRAMS_LABEL = "External Node Sum Dependent Cladograms";
+ static final String SHOW_DOMAIN_LABELS_LABEL = "Domain Labels";
+ static final String SHOW_ANN_REF_SOURCE_LABEL = "Seq Annotation Ref Sources";
+ static final String COLOR_LABELS_TIP = "To use parent branch colors for node labels as well, need to turn off taxonomy dependent colorization and turn on branch colorization for this to become apparent";
+ static final String ABBREV_SN_LABEL = "Abbreviate Scientific Taxonomic Names";
+ static final String TAXONOMY_COLORIZE_NODE_SHAPES_LABEL = "Colorize Node Shapes According to Taxonomy";
+ static final String CYCLE_NODE_SHAPE_LABEL = "Cycle Node Shapes";
+ static final String CYCLE_NODE_FILL_LABEL = "Cycle Node Fill Type";
+ static final String CHOOSE_NODE_SIZE_LABEL = "Choose Node Shape Size";
+ static final String SHOW_CONF_STDDEV_LABEL = "Confidence Standard Deviations";
+ static final String USE_BRACKETS_FOR_CONF_IN_NH_LABEL = "Use Brackets for Confidence Values";
+ static final String USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL = "Use Internal Node Names for Confidence Values";
+ static final String SHOW_BASIC_TREE_INFORMATION_LABEL = "Basic Tree Information";
+ static final String RIGHT_LINE_UP_DOMAINS = "Right-align Domain Architectures";
+ static final String LINE_UP_RENDERABLE_DATA = "Line Up Diagrams (such as Domain Architectures)";
+ static final String INFER_ANCESTOR_TAXONOMIES = "Infer Ancestor Taxonomies";
+ static final String OBTAIN_DETAILED_TAXONOMIC_INFORMATION = "Obtain Detailed Taxonomic Information";
+ JMenuBar _jmenubar;
+ JMenu _file_jmenu;
+ JMenu _tools_menu;
+ JMenu _view_jmenu;
+ JMenu _options_jmenu;
+ JMenu _font_size_menu;
+ JMenu _help_jmenu;
+ JMenuItem[] _load_phylogeny_from_webservice_menu_items;
+ // Analysis menu
+ JMenu _analysis_menu;
+ JMenuItem _load_species_tree_item;
+ JMenuItem _gsdi_item;
+ JMenuItem _gsdir_item;
+ JMenuItem _lineage_inference;
+ // file menu:
+ JMenuItem _open_item;
+ JMenuItem _open_url_item;
+ JMenuItem _save_item;
+ JMenuItem _save_all_item;
+ JMenuItem _close_item;
+ JMenuItem _exit_item;
+ JMenuItem _new_item;
+ JMenuItem _print_item;
+ JMenuItem _write_to_pdf_item;
+ JMenuItem _write_to_jpg_item;
+ JMenuItem _write_to_gif_item;
+ JMenuItem _write_to_tif_item;
+ JMenuItem _write_to_png_item;
+ JMenuItem _write_to_bmp_item;
+ // tools menu:
+ JMenuItem _midpoint_root_item;
+ JMenuItem _taxcolor_item;
+ JMenuItem _confcolor_item;
+ JMenuItem _color_rank_jmi;
+ JMenuItem _collapse_species_specific_subtrees;
+ JMenuItem _obtain_detailed_taxonomic_information_jmi;
+ JMenuItem _obtain_detailed_taxonomic_information_deleting_jmi;
+ JMenuItem _obtain_seq_information_jmi;
+ JMenuItem _move_node_names_to_tax_sn_jmi;
+ JMenuItem _move_node_names_to_seq_names_jmi;
+ JMenuItem _extract_tax_code_from_node_names_jmi;
+ JMenuItem _annotate_item;
+ JMenuItem _remove_branch_color_item;
+ JMenuItem _remove_visual_styles_item;
+ JMenuItem _delete_selected_nodes_item;
+ JMenuItem _delete_not_selected_nodes_item;
+ // font size menu:
+ JMenuItem _super_tiny_fonts_item;
+ JMenuItem _tiny_fonts_item;
+ JMenuItem _small_fonts_item;
+ JMenuItem _medium_fonts_item;
+ JMenuItem _large_fonts_item;
+ // options menu:
+ // _ screen and print
+ JMenuItem _choose_font_mi;
+ JMenuItem _switch_colors_mi;
+ JCheckBoxMenuItem _label_direction_cbmi;
+ // _ screen display
+ JCheckBoxMenuItem _screen_antialias_cbmi;
+ JCheckBoxMenuItem _background_gradient_cbmi;
+ JRadioButtonMenuItem _non_lined_up_cladograms_rbmi;
+ JRadioButtonMenuItem _uniform_cladograms_rbmi;
+ JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi;
+ JCheckBoxMenuItem _color_by_taxonomic_group_cbmi;
+ JCheckBoxMenuItem _show_scale_cbmi; //TODO fix me
+ JCheckBoxMenuItem _show_overview_cbmi;
+ JCheckBoxMenuItem _show_domain_labels;
+ JCheckBoxMenuItem _show_annotation_ref_source;
+ JCheckBoxMenuItem _abbreviate_scientific_names;
+ JCheckBoxMenuItem _color_labels_same_as_parent_branch;
+ JMenuItem _overview_placment_mi;
+ JMenuItem _choose_minimal_confidence_mi;
+ JCheckBoxMenuItem _show_default_node_shapes_internal_cbmi;
+ JCheckBoxMenuItem _show_default_node_shapes_external_cbmi;
+ JCheckBoxMenuItem _show_default_node_shapes_for_marked_cbmi;
+ JMenuItem _cycle_node_shape_mi;
+ JMenuItem _cycle_node_fill_mi;
+ JMenuItem _choose_node_size_mi;
+ JMenuItem _cycle_data_return;
+ JCheckBoxMenuItem _show_confidence_stddev_cbmi;
+ JCheckBoxMenuItem _right_line_up_domains_cbmi;
+ JCheckBoxMenuItem _line_up_renderable_data_cbmi;
+ // _ print
+ JCheckBoxMenuItem _graphics_export_visible_only_cbmi;
+ JCheckBoxMenuItem _antialias_print_cbmi;
+ JCheckBoxMenuItem _print_black_and_white_cbmi;
+ //JMenuItem _print_size_mi;
+ JMenuItem _choose_pdf_width_mi;
+ // _ parsing
+ JCheckBoxMenuItem _internal_number_are_confidence_for_nh_parsing_cbmi;
+ JRadioButtonMenuItem _extract_taxonomy_no_rbmi;
+ JRadioButtonMenuItem _extract_taxonomy_agressive_rbmi;
+ JRadioButtonMenuItem _extract_taxonomy_pfam_strict_rbmi;
+ JRadioButtonMenuItem _extract_taxonomy_pfam_relaxed_rbmi;
+ JCheckBoxMenuItem _replace_underscores_cbmi;
+ JCheckBoxMenuItem _allow_errors_in_distance_to_parent_cbmi;
+ JCheckBoxMenuItem _use_brackets_for_conf_in_nh_export_cbmi;
+ JCheckBoxMenuItem _use_internal_names_for_conf_in_nh_export_cbmi;
+ JCheckBoxMenuItem _parse_beast_style_extended_nexus_tags_cbmi;
+ // _ search
+ JCheckBoxMenuItem _search_case_senstive_cbmi;
+ JCheckBoxMenuItem _search_whole_words_only_cbmi;
+ JCheckBoxMenuItem _inverse_search_result_cbmi;
+ JCheckBoxMenuItem _search_with_regex_cbmi;
+ JCheckBoxMenuItem _color_all_found_nodes_when_coloring_subtree_cbmi;
+ // type menu:
+ JMenu _type_menu;
+ JCheckBoxMenuItem _rectangular_type_cbmi;
+ JCheckBoxMenuItem _triangular_type_cbmi;
+ JCheckBoxMenuItem _curved_type_cbmi;
+ JCheckBoxMenuItem _convex_type_cbmi;
+ JCheckBoxMenuItem _euro_type_cbmi;
+ JCheckBoxMenuItem _rounded_type_cbmi;
+ JCheckBoxMenuItem _unrooted_type_cbmi;
+ JCheckBoxMenuItem _circular_type_cbmi;
+ // view as text menu:
+ JMenuItem _view_as_NH_item;
+ JMenuItem _view_as_XML_item;
+ JMenuItem _view_as_nexus_item;
+ JMenuItem _display_basic_information_item;
+ // help menu:
+ JMenuItem _about_item;
+ JMenuItem _help_item;
+ JMenuItem _website_item;
+ JMenuItem _phyloxml_website_item;
+ JMenuItem _phyloxml_ref_item;
+ JMenuItem _aptx_ref_item;
+ //
+ File _current_dir;
+ JFileChooser _writetopdf_filechooser;
+ JFileChooser _save_filechooser;
+ JFileChooser _writetographics_filechooser;
+ // process menu:
+ JMenu _process_menu;
+ MainPanel _mainpanel;
+ Container _contentpane;
+ final LinkedList<TextFrame> _textframes = new LinkedList<TextFrame>(); ;
+ Configuration _configuration;
+ Options _options;
+ private Phylogeny _species_tree;
+ InferenceManager _inference_manager;
+ final ProcessPool _process_pool;
+ private String _previous_node_annotation_ref;
+
+ MainFrame() {
+ _process_pool = ProcessPool.createInstance();
+ _writetopdf_filechooser = new JFileChooser();
+ _writetopdf_filechooser.setMultiSelectionEnabled( false );
+ _writetopdf_filechooser.addChoosableFileFilter( pdffilter );
+ _writetographics_filechooser = new JFileChooser();
+ _writetographics_filechooser.setMultiSelectionEnabled( false );
+ _writetographics_filechooser.addChoosableFileFilter( graphicsfilefilter );
+ _save_filechooser = new JFileChooser();
+ _save_filechooser.setMultiSelectionEnabled( false );
+ _save_filechooser.setFileFilter( xmlfilter );
+ _save_filechooser.addChoosableFileFilter( nhfilter );
+ _save_filechooser.addChoosableFileFilter( nexusfilter );
+ _save_filechooser.addChoosableFileFilter( _save_filechooser.getAcceptAllFileFilter() );
+ try {
+ final String home_dir = System.getProperty( "user.home" );
+ _save_filechooser.setCurrentDirectory( new File( home_dir ) );
+ _writetopdf_filechooser.setCurrentDirectory( new File( home_dir ) );
+ _writetographics_filechooser.setCurrentDirectory( new File( home_dir ) );
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace();
+ // Do nothing. Not important.
+ }
+ }
+
+ /**
+ * Action performed.
+ */
+ @Override
+ public void actionPerformed( final ActionEvent e ) {
+ final Object o = e.getSource();
+ boolean is_applet = false;
+ JApplet applet = null;
+ if ( getCurrentTreePanel() != null ) {
+ is_applet = getCurrentTreePanel().isApplet();
+ if ( is_applet ) {
+ applet = getCurrentTreePanel().obtainApplet();
+ }
+ }
+ if ( o == _exit_item ) {
+ close();
+ }
+ else if ( o == _gsdi_item ) {
+ if ( isSubtreeDisplayed() ) {
+ return;
+ }
+ executeGSDI();
+ }
+ else if ( o == _gsdir_item ) {
+ if ( isSubtreeDisplayed() ) {
+ return;
+ }
+ executeGSDIR();
+ }
+ else if ( o == _taxcolor_item ) {
+ taxColor();
+ }
+ else if ( o == _confcolor_item ) {
+ confColor();
+ }
+ else if ( o == _color_rank_jmi ) {
+ colorRank();
+ }
+ else if ( o == _collapse_species_specific_subtrees ) {
+ if ( isSubtreeDisplayed() ) {
+ return;
+ }
+ if ( getCurrentTreePanel() != null ) {
+ getCurrentTreePanel().collapseSpeciesSpecificSubtrees();
+ }
+ }
+ else if ( o == _remove_branch_color_item ) {
+ if ( isSubtreeDisplayed() ) {
+ return;
+ }
+ removeBranchColors();
+ }
+ else if ( o == _remove_visual_styles_item ) {
+ if ( isSubtreeDisplayed() ) {
+ return;
+ }
+ removeVisualStyles();
+ }
+ else if ( o == _midpoint_root_item ) {
+ if ( isSubtreeDisplayed() ) {
+ return;
+ }
+ midpointRoot();
+ }
+ else if ( o == _delete_selected_nodes_item ) {
+ if ( isSubtreeDisplayed() ) {
+ return;
+ }
+ deleteSelectedNodes( true );
+ }
+ else if ( o == _delete_not_selected_nodes_item ) {
+ if ( isSubtreeDisplayed() ) {
+ return;
+ }
+ deleteSelectedNodes( false );
+ }
+ else if ( o == _annotate_item ) {
+ annotateSequences();
+ }
+ else if ( o == _switch_colors_mi ) {
+ switchColors();
+ }
+ else if ( o == _display_basic_information_item ) {
+ if ( getCurrentTreePanel() != null ) {
+ displayBasicInformation( getCurrentTreePanel().getTreeFile() );
+ }
+ }
+ else if ( o == _view_as_NH_item ) {
+ viewAsNH();
+ }
+ else if ( o == _view_as_XML_item ) {
+ viewAsXML();
+ }
+ else if ( o == _view_as_nexus_item ) {
+ viewAsNexus();
+ }
+ else if ( o == _super_tiny_fonts_item ) {
+ if ( getCurrentTreePanel() != null ) {
+ getCurrentTreePanel().setSuperTinyFonts();
+ getCurrentTreePanel().repaint();
+ }
+ }
+ else if ( o == _tiny_fonts_item ) {
+ if ( getCurrentTreePanel() != null ) {
+ getCurrentTreePanel().setTinyFonts();
+ getCurrentTreePanel().repaint();
+ }
+ }
+ else if ( o == _small_fonts_item ) {
+ if ( getCurrentTreePanel() != null ) {
+ getCurrentTreePanel().setSmallFonts();
+ getCurrentTreePanel().repaint();
+ }
+ }
+ else if ( o == _medium_fonts_item ) {
+ if ( getCurrentTreePanel() != null ) {
+ getCurrentTreePanel().setMediumFonts();
+ getCurrentTreePanel().repaint();
+ }
+ }
+ else if ( o == _large_fonts_item ) {
+ if ( getCurrentTreePanel() != null ) {
+ getCurrentTreePanel().setLargeFonts();
+ getCurrentTreePanel().repaint();
+ }
+ }
+ else if ( o == _choose_font_mi ) {
+ chooseFont();
+ }
+ else if ( o == _choose_minimal_confidence_mi ) {
+ chooseMinimalConfidence();
+ }
+ else if ( o == _choose_node_size_mi ) {
+ chooseNodeSize( getOptions(), this );
+ }
+ else if ( o == _overview_placment_mi ) {
+ MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );
+ }
+ else if ( o == _cycle_node_fill_mi ) {
+ MainFrame.cycleNodeFill( getOptions() );
+ }
+ else if ( o == _cycle_node_shape_mi ) {
+ MainFrame.cycleNodeShape( getOptions() );
+ }
+ else if ( o == _cycle_data_return ) {
+ MainFrame.cycleNodeDataReturn( getOptions(), getConfiguration() );
+ }
+ else if ( o == _screen_antialias_cbmi ) {
+ updateOptions( getOptions() );
+ updateScreenTextAntialias( getMainPanel().getTreePanels() );
+ }
+ else if ( o == _background_gradient_cbmi ) {
+ updateOptions( getOptions() );
+ }
+ else if ( o == _show_domain_labels ) {
+ updateOptions( getOptions() );
+ }
+ else if ( o == _show_annotation_ref_source ) {
+ updateOptions( getOptions() );
+ }
+ else if ( o == _abbreviate_scientific_names ) {
+ updateOptions( getOptions() );
+ }
+ else if ( o == _color_labels_same_as_parent_branch ) {
+ updateOptions( getOptions() );
+ }
+ else if ( o == _show_default_node_shapes_internal_cbmi ) {
+ updateOptions( getOptions() );
+ }
+ else if ( o == _show_default_node_shapes_external_cbmi ) {
+ updateOptions( getOptions() );
+ }
+ else if ( o == _show_default_node_shapes_for_marked_cbmi ) {
+ updateOptions( getOptions() );
+ }
+ else if ( o == _non_lined_up_cladograms_rbmi ) {
+ updateOptions( getOptions() );
+ showWhole();
+ }
+ else if ( o == _uniform_cladograms_rbmi ) {
+ updateOptions( getOptions() );
+ showWhole();
+ }
+ else if ( o == _ext_node_dependent_cladogram_rbmi ) {
+ updateOptions( getOptions() );
+ showWhole();
+ }
+ else if ( o == _search_case_senstive_cbmi ) {
+ updateOptions( getOptions() );
+ getMainPanel().getControlPanel().search0();
+ getMainPanel().getControlPanel().search1();
+ }
+ else if ( o == _search_whole_words_only_cbmi ) {
+ if ( ( _search_with_regex_cbmi != null ) && _search_whole_words_only_cbmi.isSelected() ) {
+ _search_with_regex_cbmi.setSelected( false );
+ }
+ updateOptions( getOptions() );
+ getMainPanel().getControlPanel().search0();
+ getMainPanel().getControlPanel().search1();
+ }
+ else if ( o == _inverse_search_result_cbmi ) {
+ updateOptions( getOptions() );
+ getMainPanel().getControlPanel().search0();
+ getMainPanel().getControlPanel().search1();
+ }
+ else if ( o == _search_with_regex_cbmi ) {
+ if ( ( _search_whole_words_only_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) {
+ _search_whole_words_only_cbmi.setSelected( false );
+ }
+ if ( ( _search_case_senstive_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) {
+ _search_case_senstive_cbmi.setSelected( true );
+ }
+ updateOptions( getOptions() );
+ getMainPanel().getControlPanel().search0();
+ getMainPanel().getControlPanel().search1();
+ }
+ else if ( o == _color_all_found_nodes_when_coloring_subtree_cbmi ) {
+ updateOptions( getOptions() );
+ }
+ else if ( o == _parse_beast_style_extended_nexus_tags_cbmi ) {
+ updateOptions( getOptions() );
+ }
+ else if ( o == _show_scale_cbmi ) {
+ updateOptions( getOptions() );
+ }
+ else if ( o == _color_by_taxonomic_group_cbmi ) {
+ updateOptions( getOptions() );
+ }
+ else if ( o == _show_confidence_stddev_cbmi ) {
+ updateOptions( getOptions() );
+ }
+ else if ( o == _use_brackets_for_conf_in_nh_export_cbmi ) {
+ if ( _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {
+ _use_internal_names_for_conf_in_nh_export_cbmi.setSelected( false );
+ }
+ updateOptions( getOptions() );
+ }
+ else if ( o == _use_internal_names_for_conf_in_nh_export_cbmi ) {
+ if ( _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {
+ _use_brackets_for_conf_in_nh_export_cbmi.setSelected( false );
+ }
+ updateOptions( getOptions() );
+ }
+ else if ( o == _label_direction_cbmi ) {
+ updateOptions( getOptions() );
+ }
+ else if ( o == _show_overview_cbmi ) {
+ updateOptions( getOptions() );
+ if ( getCurrentTreePanel() != null ) {
+ getCurrentTreePanel().updateOvSizes();
+ }
+ }
+ else if ( o == _line_up_renderable_data_cbmi ) {
+ if ( !_line_up_renderable_data_cbmi.isSelected() ) {
+ _right_line_up_domains_cbmi.setSelected( false );
+ }
+ updateOptions( getOptions() );
+ }
+ else if ( o == _right_line_up_domains_cbmi ) {
+ if ( _right_line_up_domains_cbmi.isSelected() ) {
+ _line_up_renderable_data_cbmi.setSelected( true );
+ }
+ updateOptions( getOptions() );
+ }
+ else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )
+ || ( o == _convex_type_cbmi ) || ( o == _euro_type_cbmi ) || ( o == _rounded_type_cbmi )
+ || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {
+ typeChanged( o );
+ }
+ else if ( o == _about_item ) {
+ about();
+ }
+ else if ( o == _help_item ) {
+ try {
+ AptxUtil.openWebsite( AptxConstants.APTX_DOC_SITE, is_applet, applet );
+ }
+ catch ( final IOException e1 ) {
+ ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() );
+ }
+ }
+ else if ( o == _website_item ) {
+ try {
+ AptxUtil.openWebsite( AptxConstants.APTX_WEB_SITE, is_applet, applet );
+ }
+ catch ( final IOException e1 ) {
+ ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() );
+ }
+ }
+ else if ( o == _phyloxml_website_item ) {
+ try {
+ AptxUtil.openWebsite( AptxConstants.PHYLOXML_WEB_SITE, is_applet, applet );
+ }
+ catch ( final IOException e1 ) {
+ ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() );
+ }
+ }
+ else if ( o == _aptx_ref_item ) {
+ try {
+ AptxUtil.openWebsite( AptxConstants.APTX_REFERENCE_URL, is_applet, applet );
+ }
+ catch ( final IOException e1 ) {
+ ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() );
+ }
+ }
+ else if ( o == _phyloxml_ref_item ) {
+ try {
+ AptxUtil.openWebsite( AptxConstants.PHYLOXML_REFERENCE_URL, is_applet, applet );
+ }
+ catch ( final IOException e1 ) {
+ ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() );
+ }
+ }
+ else if ( o == _write_to_pdf_item ) {
+ final File curr_dir = writeToPdf( _mainpanel.getCurrentPhylogeny(),
+ getMainPanel(),
+ _writetopdf_filechooser,
+ _current_dir,
+ getContentPane(),
+ this );
+ if ( curr_dir != null ) {
+ setCurrentDir( curr_dir );
+ }
+ }
+ else if ( o == _save_all_item ) {
+ writeAllToFile();
+ }
+ else if ( o == _write_to_jpg_item ) {
+ final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(),
+ GraphicsExportType.JPG,
+ _mainpanel,
+ _writetographics_filechooser,
+ this,
+ getContentPane(),
+ _current_dir );
+ if ( new_dir != null ) {
+ setCurrentDir( new_dir );
+ }
+ }
+ else if ( o == _write_to_gif_item ) {
+ final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(),
+ GraphicsExportType.GIF,
+ _mainpanel,
+ _writetographics_filechooser,
+ this,
+ getContentPane(),
+ _current_dir );
+ if ( new_dir != null ) {
+ setCurrentDir( new_dir );
+ }
+ }
+ else if ( o == _write_to_tif_item ) {
+ final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(),
+ GraphicsExportType.TIFF,
+ _mainpanel,
+ _writetographics_filechooser,
+ this,
+ getContentPane(),
+ _current_dir );
+ if ( new_dir != null ) {
+ setCurrentDir( new_dir );
+ }
+ }
+ else if ( o == _write_to_bmp_item ) {
+ final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(),
+ GraphicsExportType.BMP,
+ _mainpanel,
+ _writetographics_filechooser,
+ this,
+ getContentPane(),
+ _current_dir );
+ if ( new_dir != null ) {
+ setCurrentDir( new_dir );
+ }
+ }
+ else if ( o == _write_to_png_item ) {
+ final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(),
+ GraphicsExportType.PNG,
+ _mainpanel,
+ _writetographics_filechooser,
+ this,
+ getContentPane(),
+ _current_dir );
+ if ( new_dir != null ) {
+ setCurrentDir( new_dir );
+ }
+ }
+ else if ( o == _print_item ) {
+ print( getCurrentTreePanel(), getOptions(), this );
+ }
+ else if ( o == _save_item ) {
+ final File new_dir = writeToFile( _mainpanel.getCurrentPhylogeny(),
+ getMainPanel(),
+ _save_filechooser,
+ _current_dir,
+ getContentPane(),
+ this );
+ if ( new_dir != null ) {
+ setCurrentDir( new_dir );
+ }
+ }
+ else if ( o == _graphics_export_visible_only_cbmi ) {
+ updateOptions( getOptions() );
+ }
+ else if ( o == _antialias_print_cbmi ) {
+ updateOptions( getOptions() );
+ }
+ else if ( o == _print_black_and_white_cbmi ) {
+ updateOptions( getOptions() );
+ }
+ else if ( o == _choose_pdf_width_mi ) {
+ choosePdfWidth();
+ }
+ else if ( o == _lineage_inference ) {
+ if ( isSubtreeDisplayed() ) {
+ JOptionPane.showMessageDialog( this,
+ "Subtree is shown.",
+ "Cannot infer ancestral taxonomies",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ executeLineageInference();
+ }
+ else {
+ if ( _load_phylogeny_from_webservice_menu_items != null ) {
+ for( int i = 0; i < _load_phylogeny_from_webservice_menu_items.length; ++i ) {
+ if ( o == _load_phylogeny_from_webservice_menu_items[ i ] ) {
+ readPhylogeniesFromWebservice( i );
+ }
+ }
+ }
+ }
+ _contentpane.repaint();
+ }
+
+ public Configuration getConfiguration() {
+ return _configuration;
+ }
+
+ /**
+ * This method returns the current external node data which
+ * has been selected by the user by clicking the "Return ..."
+ * menu item. This method is expected to be called from Javascript or
+ * something like it.
+ *
+ * @return current external node data as String
+ */
+ public String getCurrentExternalNodesDataBuffer() {
+ return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();
+ }
+
+ public int getCurrentExternalNodesDataBufferChangeCounter() {
+ return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();
+ }
+
+ public int getCurrentExternalNodesDataBufferLength() {
+ return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();
+ }
+
+ public InferenceManager getInferenceManager() {
+ return _inference_manager;
+ }
+
+ public MainPanel getMainPanel() {
+ return _mainpanel;
+ }
+
+ public Options getOptions() {
+ return _options;
+ }
+
+ public ProcessPool getProcessPool() {
+ return _process_pool;
+ }
+
+ public void showTextFrame( final String s, final String title ) {
+ checkTextFrames();
+ _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );
+ }
+
+ public void showWhole() {
+ _mainpanel.getControlPanel().showWhole();
+ }
+
+ public void updateProcessMenu() {
+ // In general Swing is not thread safe.
+ // See "Swing's Threading Policy".
+ SwingUtilities.invokeLater( new Runnable() {
+
+ @Override
+ public void run() {
+ doUpdateProcessMenu();
+ }
+ } );
+ }
+
+ private void annotateSequences() {
+ if ( getCurrentTreePanel() != null ) {
+ List<PhylogenyNode> nodes = null;
+ if ( ( getCurrentTreePanel().getFoundNodes0() != null )
+ || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {
+ nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();
+ }
+ if ( ( nodes == null ) || nodes.isEmpty() ) {
+ JOptionPane
+ .showMessageDialog( this,
+ "Need to select nodes, either via direct selection or via the \"Search\" function",
+ "No nodes selected for annotation",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ final Phylogeny phy = getMainPanel().getCurrentPhylogeny();
+ if ( ( phy != null ) && !phy.isEmpty() ) {
+ final JTextField ref_field = new JTextField( 10 );
+ final JTextField desc_filed = new JTextField( 20 );
+ ref_field.setText( ForesterUtil.isEmpty( getPreviousNodeAnnotationReference() ) ? ""
+ : getPreviousNodeAnnotationReference() );
+ final JPanel my_panel = new JPanel();
+ my_panel.add( new JLabel( "Reference " ) );
+ my_panel.add( ref_field );
+ my_panel.add( Box.createHorizontalStrut( 15 ) );
+ my_panel.add( new JLabel( "Description " ) );
+ my_panel.add( desc_filed );
+ final int result = JOptionPane.showConfirmDialog( null,
+ my_panel,
+ "Enter the sequence annotation(s) for the "
+ + nodes.size() + " selected nodes",
+ JOptionPane.OK_CANCEL_OPTION );
+ if ( result == JOptionPane.OK_OPTION ) {
+ String ref = ref_field.getText();
+ String desc = desc_filed.getText();
+ if ( !ForesterUtil.isEmpty( ref ) ) {
+ ref = ref.trim();
+ ref = ref.replaceAll( "\\s+", " " );
+ if ( ( ref.indexOf( ':' ) < 1 ) || ( ref.indexOf( ':' ) > ( ref.length() - 2 ) )
+ || ( ref.length() < 3 ) ) {
+ JOptionPane.showMessageDialog( this,
+ "Reference needs to be in the form of \"GO:1234567\"",
+ "Illegal Format for Annotation Reference",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ }
+ if ( ref != null ) {
+ setPreviousNodeAnnotationReference( ref );
+ }
+ if ( desc != null ) {
+ desc = desc.trim();
+ desc = desc.replaceAll( "\\s+", " " );
+ }
+ if ( !ForesterUtil.isEmpty( ref ) || !ForesterUtil.isEmpty( desc ) ) {
+ for( final PhylogenyNode n : nodes ) {
+ ForesterUtil.ensurePresenceOfSequence( n );
+ final Annotation ann = ForesterUtil.isEmpty( ref ) ? new Annotation()
+ : new Annotation( ref );
+ if ( !ForesterUtil.isEmpty( desc ) ) {
+ ann.setDesc( desc );
+ }
+ n.getNodeData().getSequence().addAnnotation( ann );
+ }
+ }
+ getMainPanel().getControlPanel().showAnnotations();
+ }
+ }
+ }
+ }
+
+ private void chooseFont() {
+ final FontChooser fc = new FontChooser();
+ fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
+ fc.showDialog( this, "Select the Base Font" );
+ getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );
+ getControlPanel().displayedPhylogenyMightHaveChanged( true );
+ getMainPanel().getCurrentTreePanel().resetPreferredSize();
+ getMainPanel().getCurrentTreePanel().updateOvSizes();
+
+ repaint();
+ }
+
+ private void chooseMinimalConfidence() {
+ final String s = ( String ) JOptionPane
+ .showInputDialog( this,
+ "Please enter the minimum for confidence values to be displayed.\n"
+ + "[current value: " + getOptions().getMinConfidenceValue() + "]\n",
+ "Minimal Confidence Value",
+ JOptionPane.QUESTION_MESSAGE,
+ null,
+ null,
+ getOptions().getMinConfidenceValue() );
+ if ( !ForesterUtil.isEmpty( s ) ) {
+ boolean success = true;
+ double m = 0.0;
+ final String m_str = s.trim();
+ if ( !ForesterUtil.isEmpty( m_str ) ) {
+ try {
+ m = Double.parseDouble( m_str );
+ }
+ catch ( final Exception ex ) {
+ success = false;
+ }
+ }
+ else {
+ success = false;
+ }
+ if ( success && ( m >= 0.0 ) ) {
+ getOptions().setMinConfidenceValue( m );
+ }
+ }
+ }
+
+ private void deleteSelectedNodes( final boolean delete ) {
+ final Phylogeny phy = getMainPanel().getCurrentPhylogeny();
+ if ( ( phy == null ) || ( phy.getNumberOfExternalNodes() < 2 ) ) {
+ return;
+ }
+ final List<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( this,
+ "Need to select external nodes, either via direct selection or via the \"Search\" function",
+ "No external nodes selected to " + function.toLowerCase(),
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ final int todo = nodes.size();
+ final int ext = phy.getNumberOfExternalNodes();
+ int res = todo;
+ if ( delete ) {
+ res = ext - todo;
+ }
+ if ( res < 1 ) {
+ JOptionPane.showMessageDialog( this,
+ "Cannot delete all nodes",
+ "Attempt to delete all nodes ",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ final int result = JOptionPane.showConfirmDialog( null, function + " " + todo
+ + " external node(s), from a total of " + ext + " external nodes," + "\nresulting in tree with " + res
+ + " nodes?", function + " external nodes", JOptionPane.OK_CANCEL_OPTION );
+ if ( result == JOptionPane.OK_OPTION ) {
+ if ( !delete ) {
+ final List<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( this,
+ file + " already exists. Overwrite?",
+ "Warning",
+ JOptionPane.OK_CANCEL_OPTION,
+ JOptionPane.WARNING_MESSAGE );
+ if ( i != JOptionPane.OK_OPTION ) {
+ return;
+ }
+ else {
+ try {
+ file.delete();
+ }
+ catch ( final Exception e ) {
+ JOptionPane.showMessageDialog( this,
+ "Failed to delete: " + file,
+ "Error",
+ JOptionPane.WARNING_MESSAGE );
+ }
+ }
+ }
+ final int count = getMainPanel().getTabbedPane().getTabCount();
+ final List<Phylogeny> trees = new ArrayList<Phylogeny>();
+ for( int i = 0; i < count; ++i ) {
+ final Phylogeny phy = getMainPanel().getPhylogeny( i );
+ if ( ForesterUtil.isEmpty( phy.getName() )
+ && !ForesterUtil.isEmpty( getMainPanel().getTabbedPane().getTitleAt( i ) ) ) {
+ phy.setName( getMainPanel().getTabbedPane().getTitleAt( i ) );
+ }
+ trees.add( phy );
+ getMainPanel().getTreePanels().get( i ).setEdited( false );
+ }
+ final PhylogenyWriter writer = new PhylogenyWriter();
+ try {
+ writer.toPhyloXML( file, trees, 0, ForesterUtil.LINE_SEPARATOR );
+ }
+ catch ( final IOException e ) {
+ JOptionPane.showMessageDialog( this,
+ "Failed to write to: " + file,
+ "Error",
+ JOptionPane.WARNING_MESSAGE );
+ }
+ }
+ }
+
+ void activateSaveAllIfNeeded() {
+ if ( ( getMainPanel().getTabbedPane() != null ) && ( getMainPanel().getTabbedPane().getTabCount() > 1 ) ) {
+ _save_all_item.setEnabled( true );
+ }
+ else {
+ _save_all_item.setEnabled( false );
+ }
+ }
+
+ void buildFileMenu() {
+ _file_jmenu = MainFrame.createMenu( "File", getConfiguration() );
+ _file_jmenu.add( _save_item = new JMenuItem( "Save Tree As..." ) );
+ _file_jmenu.addSeparator();
+ _file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) );
+ if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" ) || AptxUtil.canWriteFormat( "TIF" ) ) {
+ _file_jmenu.add( _write_to_tif_item = new JMenuItem( "Export to TIFF file..." ) );
+ }
+ _file_jmenu.add( _write_to_png_item = new JMenuItem( "Export to PNG file..." ) );
+ _file_jmenu.add( _write_to_jpg_item = new JMenuItem( "Export to JPG file..." ) );
+ if ( AptxUtil.canWriteFormat( "gif" ) ) {
+ _file_jmenu.add( _write_to_gif_item = new JMenuItem( "Export to GIF file..." ) );
+ }
+ if ( AptxUtil.canWriteFormat( "bmp" ) ) {
+ _file_jmenu.add( _write_to_bmp_item = new JMenuItem( "Export to BMP file..." ) );
+ }
+ _file_jmenu.addSeparator();
+ _file_jmenu.add( _print_item = new JMenuItem( "Print..." ) );
+ _file_jmenu.addSeparator();
+ _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );
+ customizeJMenuItem( _save_item );
+ customizeJMenuItem( _write_to_pdf_item );
+ customizeJMenuItem( _write_to_png_item );
+ customizeJMenuItem( _write_to_jpg_item );
+ customizeJMenuItem( _write_to_gif_item );
+ customizeJMenuItem( _write_to_tif_item );
+ customizeJMenuItem( _write_to_bmp_item );
+ customizeJMenuItem( _print_item );
+ customizeJMenuItem( _exit_item );
+ _jmenubar.add( _file_jmenu );
+ }
+
+ void buildFontSizeMenu() {
+ _font_size_menu = createMenu( FONT_SIZE_MENU_LABEL, getConfiguration() );
+ _font_size_menu.add( _super_tiny_fonts_item = new JMenuItem( "Super Tiny Fonts" ) );
+ _font_size_menu.add( _tiny_fonts_item = new JMenuItem( "Tiny Fonts" ) );
+ _font_size_menu.add( _small_fonts_item = new JMenuItem( "Small Fonts" ) );
+ _font_size_menu.add( _medium_fonts_item = new JMenuItem( "Medium Fonts" ) );
+ _font_size_menu.add( _large_fonts_item = new JMenuItem( "Large Fonts" ) );
+ customizeJMenuItem( _super_tiny_fonts_item );
+ customizeJMenuItem( _tiny_fonts_item );
+ customizeJMenuItem( _small_fonts_item );
+ customizeJMenuItem( _medium_fonts_item );
+ customizeJMenuItem( _large_fonts_item );
+ _jmenubar.add( _font_size_menu );
+ }
+
+ void buildHelpMenu() {
+ _help_jmenu = createMenu( "Help", getConfiguration() );
+ _help_jmenu.add( _help_item = new JMenuItem( "Documentation" ) );
+ _help_jmenu.addSeparator();
+ _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );
+ _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" ); //TODO need to add this...
+ _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );
+ _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );
+ _help_jmenu.addSeparator();
+ _help_jmenu.add( _about_item = new JMenuItem( "About" ) );
+ customizeJMenuItem( _help_item );
+ customizeJMenuItem( _website_item );
+ customizeJMenuItem( _phyloxml_website_item );
+ customizeJMenuItem( _aptx_ref_item );
+ customizeJMenuItem( _phyloxml_ref_item );
+ customizeJMenuItem( _about_item );
+ _phyloxml_ref_item.setToolTipText( PHYLOXML_REF_TOOL_TIP );
+ _aptx_ref_item.setToolTipText( APTX_REF_TOOL_TIP );
+ _jmenubar.add( _help_jmenu );
+ }
+
+ void buildTypeMenu() {
+ _type_menu = createMenu( TYPE_MENU_HEADER, getConfiguration() );
+ _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );
+ _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );
+ _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );
+ _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );
+ _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );
+ _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );
+ _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );
+ _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );
+ customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );
+ customizeCheckBoxMenuItem( _triangular_type_cbmi, false );
+ customizeCheckBoxMenuItem( _euro_type_cbmi, false );
+ customizeCheckBoxMenuItem( _rounded_type_cbmi, false );
+ customizeCheckBoxMenuItem( _curved_type_cbmi, false );
+ customizeCheckBoxMenuItem( _convex_type_cbmi, false );
+ customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );
+ customizeCheckBoxMenuItem( _circular_type_cbmi, false );
+ _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
+ _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
+ initializeTypeMenu( getOptions() );
+ _jmenubar.add( _type_menu );
+ }
+
+ void buildViewMenu() {
+ _view_jmenu = createMenu( "View", getConfiguration() );
+ _view_jmenu.add( _display_basic_information_item = new JMenuItem( SHOW_BASIC_TREE_INFORMATION_LABEL ) );
+ _view_jmenu.addSeparator();
+ _view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) );
+ _view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) );
+ _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "as Nexus" ) );
+ customizeJMenuItem( _display_basic_information_item );
+ customizeJMenuItem( _view_as_NH_item );
+ customizeJMenuItem( _view_as_XML_item );
+ customizeJMenuItem( _view_as_nexus_item );
+ _jmenubar.add( _view_jmenu );
+ }
+
+ void checkTextFrames() {
+ if ( _textframes.size() > 5 ) {
+ try {
+ if ( _textframes.getFirst() != null ) {
+ _textframes.getFirst().removeMe();
+ }
+ else {
+ _textframes.removeFirst();
+ }
+ }
+ catch ( final NoSuchElementException e ) {
+ // Ignore.
+ }
+ }
+ }
+
+ void choosePdfWidth() {
+ final String s = ( String ) JOptionPane.showInputDialog( this,
+ "Please enter the default line width for PDF export.\n"
+ + "[current value: "
+ + getOptions().getPrintLineWidth() + "]\n",
+ "Line Width for PDF Export",
+ JOptionPane.QUESTION_MESSAGE,
+ null,
+ null,
+ getOptions().getPrintLineWidth() );
+ if ( !ForesterUtil.isEmpty( s ) ) {
+ boolean success = true;
+ float f = 0.0f;
+ final String m_str = s.trim();
+ if ( !ForesterUtil.isEmpty( m_str ) ) {
+ try {
+ f = Float.parseFloat( m_str );
+ }
+ catch ( final Exception ex ) {
+ success = false;
+ }
+ }
+ else {
+ success = false;
+ }
+ if ( success && ( f > 0.0 ) ) {
+ getOptions().setPrintLineWidth( f );
+ }
+ }
+ }
+
+ void close() {
+ removeAllTextFrames();
+ if ( _mainpanel != null ) {
+ _mainpanel.terminate();
+ }
+ if ( _contentpane != null ) {
+ _contentpane.removeAll();
+ }
+ setVisible( false );
+ dispose();
+ }
+
+ void colorRank() {
+ if ( _mainpanel.getCurrentTreePanel() != null ) {
+ final String[] ranks = AptxUtil.getAllPossibleRanks();
+ final String rank = ( String ) JOptionPane
+ .showInputDialog( this,
+ "What rank should the colorization be based on",
+ "Rank Selection",
+ JOptionPane.QUESTION_MESSAGE,
+ null,
+ ranks,
+ null );
+ if ( !ForesterUtil.isEmpty( rank ) ) {
+ _mainpanel.getCurrentTreePanel().colorRank( rank );
+ }
+ }
+ }
+
+ void confColor() {
+ if ( _mainpanel.getCurrentTreePanel() != null ) {
+ _mainpanel.getCurrentTreePanel().confColor();
+ }
+ }
+
+ void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {
+ if ( item != null ) {
+ item.setFont( MainFrame.menu_font );
+ if ( !getConfiguration().isUseNativeUI() ) {
+ item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
+ item.setForeground( getConfiguration().getGuiMenuTextColor() );
+ }
+ item.setSelected( is_selected );
+ item.addActionListener( this );
+ }
+ }
+
+ JMenuItem customizeJMenuItem( final JMenuItem jmi ) {
+ if ( jmi != null ) {
+ jmi.setFont( MainFrame.menu_font );
+ if ( !getConfiguration().isUseNativeUI() ) {
+ jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
+ jmi.setForeground( getConfiguration().getGuiMenuTextColor() );
+ }
+ jmi.addActionListener( this );
+ }
+ return jmi;
+ }
+
+ void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {
+ if ( item != null ) {
+ item.setFont( MainFrame.menu_font );
+ if ( !getConfiguration().isUseNativeUI() ) {
+ item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
+ item.setForeground( getConfiguration().getGuiMenuTextColor() );
+ }
+ item.setSelected( is_selected );
+ item.addActionListener( this );
+ }
+ }
+
+ void displayBasicInformation( final File treefile ) {
+ if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
+ String title = "Basic Information";
+ if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
+ title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\"";
+ }
+ showTextFrame( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny(), treefile ), title );
+ }
+ }
+
+ void exceptionOccuredDuringOpenFile( final Exception e ) {
+ try {
+ _mainpanel.getCurrentTreePanel().setArrowCursor();
+ }
+ catch ( final Exception ex ) {
+ // Do nothing.
+ }
+ JOptionPane.showMessageDialog( this,
+ ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
+ "Error during File|Open",
+ JOptionPane.ERROR_MESSAGE );
+ }
+
+ void executeGSDI() {
+ if ( !isOKforSDI( false, true ) ) {
+ return;
+ }
+ if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
+ JOptionPane.showMessageDialog( this,
+ "Gene tree is not rooted.",
+ "Cannot execute GSDI",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
+ gene_tree.setAllNodesToNotCollapse();
+ gene_tree.recalculateNumberOfExternalDescendants( false );
+ GSDI gsdi = null;
+ final Phylogeny species_tree = getSpeciesTree().copy();
+ try {
+ gsdi = new GSDI( gene_tree, species_tree, false, true, true, true );
+ }
+ catch ( final SDIException e ) {
+ JOptionPane.showMessageDialog( this,
+ e.getLocalizedMessage(),
+ "Error during GSDI",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ catch ( final Exception e ) {
+ AptxUtil.unexpectedException( e );
+ return;
+ }
+ gene_tree.setRerootable( false );
+ gene_tree.clearHashIdToNodeMap();
+ gene_tree.recalculateNumberOfExternalDescendants( true );
+ _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null );
+ getMainPanel().getControlPanel().setShowEvents( true );
+ showWhole();
+ final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
+ _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
+ showWhole();
+ _mainpanel.getTabbedPane().setSelectedIndex( selected );
+ showWhole();
+ _mainpanel.getCurrentTreePanel().setEdited( true );
+ final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
+ if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) {
+ JOptionPane.showMessageDialog( this,
+ "Duplications: " + gsdi.getDuplicationsSum() + "\n"
+ + "Potential duplications: "
+ + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
+ + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
+ + "Stripped gene tree nodes: "
+ + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
+ + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
+ + "Number of polytomies in species tree used: " + poly + "\n",
+ "GSDI successfully completed",
+ JOptionPane.WARNING_MESSAGE );
+ }
+ else {
+ JOptionPane.showMessageDialog( this,
+ "Duplications: " + gsdi.getDuplicationsSum() + "\n"
+ + "Potential duplications: "
+ + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
+ + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
+ + "Stripped gene tree nodes: "
+ + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
+ + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
+ + "Number of polytomies in species tree used: " + poly + "\n",
+ "GSDI successfully completed",
+ JOptionPane.INFORMATION_MESSAGE );
+ }
+ }
+
+ void executeGSDIR() {
+ if ( !isOKforSDI( false, false ) ) {
+ return;
+ }
+ final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() );
+ if ( ( p > 0 )
+ && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) {
+ JOptionPane.showMessageDialog( this,
+ "Gene tree is not completely binary",
+ "Cannot execute GSDI",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
+ gene_tree.setAllNodesToNotCollapse();
+ gene_tree.recalculateNumberOfExternalDescendants( false );
+ GSDIR gsdir = null;
+ final Phylogeny species_tree = getSpeciesTree().copy();
+ try {
+ gsdir = new GSDIR( gene_tree, species_tree, true, true, true );
+ }
+ catch ( final SDIException e ) {
+ JOptionPane.showMessageDialog( this,
+ e.getLocalizedMessage(),
+ "Error during GSDIR",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ catch ( final Exception e ) {
+ AptxUtil.unexpectedException( e );
+ return;
+ }
+ final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree();
+ result_gene_tree.setRerootable( false );
+ result_gene_tree.clearHashIdToNodeMap();
+ result_gene_tree.recalculateNumberOfExternalDescendants( true );
+ PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );
+ _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );
+ getMainPanel().getControlPanel().setShowEvents( true );
+ showWhole();
+ final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
+ _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
+ showWhole();
+ _mainpanel.getTabbedPane().setSelectedIndex( selected );
+ showWhole();
+ _mainpanel.getCurrentTreePanel().setEdited( true );
+ final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
+ if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) {
+ JOptionPane.showMessageDialog( this,
+ "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
+ + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
+ + "Stripped gene tree nodes: "
+ + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
+ + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
+ + "Number of polytomies in species tree used: " + poly + "\n",
+ "GSDIR successfully completed",
+ JOptionPane.WARNING_MESSAGE );
+ }
+ else {
+ JOptionPane.showMessageDialog( this,
+ "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
+ + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
+ + "Stripped gene tree nodes: "
+ + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
+ + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
+ + "Number of polytomies in species tree used: " + poly + "\n",
+ "GSDIR successfully completed",
+ JOptionPane.INFORMATION_MESSAGE );
+ }
+ }
+
+ void executeLineageInference() {
+ if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) {
+ return;
+ }
+ if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
+ JOptionPane.showMessageDialog( this,
+ "Phylogeny is not rooted.",
+ "Cannot infer ancestral taxonomies",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ final AncestralTaxonomyInferrer inferrer = new AncestralTaxonomyInferrer( this,
+ _mainpanel.getCurrentTreePanel(),
+ _mainpanel.getCurrentPhylogeny()
+ .copy() );
+ new Thread( inferrer ).start();
+ }
+
+ boolean GAndSDoHaveMoreThanOneSpeciesInComman( final Phylogeny gene_tree ) {
+ if ( ( gene_tree == null ) || gene_tree.isEmpty() ) {
+ JOptionPane.showMessageDialog( this,
+ "Gene tree and species tree have no species in common.",
+ "Error during SDI",
+ JOptionPane.ERROR_MESSAGE );
+ return false;
+ }
+ else if ( gene_tree.getNumberOfExternalNodes() < 2 ) {
+ JOptionPane.showMessageDialog( this,
+ "Gene tree and species tree have only one species in common.",
+ "Error during SDI",
+ JOptionPane.ERROR_MESSAGE );
+ return false;
+ }
+ else {
+ return true;
+ }
+ }
+
+ ControlPanel getControlPanel() {
+ return getMainPanel().getControlPanel();
+ }
+
+ File getCurrentDir() {
+ if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
+ if ( ForesterUtil.isWindows() ) {
+ try {
+ _current_dir = new File( WindowsUtils.getCurrentUserDesktopPath() );
+ }
+ catch ( final Exception e ) {
+ _current_dir = null;
+ }
+ }
+ }
+ if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
+ if ( System.getProperty( "user.home" ) != null ) {
+ _current_dir = new File( System.getProperty( "user.home" ) );
+ }
+ else if ( System.getProperty( "user.dir" ) != null ) {
+ _current_dir = new File( System.getProperty( "user.dir" ) );
+ }
+ }
+ return _current_dir;
+ }
+
+ TreePanel getCurrentTreePanel() {
+ return getMainPanel().getCurrentTreePanel();
+ }
+
+ JMenu getHelpMenu() {
+ return _help_jmenu;
+ }
+
+ JCheckBoxMenuItem getlabelDirectionCbmi() {
+ return _label_direction_cbmi;
+ }
+
+ JMenuBar getMenuBarOfMainFrame() {
+ return _jmenubar;
+ }
+
+ final Phylogeny getSpeciesTree() {
+ return _species_tree;
+ }
+
+ void initializeTypeMenu( final Options options ) {
+ setTypeMenuToAllUnselected();
+ switch ( options.getPhylogenyGraphicsType() ) {
+ case CONVEX:
+ _convex_type_cbmi.setSelected( true );
+ break;
+ case CURVED:
+ _curved_type_cbmi.setSelected( true );
+ break;
+ case EURO_STYLE:
+ _euro_type_cbmi.setSelected( true );
+ break;
+ case ROUNDED:
+ _rounded_type_cbmi.setSelected( true );
+ break;
+ case TRIANGULAR:
+ _triangular_type_cbmi.setSelected( true );
+ break;
+ case UNROOTED:
+ _unrooted_type_cbmi.setSelected( true );
+ break;
+ case CIRCULAR:
+ _circular_type_cbmi.setSelected( true );
+ break;
+ default:
+ _rectangular_type_cbmi.setSelected( true );
+ break;
+ }
+ }
+
+ boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {
+ if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {
+ return false;
+ }
+ else if ( ( getSpeciesTree() == null ) || getSpeciesTree().isEmpty() ) {
+ JOptionPane.showMessageDialog( this,
+ "No species tree loaded",
+ "Cannot execute GSDI",
+ JOptionPane.ERROR_MESSAGE );
+ return false;
+ }
+ else if ( species_tree_has_to_binary && !getSpeciesTree().isCompletelyBinary() ) {
+ JOptionPane.showMessageDialog( this,
+ "Species tree is not completely binary",
+ "Cannot execute GSDI",
+ JOptionPane.ERROR_MESSAGE );
+ return false;
+ }
+ else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {
+ JOptionPane.showMessageDialog( this,
+ "Gene tree is not completely binary",
+ "Cannot execute GSDI",
+ JOptionPane.ERROR_MESSAGE );
+ return false;
+ }
+ else {
+ return true;
+ }
+ }
+
+ boolean isSubtreeDisplayed() {
+ if ( getCurrentTreePanel() != null ) {
+ if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {
+ JOptionPane
+ .showMessageDialog( this,
+ "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",
+ "Operation can not be exectuted on a sub-tree",
+ JOptionPane.WARNING_MESSAGE );
+ return true;
+ }
+ }
+ return false;
+ }
+
+ void midpointRoot() {
+ if ( _mainpanel.getCurrentTreePanel() != null ) {
+ _mainpanel.getCurrentTreePanel().midpointRoot();
+ }
+ }
+
+ void readPhylogeniesFromWebservice( final int i ) {
+ final UrlTreeReader reader = new UrlTreeReader( this, i );
+ new Thread( reader ).start();
+ }
+
+ void removeAllTextFrames() {
+ for( final TextFrame tf : _textframes ) {
+ if ( tf != null ) {
+ tf.close();
+ }
+ }
+ _textframes.clear();
+ }
+
+ void resetSearch() {
+ getMainPanel().getCurrentTreePanel().setFoundNodes0( null );
+ getMainPanel().getCurrentTreePanel().setFoundNodes1( null );
+ getMainPanel().getControlPanel().setSearchFoundCountsOnLabel0( 0 );
+ getMainPanel().getControlPanel().getSearchFoundCountsLabel0().setVisible( false );
+ getMainPanel().getControlPanel().getSearchTextField0().setText( "" );
+ getMainPanel().getControlPanel().getSearchResetButton0().setEnabled( false );
+ getMainPanel().getControlPanel().getSearchResetButton0().setVisible( false );
+ getMainPanel().getControlPanel().setSearchFoundCountsOnLabel1( 0 );
+ getMainPanel().getControlPanel().getSearchFoundCountsLabel1().setVisible( false );
+ getMainPanel().getControlPanel().getSearchTextField1().setText( "" );
+ getMainPanel().getControlPanel().getSearchResetButton1().setEnabled( false );
+ getMainPanel().getControlPanel().getSearchResetButton1().setVisible( false );
+ }
+
+ void setConfiguration( final Configuration configuration ) {
+ _configuration = configuration;
+ }
+
+ void setCurrentDir( final File current_dir ) {
+ _current_dir = current_dir;
+ }
+
+ void setInferenceManager( final InferenceManager i ) {
+ _inference_manager = i;
+ }
+
+ void setOptions( final Options options ) {
+ _options = options;
+ }
+
+ void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {
+ setTypeMenuToAllUnselected();
+ switch ( type ) {
+ case CIRCULAR:
+ _circular_type_cbmi.setSelected( true );
+ break;
+ case CONVEX:
+ _convex_type_cbmi.setSelected( true );
+ break;
+ case CURVED:
+ _curved_type_cbmi.setSelected( true );
+ break;
+ case EURO_STYLE:
+ _euro_type_cbmi.setSelected( true );
+ break;
+ case ROUNDED:
+ _rounded_type_cbmi.setSelected( true );
+ break;
+ case RECTANGULAR:
+ _rectangular_type_cbmi.setSelected( true );
+ break;
+ case TRIANGULAR:
+ _triangular_type_cbmi.setSelected( true );
+ break;
+ case UNROOTED:
+ _unrooted_type_cbmi.setSelected( true );
+ break;
+ default:
+ throw new IllegalArgumentException( "unknown type: " + type );
+ }
+ }
+
+ final void setSpeciesTree( final Phylogeny species_tree ) {
+ _species_tree = species_tree;
+ }
+
+ void setTypeMenuToAllUnselected() {
+ _convex_type_cbmi.setSelected( false );
+ _curved_type_cbmi.setSelected( false );
+ _euro_type_cbmi.setSelected( false );
+ _rounded_type_cbmi.setSelected( false );
+ _triangular_type_cbmi.setSelected( false );
+ _rectangular_type_cbmi.setSelected( false );
+ _unrooted_type_cbmi.setSelected( false );
+ _circular_type_cbmi.setSelected( false );
+ }
+
+ void switchColors() {
+ final TreeColorSet colorset = _mainpanel.getTreeColorSet();
+ final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );
+ csc.setVisible( true );
+ }
+
+ void taxColor() {
+ if ( _mainpanel.getCurrentTreePanel() != null ) {
+ _mainpanel.getCurrentTreePanel().taxColor();
+ }
+ }
+
+ void typeChanged( final Object o ) {
+ updateTypeCheckboxes( getOptions(), o );
+ updateOptions( getOptions() );
+ if ( getCurrentTreePanel() != null ) {
+ final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();
+ final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();
+ if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
+ || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )
+ || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
+ || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {
+ getCurrentTreePanel().getControlPanel().showWhole();
+ }
+ if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
+ getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );
+ }
+ else {
+ getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );
+ }
+ getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );
+ updateScreenTextAntialias( getMainPanel().getTreePanels() );
+ if ( getCurrentTreePanel().getControlPanel().getDynamicallyHideData() != null ) {
+ if ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
+ getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( false );
+ }
+ else {
+ getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( true );
+ }
+ }
+ }
+ }
+
+ void updateOptions( final Options options ) {
+ options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );
+ options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
+ && _background_gradient_cbmi.isSelected() );
+ options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
+ options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null )
+ && _show_annotation_ref_source.isSelected() );
+ options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
+ && _abbreviate_scientific_names.isSelected() );
+ options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
+ && _color_labels_same_as_parent_branch.isSelected() );
+ options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )
+ && _show_default_node_shapes_internal_cbmi.isSelected() );
+ options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )
+ && _show_default_node_shapes_external_cbmi.isSelected() );
+ options.setShowDefaultNodeShapesForMarkedNodes( ( _show_default_node_shapes_for_marked_cbmi != null )
+ && _show_default_node_shapes_for_marked_cbmi.isSelected() );
+ if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
+ options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
+ }
+ else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {
+ options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
+ }
+ else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {
+ options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
+ }
+ options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )
+ && _search_case_senstive_cbmi.isSelected() );
+ if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {
+ options.setShowScale( _show_scale_cbmi.isSelected() );
+ }
+ if ( _label_direction_cbmi != null ) {
+ if ( _label_direction_cbmi.isSelected() ) {
+ options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
+ }
+ else {
+ options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
+ }
+ }
+ options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
+ options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )
+ && _show_confidence_stddev_cbmi.isSelected() );
+ if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) {
+ options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() );
+ }
+ options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() );
+ if ( ( _use_brackets_for_conf_in_nh_export_cbmi != null )
+ && _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {
+ options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );
+ }
+ else if ( ( _use_internal_names_for_conf_in_nh_export_cbmi != null )
+ && _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {
+ options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );
+ }
+ else {
+ options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );
+ }
+ options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null )
+ && _print_black_and_white_cbmi.isSelected() );
+ options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null )
+ && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );
+ if ( ( _extract_taxonomy_pfam_strict_rbmi != null ) && _extract_taxonomy_pfam_strict_rbmi.isSelected() ) {
+ options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ }
+ else if ( ( _extract_taxonomy_pfam_relaxed_rbmi != null ) && _extract_taxonomy_pfam_relaxed_rbmi.isSelected() ) {
+ options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ }
+ else if ( ( _extract_taxonomy_agressive_rbmi != null ) && _extract_taxonomy_agressive_rbmi.isSelected() ) {
+ options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );
+ }
+ else if ( ( _extract_taxonomy_no_rbmi != null ) && _extract_taxonomy_no_rbmi.isSelected() ) {
+ options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );
+ }
+ options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )
+ && _replace_underscores_cbmi.isSelected() );
+ options.setAllowErrorsInDistanceToParent( ( _allow_errors_in_distance_to_parent_cbmi != null )
+ && _allow_errors_in_distance_to_parent_cbmi.isSelected() );
+ options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
+ && _search_whole_words_only_cbmi.isSelected() );
+ options.setSearchWithRegex( ( _search_with_regex_cbmi != null ) && _search_with_regex_cbmi.isSelected() );
+ options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
+ && _inverse_search_result_cbmi.isSelected() );
+ if ( _graphics_export_visible_only_cbmi != null ) {
+ options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_cbmi.isSelected() );
+ }
+ if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
+ }
+ else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
+ }
+ else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
+ }
+ else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
+ }
+ else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
+ }
+ else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
+ }
+ else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
+ }
+ else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
+ }
+ if ( ( _right_line_up_domains_cbmi != null ) && _right_line_up_domains_cbmi.isEnabled() ) {
+ options.setRightLineUpDomains( _right_line_up_domains_cbmi.isSelected() );
+ }
+ if ( ( _line_up_renderable_data_cbmi != null ) && _line_up_renderable_data_cbmi.isEnabled() ) {
+ options.setLineUpRendarableNodeData( _line_up_renderable_data_cbmi.isSelected() );
+ }
+ if ( ( _color_all_found_nodes_when_coloring_subtree_cbmi != null ) && _color_all_found_nodes_when_coloring_subtree_cbmi.isEnabled() ) {
+ options.setColorAllFoundNodesWhenColoringSubtree( _color_all_found_nodes_when_coloring_subtree_cbmi.isSelected() );
+ }
+ if ( ( _parse_beast_style_extended_nexus_tags_cbmi != null ) && _parse_beast_style_extended_nexus_tags_cbmi.isEnabled() ) {
+ options.setParseBeastStyleExtendedNexusTags(_parse_beast_style_extended_nexus_tags_cbmi.isSelected() );
+ }
+ }
+
+ void updateTypeCheckboxes( final Options options, final Object o ) {
+ setTypeMenuToAllUnselected();
+ ( ( JCheckBoxMenuItem ) o ).setSelected( true );
+ }
+
+ void viewAsNexus() {
+ if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
+ String title = "Nexus";
+ if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
+ title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
+ }
+ showTextFrame( _mainpanel.getCurrentPhylogeny().toNexus( getOptions().getNhConversionSupportValueStyle() ),
+ title );
+ }
+ }
+
+ void viewAsNH() {
+ if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
+ String title = "New Hampshire";
+ if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
+ title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
+ }
+ showTextFrame( _mainpanel.getCurrentPhylogeny().toNewHampshire( getOptions()
+ .getNhConversionSupportValueStyle() ),
+ title );
+ }
+ }
+
+ void viewAsXML() {
+ if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
+ String title = "phyloXML";
+ if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
+ title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
+ }
+ showTextFrame( _mainpanel.getCurrentPhylogeny().toPhyloXML( 0 ), title );
+ }
+ }
+
+ private static void cycleNodeDataReturn( final Options op, final Configuration conf ) {
+ switch ( op.getExtDescNodeDataToReturn() ) {
+ case UNKNOWN:
+ op.setExtDescNodeDataToReturn( NodeDataField.DOMAINS_ALL );
+ break;
+ case DOMAINS_ALL:
+ op.setExtDescNodeDataToReturn( NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN );
+ break;
+ case DOMAINS_COLLAPSED_PER_PROTEIN:
+ op.setExtDescNodeDataToReturn( NodeDataField.SEQ_ANNOTATIONS );
+ break;
+ case SEQ_ANNOTATIONS:
+ op.setExtDescNodeDataToReturn( NodeDataField.GO_TERM_IDS );
+ break;
+ case GO_TERM_IDS:
+ op.setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_MOL_SEQ_FASTA );
+ break;
+ case SEQUENCE_MOL_SEQ_FASTA:
+ if ( ( conf != null ) && ( conf.getExtDescNodeDataToReturn() != null )
+ && ( conf.getExtDescNodeDataToReturn() != NodeDataField.DOMAINS_ALL )
+ && ( conf.getExtDescNodeDataToReturn() != NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN )
+ && ( conf.getExtDescNodeDataToReturn() != NodeDataField.SEQ_ANNOTATIONS )
+ && ( conf.getExtDescNodeDataToReturn() != NodeDataField.GO_TERM_IDS )
+ && ( conf.getExtDescNodeDataToReturn() != NodeDataField.SEQUENCE_MOL_SEQ_FASTA ) ) {
+ op.setExtDescNodeDataToReturn( conf.getExtDescNodeDataToReturn() );
+ }
+ else {
+ op.setExtDescNodeDataToReturn( NodeDataField.UNKNOWN );
+ }
+ break;
+ default:
+ op.setExtDescNodeDataToReturn( NodeDataField.UNKNOWN );
+ }
+ }
+
+ /**
+ * Display the about box.
+ */
+ static void about() {
+ final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + AptxConstants.VERSION + "\n" );
+ about.append( "Copyright (C) 2016 Christian M Zmasek\n" );
+ about.append( "All Rights Reserved\n" );
+ about.append( "License: GNU Lesser General Public License (LGPL)\n" );
+ about.append( "Last modified: " + AptxConstants.PRG_DATE + "\n" );
+ about.append( "Based on: " + ForesterUtil.getForesterLibraryInformation() + "\n" );
+ about.append( "phyloXML version : " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
+ about.append( "phyloXML location: " + ForesterConstants.PHYLO_XML_LOCATION + "\n" );
+ if ( !ForesterUtil.isEmpty( ForesterUtil.JAVA_VERSION ) && !ForesterUtil.isEmpty( ForesterUtil.JAVA_VENDOR ) ) {
+ about.append( "[your Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]\n" );
+ }
+ if ( !ForesterUtil.isEmpty( ForesterUtil.OS_NAME ) && !ForesterUtil.isEmpty( ForesterUtil.OS_ARCH )
+ && !ForesterUtil.isEmpty( ForesterUtil.OS_VERSION ) ) {
+ about.append( "[your OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " "
+ + ForesterUtil.OS_VERSION + "]\n" );
+ }
+ final Runtime rt = java.lang.Runtime.getRuntime();
+ final long free_memory = rt.freeMemory() / 1000000;
+ final long total_memory = rt.totalMemory() / 1000000;
+ about.append( "[free memory: " + free_memory + "MB, total memory: " + total_memory + "MB]\n" );
+ about.append( "[locale: " + Locale.getDefault() + "]\n" );
+ about.append( "References:\n" );
+ about.append( AptxConstants.PHYLOXML_REFERENCE_SHORT + "\n" );
+ about.append( "For more information & download:\n" );
+ about.append( AptxConstants.APTX_WEB_SITE + "\n" );
+ about.append( "Documentation:\n" );
+ about.append( AptxConstants.APTX_DOC_SITE + "\n" );
+ about.append( "Comments: " + AptxConstants.AUTHOR_EMAIL );
+ JOptionPane.showMessageDialog( null, about, AptxConstants.PRG_NAME, JOptionPane.PLAIN_MESSAGE );
+ }
+
+ static void chooseNodeSize( final Options options, final Component parent ) {
+ final String s = ( String ) JOptionPane.showInputDialog( parent,
+ "Please enter the default size for node shapes.\n"
+ + "[current value: "
+ + options.getDefaultNodeShapeSize() + "]\n",
+ "Node Shape Size",
+ JOptionPane.QUESTION_MESSAGE,
+ null,
+ null,
+ options.getDefaultNodeShapeSize() );
+ if ( !ForesterUtil.isEmpty( s ) ) {
+ boolean success = true;
+ double m = 0.0;
+ final String m_str = s.trim();
+ if ( !ForesterUtil.isEmpty( m_str ) ) {
+ try {
+ m = Double.parseDouble( m_str );
+ }
+ catch ( final Exception ex ) {
+ success = false;
+ }
+ }
+ else {
+ success = false;
+ }
+ if ( success && ( m >= 0.0 ) ) {
+ final short size = ForesterUtil.roundToShort( m );
+ if ( size >= 0.0 ) {
+ options.setDefaultNodeShapeSize( size );
+ }
+ }
+ }
+ }
+
+ static String createCurrentFontDesc( final TreeFontSet tree_font_set ) {
+ return tree_font_set.getLargeFont().getFamily() + " " + tree_font_set.getLargeFont().getSize();
+ }
+
+ static JMenu createMenu( final String title, final Configuration conf ) {
+ final JMenu jmenu = new JMenu( title );
+ if ( !conf.isUseNativeUI() ) {
+ jmenu.setFont( MainFrame.menu_font );
+ jmenu.setBackground( conf.getGuiMenuBackgroundColor() );
+ jmenu.setForeground( conf.getGuiMenuTextColor() );
+ }
+ return jmenu;
+ }
+
+ static JMenuItem customizeMenuItemAsLabel( final JMenuItem label, final Configuration configuration ) {
+ label.setFont( MainFrame.menu_font.deriveFont( Font.BOLD ) );
+ if ( !configuration.isUseNativeUI() ) {
+ label.setBackground( configuration.getGuiMenuBackgroundColor() );
+ label.setForeground( configuration.getGuiMenuTextColor() );
+ label.setOpaque( true );
+ }
+ label.setSelected( false );
+ label.setEnabled( false );
+ return label;
+ }
+
+ static void cycleNodeFill( final Options op ) {
+ switch ( op.getDefaultNodeFill() ) {
+ case GRADIENT:
+ op.setDefaultNodeFill( NodeFill.SOLID );
+ break;
+ case NONE:
+ op.setDefaultNodeFill( NodeFill.GRADIENT );
+ break;
+ case SOLID:
+ op.setDefaultNodeFill( NodeFill.NONE );
+ break;
+ default:
+ throw new RuntimeException( "unknown fill: " + op.getDefaultNodeFill() );
+ }
+ }
+
+ static void cycleNodeShape( final Options op ) {
+ switch ( op.getDefaultNodeShape() ) {
+ case CIRCLE:
+ op.setDefaultNodeShape( NodeShape.RECTANGLE );
+ break;
+ case RECTANGLE:
+ op.setDefaultNodeShape( NodeShape.CIRCLE );
+ break;
+ default:
+ throw new RuntimeException( "unknown shape: " + op.getDefaultNodeShape() );
+ }
+ }
+
+ static void cycleOverview( final Options op, final TreePanel tree_panel ) {
+ switch ( op.getOvPlacement() ) {
+ case LOWER_LEFT:
+ op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
+ break;
+ case LOWER_RIGHT:
+ op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );
+ break;
+ case UPPER_LEFT:
+ op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );
+ break;
+ case UPPER_RIGHT:
+ op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );
+ break;
+ default:
+ throw new RuntimeException( "unknown placement: " + op.getOvPlacement() );
+ }
+ if ( tree_panel != null ) {
+ tree_panel.updateOvSettings();
+ }
+ }
+
+ static void exceptionOccuredDuringSaveAs( final Exception e, final TreePanel tp, final Component comp ) {
+ try {
+ tp.setArrowCursor();
+ }
+ catch ( final Exception ex ) {
+ // Do nothing.
+ }
+ JOptionPane.showMessageDialog( comp, "Exception" + e, "Error during File|SaveAs", JOptionPane.ERROR_MESSAGE );
+ }
+
+ static void print( final TreePanel tp, final Options op, final Component c ) {
+ if ( ( tp == null ) || ( tp.getPhylogeny() == null ) || tp.getPhylogeny().isEmpty() ) {
+ return;
+ }
+ final String job_name = AptxConstants.PRG_NAME;
+ boolean error = false;
+ String printer_name = null;
+ try {
+ printer_name = Printer.print( tp, job_name );
+ }
+ catch ( final Exception e ) {
+ error = true;
+ JOptionPane.showMessageDialog( c, e.getMessage(), "Printing Error", JOptionPane.ERROR_MESSAGE );
+ }
+ if ( !error && ( printer_name != null ) ) {
+ String msg = "Printing data sent to printer";
+ if ( printer_name.length() > 1 ) {
+ msg += " [" + printer_name + "]";
+ }
+ JOptionPane.showMessageDialog( c, msg, "Printing...", JOptionPane.INFORMATION_MESSAGE );
+ }
+ if ( !op.isPrintUsingActualSize() ) {
+ tp.getControlPanel().showWhole();
+ }
+ }
+
+ static void printPhylogenyToPdf( final String file_name,
+ final Options opts,
+ final TreePanel tp,
+ final Component comp ) {
+
+ String pdf_written_to = "";
+ boolean error = false;
+ try {
+ if ( opts.isPrintUsingActualSize() ) {
+ pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name, tp, tp.getWidth() , tp.getHeight() );
+ }
+ else {
+ // Never false.
+ }
+ }
+ catch ( final IOException e ) {
+ error = true;
+ JOptionPane.showMessageDialog( comp, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );
+ }
+ if ( !error ) {
+ if ( !ForesterUtil.isEmpty( pdf_written_to ) ) {
+ JOptionPane.showMessageDialog( comp,
+ "Wrote PDF to: " + pdf_written_to,
+ "Information",
+ JOptionPane.INFORMATION_MESSAGE );
+ }
+ else {
+ JOptionPane.showMessageDialog( comp,
+ "There was an unknown problem when attempting to write to PDF file: \""
+ + file_name + "\"",
+ "Error",
+ JOptionPane.ERROR_MESSAGE );
+ }
+ }
+ if ( !opts.isPrintUsingActualSize() ) {
+ tp.getControlPanel().showWhole();
+ }
+ }
+
+ static void setCycleDataReturnMenuItem( final JMenuItem mi, final Options options ) {
+ if ( ( options != null ) && ( options.getExtDescNodeDataToReturn() != null ) ) {
+ mi.setText( "Cycle Node Return Data... (current: " + options.getExtDescNodeDataToReturn().toString() + ")" );
+ }
+ else {
+ mi.setText( "Cycle Node Return Data..." );
+ }
+ }
+
+ static void setCycleNodeFillMenuItem( final JMenuItem mi, final Options options ) {
+ if ( ( options != null ) && ( options.getDefaultNodeFill() != null ) ) {
+ mi.setText( "Cycle Node Shape Fill Type... (current: "
+ + options.getDefaultNodeFill().toString().toLowerCase() + ")" );
+ }
+ else {
+ mi.setText( "Cycle Node Shape Fill Type..." );
+ }
+ }
+
+ static void setCycleNodeShapeMenuItem( final JMenuItem mi, final Options options ) {
+ if ( ( options != null ) && ( options.getDefaultNodeShape() != null ) ) {
+ mi.setText( "Cycle Node Shape Fill Type... (current: "
+ + options.getDefaultNodeShape().toString().toLowerCase() + ")" );
+ }
+ else {
+ mi.setText( "Cycle Node Shape Fill Type..." );
+ }
+ }
+
+ static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) {
+ if ( ( options != null ) && ( options.getOvPlacement() != null ) ) {
+ mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" );
+ }
+ else {
+ mi.setText( "Cycle Overview Placement..." );
+ }
+ }
+
+ static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) {
+ if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) {
+ mi.setText( "Select Color Scheme... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName()
+ + ")" );
+ }
+ else {
+ mi.setText( "Select Color Scheme..." );
+ }
+ }
+
+ static void setTextForFontChooserMenuItem( final JMenuItem mi, final String font_desc ) {
+ mi.setText( "Select Default Font... (current: " + font_desc + ")" );
+ }
+
+ static void setTextForPdfLineWidthChooserMenuItem( final JMenuItem mi, final Options o ) {
+ mi.setText( "Enter Default Line Width for PDF Export... (current: " + o.getPrintLineWidth() + ")" );
+ }
+
+ static void setTextMinSupportMenuItem( final JMenuItem mi, final Options options, final TreePanel current_tree_panel ) {
+ if ( ( current_tree_panel == null ) || ( current_tree_panel.getPhylogeny() == null ) ) {
+ mi.setEnabled( true );
+ }
+ else if ( AptxUtil.isHasAtLeastOneBranchWithSupportValues( current_tree_panel.getPhylogeny() ) ) {
+ mi.setEnabled( true );
+ }
+ else {
+ mi.setEnabled( false );
+ }
+ mi.setText( "Enter Min Confidence Value... (current: " + options.getMinConfidenceValue() + ")" );
+ }
+
+ static void setTextNodeSizeMenuItem( final JMenuItem mi, final Options options ) {
+ mi.setText( "Enter Default Node Shape Size... (current: " + options.getDefaultNodeShapeSize() + ")" );
+ }
+
+ static void updateScreenTextAntialias( final List<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
-// $Id:\r
-// FORESTER -- software libraries and applications\r
-// for evolutionary biology research and applications.\r
-//\r
-// Copyright (C) 2008-2009 Christian M. Zmasek\r
-// Copyright (C) 2008-2009 Burnham Institute for Medical Research\r
-// Copyright (C) 2003-2007 Ethalinda K.S. Cannon\r
-// All rights reserved\r
-//\r
-// This library is free software; you can redistribute it and/or\r
-// modify it under the terms of the GNU Lesser General Public\r
-// License as published by the Free Software Foundation; either\r
-// version 2.1 of the License, or (at your option) any later version.\r
-//\r
-// This library is distributed in the hope that it will be useful,\r
-// but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU\r
-// Lesser General Public License for more details.\r
-//\r
-// You should have received a copy of the GNU Lesser General Public\r
-// License along with this library; if not, write to the Free Software\r
-// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-//\r
-// Contact: phylosoft @ gmail . com\r
-// WWW: https://sites.google.com/site/cmzmasek/home/software/forester\r
-\r
-package org.forester.archaeopteryx;\r
-\r
-import java.awt.BorderLayout;\r
-import java.awt.Font;\r
-import java.awt.event.ActionEvent;\r
-import java.awt.event.ComponentAdapter;\r
-import java.awt.event.ComponentEvent;\r
-import java.awt.event.WindowAdapter;\r
-import java.awt.event.WindowEvent;\r
-import java.io.File;\r
-import java.io.FileInputStream;\r
-import java.io.IOException;\r
-import java.io.InputStream;\r
-import java.net.MalformedURLException;\r
-import java.net.URL;\r
-import java.util.ArrayList;\r
-import java.util.HashSet;\r
-import java.util.List;\r
-import java.util.Set;\r
-\r
-import javax.swing.ButtonGroup;\r
-import javax.swing.JCheckBoxMenuItem;\r
-import javax.swing.JFileChooser;\r
-import javax.swing.JMenu;\r
-import javax.swing.JMenuBar;\r
-import javax.swing.JMenuItem;\r
-import javax.swing.JOptionPane;\r
-import javax.swing.JRadioButtonMenuItem;\r
-import javax.swing.UIManager;\r
-import javax.swing.UnsupportedLookAndFeelException;\r
-import javax.swing.WindowConstants;\r
-import javax.swing.event.ChangeEvent;\r
-import javax.swing.event.ChangeListener;\r
-\r
-import org.forester.analysis.TaxonomyDataManager;\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.PhyloInferenceDialog;\r
-import org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions;\r
-import org.forester.archaeopteryx.tools.PhylogeneticInferrer;\r
-import org.forester.archaeopteryx.tools.SequenceDataRetriver;\r
-import org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient;\r
-import org.forester.archaeopteryx.webservices.WebservicesManager;\r
-import org.forester.io.parsers.FastaParser;\r
-import org.forester.io.parsers.GeneralMsaParser;\r
-import org.forester.io.parsers.PhylogenyParser;\r
-import org.forester.io.parsers.nexus.NexusPhylogeniesParser;\r
-import org.forester.io.parsers.nhx.NHXParser;\r
-import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;\r
-import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;\r
-import org.forester.io.parsers.phyloxml.PhyloXmlParser;\r
-import org.forester.io.parsers.phyloxml.PhyloXmlUtil;\r
-import org.forester.io.parsers.tol.TolParser;\r
-import org.forester.io.parsers.util.ParserUtils;\r
-import org.forester.io.writers.SequenceWriter;\r
-import org.forester.msa.Msa;\r
-import org.forester.msa.MsaFormatException;\r
-import org.forester.phylogeny.Phylogeny;\r
-import org.forester.phylogeny.PhylogenyMethods;\r
-import org.forester.phylogeny.PhylogenyNode;\r
-import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;\r
-import org.forester.phylogeny.data.Confidence;\r
-import org.forester.phylogeny.data.PhylogenyDataUtil;\r
-import org.forester.phylogeny.data.Sequence;\r
-import org.forester.phylogeny.data.Taxonomy;\r
-import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;\r
-import org.forester.phylogeny.factories.PhylogenyFactory;\r
-import org.forester.phylogeny.iterators.PhylogenyNodeIterator;\r
-import org.forester.sequence.MolecularSequence;\r
-import org.forester.util.BasicDescriptiveStatistics;\r
-import org.forester.util.BasicTable;\r
-import org.forester.util.BasicTableParser;\r
-import org.forester.util.DescriptiveStatistics;\r
-import org.forester.util.ForesterUtil;\r
-\r
-public final class MainFrameApplication extends MainFrame {\r
-\r
- private final static int FRAME_X_SIZE = 800;\r
- private final static int FRAME_Y_SIZE = 800;\r
- // Filters for the file-open dialog (classes defined in this file)\r
- private static final long serialVersionUID = -799735726778865234L;\r
- private static final boolean PREPROCESS_TREES = false;\r
- private final JFileChooser _values_filechooser;\r
- private final JFileChooser _sequences_filechooser;\r
- private final JFileChooser _open_filechooser;\r
- private final JFileChooser _msa_filechooser;\r
- private final JFileChooser _seqs_pi_filechooser;\r
- private final JFileChooser _open_filechooser_for_species_tree;\r
- // Application-only print menu items\r
- private JMenuItem _collapse_below_threshold;\r
- private JMenuItem _collapse_below_branch_length;\r
- private ButtonGroup _radio_group_1;\r
- private ButtonGroup _radio_group_2;\r
- // Others:\r
- double _min_not_collapse = AptxConstants.MIN_NOT_COLLAPSE_DEFAULT;\r
- double _min_not_collapse_bl = 0.001;\r
- // Phylogeny Inference menu\r
- private JMenu _inference_menu;\r
- private JMenuItem _inference_from_msa_item;\r
- private JMenuItem _inference_from_seqs_item;\r
- // Phylogeny Inference\r
- private PhylogeneticInferenceOptions _phylogenetic_inference_options = null;\r
- private Msa _msa = null;\r
- private File _msa_file = null;\r
- private List<MolecularSequence> _seqs = null;\r
- private File _seqs_file = null;\r
- JMenuItem _read_values_jmi;\r
- JMenuItem _read_seqs_jmi;\r
-\r
- private MainFrameApplication( final Phylogeny[] phys, final Configuration config ) {\r
- _configuration = config;\r
- if ( _configuration == null ) {\r
- throw new IllegalArgumentException( "configuration is null" );\r
- }\r
- setVisible( false );\r
- setOptions( Options.createInstance( _configuration ) );\r
- _mainpanel = new MainPanel( _configuration, this );\r
- _open_filechooser = null;\r
- _open_filechooser_for_species_tree = null;\r
- _save_filechooser = null;\r
- _writetopdf_filechooser = null;\r
- _writetographics_filechooser = null;\r
- _msa_filechooser = null;\r
- _seqs_pi_filechooser = null;\r
- _values_filechooser = null;\r
- _sequences_filechooser = null;\r
- _jmenubar = new JMenuBar();\r
- buildFileMenu();\r
- buildTypeMenu();\r
- _contentpane = getContentPane();\r
- _contentpane.setLayout( new BorderLayout() );\r
- _contentpane.add( _mainpanel, BorderLayout.CENTER );\r
- // App is this big\r
- setSize( MainFrameApplication.FRAME_X_SIZE, MainFrameApplication.FRAME_Y_SIZE );\r
- // The window listener\r
- setDefaultCloseOperation( WindowConstants.DO_NOTHING_ON_CLOSE );\r
- addWindowListener( new WindowAdapter() {\r
-\r
- @Override\r
- public void windowClosing( final WindowEvent e ) {\r
- exit();\r
- }\r
- } );\r
- // setVisible( true );\r
- if ( ( phys != null ) && ( phys.length > 0 ) ) {\r
- AptxUtil.addPhylogeniesToTabs( phys, "", null, _configuration, _mainpanel );\r
- validate();\r
- getMainPanel().getControlPanel().showWholeAll();\r
- getMainPanel().getControlPanel().showWhole();\r
- }\r
- //activateSaveAllIfNeeded();\r
- // ...and its children\r
- _contentpane.repaint();\r
- }\r
-\r
- private MainFrameApplication( final Phylogeny[] phys, final Configuration config, final String title ) {\r
- this( phys, config, title, null );\r
- }\r
-\r
- private MainFrameApplication( final Phylogeny[] phys,\r
- final Configuration config,\r
- final String title,\r
- final File current_dir ) {\r
- super();\r
- _configuration = config;\r
- if ( _configuration == null ) {\r
- throw new IllegalArgumentException( "configuration is null" );\r
- }\r
- try {\r
- if ( _configuration.isUseNativeUI() ) {\r
- UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );\r
- }\r
- else {\r
- UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );\r
- }\r
- }\r
- catch ( final UnsupportedLookAndFeelException e ) {\r
- AptxUtil.dieWithSystemError( "unsupported look and feel: " + e.toString() );\r
- }\r
- catch ( final ClassNotFoundException e ) {\r
- AptxUtil.dieWithSystemError( "class not found exception: " + e.toString() );\r
- }\r
- catch ( final InstantiationException e ) {\r
- AptxUtil.dieWithSystemError( "instantiation exception: " + e.toString() );\r
- }\r
- catch ( final IllegalAccessException e ) {\r
- AptxUtil.dieWithSystemError( "illegal access exception: " + e.toString() );\r
- }\r
- if ( ( current_dir != null ) && current_dir.canRead() && current_dir.isDirectory() ) {\r
- setCurrentDir( current_dir );\r
- }\r
- // hide until everything is ready\r
- setVisible( false );\r
- setOptions( Options.createInstance( _configuration ) );\r
- setInferenceManager( InferenceManager.createInstance( _configuration ) );\r
- setPhylogeneticInferenceOptions( PhylogeneticInferenceOptions.createInstance( _configuration ) );\r
- // set title\r
- setTitle( AptxConstants.PRG_NAME + " " + AptxConstants.VERSION + " (" + AptxConstants.PRG_DATE + ")" );\r
- _mainpanel = new MainPanel( _configuration, this );\r
- // The file dialogs\r
- _open_filechooser = new JFileChooser();\r
- _open_filechooser.setMultiSelectionEnabled( true );\r
- _open_filechooser.addChoosableFileFilter( MainFrame.xmlfilter );\r
- _open_filechooser.addChoosableFileFilter( MainFrame.nhxfilter );\r
- _open_filechooser.addChoosableFileFilter( MainFrame.nhfilter );\r
- _open_filechooser.addChoosableFileFilter( MainFrame.nexusfilter );\r
- _open_filechooser.addChoosableFileFilter( MainFrame.tolfilter );\r
- _open_filechooser.addChoosableFileFilter( _open_filechooser.getAcceptAllFileFilter() );\r
- _open_filechooser.setFileFilter( MainFrame.defaultfilter );\r
- _open_filechooser_for_species_tree = new JFileChooser();\r
- _open_filechooser_for_species_tree.setMultiSelectionEnabled( false );\r
- _open_filechooser_for_species_tree.addChoosableFileFilter( MainFrame.xmlfilter );\r
- _open_filechooser_for_species_tree.addChoosableFileFilter( MainFrame.tolfilter );\r
- _open_filechooser_for_species_tree.setFileFilter( MainFrame.xmlfilter );\r
- // Msa:\r
- _msa_filechooser = new JFileChooser();\r
- _msa_filechooser.setName( "Read Multiple Sequence Alignment File" );\r
- _msa_filechooser.setMultiSelectionEnabled( false );\r
- _msa_filechooser.addChoosableFileFilter( _msa_filechooser.getAcceptAllFileFilter() );\r
- _msa_filechooser.addChoosableFileFilter( MainFrame.msafilter );\r
- // Seqs:\r
- _seqs_pi_filechooser = new JFileChooser();\r
- _seqs_pi_filechooser.setName( "Read Sequences File" );\r
- _seqs_pi_filechooser.setMultiSelectionEnabled( false );\r
- _seqs_pi_filechooser.addChoosableFileFilter( _seqs_pi_filechooser.getAcceptAllFileFilter() );\r
- _seqs_pi_filechooser.addChoosableFileFilter( MainFrame.seqsfilter );\r
- // Expression\r
- _values_filechooser = new JFileChooser();\r
- _values_filechooser.setMultiSelectionEnabled( false );\r
- // Sequences\r
- _sequences_filechooser = new JFileChooser();\r
- _sequences_filechooser.setMultiSelectionEnabled( false );\r
- try {\r
- final String home_dir = System.getProperty( "user.home" );\r
- _open_filechooser.setCurrentDirectory( new File( home_dir ) );\r
- _open_filechooser_for_species_tree.setCurrentDirectory( new File( home_dir ) );\r
- _msa_filechooser.setCurrentDirectory( new File( home_dir ) );\r
- _seqs_pi_filechooser.setCurrentDirectory( new File( home_dir ) );\r
- _values_filechooser.setCurrentDirectory( new File( home_dir ) );\r
- _sequences_filechooser.setCurrentDirectory( new File( home_dir ) );\r
- }\r
- catch ( final Exception e ) {\r
- e.printStackTrace();\r
- // Do nothing. Not important.\r
- }\r
- // build the menu bar\r
- _jmenubar = new JMenuBar();\r
- if ( !_configuration.isUseNativeUI() ) {\r
- _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
- }\r
- buildFileMenu();\r
- if ( AptxConstants.__ALLOW_PHYLOGENETIC_INFERENCE ) {\r
- buildPhylogeneticInferenceMenu();\r
- }\r
- buildAnalysisMenu();\r
- buildToolsMenu();\r
- buildViewMenu();\r
- buildFontSizeMenu();\r
- buildOptionsMenu();\r
- buildTypeMenu();\r
- buildHelpMenu();\r
- setJMenuBar( _jmenubar );\r
- _jmenubar.add( _help_jmenu );\r
- _contentpane = getContentPane();\r
- _contentpane.setLayout( new BorderLayout() );\r
- _contentpane.add( _mainpanel, BorderLayout.CENTER );\r
- // App is this big\r
- setSize( MainFrameApplication.FRAME_X_SIZE, MainFrameApplication.FRAME_Y_SIZE );\r
- // addWindowFocusListener( new WindowAdapter() {\r
- //\r
- // @Override\r
- // public void windowGainedFocus( WindowEvent e ) {\r
- // requestFocusInWindow();\r
- // }\r
- // } );\r
- // The window listener\r
- setDefaultCloseOperation( WindowConstants.DO_NOTHING_ON_CLOSE );\r
- addWindowListener( new WindowAdapter() {\r
-\r
- @Override\r
- public void windowClosing( final WindowEvent e ) {\r
- if ( isUnsavedDataPresent() ) {\r
- final int r = JOptionPane.showConfirmDialog( null,\r
- "Exit despite potentially unsaved changes?",\r
- "Exit?",\r
- JOptionPane.YES_NO_OPTION );\r
- if ( r != JOptionPane.YES_OPTION ) {\r
- return;\r
- }\r
- }\r
- else {\r
- final int r = JOptionPane.showConfirmDialog( null,\r
- "Exit Archaeopteryx?",\r
- "Exit?",\r
- JOptionPane.YES_NO_OPTION );\r
- if ( r != JOptionPane.YES_OPTION ) {\r
- return;\r
- }\r
- }\r
- exit();\r
- }\r
- } );\r
- // The component listener\r
- addComponentListener( new ComponentAdapter() {\r
-\r
- @Override\r
- public void componentResized( final ComponentEvent e ) {\r
- if ( _mainpanel.getCurrentTreePanel() != null ) {\r
- _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel()\r
- .getWidth(),\r
- _mainpanel.getCurrentTreePanel()\r
- .getHeight() );\r
- }\r
- }\r
- } );\r
- requestFocusInWindow();\r
- // addKeyListener( this );\r
- setVisible( true );\r
- if ( ( phys != null ) && ( phys.length > 0 ) ) {\r
- AptxUtil.addPhylogeniesToTabs( phys, title, null, _configuration, _mainpanel );\r
- validate();\r
- getMainPanel().getControlPanel().showWholeAll();\r
- getMainPanel().getControlPanel().showWhole();\r
- }\r
- activateSaveAllIfNeeded();\r
- // ...and its children\r
- _contentpane.repaint();\r
- System.gc();\r
- }\r
-\r
- private MainFrameApplication( final Phylogeny[] phys, final String config_file, final String title ) {\r
- // Reads the config file (false, false => not url, not applet):\r
- this( phys, new Configuration( config_file, false, false, true ), title );\r
- }\r
-\r
- @Override\r
- public void actionPerformed( final ActionEvent e ) {\r
- try {\r
- super.actionPerformed( e );\r
- final Object o = e.getSource();\r
- // Handle app-specific actions here:\r
- if ( o == _open_item ) {\r
- readPhylogeniesFromFile();\r
- }\r
- if ( o == _open_url_item ) {\r
- readPhylogeniesFromURL();\r
- }\r
- else if ( o == _new_item ) {\r
- newTree();\r
- }\r
- else if ( o == _close_item ) {\r
- closeCurrentPane();\r
- }\r
- else if ( o == _load_species_tree_item ) {\r
- readSpeciesTreeFromFile();\r
- }\r
- else if ( o == _obtain_detailed_taxonomic_information_jmi ) {\r
- if ( isSubtreeDisplayed() ) {\r
- return;\r
- }\r
- obtainDetailedTaxonomicInformation();\r
- }\r
- else if ( o == _obtain_detailed_taxonomic_information_deleting_jmi ) {\r
- if ( isSubtreeDisplayed() ) {\r
- return;\r
- }\r
- obtainDetailedTaxonomicInformationDelete();\r
- }\r
- else if ( o == _obtain_seq_information_jmi ) {\r
- obtainSequenceInformation();\r
- }\r
- else if ( o == _read_values_jmi ) {\r
- if ( isSubtreeDisplayed() ) {\r
- return;\r
- }\r
- addExpressionValuesFromFile();\r
- }\r
- else if ( o == _read_seqs_jmi ) {\r
- if ( isSubtreeDisplayed() ) {\r
- return;\r
- }\r
- addSequencesFromFile();\r
- }\r
- else if ( o == _move_node_names_to_tax_sn_jmi ) {\r
- moveNodeNamesToTaxSn();\r
- }\r
- else if ( o == _move_node_names_to_seq_names_jmi ) {\r
- moveNodeNamesToSeqNames();\r
- }\r
- else if ( o == _extract_tax_code_from_node_names_jmi ) {\r
- extractTaxDataFromNodeNames();\r
- }\r
- else if ( o == _internal_number_are_confidence_for_nh_parsing_cbmi ) {\r
- updateOptions( getOptions() );\r
- }\r
- else if ( o == _replace_underscores_cbmi ) {\r
- if ( ( _extract_taxonomy_no_rbmi != null ) && !_extract_taxonomy_no_rbmi.isSelected() ) {\r
- _extract_taxonomy_no_rbmi.setSelected( true );\r
- }\r
- updateOptions( getOptions() );\r
- }\r
- else if ( o == _allow_errors_in_distance_to_parent_cbmi ) {\r
- updateOptions( getOptions() );\r
- }\r
- else if ( o == _collapse_below_threshold ) {\r
- if ( isSubtreeDisplayed() ) {\r
- return;\r
- }\r
- collapseBelowThreshold();\r
- }\r
- else if ( o == _collapse_below_branch_length ) {\r
- if ( isSubtreeDisplayed() ) {\r
- return;\r
- }\r
- collapseBelowBranchLengthThreshold();\r
- }\r
- else if ( ( o == _extract_taxonomy_pfam_strict_rbmi ) || ( o == _extract_taxonomy_pfam_relaxed_rbmi )\r
- || ( o == _extract_taxonomy_agressive_rbmi ) ) {\r
- if ( _replace_underscores_cbmi != null ) {\r
- _replace_underscores_cbmi.setSelected( false );\r
- }\r
- updateOptions( getOptions() );\r
- }\r
- else if ( o == _extract_taxonomy_no_rbmi ) {\r
- updateOptions( getOptions() );\r
- }\r
- else if ( o == _inference_from_msa_item ) {\r
- executePhyleneticInference( false );\r
- }\r
- else if ( o == _inference_from_seqs_item ) {\r
- executePhyleneticInference( true );\r
- }\r
- _contentpane.repaint();\r
- }\r
- catch ( final Exception ex ) {\r
- AptxUtil.unexpectedException( ex );\r
- }\r
- catch ( final Error err ) {\r
- AptxUtil.unexpectedError( err );\r
- }\r
- }\r
-\r
- public void end() {\r
- _mainpanel.terminate();\r
- _contentpane.removeAll();\r
- setVisible( false );\r
- dispose();\r
- }\r
-\r
- @Override\r
- public MainPanel getMainPanel() {\r
- return _mainpanel;\r
- }\r
-\r
- public Msa getMsa() {\r
- return _msa;\r
- }\r
-\r
- public File getMsaFile() {\r
- return _msa_file;\r
- }\r
-\r
- public List<MolecularSequence> getSeqs() {\r
- return _seqs;\r
- }\r
-\r
- public File getSeqsFile() {\r
- return _seqs_file;\r
- }\r
-\r
- public void readMsaFromFile() {\r
- // Set an initial directory if none set yet\r
- final File my_dir = getCurrentDir();\r
- _msa_filechooser.setMultiSelectionEnabled( false );\r
- // Open file-open dialog and set current directory\r
- if ( my_dir != null ) {\r
- _msa_filechooser.setCurrentDirectory( my_dir );\r
- }\r
- final int result = _msa_filechooser.showOpenDialog( _contentpane );\r
- // All done: get the msa\r
- final File file = _msa_filechooser.getSelectedFile();\r
- setCurrentDir( _msa_filechooser.getCurrentDirectory() );\r
- if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
- setMsaFile( null );\r
- setMsa( null );\r
- Msa msa = null;\r
- try {\r
- final InputStream is = new FileInputStream( file );\r
- if ( FastaParser.isLikelyFasta( file ) ) {\r
- msa = FastaParser.parseMsa( is );\r
- }\r
- else {\r
- msa = GeneralMsaParser.parse( is );\r
- }\r
- }\r
- catch ( final MsaFormatException e ) {\r
- setArrowCursor();\r
- JOptionPane.showMessageDialog( this,\r
- e.getLocalizedMessage(),\r
- "Multiple sequence alignment format error",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- catch ( final IOException e ) {\r
- setArrowCursor();\r
- JOptionPane.showMessageDialog( this,\r
- e.getLocalizedMessage(),\r
- "Failed to read multiple sequence alignment",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- catch ( final IllegalArgumentException e ) {\r
- setArrowCursor();\r
- JOptionPane.showMessageDialog( this,\r
- e.getLocalizedMessage(),\r
- "Unexpected error during reading of multiple sequence alignment",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- catch ( final Exception e ) {\r
- setArrowCursor();\r
- e.printStackTrace();\r
- JOptionPane.showMessageDialog( this,\r
- e.getLocalizedMessage(),\r
- "Unexpected error during reading of multiple sequence alignment",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- if ( ( msa == null ) || ( msa.getNumberOfSequences() < 1 ) ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Multiple sequence alignment is empty",\r
- "Illegal Multiple Sequence Alignment",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- if ( msa.getNumberOfSequences() < 4 ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Multiple sequence alignment needs to contain at least 3 sequences",\r
- "Illegal multiple sequence alignment",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- if ( msa.getLength() < 2 ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Multiple sequence alignment needs to contain at least 2 residues",\r
- "Illegal multiple sequence alignment",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- System.gc();\r
- setMsaFile( _msa_filechooser.getSelectedFile() );\r
- setMsa( msa );\r
- }\r
- }\r
-\r
- public void readSeqsFromFileforPI() {\r
- // Set an initial directory if none set yet\r
- final File my_dir = getCurrentDir();\r
- _seqs_pi_filechooser.setMultiSelectionEnabled( false );\r
- // Open file-open dialog and set current directory\r
- if ( my_dir != null ) {\r
- _seqs_pi_filechooser.setCurrentDirectory( my_dir );\r
- }\r
- final int result = _seqs_pi_filechooser.showOpenDialog( _contentpane );\r
- // All done: get the seqs\r
- final File file = _seqs_pi_filechooser.getSelectedFile();\r
- setCurrentDir( _seqs_pi_filechooser.getCurrentDirectory() );\r
- if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
- setSeqsFile( null );\r
- setSeqs( null );\r
- List<MolecularSequence> seqs = null;\r
- try {\r
- if ( FastaParser.isLikelyFasta( new FileInputStream( file ) ) ) {\r
- seqs = FastaParser.parse( new FileInputStream( file ) );\r
- for( final MolecularSequence seq : seqs ) {\r
- System.out.println( SequenceWriter.toFasta( seq, 60 ) );\r
- }\r
- }\r
- else {\r
- //TODO error\r
- }\r
- }\r
- catch ( final MsaFormatException e ) {\r
- setArrowCursor();\r
- JOptionPane.showMessageDialog( this,\r
- e.getLocalizedMessage(),\r
- "Multiple sequence file format error",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- catch ( final IOException e ) {\r
- setArrowCursor();\r
- JOptionPane.showMessageDialog( this,\r
- e.getLocalizedMessage(),\r
- "Failed to read multiple sequence file",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- catch ( final IllegalArgumentException e ) {\r
- setArrowCursor();\r
- JOptionPane.showMessageDialog( this,\r
- e.getLocalizedMessage(),\r
- "Unexpected error during reading of multiple sequence file",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- catch ( final Exception e ) {\r
- setArrowCursor();\r
- e.printStackTrace();\r
- JOptionPane.showMessageDialog( this,\r
- e.getLocalizedMessage(),\r
- "Unexpected error during reading of multiple sequence file",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- if ( ( seqs == null ) || ( seqs.size() < 1 ) ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Multiple sequence file is empty",\r
- "Illegal multiple sequence file",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- if ( seqs.size() < 4 ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Multiple sequence file needs to contain at least 3 sequences",\r
- "Illegal multiple sequence file",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- // if ( msa.getLength() < 2 ) {\r
- // JOptionPane.showMessageDialog( this,\r
- // "Multiple sequence alignment needs to contain at least 2 residues",\r
- // "Illegal multiple sequence file",\r
- // JOptionPane.ERROR_MESSAGE );\r
- // return;\r
- // }\r
- System.gc();\r
- setSeqsFile( _seqs_pi_filechooser.getSelectedFile() );\r
- setSeqs( seqs );\r
- }\r
- }\r
-\r
- private void addExpressionValuesFromFile() {\r
- if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Need to load evolutionary tree first",\r
- "Can Not Read Expression Values",\r
- JOptionPane.WARNING_MESSAGE );\r
- return;\r
- }\r
- final File my_dir = getCurrentDir();\r
- if ( my_dir != null ) {\r
- _values_filechooser.setCurrentDirectory( my_dir );\r
- }\r
- final int result = _values_filechooser.showOpenDialog( _contentpane );\r
- final File file = _values_filechooser.getSelectedFile();\r
- if ( ( file != null ) && ( file.length() > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
- BasicTable<String> t = null;\r
- try {\r
- t = BasicTableParser.parse( file, '\t' );\r
- if ( t.getNumberOfColumns() < 2 ) {\r
- t = BasicTableParser.parse( file, ',' );\r
- }\r
- if ( t.getNumberOfColumns() < 2 ) {\r
- t = BasicTableParser.parse( file, ' ' );\r
- }\r
- }\r
- catch ( final IOException e ) {\r
- JOptionPane.showMessageDialog( this,\r
- e.getMessage(),\r
- "Could Not Read Expression Value Table",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- if ( t.getNumberOfColumns() < 2 ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Table contains " + t.getNumberOfColumns() + " column(s)",\r
- "Problem with Expression Value Table",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- if ( t.getNumberOfRows() < 1 ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Table contains zero rows",\r
- "Problem with Expression Value Table",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- final Phylogeny phy = getCurrentTreePanel().getPhylogeny();\r
- if ( t.getNumberOfRows() != phy.getNumberOfExternalNodes() ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Table contains " + t.getNumberOfRows() + " rows, but tree contains "\r
- + phy.getNumberOfExternalNodes() + " external nodes",\r
- "Warning",\r
- JOptionPane.WARNING_MESSAGE );\r
- }\r
- final DescriptiveStatistics stats = new BasicDescriptiveStatistics();\r
- int not_found = 0;\r
- for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {\r
- final PhylogenyNode node = iter.next();\r
- final String node_name = node.getName();\r
- if ( !ForesterUtil.isEmpty( node_name ) ) {\r
- int row = -1;\r
- try {\r
- row = t.findRow( node_name );\r
- }\r
- catch ( final IllegalArgumentException e ) {\r
- JOptionPane\r
- .showMessageDialog( this,\r
- e.getMessage(),\r
- "Error Mapping Node Identifiers to Expression Value Identifiers",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- if ( row < 0 ) {\r
- if ( node.isExternal() ) {\r
- not_found++;\r
- }\r
- continue;\r
- }\r
- final List<Double> l = new ArrayList<Double>();\r
- for( int col = 1; col < t.getNumberOfColumns(); ++col ) {\r
- double d = -100;\r
- try {\r
- d = Double.parseDouble( t.getValueAsString( col, row ) );\r
- }\r
- catch ( final NumberFormatException e ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Could not parse \"" + t.getValueAsString( col, row )\r
- + "\" into a decimal value",\r
- "Issue with Expression Value Table",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- stats.addValue( d );\r
- l.add( d );\r
- }\r
- if ( !l.isEmpty() ) {\r
- if ( node.getNodeData().getProperties() != null ) {\r
- node.getNodeData().getProperties()\r
- .removePropertiesWithGivenReferencePrefix( PhyloXmlUtil.VECTOR_PROPERTY_REF );\r
- }\r
- node.getNodeData().setVector( l );\r
- }\r
- }\r
- }\r
- if ( not_found > 0 ) {\r
- JOptionPane.showMessageDialog( this, "Could not fine expression values for " + not_found\r
- + " external node(s)", "Warning", JOptionPane.WARNING_MESSAGE );\r
- }\r
- getCurrentTreePanel().setStatisticsForExpressionValues( stats );\r
- }\r
- }\r
-\r
- private void addSequencesFromFile() {\r
- if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Need to load evolutionary tree first",\r
- "Can Not Read Sequences",\r
- JOptionPane.WARNING_MESSAGE );\r
- return;\r
- }\r
- final File my_dir = getCurrentDir();\r
- if ( my_dir != null ) {\r
- _sequences_filechooser.setCurrentDirectory( my_dir );\r
- }\r
- final int result = _sequences_filechooser.showOpenDialog( _contentpane );\r
- final File file = _sequences_filechooser.getSelectedFile();\r
- List<MolecularSequence> seqs = null;\r
- if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
- try {\r
- final FileInputStream fis1 = new FileInputStream( file );\r
- if ( FastaParser.isLikelyFasta( fis1 ) ) {\r
- final FileInputStream fis2 = new FileInputStream( file );\r
- seqs = FastaParser.parse( fis2 );\r
- try {\r
- fis2.close();\r
- }\r
- catch ( final Exception e ) {\r
- // Ignore.\r
- }\r
- }\r
- else {\r
- JOptionPane.showMessageDialog( this,\r
- "Format does not appear to be Fasta",\r
- "Multiple sequence file format error",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- try {\r
- fis1.close();\r
- }\r
- catch ( final Exception e ) {\r
- // Ignore.\r
- }\r
- }\r
- catch ( final MsaFormatException e ) {\r
- setArrowCursor();\r
- JOptionPane.showMessageDialog( this,\r
- e.getLocalizedMessage(),\r
- "Multiple sequence file format error",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- catch ( final IOException e ) {\r
- setArrowCursor();\r
- JOptionPane.showMessageDialog( this,\r
- e.getLocalizedMessage(),\r
- "Failed to read multiple sequence file",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- catch ( final Exception e ) {\r
- setArrowCursor();\r
- e.printStackTrace();\r
- JOptionPane.showMessageDialog( this,\r
- e.getLocalizedMessage(),\r
- "Unexpected error during reading of multiple sequence file",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- if ( ( seqs == null ) || ( seqs.size() < 1 ) ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Multiple sequence file is empty",\r
- "Empty multiple sequence file",\r
- JOptionPane.ERROR_MESSAGE );\r
- setArrowCursor();\r
- return;\r
- }\r
- }\r
- if ( seqs != null ) {\r
- for( final MolecularSequence seq : seqs ) {\r
- System.out.println( seq.getIdentifier() );\r
- }\r
- final Phylogeny phy = getCurrentTreePanel().getPhylogeny();\r
- int total_counter = 0;\r
- int attached_counter = 0;\r
- for( final MolecularSequence seq : seqs ) {\r
- ++total_counter;\r
- final String seq_name = seq.getIdentifier();\r
- if ( !ForesterUtil.isEmpty( seq_name ) ) {\r
- List<PhylogenyNode> nodes = phy.getNodesViaSequenceName( seq_name );\r
- if ( nodes.isEmpty() ) {\r
- nodes = phy.getNodesViaSequenceSymbol( seq_name );\r
- }\r
- if ( nodes.isEmpty() ) {\r
- nodes = phy.getNodesViaGeneName( seq_name );\r
- }\r
- if ( nodes.isEmpty() ) {\r
- nodes = phy.getNodes( seq_name );\r
- }\r
- if ( nodes.size() > 1 ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Sequence name \"" + seq_name + "\" is not unique",\r
- "Sequence name not unique",\r
- JOptionPane.ERROR_MESSAGE );\r
- setArrowCursor();\r
- return;\r
- }\r
- final String[] a = seq_name.split( "\\s" );\r
- if ( nodes.isEmpty() && ( a.length > 1 ) ) {\r
- final String seq_name_split = a[ 0 ];\r
- nodes = phy.getNodesViaSequenceName( seq_name_split );\r
- if ( nodes.isEmpty() ) {\r
- nodes = phy.getNodesViaSequenceSymbol( seq_name_split );\r
- }\r
- if ( nodes.isEmpty() ) {\r
- nodes = phy.getNodes( seq_name_split );\r
- }\r
- if ( nodes.size() > 1 ) {\r
- JOptionPane.showMessageDialog( this, "Split sequence name \"" + seq_name_split\r
- + "\" is not unique", "Sequence name not unique", JOptionPane.ERROR_MESSAGE );\r
- setArrowCursor();\r
- return;\r
- }\r
- }\r
- if ( nodes.size() == 1 ) {\r
- ++attached_counter;\r
- final PhylogenyNode n = nodes.get( 0 );\r
- if ( !n.getNodeData().isHasSequence() ) {\r
- n.getNodeData().addSequence( new org.forester.phylogeny.data.Sequence() );\r
- }\r
- n.getNodeData().getSequence().setMolecularSequence( seq.getMolecularSequenceAsString() );\r
- if ( ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) {\r
- n.getNodeData().getSequence().setName( seq_name );\r
- }\r
- }\r
- }\r
- }\r
- if ( attached_counter > 0 ) {\r
- int ext_nodes = 0;\r
- int ext_nodes_with_seq = 0;\r
- for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {\r
- ++ext_nodes;\r
- final PhylogenyNode n = iter.next();\r
- if ( n.getNodeData().isHasSequence()\r
- && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getMolecularSequence() ) ) {\r
- ++ext_nodes_with_seq;\r
- }\r
- }\r
- final String s;\r
- if ( ext_nodes == ext_nodes_with_seq ) {\r
- s = "All " + ext_nodes_with_seq + " external nodes now have a molecular sequence attached to them.";\r
- }\r
- else {\r
- s = ext_nodes_with_seq + " out of " + ext_nodes\r
- + " external nodes now have a molecular sequence attached to them.";\r
- }\r
- if ( ( attached_counter == total_counter ) && ( ext_nodes == ext_nodes_with_seq ) ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Attached all " + total_counter + " sequences to tree nodes.\n" + s,\r
- "All sequences attached",\r
- JOptionPane.INFORMATION_MESSAGE );\r
- }\r
- else {\r
- JOptionPane.showMessageDialog( this, "Attached " + attached_counter\r
- + " sequences out of a total of " + total_counter + " sequences.\n" + s, attached_counter\r
- + " sequences attached", JOptionPane.WARNING_MESSAGE );\r
- }\r
- }\r
- else {\r
- JOptionPane.showMessageDialog( this, "No maching tree node for any of the " + total_counter\r
- + " sequences", "Could not attach any sequences", JOptionPane.ERROR_MESSAGE );\r
- }\r
- }\r
- }\r
-\r
- private void closeCurrentPane() {\r
- if ( getMainPanel().getCurrentTreePanel() != null ) {\r
- if ( getMainPanel().getCurrentTreePanel().isEdited() ) {\r
- final int r = JOptionPane.showConfirmDialog( this,\r
- "Close tab despite potentially unsaved changes?",\r
- "Close Tab?",\r
- JOptionPane.YES_NO_OPTION );\r
- if ( r != JOptionPane.YES_OPTION ) {\r
- return;\r
- }\r
- }\r
- getMainPanel().closeCurrentPane();\r
- activateSaveAllIfNeeded();\r
- }\r
- }\r
-\r
- private void collapse( final Phylogeny phy ) {\r
- final PhylogenyNodeIterator it = phy.iteratorPostorder();\r
- final List<PhylogenyNode> to_be_removed = new ArrayList<PhylogenyNode>();\r
- double min_support = Double.MAX_VALUE;\r
- boolean conf_present = false;\r
- while ( it.hasNext() ) {\r
- final PhylogenyNode n = it.next();\r
- if ( !n.isExternal() && !n.isRoot() ) {\r
- final List<Confidence> c = n.getBranchData().getConfidences();\r
- if ( ( c != null ) && ( c.size() > 0 ) ) {\r
- conf_present = true;\r
- double max = 0;\r
- for( final Confidence confidence : c ) {\r
- if ( confidence.getValue() > max ) {\r
- max = confidence.getValue();\r
- }\r
- }\r
- if ( max < getMinNotCollapseConfidenceValue() ) {\r
- to_be_removed.add( n );\r
- }\r
- if ( max < min_support ) {\r
- min_support = max;\r
- }\r
- }\r
- }\r
- }\r
- if ( conf_present ) {\r
- for( final PhylogenyNode node : to_be_removed ) {\r
- PhylogenyMethods.removeNode( node, phy );\r
- }\r
- if ( to_be_removed.size() > 0 ) {\r
- phy.externalNodesHaveChanged();\r
- phy.clearHashIdToNodeMap();\r
- phy.recalculateNumberOfExternalDescendants( true );\r
- getCurrentTreePanel().resetNodeIdToDistToLeafMap();\r
- getCurrentTreePanel().updateSetOfCollapsedExternalNodes();\r
- getCurrentTreePanel().calculateLongestExtNodeInfo();\r
- getCurrentTreePanel().setNodeInPreorderToNull();\r
- getCurrentTreePanel().recalculateMaxDistanceToRoot();\r
- getCurrentTreePanel().resetPreferredSize();\r
- getCurrentTreePanel().setEdited( true );\r
- getCurrentTreePanel().repaint();\r
- repaint();\r
- }\r
- if ( to_be_removed.size() > 0 ) {\r
- JOptionPane.showMessageDialog( this, "Collapsed " + to_be_removed.size()\r
- + " branches with\nconfidence values below " + getMinNotCollapseConfidenceValue(), "Collapsed "\r
- + to_be_removed.size() + " branches", JOptionPane.INFORMATION_MESSAGE );\r
- }\r
- else {\r
- JOptionPane.showMessageDialog( this, "No branch collapsed,\nminimum confidence value per branch is "\r
- + min_support, "No branch collapsed", JOptionPane.INFORMATION_MESSAGE );\r
- }\r
- }\r
- else {\r
- JOptionPane.showMessageDialog( this,\r
- "No branch collapsed because no confidence values present",\r
- "No confidence values present",\r
- JOptionPane.INFORMATION_MESSAGE );\r
- }\r
- }\r
-\r
- private void collapseBelowBranchLengthThreshold() {\r
- if ( getCurrentTreePanel() != null ) {\r
- final Phylogeny phy = getCurrentTreePanel().getPhylogeny();\r
- if ( ( phy != null ) && !phy.isEmpty() ) {\r
- final String s = ( String ) JOptionPane\r
- .showInputDialog( this,\r
- "Please enter the minimum branch length value\n",\r
- "Minimal Branch Length Value",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null,\r
- null,\r
- getMinNotCollapseBlValue() );\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
- setMinNotCollapseBlValue( m );\r
- collapseBl( phy );\r
- }\r
- }\r
- }\r
- }\r
- }\r
-\r
- private void collapseBelowThreshold() {\r
- if ( getCurrentTreePanel() != null ) {\r
- final Phylogeny phy = getCurrentTreePanel().getPhylogeny();\r
- if ( ( phy != null ) && !phy.isEmpty() ) {\r
- final String s = ( String ) JOptionPane.showInputDialog( this,\r
- "Please enter the minimum confidence value\n",\r
- "Minimal Confidence Value",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null,\r
- null,\r
- getMinNotCollapseConfidenceValue() );\r
- if ( !ForesterUtil.isEmpty( s ) ) {\r
- boolean success = true;\r
- double m = 0.0;\r
- final String m_str = s.trim();\r
- if ( !ForesterUtil.isEmpty( m_str ) ) {\r
- try {\r
- m = Double.parseDouble( m_str );\r
- }\r
- catch ( final Exception ex ) {\r
- success = false;\r
- }\r
- }\r
- else {\r
- success = false;\r
- }\r
- if ( success && ( m >= 0.0 ) ) {\r
- setMinNotCollapseConfidenceValue( m );\r
- collapse( phy );\r
- }\r
- }\r
- }\r
- }\r
- }\r
-\r
- private void collapseBl( final Phylogeny phy ) {\r
- final PhylogenyNodeIterator it = phy.iteratorPostorder();\r
- final List<PhylogenyNode> to_be_removed = new ArrayList<PhylogenyNode>();\r
- double min_bl = Double.MAX_VALUE;\r
- boolean bl_present = false;\r
- while ( it.hasNext() ) {\r
- final PhylogenyNode n = it.next();\r
- if ( !n.isExternal() && !n.isRoot() ) {\r
- final double bl = n.getDistanceToParent();\r
- if ( bl != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {\r
- bl_present = true;\r
- if ( bl < getMinNotCollapseBlValue() ) {\r
- to_be_removed.add( n );\r
- }\r
- if ( bl < min_bl ) {\r
- min_bl = bl;\r
- }\r
- }\r
- }\r
- }\r
- if ( bl_present ) {\r
- for( final PhylogenyNode node : to_be_removed ) {\r
- PhylogenyMethods.removeNode( node, phy );\r
- }\r
- if ( to_be_removed.size() > 0 ) {\r
- phy.externalNodesHaveChanged();\r
- phy.clearHashIdToNodeMap();\r
- phy.recalculateNumberOfExternalDescendants( true );\r
- getCurrentTreePanel().resetNodeIdToDistToLeafMap();\r
- getCurrentTreePanel().updateSetOfCollapsedExternalNodes();\r
- getCurrentTreePanel().calculateLongestExtNodeInfo();\r
- getCurrentTreePanel().setNodeInPreorderToNull();\r
- getCurrentTreePanel().recalculateMaxDistanceToRoot();\r
- getCurrentTreePanel().resetPreferredSize();\r
- getCurrentTreePanel().setEdited( true );\r
- getCurrentTreePanel().repaint();\r
- repaint();\r
- }\r
- if ( to_be_removed.size() > 0 ) {\r
- JOptionPane.showMessageDialog( this, "Collapsed " + to_be_removed.size()\r
- + " branches with\nbranch length values below " + getMinNotCollapseBlValue(), "Collapsed "\r
- + to_be_removed.size() + " branches", JOptionPane.INFORMATION_MESSAGE );\r
- }\r
- else {\r
- JOptionPane.showMessageDialog( this,\r
- "No branch collapsed,\nminimum branch length is " + min_bl,\r
- "No branch collapsed",\r
- JOptionPane.INFORMATION_MESSAGE );\r
- }\r
- }\r
- else {\r
- JOptionPane.showMessageDialog( this,\r
- "No branch collapsed because no branch length values present",\r
- "No branch length values present",\r
- JOptionPane.INFORMATION_MESSAGE );\r
- }\r
- }\r
-\r
- private PhyloXmlParser createPhyloXmlParser() {\r
- PhyloXmlParser xml_parser = null;\r
- if ( getConfiguration().isValidatePhyloXmlAgainstSchema() ) {\r
- try {\r
- xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();\r
- }\r
- catch ( final Exception e ) {\r
- JOptionPane.showMessageDialog( this,\r
- e.getLocalizedMessage(),\r
- "failed to create validating XML parser",\r
- JOptionPane.WARNING_MESSAGE );\r
- }\r
- }\r
- if ( xml_parser == null ) {\r
- xml_parser = PhyloXmlParser.createPhyloXmlParser();\r
- }\r
- return xml_parser;\r
- }\r
-\r
- private void executePhyleneticInference( final boolean from_unaligned_seqs ) {\r
- final PhyloInferenceDialog dialog = new PhyloInferenceDialog( this,\r
- getPhylogeneticInferenceOptions(),\r
- from_unaligned_seqs );\r
- dialog.activate();\r
- if ( dialog.getValue() == JOptionPane.OK_OPTION ) {\r
- if ( !from_unaligned_seqs ) {\r
- if ( getMsa() != null ) {\r
- final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getMsa(),\r
- getPhylogeneticInferenceOptions()\r
- .copy(), this );\r
- new Thread( inferrer ).start();\r
- }\r
- else {\r
- JOptionPane.showMessageDialog( this,\r
- "No multiple sequence alignment selected",\r
- "Phylogenetic Inference Not Launched",\r
- JOptionPane.WARNING_MESSAGE );\r
- }\r
- }\r
- else {\r
- if ( getSeqs() != null ) {\r
- final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getSeqs(),\r
- getPhylogeneticInferenceOptions()\r
- .copy(), this );\r
- new Thread( inferrer ).start();\r
- }\r
- else {\r
- JOptionPane.showMessageDialog( this,\r
- "No input sequences selected",\r
- "Phylogenetic Inference Not Launched",\r
- JOptionPane.WARNING_MESSAGE );\r
- }\r
- }\r
- }\r
- }\r
-\r
- private void extractTaxDataFromNodeNames() throws PhyloXmlDataFormatException {\r
- final StringBuilder sb = new StringBuilder();\r
- final StringBuilder sb_failed = new StringBuilder();\r
- int counter = 0;\r
- int counter_failed = 0;\r
- if ( getCurrentTreePanel() != null ) {\r
- final Phylogeny phy = getCurrentTreePanel().getPhylogeny();\r
- if ( ( phy != null ) && !phy.isEmpty() ) {\r
- final PhylogenyNodeIterator it = phy.iteratorExternalForward();\r
- while ( it.hasNext() ) {\r
- final PhylogenyNode n = it.next();\r
- final String name = n.getName().trim();\r
- if ( !ForesterUtil.isEmpty( name ) ) {\r
- final String nt = ParserUtils.extractTaxonomyDataFromNodeName( n,\r
- TAXONOMY_EXTRACTION.AGGRESSIVE );\r
- if ( !ForesterUtil.isEmpty( nt ) ) {\r
- if ( counter < 15 ) {\r
- sb.append( name + ": " + nt + "\n" );\r
- }\r
- else if ( counter == 15 ) {\r
- sb.append( "...\n" );\r
- }\r
- counter++;\r
- }\r
- else {\r
- if ( counter_failed < 15 ) {\r
- sb_failed.append( name + "\n" );\r
- }\r
- else if ( counter_failed == 15 ) {\r
- sb_failed.append( "...\n" );\r
- }\r
- counter_failed++;\r
- }\r
- }\r
- }\r
- if ( counter > 0 ) {\r
- String failed = "";\r
- String all = "all ";\r
- if ( counter_failed > 0 ) {\r
- all = "";\r
- failed = "\nCould not extract taxonomic data for " + counter_failed\r
- + " named external nodes:\n" + sb_failed;\r
- }\r
- JOptionPane.showMessageDialog( this,\r
- "Extracted taxonomic data from " + all + counter\r
- + " named external nodes:\n" + sb.toString() + failed,\r
- "Taxonomic Data Extraction Completed",\r
- counter_failed > 0 ? JOptionPane.WARNING_MESSAGE\r
- : JOptionPane.INFORMATION_MESSAGE );\r
- }\r
- else {\r
- JOptionPane\r
- .showMessageDialog( this,\r
- "Could not extract any taxonomic data.\nMaybe node names are empty\n"\r
- + "or not in the forms \"XYZ_CAEEL\", \"XYZ_6239\", or \"XYZ_Caenorhabditis_elegans\"\n"\r
- + "or nodes already have taxonomic data?\n",\r
- "No Taxonomic Data Extracted",\r
- JOptionPane.ERROR_MESSAGE );\r
- }\r
- }\r
- }\r
- }\r
-\r
- private double getMinNotCollapseBlValue() {\r
- return _min_not_collapse_bl;\r
- }\r
-\r
- private double getMinNotCollapseConfidenceValue() {\r
- return _min_not_collapse;\r
- }\r
-\r
- private PhylogeneticInferenceOptions getPhylogeneticInferenceOptions() {\r
- if ( _phylogenetic_inference_options == null ) {\r
- _phylogenetic_inference_options = new PhylogeneticInferenceOptions();\r
- }\r
- return _phylogenetic_inference_options;\r
- }\r
-\r
- private boolean isUnsavedDataPresent() {\r
- final List<TreePanel> tps = getMainPanel().getTreePanels();\r
- for( final TreePanel tp : tps ) {\r
- if ( tp.isEdited() ) {\r
- return true;\r
- }\r
- }\r
- return false;\r
- }\r
-\r
- private void moveNodeNamesToSeqNames() throws PhyloXmlDataFormatException {\r
- if ( getCurrentTreePanel() != null ) {\r
- final Phylogeny phy = getCurrentTreePanel().getPhylogeny();\r
- if ( ( phy != null ) && !phy.isEmpty() ) {\r
- PhylogenyMethods\r
- .transferNodeNameToField( phy, PhylogenyMethods.PhylogenyNodeField.SEQUENCE_NAME, false );\r
- }\r
- }\r
- }\r
-\r
- private void moveNodeNamesToTaxSn() throws PhyloXmlDataFormatException {\r
- if ( getCurrentTreePanel() != null ) {\r
- final Phylogeny phy = getCurrentTreePanel().getPhylogeny();\r
- if ( ( phy != null ) && !phy.isEmpty() ) {\r
- PhylogenyMethods.transferNodeNameToField( phy,\r
- PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME,\r
- false );\r
- }\r
- }\r
- }\r
-\r
- private void newTree() {\r
- final Phylogeny[] phys = new Phylogeny[ 1 ];\r
- final Phylogeny phy = new Phylogeny();\r
- final PhylogenyNode node = new PhylogenyNode();\r
- phy.setRoot( node );\r
- phy.setRooted( true );\r
- phys[ 0 ] = phy;\r
- AptxUtil.addPhylogeniesToTabs( phys, "", "", getConfiguration(), getMainPanel() );\r
- _mainpanel.getControlPanel().showWhole();\r
- _mainpanel.getCurrentTreePanel().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );\r
- _mainpanel.getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );\r
- if ( getMainPanel().getMainFrame() == null ) {\r
- // Must be "E" applet version.\r
- ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() )\r
- .setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );\r
- }\r
- else {\r
- getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );\r
- }\r
- activateSaveAllIfNeeded();\r
- System.gc();\r
- }\r
-\r
- private void obtainDetailedTaxonomicInformation() {\r
- if ( getCurrentTreePanel() != null ) {\r
- final Phylogeny phy = getCurrentTreePanel().getPhylogeny();\r
- if ( ( phy != null ) && !phy.isEmpty() ) {\r
- final TaxonomyDataManager t = new TaxonomyDataManager( this,\r
- _mainpanel.getCurrentTreePanel(),\r
- phy.copy(),\r
- false,\r
- true );\r
- new Thread( t ).start();\r
- }\r
- }\r
- }\r
-\r
- private void obtainDetailedTaxonomicInformationDelete() {\r
- if ( getCurrentTreePanel() != null ) {\r
- final Phylogeny phy = getCurrentTreePanel().getPhylogeny();\r
- if ( ( phy != null ) && !phy.isEmpty() ) {\r
- final TaxonomyDataManager t = new TaxonomyDataManager( this,\r
- _mainpanel.getCurrentTreePanel(),\r
- phy.copy(),\r
- true,\r
- true );\r
- new Thread( t ).start();\r
- }\r
- }\r
- }\r
-\r
- private void obtainSequenceInformation() {\r
- if ( getCurrentTreePanel() != null ) {\r
- final Phylogeny phy = getCurrentTreePanel().getPhylogeny();\r
- if ( ( phy != null ) && !phy.isEmpty() ) {\r
- final SequenceDataRetriver u = new SequenceDataRetriver( this,\r
- _mainpanel.getCurrentTreePanel(),\r
- phy.copy() );\r
- new Thread( u ).start();\r
- }\r
- }\r
- }\r
-\r
- private void preProcessTreesUponReading( final Phylogeny[] phys ) {\r
- for( final Phylogeny phy : phys ) {\r
- if ( ( phy != null ) && !phy.isEmpty() ) {\r
- for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) {\r
- final PhylogenyNode n = it.next();\r
- if ( n.isExternal() ) {\r
- if ( n.getNodeData().isHasSequence() ) {\r
- final Sequence s = n.getNodeData().getSequence();\r
- if ( ForesterUtil.isEmpty( s.getGeneName() ) || s.getGeneName().startsWith( "LOC" ) ) {\r
- if ( ( s.getAccession() != null )\r
- && !ForesterUtil.isEmpty( s.getAccession().getValue() ) ) {\r
- s.setGeneName( s.getAccession().getValue() );\r
- }\r
- else if ( !ForesterUtil.isEmpty( n.getName() ) ) {\r
- s.setGeneName( n.getName() );\r
- }\r
- }\r
- }\r
- }\r
- }\r
- }\r
- }\r
- }\r
-\r
- private void readPhylogeniesFromFile() {\r
- boolean exception = false;\r
- Phylogeny[] phys = null;\r
- // Set an initial directory if none set yet\r
- final File my_dir = getCurrentDir();\r
- // Open file-open dialog and set current directory\r
- if ( my_dir != null ) {\r
- _open_filechooser.setCurrentDirectory( my_dir );\r
- }\r
- final int result = _open_filechooser.showOpenDialog( _contentpane );\r
- // All done: get the file\r
- final File[] files = _open_filechooser.getSelectedFiles();\r
- setCurrentDir( _open_filechooser.getCurrentDirectory() );\r
- boolean nhx_or_nexus = false;\r
- if ( ( files != null ) && ( files.length > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
- for( final File file : files ) {\r
- if ( ( file != null ) && !file.isDirectory() ) {\r
- if ( _mainpanel.getCurrentTreePanel() != null ) {\r
- _mainpanel.getCurrentTreePanel().setWaitCursor();\r
- }\r
- else {\r
- _mainpanel.setWaitCursor();\r
- }\r
- if ( ( _open_filechooser.getFileFilter() == MainFrame.nhfilter )\r
- || ( _open_filechooser.getFileFilter() == MainFrame.nhxfilter ) ) {\r
- try {\r
- final NHXParser nhx = new NHXParser();\r
- setSpecialOptionsForNhxParser( nhx );\r
- phys = PhylogenyMethods.readPhylogenies( nhx, file );\r
- nhx_or_nexus = true;\r
- }\r
- catch ( final Exception e ) {\r
- exception = true;\r
- exceptionOccuredDuringOpenFile( e );\r
- }\r
- }\r
- else if ( _open_filechooser.getFileFilter() == MainFrame.xmlfilter ) {\r
- warnIfNotPhyloXmlValidation( getConfiguration() );\r
- try {\r
- final PhyloXmlParser xml_parser = createPhyloXmlParser();\r
- phys = PhylogenyMethods.readPhylogenies( xml_parser, file );\r
- }\r
- catch ( final Exception e ) {\r
- exception = true;\r
- exceptionOccuredDuringOpenFile( e );\r
- }\r
- }\r
- else if ( _open_filechooser.getFileFilter() == MainFrame.tolfilter ) {\r
- try {\r
- phys = PhylogenyMethods.readPhylogenies( new TolParser(), file );\r
- }\r
- catch ( final Exception e ) {\r
- exception = true;\r
- exceptionOccuredDuringOpenFile( e );\r
- }\r
- }\r
- else if ( _open_filechooser.getFileFilter() == MainFrame.nexusfilter ) {\r
- try {\r
- final NexusPhylogeniesParser nex = new NexusPhylogeniesParser();\r
- setSpecialOptionsForNexParser( nex );\r
- phys = PhylogenyMethods.readPhylogenies( nex, file );\r
- nhx_or_nexus = true;\r
- }\r
- catch ( final Exception e ) {\r
- exception = true;\r
- exceptionOccuredDuringOpenFile( e );\r
- }\r
- }\r
- // "*.*":\r
- else {\r
- try {\r
- final PhylogenyParser parser = ParserUtils\r
- .createParserDependingOnFileType( file, getConfiguration()\r
- .isValidatePhyloXmlAgainstSchema() );\r
- if ( parser instanceof NexusPhylogeniesParser ) {\r
- final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) parser;\r
- setSpecialOptionsForNexParser( nex );\r
- nhx_or_nexus = true;\r
- }\r
- else if ( parser instanceof NHXParser ) {\r
- final NHXParser nhx = ( NHXParser ) parser;\r
- setSpecialOptionsForNhxParser( nhx );\r
- nhx_or_nexus = true;\r
- }\r
- else if ( parser instanceof PhyloXmlParser ) {\r
- warnIfNotPhyloXmlValidation( getConfiguration() );\r
- }\r
- phys = PhylogenyMethods.readPhylogenies( parser, file );\r
- }\r
- catch ( final Exception e ) {\r
- exception = true;\r
- exceptionOccuredDuringOpenFile( e );\r
- }\r
- }\r
- if ( _mainpanel.getCurrentTreePanel() != null ) {\r
- _mainpanel.getCurrentTreePanel().setArrowCursor();\r
- }\r
- else {\r
- _mainpanel.setArrowCursor();\r
- }\r
- if ( !exception && ( phys != null ) && ( phys.length > 0 ) ) {\r
- boolean one_desc = false;\r
- if ( nhx_or_nexus ) {\r
- for( final Phylogeny phy : phys ) {\r
- if ( getOptions().isInternalNumberAreConfidenceForNhParsing() ) {\r
- PhylogenyMethods.transferInternalNodeNamesToConfidence( phy, "" );\r
- }\r
- if ( PhylogenyMethods.getMinimumDescendentsPerInternalNodes( phy ) == 1 ) {\r
- one_desc = true;\r
- break;\r
- }\r
- }\r
- }\r
- if ( PREPROCESS_TREES ) {\r
- preProcessTreesUponReading( phys );\r
- }\r
- AptxUtil.addPhylogeniesToTabs( phys,\r
- file.getName(),\r
- file.getAbsolutePath(),\r
- getConfiguration(),\r
- getMainPanel() );\r
- _mainpanel.getControlPanel().showWhole();\r
- if ( nhx_or_nexus && one_desc ) {\r
- JOptionPane\r
- .showMessageDialog( this,\r
- "One or more trees contain (a) node(s) with one descendant, "\r
- + ForesterUtil.LINE_SEPARATOR\r
- + "possibly indicating illegal parentheses within node names.",\r
- "Warning: Possible Error in New Hampshire Formatted Data",\r
- JOptionPane.WARNING_MESSAGE );\r
- }\r
- }\r
- }\r
- }\r
- }\r
- activateSaveAllIfNeeded();\r
- System.gc();\r
- }\r
-\r
- private void readSpeciesTreeFromFile() {\r
- Phylogeny t = null;\r
- boolean exception = false;\r
- final File my_dir = getCurrentDir();\r
- _open_filechooser_for_species_tree.setSelectedFile( new File( "" ) );\r
- if ( my_dir != null ) {\r
- _open_filechooser_for_species_tree.setCurrentDirectory( my_dir );\r
- }\r
- final int result = _open_filechooser_for_species_tree.showOpenDialog( _contentpane );\r
- final File file = _open_filechooser_for_species_tree.getSelectedFile();\r
- if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
- if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrame.xmlfilter ) {\r
- try {\r
- final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( PhyloXmlParser\r
- .createPhyloXmlParserXsdValidating(), file );\r
- t = trees[ 0 ];\r
- }\r
- catch ( final Exception e ) {\r
- exception = true;\r
- exceptionOccuredDuringOpenFile( e );\r
- }\r
- }\r
- else if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrame.tolfilter ) {\r
- try {\r
- final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new TolParser(), file );\r
- t = trees[ 0 ];\r
- }\r
- catch ( final Exception e ) {\r
- exception = true;\r
- exceptionOccuredDuringOpenFile( e );\r
- }\r
- }\r
- // "*.*":\r
- else {\r
- try {\r
- final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( PhyloXmlParser\r
- .createPhyloXmlParserXsdValidating(), file );\r
- t = trees[ 0 ];\r
- }\r
- catch ( final Exception e ) {\r
- exception = true;\r
- exceptionOccuredDuringOpenFile( e );\r
- }\r
- }\r
- if ( !exception && ( t != null ) && !t.isRooted() ) {\r
- exception = true;\r
- t = null;\r
- JOptionPane.showMessageDialog( this,\r
- "Species tree is not rooted",\r
- "Species tree not loaded",\r
- JOptionPane.ERROR_MESSAGE );\r
- }\r
- if ( !exception && ( t != null ) ) {\r
- final Set<Taxonomy> tax_set = new HashSet<Taxonomy>();\r
- for( final PhylogenyNodeIterator it = t.iteratorExternalForward(); it.hasNext(); ) {\r
- final PhylogenyNode node = it.next();\r
- if ( !node.getNodeData().isHasTaxonomy() ) {\r
- exception = true;\r
- t = null;\r
- JOptionPane\r
- .showMessageDialog( this,\r
- "Species tree contains external node(s) without taxonomy information",\r
- "Species tree not loaded",\r
- JOptionPane.ERROR_MESSAGE );\r
- break;\r
- }\r
- else {\r
- if ( tax_set.contains( node.getNodeData().getTaxonomy() ) ) {\r
- exception = true;\r
- t = null;\r
- JOptionPane.showMessageDialog( this,\r
- "Taxonomy ["\r
- + node.getNodeData().getTaxonomy().asSimpleText()\r
- + "] is not unique in species tree",\r
- "Species tree not loaded",\r
- JOptionPane.ERROR_MESSAGE );\r
- break;\r
- }\r
- else {\r
- tax_set.add( node.getNodeData().getTaxonomy() );\r
- }\r
- }\r
- }\r
- }\r
- if ( !exception && ( t != null ) ) {\r
- setSpeciesTree( t );\r
- JOptionPane.showMessageDialog( this,\r
- "Species tree successfully loaded",\r
- "Species tree loaded",\r
- JOptionPane.INFORMATION_MESSAGE );\r
- }\r
- _contentpane.repaint();\r
- System.gc();\r
- }\r
- }\r
-\r
- private void setArrowCursor() {\r
- try {\r
- _mainpanel.getCurrentTreePanel().setArrowCursor();\r
- }\r
- catch ( final Exception ex ) {\r
- // Do nothing.\r
- }\r
- }\r
-\r
- private void setMinNotCollapseBlValue( final double min_not_collapse_bl ) {\r
- _min_not_collapse_bl = min_not_collapse_bl;\r
- }\r
-\r
- private void setMinNotCollapseConfidenceValue( final double min_not_collapse ) {\r
- _min_not_collapse = min_not_collapse;\r
- }\r
-\r
- private void setPhylogeneticInferenceOptions( final PhylogeneticInferenceOptions phylogenetic_inference_options ) {\r
- _phylogenetic_inference_options = phylogenetic_inference_options;\r
- }\r
-\r
- private void setSpecialOptionsForNexParser( final NexusPhylogeniesParser nex ) {\r
- nex.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );\r
- nex.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() );\r
- }\r
-\r
- private void setSpecialOptionsForNhxParser( final NHXParser nhx ) {\r
- nhx.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );\r
- nhx.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() );\r
- nhx.setAllowErrorsInDistanceToParent( getOptions().isAllowErrorsInDistanceToParent() );\r
- }\r
-\r
- void buildAnalysisMenu() {\r
- _analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );\r
- _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );\r
- _analysis_menu.add( _gsdir_item = new JMenuItem( "GSDIR (GSDI with re-rooting)" ) );\r
- _analysis_menu.add( _load_species_tree_item = new JMenuItem( "Load Species Tree..." ) );\r
- customizeJMenuItem( _gsdi_item );\r
- customizeJMenuItem( _gsdir_item );\r
- customizeJMenuItem( _load_species_tree_item );\r
- _analysis_menu.addSeparator();\r
- _analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) );\r
- customizeJMenuItem( _lineage_inference );\r
- _lineage_inference.setToolTipText( "Inference of ancestor taxonomies/lineages" );\r
- _jmenubar.add( _analysis_menu );\r
- }\r
-\r
- @Override\r
- void buildFileMenu() {\r
- _file_jmenu = MainFrame.createMenu( "File", getConfiguration() );\r
- _file_jmenu.add( _open_item = new JMenuItem( "Read Tree from File..." ) );\r
- _file_jmenu.addSeparator();\r
- _file_jmenu.add( _open_url_item = new JMenuItem( "Read Tree from URL/Webservice..." ) );\r
- _file_jmenu.addSeparator();\r
- final WebservicesManager webservices_manager = WebservicesManager.getInstance();\r
- _load_phylogeny_from_webservice_menu_items = new JMenuItem[ webservices_manager\r
- .getAvailablePhylogeniesWebserviceClients().size() ];\r
- for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {\r
- final PhylogeniesWebserviceClient client = webservices_manager.getAvailablePhylogeniesWebserviceClient( i );\r
- _load_phylogeny_from_webservice_menu_items[ i ] = new JMenuItem( client.getMenuName() );\r
- _file_jmenu.add( _load_phylogeny_from_webservice_menu_items[ i ] );\r
- }\r
- if ( getConfiguration().isEditable() ) {\r
- _file_jmenu.addSeparator();\r
- _file_jmenu.add( _new_item = new JMenuItem( "New" ) );\r
- _new_item.setToolTipText( "to create a new tree with one node, as source for manual tree construction" );\r
- }\r
- _file_jmenu.addSeparator();\r
- _file_jmenu.add( _save_item = new JMenuItem( "Save Tree As..." ) );\r
- _file_jmenu.add( _save_all_item = new JMenuItem( "Save All Trees As..." ) );\r
- _save_all_item.setToolTipText( "Write all phylogenies to one file." );\r
- _save_all_item.setEnabled( false );\r
- _file_jmenu.addSeparator();\r
- _file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) );\r
- if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" ) || AptxUtil.canWriteFormat( "TIF" ) ) {\r
- _file_jmenu.add( _write_to_tif_item = new JMenuItem( "Export to TIFF file..." ) );\r
- }\r
- _file_jmenu.add( _write_to_png_item = new JMenuItem( "Export to PNG file..." ) );\r
- _file_jmenu.add( _write_to_jpg_item = new JMenuItem( "Export to JPG file..." ) );\r
- if ( AptxUtil.canWriteFormat( "gif" ) ) {\r
- _file_jmenu.add( _write_to_gif_item = new JMenuItem( "Export to GIF file..." ) );\r
- }\r
- if ( AptxUtil.canWriteFormat( "bmp" ) ) {\r
- _file_jmenu.add( _write_to_bmp_item = new JMenuItem( "Export to BMP file..." ) );\r
- }\r
- _file_jmenu.addSeparator();\r
- _file_jmenu.add( _print_item = new JMenuItem( "Print..." ) );\r
- _file_jmenu.addSeparator();\r
- _file_jmenu.add( _close_item = new JMenuItem( "Close Tab" ) );\r
- _close_item.setToolTipText( "To close the current pane." );\r
- _close_item.setEnabled( true );\r
- _file_jmenu.addSeparator();\r
- _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );\r
- customizeJMenuItem( _open_item );\r
- _open_item\r
- .setFont( new Font( _open_item.getFont().getFontName(), Font.BOLD, _open_item.getFont().getSize() + 4 ) );\r
- customizeJMenuItem( _open_url_item );\r
- for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {\r
- customizeJMenuItem( _load_phylogeny_from_webservice_menu_items[ i ] );\r
- }\r
- customizeJMenuItem( _save_item );\r
- if ( getConfiguration().isEditable() ) {\r
- customizeJMenuItem( _new_item );\r
- }\r
- customizeJMenuItem( _close_item );\r
- customizeJMenuItem( _save_all_item );\r
- customizeJMenuItem( _write_to_pdf_item );\r
- customizeJMenuItem( _write_to_png_item );\r
- customizeJMenuItem( _write_to_jpg_item );\r
- customizeJMenuItem( _write_to_gif_item );\r
- customizeJMenuItem( _write_to_tif_item );\r
- customizeJMenuItem( _write_to_bmp_item );\r
- customizeJMenuItem( _print_item );\r
- customizeJMenuItem( _exit_item );\r
- _jmenubar.add( _file_jmenu );\r
- }\r
-\r
- void buildOptionsMenu() {\r
- _options_jmenu = MainFrame.createMenu( OPTIONS_HEADER, getConfiguration() );\r
- _options_jmenu.addChangeListener( new ChangeListener() {\r
-\r
- @Override\r
- public void stateChanged( final ChangeEvent e ) {\r
- MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );\r
- MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );\r
- MainFrame\r
- .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );\r
- MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame\r
- .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );\r
- // MainFrame.setTextForGraphicsSizeChooserMenuItem( _print_size_mi, getOptions() );\r
- MainFrame.setTextForPdfLineWidthChooserMenuItem( _choose_pdf_width_mi, getOptions() );\r
- MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );\r
- MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );\r
- MainFrame.setCycleDataReturnMenuItem( _cycle_data_return, getOptions() );\r
- MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );\r
- try {\r
- getMainPanel().getControlPanel().setVisibilityOfDomainStrucureCB();\r
- getMainPanel().getControlPanel().setVisibilityOfX();\r
- }\r
- catch ( final Exception ignore ) {\r
- // do nothing, not important.\r
- }\r
- }\r
- } );\r
- _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( DISPLAY_SUBHEADER ), getConfiguration() ) );\r
- _options_jmenu\r
- .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );\r
- _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );\r
- _options_jmenu.add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( NON_LINED_UP_CLADOGRAMS_LABEL ) );\r
- _radio_group_1 = new ButtonGroup();\r
- _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );\r
- _radio_group_1.add( _uniform_cladograms_rbmi );\r
- _radio_group_1.add( _non_lined_up_cladograms_rbmi );\r
- _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( SHOW_OVERVIEW_LABEL ) );\r
- _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( DISPLAY_SCALE_LABEL ) );\r
- _options_jmenu\r
- .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_INT ) );\r
- _options_jmenu\r
- .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_EXT ) );\r
- _options_jmenu\r
- .add( _show_default_node_shapes_for_marked_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_MARKED ) );\r
- _options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) );\r
- if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {\r
- _options_jmenu.add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) );\r
- _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) );\r
- }\r
- _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( SHOW_ANN_REF_SOURCE_LABEL ) );\r
- _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( SHOW_CONF_STDDEV_LABEL ) );\r
- _options_jmenu.add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( COLOR_BY_TAXONOMIC_GROUP ) );\r
- _options_jmenu.add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( COLOR_LABELS_LABEL ) );\r
- _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );\r
- _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( ABBREV_SN_LABEL ) );\r
- _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( LABEL_DIRECTION_LABEL ) );\r
- _label_direction_cbmi.setToolTipText( LABEL_DIRECTION_TIP );\r
- _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( SCREEN_ANTIALIAS_LABEL ) );\r
- _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( BG_GRAD_LABEL ) );\r
- _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );\r
- _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );\r
- _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );\r
- _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );\r
- _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );\r
- _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );\r
- _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );\r
- _options_jmenu.addSeparator();\r
- _options_jmenu.add( _cycle_data_return = new JMenuItem( "Cycle Data Return" ) );\r
- _options_jmenu.addSeparator();\r
- _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( SEARCH_SUBHEADER ), getConfiguration() ) );\r
- _options_jmenu.add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( SEARCH_CASE_SENSITIVE_LABEL ) );\r
- _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( SEARCH_TERMS_ONLY_LABEL ) );\r
- _options_jmenu.add( _search_with_regex_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_REGEX_LABEL ) );\r
- _search_with_regex_cbmi.setToolTipText( MainFrame.SEARCH_WITH_REGEX_TIP );\r
- _options_jmenu.add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( INVERSE_SEARCH_RESULT_LABEL ) );\r
- _options_jmenu.add( _color_all_found_nodes_when_coloring_subtree_cbmi = new JCheckBoxMenuItem( "Colorize All Found Nodes When Colorizing Subtree(s)" ) ); \r
- _options_jmenu.addSeparator();\r
- _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Graphics Export & Printing:" ),\r
- getConfiguration() ) );\r
- _options_jmenu.add( _antialias_print_cbmi = new JCheckBoxMenuItem( "Antialias" ) );\r
- _options_jmenu.add( _print_black_and_white_cbmi = new JCheckBoxMenuItem( "Export in Black and White" ) );\r
- //_options_jmenu\r
- //.add( _print_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PDF export and Printing" ) );\r
- //_options_jmenu\r
- //.add( _graphics_export_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PNG, JPG, and GIF export" ) );\r
- _options_jmenu\r
- .add( _graphics_export_visible_only_cbmi = new JCheckBoxMenuItem( "Limit to Visible ('Screenshot') for PNG, JPG, and GIF export" ) );\r
- // _options_jmenu.add( _print_size_mi = new JMenuItem( "" ) );\r
- _options_jmenu.add( _choose_pdf_width_mi = new JMenuItem( "" ) );\r
- _options_jmenu.addSeparator();\r
- _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/NHX/Nexus Read:" ), getConfiguration() ) );\r
- _options_jmenu\r
- .add( _internal_number_are_confidence_for_nh_parsing_cbmi = new JCheckBoxMenuItem( "Internal Node Names are Confidence Values" ) );\r
- _options_jmenu.add( _replace_underscores_cbmi = new JCheckBoxMenuItem( "Replace Underscores with Spaces" ) );\r
- _options_jmenu\r
- .add( _allow_errors_in_distance_to_parent_cbmi = new JCheckBoxMenuItem( "Ignore Distance Values Format Errors" ) );\r
- _options_jmenu.add( _extract_taxonomy_no_rbmi = new JRadioButtonMenuItem( "No Taxonomy Extraction" ) );\r
- _options_jmenu\r
- .add( _extract_taxonomy_pfam_strict_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style Node Names" ) );\r
- _options_jmenu\r
- .add( _extract_taxonomy_pfam_relaxed_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style like Node Names" ) );\r
- _options_jmenu\r
- .add( _extract_taxonomy_agressive_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids/Scientific Names from Node Names" ) );\r
- _extract_taxonomy_pfam_strict_rbmi\r
- .setToolTipText( "To extract taxonomy codes/ids from node names in the form of e.g. \"BCL2_MOUSE/123-304\" or \"BCL2_10090/123-304\"" );\r
- _extract_taxonomy_pfam_relaxed_rbmi\r
- .setToolTipText( "To extract taxonomy codes/ids from node names in the form of e.g. \"bax_MOUSE\" or \"bax_10090\"" );\r
- _extract_taxonomy_agressive_rbmi\r
- .setToolTipText( "To extract taxonomy codes/ids or scientific names from node names in the form of e.g. \"MOUSE\" or \"10090\" or \"xyz_Nematostella_vectensis\"" );\r
- _radio_group_2 = new ButtonGroup();\r
- _radio_group_2.add( _extract_taxonomy_no_rbmi );\r
- _radio_group_2.add( _extract_taxonomy_pfam_strict_rbmi );\r
- _radio_group_2.add( _extract_taxonomy_pfam_relaxed_rbmi );\r
- _radio_group_2.add( _extract_taxonomy_agressive_rbmi );\r
- _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/Nexus Save:" ), getConfiguration() ) );\r
- _options_jmenu\r
- .add( _use_brackets_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_BRACKETS_FOR_CONF_IN_NH_LABEL ) );\r
- _use_brackets_for_conf_in_nh_export_cbmi\r
- .setToolTipText( "e.g. \"0.1[90]\" for a branch with support 90 and a length of 0.1" );\r
- _options_jmenu\r
- .add( _use_internal_names_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL ) );\r
- customizeJMenuItem( _choose_font_mi );\r
- customizeJMenuItem( _choose_minimal_confidence_mi );\r
- customizeJMenuItem( _switch_colors_mi );\r
- // customizeJMenuItem( _print_size_mi );\r
- customizeJMenuItem( _choose_pdf_width_mi );\r
- customizeJMenuItem( _overview_placment_mi );\r
- customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions()\r
- .isShowDefaultNodeShapesExternal() );\r
- customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()\r
- .isShowDefaultNodeShapesInternal() );\r
- customizeCheckBoxMenuItem( _show_default_node_shapes_for_marked_cbmi, getOptions()\r
- .isShowDefaultNodeShapesForMarkedNodes() );\r
- customizeJMenuItem( _cycle_node_shape_mi );\r
- customizeJMenuItem( _cycle_node_fill_mi );\r
- customizeJMenuItem( _choose_node_size_mi );\r
- customizeJMenuItem( _cycle_data_return );\r
- customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );\r
- customizeCheckBoxMenuItem( _color_by_taxonomic_group_cbmi, getOptions().isColorByTaxonomicGroup() );\r
- customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );\r
- customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );\r
- customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );\r
- customizeCheckBoxMenuItem( _show_annotation_ref_source, getOptions().isShowAnnotationRefSource() );\r
- customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );\r
- customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );\r
- customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );\r
- customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,\r
- getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );\r
- customizeRadioButtonMenuItem( _uniform_cladograms_rbmi,\r
- getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );\r
- customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,\r
- getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );\r
- customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );\r
- customizeCheckBoxMenuItem( _label_direction_cbmi,\r
- getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );\r
- customizeCheckBoxMenuItem( _antialias_print_cbmi, getOptions().isAntialiasPrint() );\r
- customizeCheckBoxMenuItem( _print_black_and_white_cbmi, getOptions().isPrintBlackAndWhite() );\r
- customizeCheckBoxMenuItem( _internal_number_are_confidence_for_nh_parsing_cbmi, getOptions()\r
- .isInternalNumberAreConfidenceForNhParsing() );\r
- customizeRadioButtonMenuItem( _extract_taxonomy_no_rbmi,\r
- getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.NO );\r
- customizeRadioButtonMenuItem( _extract_taxonomy_pfam_strict_rbmi,\r
- getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );\r
- customizeRadioButtonMenuItem( _extract_taxonomy_pfam_relaxed_rbmi,\r
- getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );\r
- customizeRadioButtonMenuItem( _extract_taxonomy_agressive_rbmi,\r
- getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.AGGRESSIVE );\r
- customizeCheckBoxMenuItem( _replace_underscores_cbmi, getOptions().isReplaceUnderscoresInNhParsing() );\r
- customizeCheckBoxMenuItem( _allow_errors_in_distance_to_parent_cbmi, getOptions()\r
- .isReplaceUnderscoresInNhParsing() );\r
- customizeCheckBoxMenuItem( _search_with_regex_cbmi, getOptions().isSearchWithRegex() );\r
- customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );\r
- customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );\r
- customizeCheckBoxMenuItem( _color_all_found_nodes_when_coloring_subtree_cbmi, getOptions().isColorAllFoundNodesWhenColoringSubtree() ); \r
- customizeCheckBoxMenuItem( _graphics_export_visible_only_cbmi, getOptions().isGraphicsExportVisibleOnly() );\r
- customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );\r
- customizeCheckBoxMenuItem( _use_brackets_for_conf_in_nh_export_cbmi, getOptions()\r
- .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );\r
- customizeCheckBoxMenuItem( _use_internal_names_for_conf_in_nh_export_cbmi, getOptions()\r
- .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );\r
- customizeCheckBoxMenuItem( _line_up_renderable_data_cbmi, getOptions().isLineUpRendarableNodeData() );\r
- customizeCheckBoxMenuItem( _right_line_up_domains_cbmi, getOptions().isRightLineUpDomains() );\r
- _jmenubar.add( _options_jmenu );\r
- }\r
-\r
- void buildPhylogeneticInferenceMenu() {\r
- final InferenceManager im = getInferenceManager();\r
- _inference_menu = MainFrame.createMenu( "Inference", getConfiguration() );\r
- _inference_menu.add( _inference_from_msa_item = new JMenuItem( "From Multiple Sequence Alignment..." ) );\r
- customizeJMenuItem( _inference_from_msa_item );\r
- _inference_from_msa_item.setToolTipText( "Basic phylogenetic inference from MSA" );\r
- if ( im.canDoMsa() ) {\r
- _inference_menu.add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences..." ) );\r
- customizeJMenuItem( _inference_from_seqs_item );\r
- _inference_from_seqs_item\r
- .setToolTipText( "Basic phylogenetic inference including multiple sequence alignment" );\r
- }\r
- else {\r
- _inference_menu\r
- .add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences (no program found)" ) );\r
- customizeJMenuItem( _inference_from_seqs_item );\r
- _inference_from_seqs_item.setEnabled( false );\r
- }\r
- _jmenubar.add( _inference_menu );\r
- }\r
-\r
- void buildToolsMenu() {\r
- _tools_menu = createMenu( "Tools", getConfiguration() );\r
- _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );\r
- customizeJMenuItem( _confcolor_item );\r
- _tools_menu.add( _color_rank_jmi = new JMenuItem( "Colorize Subtrees via Taxonomic Rank" ) );\r
- customizeJMenuItem( _color_rank_jmi );\r
- _color_rank_jmi.setToolTipText( "for example, at \"Class\" level, colorize mammal specific subtree red" );\r
- _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );\r
- customizeJMenuItem( _taxcolor_item );\r
- _tools_menu.addSeparator();\r
- _tools_menu.add( _remove_visual_styles_item = new JMenuItem( "Delete All Visual Styles From Nodes" ) );\r
- _remove_visual_styles_item\r
- .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny" );\r
- customizeJMenuItem( _remove_visual_styles_item );\r
- _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete All Colors From Branches" ) );\r
- _remove_branch_color_item.setToolTipText( "To remove all branch color values from the current phylogeny" );\r
- customizeJMenuItem( _remove_branch_color_item );\r
- _tools_menu.addSeparator();\r
- _tools_menu.add( _annotate_item = new JMenuItem( "Annotate Sequences of Selected Nodes" ) );\r
- customizeJMenuItem( _annotate_item );\r
- _tools_menu.addSeparator();\r
- _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );\r
- customizeJMenuItem( _midpoint_root_item );\r
- _tools_menu.addSeparator();\r
- _tools_menu.add( _delete_selected_nodes_item = new JMenuItem( "Delete Selected Nodes" ) );\r
- _delete_selected_nodes_item.setToolTipText( "To delete all selected external nodes" );\r
- customizeJMenuItem( _delete_selected_nodes_item );\r
- _tools_menu.add( _delete_not_selected_nodes_item = new JMenuItem( "Retain Selected Nodes" ) );\r
- _delete_not_selected_nodes_item.setToolTipText( "To delete all not selected external nodes" );\r
- customizeJMenuItem( _delete_not_selected_nodes_item );\r
- _tools_menu.addSeparator();\r
- _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );\r
- customizeJMenuItem( _collapse_species_specific_subtrees );\r
- _collapse_species_specific_subtrees.setToolTipText( "To (reversibly) collapse species-specific subtrees" );\r
- _tools_menu\r
- .add( _collapse_below_threshold = new JMenuItem( "Collapse Branches with Confidence Below Threshold into Multifurcations" ) );\r
- customizeJMenuItem( _collapse_below_threshold );\r
- _collapse_below_threshold\r
- .setToolTipText( "To (permanently) collapse branches with confidence values below a threshold into multifurcations (in the case of multiple confidences per branch: without at least one confidence value above a threshold)" );\r
- //\r
- _tools_menu\r
- .add( _collapse_below_branch_length = new JMenuItem( "Collapse Branches with Branch Lengths Below Threshold into Multifurcations" ) );\r
- customizeJMenuItem( _collapse_below_branch_length );\r
- _collapse_below_branch_length\r
- .setToolTipText( "To (permanently) collapse branches with branches with branch lengths below a threshold into multifurcations" );\r
- //\r
- _tools_menu.addSeparator();\r
- _tools_menu\r
- .add( _extract_tax_code_from_node_names_jmi = new JMenuItem( "Extract Taxonomic Data from Node Names" ) );\r
- customizeJMenuItem( _extract_tax_code_from_node_names_jmi );\r
- _extract_tax_code_from_node_names_jmi\r
- .setToolTipText( "To extract SwissProt/Uniprot taxonomic codes (mnemonics) from nodes names in the form of 'xyz_CAEEL', Uniprot/NCBI identifiers form of 'xyz_6239', or scientific names form of 'xyz_Caenorhabditis_elegans'" );\r
- _tools_menu\r
- .add( _move_node_names_to_tax_sn_jmi = new JMenuItem( "Transfer Node Names to Taxonomic Scientific Names" ) );\r
- customizeJMenuItem( _move_node_names_to_tax_sn_jmi );\r
- _move_node_names_to_tax_sn_jmi.setToolTipText( "To interpret node names as taxonomic scientific names" );\r
- _tools_menu.add( _move_node_names_to_seq_names_jmi = new JMenuItem( "Transfer Node Names to Sequence Names" ) );\r
- customizeJMenuItem( _move_node_names_to_seq_names_jmi );\r
- _move_node_names_to_seq_names_jmi.setToolTipText( "To interpret node names as sequence (protein, gene) names" );\r
- _tools_menu.addSeparator();\r
- _tools_menu.add( _obtain_seq_information_jmi = new JMenuItem( "Obtain Sequence Information" ) );\r
- customizeJMenuItem( _obtain_seq_information_jmi );\r
- _obtain_seq_information_jmi.setToolTipText( "To add additional sequence information" );\r
- _tools_menu\r
- .add( _obtain_detailed_taxonomic_information_jmi = new JMenuItem( OBTAIN_DETAILED_TAXONOMIC_INFORMATION ) );\r
- customizeJMenuItem( _obtain_detailed_taxonomic_information_jmi );\r
- _obtain_detailed_taxonomic_information_jmi\r
- .setToolTipText( "To add additional taxonomic information (from UniProt Taxonomy)" );\r
- _tools_menu\r
- .add( _obtain_detailed_taxonomic_information_deleting_jmi = new JMenuItem( "Obtain Detailed Taxonomic Information (deletes nodes!)" ) );\r
- customizeJMenuItem( _obtain_detailed_taxonomic_information_deleting_jmi );\r
- _obtain_detailed_taxonomic_information_deleting_jmi\r
- .setToolTipText( "To add additional taxonomic information, deletes nodes for which taxonomy cannot found (from UniProt Taxonomy)" );\r
- _tools_menu.addSeparator();\r
- _tools_menu.add( _read_values_jmi = new JMenuItem( "Attach Vector/Expression Values" ) );\r
- customizeJMenuItem( _read_values_jmi );\r
- _read_values_jmi.setToolTipText( "To attach vector (e.g. gene expression) values to tree nodes (beta)" );\r
- _jmenubar.add( _tools_menu );\r
- _tools_menu.add( _read_seqs_jmi = new JMenuItem( "Attach Molecular Sequences" ) );\r
- customizeJMenuItem( _read_seqs_jmi );\r
- _read_seqs_jmi\r
- .setToolTipText( "To attach molecular sequences to tree nodes (from Fasta-formatted file) (beta)" );\r
- _jmenubar.add( _tools_menu );\r
- }\r
-\r
- @Override\r
- void close() {\r
- if ( isUnsavedDataPresent() ) {\r
- final int r = JOptionPane.showConfirmDialog( this,\r
- "Exit despite potentially unsaved changes?",\r
- "Exit?",\r
- JOptionPane.YES_NO_OPTION );\r
- if ( r != JOptionPane.YES_OPTION ) {\r
- return;\r
- }\r
- }\r
- exit();\r
- }\r
-\r
- void exit() {\r
- removeAllTextFrames();\r
- _mainpanel.terminate();\r
- _contentpane.removeAll();\r
- setVisible( false );\r
- dispose();\r
- // System.exit( 0 ); //TODO reconfirm that this is OK, then remove.\r
- }\r
-\r
- void readPhylogeniesFromURL() {\r
- URL url = null;\r
- Phylogeny[] phys = null;\r
- final String message = "Please enter a complete URL, for example \"http://purl.org/phylo/treebase/phylows/study/TB2:S15480?format=nexus\"";\r
- final String url_string = JOptionPane.showInputDialog( this,\r
- message,\r
- "Use URL/webservice to obtain a phylogeny",\r
- JOptionPane.QUESTION_MESSAGE );\r
- boolean nhx_or_nexus = false;\r
- if ( ( url_string != null ) && ( url_string.length() > 0 ) ) {\r
- try {\r
- url = new URL( url_string );\r
- PhylogenyParser parser = null;\r
- if ( url.getHost().toLowerCase().indexOf( "tolweb" ) >= 0 ) {\r
- parser = new TolParser();\r
- }\r
- else {\r
- parser = ParserUtils.createParserDependingOnUrlContents( url, getConfiguration()\r
- .isValidatePhyloXmlAgainstSchema() );\r
- }\r
- if ( parser instanceof NexusPhylogeniesParser ) {\r
- nhx_or_nexus = true;\r
- }\r
- else if ( parser instanceof NHXParser ) {\r
- nhx_or_nexus = true;\r
- }\r
- if ( _mainpanel.getCurrentTreePanel() != null ) {\r
- _mainpanel.getCurrentTreePanel().setWaitCursor();\r
- }\r
- else {\r
- _mainpanel.setWaitCursor();\r
- }\r
- final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();\r
- phys = factory.create( url.openStream(), parser );\r
- }\r
- catch ( final MalformedURLException e ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Malformed URL: " + url + "\n" + e.getLocalizedMessage(),\r
- "Malformed URL",\r
- JOptionPane.ERROR_MESSAGE );\r
- }\r
- catch ( final IOException e ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Could not read from " + url + "\n"\r
- + ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),\r
- "Failed to read URL",\r
- JOptionPane.ERROR_MESSAGE );\r
- }\r
- catch ( final Exception e ) {\r
- JOptionPane.showMessageDialog( this,\r
- ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),\r
- "Unexpected Exception",\r
- JOptionPane.ERROR_MESSAGE );\r
- }\r
- finally {\r
- if ( _mainpanel.getCurrentTreePanel() != null ) {\r
- _mainpanel.getCurrentTreePanel().setArrowCursor();\r
- }\r
- else {\r
- _mainpanel.setArrowCursor();\r
- }\r
- }\r
- if ( ( phys != null ) && ( phys.length > 0 ) ) {\r
- if ( nhx_or_nexus && getOptions().isInternalNumberAreConfidenceForNhParsing() ) {\r
- for( final Phylogeny phy : phys ) {\r
- PhylogenyMethods.transferInternalNodeNamesToConfidence( phy, "" );\r
- }\r
- }\r
- AptxUtil.addPhylogeniesToTabs( phys,\r
- new File( url.getFile() ).getName(),\r
- new File( url.getFile() ).toString(),\r
- getConfiguration(),\r
- getMainPanel() );\r
- _mainpanel.getControlPanel().showWhole();\r
- }\r
- }\r
- activateSaveAllIfNeeded();\r
- System.gc();\r
- }\r
-\r
- void setMsa( final Msa msa ) {\r
- _msa = msa;\r
- }\r
-\r
- void setMsaFile( final File msa_file ) {\r
- _msa_file = msa_file;\r
- }\r
-\r
- void setSeqs( final List<MolecularSequence> seqs ) {\r
- _seqs = seqs;\r
- }\r
-\r
- void setSeqsFile( final File seqs_file ) {\r
- _seqs_file = seqs_file;\r
- }\r
-\r
- public static MainFrameApplication createInstance( final Phylogeny[] phys, final Configuration config ) {\r
- return new MainFrameApplication( phys, config );\r
- }\r
-\r
- public static MainFrame createInstance( final Phylogeny[] phys,\r
- final Configuration config,\r
- final String title,\r
- final File current_dir ) {\r
- return new MainFrameApplication( phys, config, title, current_dir );\r
- }\r
-\r
- static MainFrame createInstance( final Phylogeny[] phys, final Configuration config, final String title ) {\r
- return new MainFrameApplication( phys, config, title );\r
- }\r
-\r
- static MainFrame createInstance( final Phylogeny[] phys, final String config_file_name, final String title ) {\r
- return new MainFrameApplication( phys, config_file_name, title );\r
- }\r
-\r
- static void warnIfNotPhyloXmlValidation( final Configuration c ) {\r
- if ( !c.isValidatePhyloXmlAgainstSchema() ) {\r
- JOptionPane\r
- .showMessageDialog( null,\r
- ForesterUtil\r
- .wordWrap( "phyloXML XSD-based validation is turned off [enable with line 'validate_against_phyloxml_xsd_schem: true' in configuration file]",\r
- 80 ),\r
- "Warning",\r
- JOptionPane.WARNING_MESSAGE );\r
- }\r
- }\r
-} // MainFrameApplication.\r
+// $Id:
+// FORESTER -- software libraries and applications
+// for evolutionary biology research and applications.
+//
+// Copyright (C) 2008-2009 Christian M. Zmasek
+// Copyright (C) 2008-2009 Burnham Institute for Medical Research
+// Copyright (C) 2003-2007 Ethalinda K.S. Cannon
+// All rights reserved
+//
+// This library is free software; you can redistribute it and/or
+// modify it under the terms of the GNU Lesser General Public
+// License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+//
+// This library is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+// Lesser General Public License for more details.
+//
+// You should have received a copy of the GNU Lesser General Public
+// License along with this library; if not, write to the Free Software
+// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+//
+// Contact: phylosoft @ gmail . com
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
+
+package org.forester.archaeopteryx;
+
+import java.awt.BorderLayout;
+import java.awt.Font;
+import java.awt.event.ActionEvent;
+import java.awt.event.ComponentAdapter;
+import java.awt.event.ComponentEvent;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import javax.swing.ButtonGroup;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JFileChooser;
+import javax.swing.JMenu;
+import javax.swing.JMenuBar;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JRadioButtonMenuItem;
+import javax.swing.UIManager;
+import javax.swing.UnsupportedLookAndFeelException;
+import javax.swing.WindowConstants;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+
+import org.forester.analysis.TaxonomyDataManager;
+import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
+import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
+import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
+import org.forester.archaeopteryx.tools.InferenceManager;
+import org.forester.archaeopteryx.tools.PhyloInferenceDialog;
+import org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions;
+import org.forester.archaeopteryx.tools.PhylogeneticInferrer;
+import org.forester.archaeopteryx.tools.SequenceDataRetriver;
+import org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient;
+import org.forester.archaeopteryx.webservices.WebservicesManager;
+import org.forester.io.parsers.FastaParser;
+import org.forester.io.parsers.GeneralMsaParser;
+import org.forester.io.parsers.PhylogenyParser;
+import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
+import org.forester.io.parsers.nhx.NHXParser;
+import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
+import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
+import org.forester.io.parsers.phyloxml.PhyloXmlParser;
+import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
+import org.forester.io.parsers.tol.TolParser;
+import org.forester.io.parsers.util.ParserUtils;
+import org.forester.io.writers.SequenceWriter;
+import org.forester.msa.Msa;
+import org.forester.msa.MsaFormatException;
+import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyMethods;
+import org.forester.phylogeny.PhylogenyNode;
+import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
+import org.forester.phylogeny.data.Confidence;
+import org.forester.phylogeny.data.PhylogenyDataUtil;
+import org.forester.phylogeny.data.Sequence;
+import org.forester.phylogeny.data.Taxonomy;
+import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
+import org.forester.phylogeny.factories.PhylogenyFactory;
+import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
+import org.forester.sequence.MolecularSequence;
+import org.forester.util.BasicDescriptiveStatistics;
+import org.forester.util.BasicTable;
+import org.forester.util.BasicTableParser;
+import org.forester.util.DescriptiveStatistics;
+import org.forester.util.ForesterUtil;
+
+public final class MainFrameApplication extends MainFrame {
+
+ private final static int FRAME_X_SIZE = 800;
+ private final static int FRAME_Y_SIZE = 800;
+ // Filters for the file-open dialog (classes defined in this file)
+ private static final long serialVersionUID = -799735726778865234L;
+ private static final boolean PREPROCESS_TREES = false;
+ private final JFileChooser _values_filechooser;
+ private final JFileChooser _sequences_filechooser;
+ private final JFileChooser _open_filechooser;
+ private final JFileChooser _msa_filechooser;
+ private final JFileChooser _seqs_pi_filechooser;
+ private final JFileChooser _open_filechooser_for_species_tree;
+ // Application-only print menu items
+ private JMenuItem _collapse_below_threshold;
+ private JMenuItem _collapse_below_branch_length;
+ private ButtonGroup _radio_group_1;
+ private ButtonGroup _radio_group_2;
+ // Others:
+ double _min_not_collapse = AptxConstants.MIN_NOT_COLLAPSE_DEFAULT;
+ double _min_not_collapse_bl = 0.001;
+ // Phylogeny Inference menu
+ private JMenu _inference_menu;
+ private JMenuItem _inference_from_msa_item;
+ private JMenuItem _inference_from_seqs_item;
+ // Phylogeny Inference
+ private PhylogeneticInferenceOptions _phylogenetic_inference_options = null;
+ private Msa _msa = null;
+ private File _msa_file = null;
+ private List<MolecularSequence> _seqs = null;
+ private File _seqs_file = null;
+ JMenuItem _read_values_jmi;
+ JMenuItem _read_seqs_jmi;
+
+ private MainFrameApplication( final Phylogeny[] phys, final Configuration config ) {
+ _configuration = config;
+ if ( _configuration == null ) {
+ throw new IllegalArgumentException( "configuration is null" );
+ }
+ setVisible( false );
+ setOptions( Options.createInstance( _configuration ) );
+ _mainpanel = new MainPanel( _configuration, this );
+ _open_filechooser = null;
+ _open_filechooser_for_species_tree = null;
+ _save_filechooser = null;
+ _writetopdf_filechooser = null;
+ _writetographics_filechooser = null;
+ _msa_filechooser = null;
+ _seqs_pi_filechooser = null;
+ _values_filechooser = null;
+ _sequences_filechooser = null;
+ _jmenubar = new JMenuBar();
+ buildFileMenu();
+ buildTypeMenu();
+ _contentpane = getContentPane();
+ _contentpane.setLayout( new BorderLayout() );
+ _contentpane.add( _mainpanel, BorderLayout.CENTER );
+ // App is this big
+ setSize( MainFrameApplication.FRAME_X_SIZE, MainFrameApplication.FRAME_Y_SIZE );
+ // The window listener
+ setDefaultCloseOperation( WindowConstants.DO_NOTHING_ON_CLOSE );
+ addWindowListener( new WindowAdapter() {
+
+ @Override
+ public void windowClosing( final WindowEvent e ) {
+ exit();
+ }
+ } );
+ // setVisible( true );
+ if ( ( phys != null ) && ( phys.length > 0 ) ) {
+ AptxUtil.addPhylogeniesToTabs( phys, "", null, _configuration, _mainpanel );
+ validate();
+ getMainPanel().getControlPanel().showWholeAll();
+ getMainPanel().getControlPanel().showWhole();
+ }
+ //activateSaveAllIfNeeded();
+ // ...and its children
+ _contentpane.repaint();
+ }
+
+ private MainFrameApplication( final Phylogeny[] phys, final Configuration config, final String title ) {
+ this( phys, config, title, null );
+ }
+
+ private MainFrameApplication( final Phylogeny[] phys,
+ final Configuration config,
+ final String title,
+ final File current_dir ) {
+ super();
+ _configuration = config;
+ if ( _configuration == null ) {
+ throw new IllegalArgumentException( "configuration is null" );
+ }
+ try {
+ if ( _configuration.isUseNativeUI() ) {
+ UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
+ }
+ else {
+ UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );
+ }
+ }
+ catch ( final UnsupportedLookAndFeelException e ) {
+ AptxUtil.dieWithSystemError( "unsupported look and feel: " + e.toString() );
+ }
+ catch ( final ClassNotFoundException e ) {
+ AptxUtil.dieWithSystemError( "class not found exception: " + e.toString() );
+ }
+ catch ( final InstantiationException e ) {
+ AptxUtil.dieWithSystemError( "instantiation exception: " + e.toString() );
+ }
+ catch ( final IllegalAccessException e ) {
+ AptxUtil.dieWithSystemError( "illegal access exception: " + e.toString() );
+ }
+ if ( ( current_dir != null ) && current_dir.canRead() && current_dir.isDirectory() ) {
+ setCurrentDir( current_dir );
+ }
+ // hide until everything is ready
+ setVisible( false );
+ setOptions( Options.createInstance( _configuration ) );
+ setInferenceManager( InferenceManager.createInstance( _configuration ) );
+ setPhylogeneticInferenceOptions( PhylogeneticInferenceOptions.createInstance( _configuration ) );
+ // set title
+ setTitle( AptxConstants.PRG_NAME + " " + AptxConstants.VERSION + " (" + AptxConstants.PRG_DATE + ")" );
+ _mainpanel = new MainPanel( _configuration, this );
+ // The file dialogs
+ _open_filechooser = new JFileChooser();
+ _open_filechooser.setMultiSelectionEnabled( true );
+ _open_filechooser.addChoosableFileFilter( MainFrame.xmlfilter );
+ _open_filechooser.addChoosableFileFilter( MainFrame.nhxfilter );
+ _open_filechooser.addChoosableFileFilter( MainFrame.nhfilter );
+ _open_filechooser.addChoosableFileFilter( MainFrame.nexusfilter );
+ _open_filechooser.addChoosableFileFilter( MainFrame.tolfilter );
+ _open_filechooser.addChoosableFileFilter( _open_filechooser.getAcceptAllFileFilter() );
+ _open_filechooser.setFileFilter( MainFrame.defaultfilter );
+ _open_filechooser_for_species_tree = new JFileChooser();
+ _open_filechooser_for_species_tree.setMultiSelectionEnabled( false );
+ _open_filechooser_for_species_tree.addChoosableFileFilter( MainFrame.xmlfilter );
+ _open_filechooser_for_species_tree.addChoosableFileFilter( MainFrame.tolfilter );
+ _open_filechooser_for_species_tree.setFileFilter( MainFrame.xmlfilter );
+ // Msa:
+ _msa_filechooser = new JFileChooser();
+ _msa_filechooser.setName( "Read Multiple Sequence Alignment File" );
+ _msa_filechooser.setMultiSelectionEnabled( false );
+ _msa_filechooser.addChoosableFileFilter( _msa_filechooser.getAcceptAllFileFilter() );
+ _msa_filechooser.addChoosableFileFilter( MainFrame.msafilter );
+ // Seqs:
+ _seqs_pi_filechooser = new JFileChooser();
+ _seqs_pi_filechooser.setName( "Read Sequences File" );
+ _seqs_pi_filechooser.setMultiSelectionEnabled( false );
+ _seqs_pi_filechooser.addChoosableFileFilter( _seqs_pi_filechooser.getAcceptAllFileFilter() );
+ _seqs_pi_filechooser.addChoosableFileFilter( MainFrame.seqsfilter );
+ // Expression
+ _values_filechooser = new JFileChooser();
+ _values_filechooser.setMultiSelectionEnabled( false );
+ // Sequences
+ _sequences_filechooser = new JFileChooser();
+ _sequences_filechooser.setMultiSelectionEnabled( false );
+ try {
+ final String home_dir = System.getProperty( "user.home" );
+ _open_filechooser.setCurrentDirectory( new File( home_dir ) );
+ _open_filechooser_for_species_tree.setCurrentDirectory( new File( home_dir ) );
+ _msa_filechooser.setCurrentDirectory( new File( home_dir ) );
+ _seqs_pi_filechooser.setCurrentDirectory( new File( home_dir ) );
+ _values_filechooser.setCurrentDirectory( new File( home_dir ) );
+ _sequences_filechooser.setCurrentDirectory( new File( home_dir ) );
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace();
+ // Do nothing. Not important.
+ }
+ // build the menu bar
+ _jmenubar = new JMenuBar();
+ if ( !_configuration.isUseNativeUI() ) {
+ _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
+ }
+ buildFileMenu();
+ if ( AptxConstants.__ALLOW_PHYLOGENETIC_INFERENCE ) {
+ buildPhylogeneticInferenceMenu();
+ }
+ buildAnalysisMenu();
+ buildToolsMenu();
+ buildViewMenu();
+ buildFontSizeMenu();
+ buildOptionsMenu();
+ buildTypeMenu();
+ buildHelpMenu();
+ setJMenuBar( _jmenubar );
+ _jmenubar.add( _help_jmenu );
+ _contentpane = getContentPane();
+ _contentpane.setLayout( new BorderLayout() );
+ _contentpane.add( _mainpanel, BorderLayout.CENTER );
+ // App is this big
+ setSize( MainFrameApplication.FRAME_X_SIZE, MainFrameApplication.FRAME_Y_SIZE );
+ // addWindowFocusListener( new WindowAdapter() {
+ //
+ // @Override
+ // public void windowGainedFocus( WindowEvent e ) {
+ // requestFocusInWindow();
+ // }
+ // } );
+ // The window listener
+ setDefaultCloseOperation( WindowConstants.DO_NOTHING_ON_CLOSE );
+ addWindowListener( new WindowAdapter() {
+
+ @Override
+ public void windowClosing( final WindowEvent e ) {
+ if ( isUnsavedDataPresent() ) {
+ final int r = JOptionPane.showConfirmDialog( null,
+ "Exit despite potentially unsaved changes?",
+ "Exit?",
+ JOptionPane.YES_NO_OPTION );
+ if ( r != JOptionPane.YES_OPTION ) {
+ return;
+ }
+ }
+ else {
+ final int r = JOptionPane.showConfirmDialog( null,
+ "Exit Archaeopteryx?",
+ "Exit?",
+ JOptionPane.YES_NO_OPTION );
+ if ( r != JOptionPane.YES_OPTION ) {
+ return;
+ }
+ }
+ exit();
+ }
+ } );
+ // The component listener
+ addComponentListener( new ComponentAdapter() {
+
+ @Override
+ public void componentResized( final ComponentEvent e ) {
+ if ( _mainpanel.getCurrentTreePanel() != null ) {
+ _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel()
+ .getWidth(),
+ _mainpanel.getCurrentTreePanel()
+ .getHeight() );
+ }
+ }
+ } );
+ requestFocusInWindow();
+ // addKeyListener( this );
+ setVisible( true );
+ if ( ( phys != null ) && ( phys.length > 0 ) ) {
+ AptxUtil.addPhylogeniesToTabs( phys, title, null, _configuration, _mainpanel );
+ validate();
+ getMainPanel().getControlPanel().showWholeAll();
+ getMainPanel().getControlPanel().showWhole();
+ }
+ activateSaveAllIfNeeded();
+ // ...and its children
+ _contentpane.repaint();
+ System.gc();
+ }
+
+ private MainFrameApplication( final Phylogeny[] phys, final String config_file, final String title ) {
+ // Reads the config file (false, false => not url, not applet):
+ this( phys, new Configuration( config_file, false, false, true ), title );
+ }
+
+ @Override
+ public void actionPerformed( final ActionEvent e ) {
+ try {
+ super.actionPerformed( e );
+ final Object o = e.getSource();
+ // Handle app-specific actions here:
+ if ( o == _open_item ) {
+ readPhylogeniesFromFile();
+ }
+ if ( o == _open_url_item ) {
+ readPhylogeniesFromURL();
+ }
+ else if ( o == _new_item ) {
+ newTree();
+ }
+ else if ( o == _close_item ) {
+ closeCurrentPane();
+ }
+ else if ( o == _load_species_tree_item ) {
+ readSpeciesTreeFromFile();
+ }
+ else if ( o == _obtain_detailed_taxonomic_information_jmi ) {
+ if ( isSubtreeDisplayed() ) {
+ return;
+ }
+ obtainDetailedTaxonomicInformation();
+ }
+ else if ( o == _obtain_detailed_taxonomic_information_deleting_jmi ) {
+ if ( isSubtreeDisplayed() ) {
+ return;
+ }
+ obtainDetailedTaxonomicInformationDelete();
+ }
+ else if ( o == _obtain_seq_information_jmi ) {
+ obtainSequenceInformation();
+ }
+ else if ( o == _read_values_jmi ) {
+ if ( isSubtreeDisplayed() ) {
+ return;
+ }
+ addExpressionValuesFromFile();
+ }
+ else if ( o == _read_seqs_jmi ) {
+ if ( isSubtreeDisplayed() ) {
+ return;
+ }
+ addSequencesFromFile();
+ }
+ else if ( o == _move_node_names_to_tax_sn_jmi ) {
+ moveNodeNamesToTaxSn();
+ }
+ else if ( o == _move_node_names_to_seq_names_jmi ) {
+ moveNodeNamesToSeqNames();
+ }
+ else if ( o == _extract_tax_code_from_node_names_jmi ) {
+ extractTaxDataFromNodeNames();
+ }
+ else if ( o == _internal_number_are_confidence_for_nh_parsing_cbmi ) {
+ updateOptions( getOptions() );
+ }
+ else if ( o == _replace_underscores_cbmi ) {
+ if ( ( _extract_taxonomy_no_rbmi != null ) && !_extract_taxonomy_no_rbmi.isSelected() ) {
+ _extract_taxonomy_no_rbmi.setSelected( true );
+ }
+ updateOptions( getOptions() );
+ }
+ else if ( o == _allow_errors_in_distance_to_parent_cbmi ) {
+ updateOptions( getOptions() );
+ }
+ else if ( o == _collapse_below_threshold ) {
+ if ( isSubtreeDisplayed() ) {
+ return;
+ }
+ collapseBelowThreshold();
+ }
+ else if ( o == _collapse_below_branch_length ) {
+ if ( isSubtreeDisplayed() ) {
+ return;
+ }
+ collapseBelowBranchLengthThreshold();
+ }
+ else if ( ( o == _extract_taxonomy_pfam_strict_rbmi ) || ( o == _extract_taxonomy_pfam_relaxed_rbmi )
+ || ( o == _extract_taxonomy_agressive_rbmi ) ) {
+ if ( _replace_underscores_cbmi != null ) {
+ _replace_underscores_cbmi.setSelected( false );
+ }
+ updateOptions( getOptions() );
+ }
+ else if ( o == _extract_taxonomy_no_rbmi ) {
+ updateOptions( getOptions() );
+ }
+ else if ( o == _inference_from_msa_item ) {
+ executePhyleneticInference( false );
+ }
+ else if ( o == _inference_from_seqs_item ) {
+ executePhyleneticInference( true );
+ }
+ _contentpane.repaint();
+ }
+ catch ( final Exception ex ) {
+ AptxUtil.unexpectedException( ex );
+ }
+ catch ( final Error err ) {
+ AptxUtil.unexpectedError( err );
+ }
+ }
+
+ public void end() {
+ _mainpanel.terminate();
+ _contentpane.removeAll();
+ setVisible( false );
+ dispose();
+ }
+
+ @Override
+ public MainPanel getMainPanel() {
+ return _mainpanel;
+ }
+
+ public Msa getMsa() {
+ return _msa;
+ }
+
+ public File getMsaFile() {
+ return _msa_file;
+ }
+
+ public List<MolecularSequence> getSeqs() {
+ return _seqs;
+ }
+
+ public File getSeqsFile() {
+ return _seqs_file;
+ }
+
+ public void readMsaFromFile() {
+ // Set an initial directory if none set yet
+ final File my_dir = getCurrentDir();
+ _msa_filechooser.setMultiSelectionEnabled( false );
+ // Open file-open dialog and set current directory
+ if ( my_dir != null ) {
+ _msa_filechooser.setCurrentDirectory( my_dir );
+ }
+ final int result = _msa_filechooser.showOpenDialog( _contentpane );
+ // All done: get the msa
+ final File file = _msa_filechooser.getSelectedFile();
+ setCurrentDir( _msa_filechooser.getCurrentDirectory() );
+ if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {
+ setMsaFile( null );
+ setMsa( null );
+ Msa msa = null;
+ try {
+ final InputStream is = new FileInputStream( file );
+ if ( FastaParser.isLikelyFasta( file ) ) {
+ msa = FastaParser.parseMsa( is );
+ }
+ else {
+ msa = GeneralMsaParser.parse( is );
+ }
+ }
+ catch ( final MsaFormatException e ) {
+ setArrowCursor();
+ JOptionPane.showMessageDialog( this,
+ e.getLocalizedMessage(),
+ "Multiple sequence alignment format error",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ catch ( final IOException e ) {
+ setArrowCursor();
+ JOptionPane.showMessageDialog( this,
+ e.getLocalizedMessage(),
+ "Failed to read multiple sequence alignment",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ catch ( final IllegalArgumentException e ) {
+ setArrowCursor();
+ JOptionPane.showMessageDialog( this,
+ e.getLocalizedMessage(),
+ "Unexpected error during reading of multiple sequence alignment",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ catch ( final Exception e ) {
+ setArrowCursor();
+ e.printStackTrace();
+ JOptionPane.showMessageDialog( this,
+ e.getLocalizedMessage(),
+ "Unexpected error during reading of multiple sequence alignment",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ if ( ( msa == null ) || ( msa.getNumberOfSequences() < 1 ) ) {
+ JOptionPane.showMessageDialog( this,
+ "Multiple sequence alignment is empty",
+ "Illegal Multiple Sequence Alignment",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ if ( msa.getNumberOfSequences() < 4 ) {
+ JOptionPane.showMessageDialog( this,
+ "Multiple sequence alignment needs to contain at least 3 sequences",
+ "Illegal multiple sequence alignment",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ if ( msa.getLength() < 2 ) {
+ JOptionPane.showMessageDialog( this,
+ "Multiple sequence alignment needs to contain at least 2 residues",
+ "Illegal multiple sequence alignment",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ System.gc();
+ setMsaFile( _msa_filechooser.getSelectedFile() );
+ setMsa( msa );
+ }
+ }
+
+ public void readSeqsFromFileforPI() {
+ // Set an initial directory if none set yet
+ final File my_dir = getCurrentDir();
+ _seqs_pi_filechooser.setMultiSelectionEnabled( false );
+ // Open file-open dialog and set current directory
+ if ( my_dir != null ) {
+ _seqs_pi_filechooser.setCurrentDirectory( my_dir );
+ }
+ final int result = _seqs_pi_filechooser.showOpenDialog( _contentpane );
+ // All done: get the seqs
+ final File file = _seqs_pi_filechooser.getSelectedFile();
+ setCurrentDir( _seqs_pi_filechooser.getCurrentDirectory() );
+ if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {
+ setSeqsFile( null );
+ setSeqs( null );
+ List<MolecularSequence> seqs = null;
+ try {
+ if ( FastaParser.isLikelyFasta( new FileInputStream( file ) ) ) {
+ seqs = FastaParser.parse( new FileInputStream( file ) );
+ for( final MolecularSequence seq : seqs ) {
+ System.out.println( SequenceWriter.toFasta( seq, 60 ) );
+ }
+ }
+ else {
+ //TODO error
+ }
+ }
+ catch ( final MsaFormatException e ) {
+ setArrowCursor();
+ JOptionPane.showMessageDialog( this,
+ e.getLocalizedMessage(),
+ "Multiple sequence file format error",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ catch ( final IOException e ) {
+ setArrowCursor();
+ JOptionPane.showMessageDialog( this,
+ e.getLocalizedMessage(),
+ "Failed to read multiple sequence file",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ catch ( final IllegalArgumentException e ) {
+ setArrowCursor();
+ JOptionPane.showMessageDialog( this,
+ e.getLocalizedMessage(),
+ "Unexpected error during reading of multiple sequence file",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ catch ( final Exception e ) {
+ setArrowCursor();
+ e.printStackTrace();
+ JOptionPane.showMessageDialog( this,
+ e.getLocalizedMessage(),
+ "Unexpected error during reading of multiple sequence file",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ if ( ( seqs == null ) || ( seqs.size() < 1 ) ) {
+ JOptionPane.showMessageDialog( this,
+ "Multiple sequence file is empty",
+ "Illegal multiple sequence file",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ if ( seqs.size() < 4 ) {
+ JOptionPane.showMessageDialog( this,
+ "Multiple sequence file needs to contain at least 3 sequences",
+ "Illegal multiple sequence file",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ // if ( msa.getLength() < 2 ) {
+ // JOptionPane.showMessageDialog( this,
+ // "Multiple sequence alignment needs to contain at least 2 residues",
+ // "Illegal multiple sequence file",
+ // JOptionPane.ERROR_MESSAGE );
+ // return;
+ // }
+ System.gc();
+ setSeqsFile( _seqs_pi_filechooser.getSelectedFile() );
+ setSeqs( seqs );
+ }
+ }
+
+ private void addExpressionValuesFromFile() {
+ if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) {
+ JOptionPane.showMessageDialog( this,
+ "Need to load evolutionary tree first",
+ "Can Not Read Expression Values",
+ JOptionPane.WARNING_MESSAGE );
+ return;
+ }
+ final File my_dir = getCurrentDir();
+ if ( my_dir != null ) {
+ _values_filechooser.setCurrentDirectory( my_dir );
+ }
+ final int result = _values_filechooser.showOpenDialog( _contentpane );
+ final File file = _values_filechooser.getSelectedFile();
+ if ( ( file != null ) && ( file.length() > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
+ BasicTable<String> t = null;
+ try {
+ t = BasicTableParser.parse( file, '\t' );
+ if ( t.getNumberOfColumns() < 2 ) {
+ t = BasicTableParser.parse( file, ',' );
+ }
+ if ( t.getNumberOfColumns() < 2 ) {
+ t = BasicTableParser.parse( file, ' ' );
+ }
+ }
+ catch ( final IOException e ) {
+ JOptionPane.showMessageDialog( this,
+ e.getMessage(),
+ "Could Not Read Expression Value Table",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ if ( t.getNumberOfColumns() < 2 ) {
+ JOptionPane.showMessageDialog( this,
+ "Table contains " + t.getNumberOfColumns() + " column(s)",
+ "Problem with Expression Value Table",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ if ( t.getNumberOfRows() < 1 ) {
+ JOptionPane.showMessageDialog( this,
+ "Table contains zero rows",
+ "Problem with Expression Value Table",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
+ if ( t.getNumberOfRows() != phy.getNumberOfExternalNodes() ) {
+ JOptionPane.showMessageDialog( this,
+ "Table contains " + t.getNumberOfRows() + " rows, but tree contains "
+ + phy.getNumberOfExternalNodes() + " external nodes",
+ "Warning",
+ JOptionPane.WARNING_MESSAGE );
+ }
+ final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
+ int not_found = 0;
+ for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
+ final PhylogenyNode node = iter.next();
+ final String node_name = node.getName();
+ if ( !ForesterUtil.isEmpty( node_name ) ) {
+ int row = -1;
+ try {
+ row = t.findRow( node_name );
+ }
+ catch ( final IllegalArgumentException e ) {
+ JOptionPane
+ .showMessageDialog( this,
+ e.getMessage(),
+ "Error Mapping Node Identifiers to Expression Value Identifiers",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ if ( row < 0 ) {
+ if ( node.isExternal() ) {
+ not_found++;
+ }
+ continue;
+ }
+ final List<Double> l = new ArrayList<Double>();
+ for( int col = 1; col < t.getNumberOfColumns(); ++col ) {
+ double d = -100;
+ try {
+ d = Double.parseDouble( t.getValueAsString( col, row ) );
+ }
+ catch ( final NumberFormatException e ) {
+ JOptionPane.showMessageDialog( this,
+ "Could not parse \"" + t.getValueAsString( col, row )
+ + "\" into a decimal value",
+ "Issue with Expression Value Table",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ stats.addValue( d );
+ l.add( d );
+ }
+ if ( !l.isEmpty() ) {
+ if ( node.getNodeData().getProperties() != null ) {
+ node.getNodeData().getProperties()
+ .removePropertiesWithGivenReferencePrefix( PhyloXmlUtil.VECTOR_PROPERTY_REF );
+ }
+ node.getNodeData().setVector( l );
+ }
+ }
+ }
+ if ( not_found > 0 ) {
+ JOptionPane.showMessageDialog( this, "Could not fine expression values for " + not_found
+ + " external node(s)", "Warning", JOptionPane.WARNING_MESSAGE );
+ }
+ getCurrentTreePanel().setStatisticsForExpressionValues( stats );
+ }
+ }
+
+ private void addSequencesFromFile() {
+ if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) {
+ JOptionPane.showMessageDialog( this,
+ "Need to load evolutionary tree first",
+ "Can Not Read Sequences",
+ JOptionPane.WARNING_MESSAGE );
+ return;
+ }
+ final File my_dir = getCurrentDir();
+ if ( my_dir != null ) {
+ _sequences_filechooser.setCurrentDirectory( my_dir );
+ }
+ final int result = _sequences_filechooser.showOpenDialog( _contentpane );
+ final File file = _sequences_filechooser.getSelectedFile();
+ List<MolecularSequence> seqs = null;
+ if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {
+ try {
+ final FileInputStream fis1 = new FileInputStream( file );
+ if ( FastaParser.isLikelyFasta( fis1 ) ) {
+ final FileInputStream fis2 = new FileInputStream( file );
+ seqs = FastaParser.parse( fis2 );
+ try {
+ fis2.close();
+ }
+ catch ( final Exception e ) {
+ // Ignore.
+ }
+ }
+ else {
+ JOptionPane.showMessageDialog( this,
+ "Format does not appear to be Fasta",
+ "Multiple sequence file format error",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ try {
+ fis1.close();
+ }
+ catch ( final Exception e ) {
+ // Ignore.
+ }
+ }
+ catch ( final MsaFormatException e ) {
+ setArrowCursor();
+ JOptionPane.showMessageDialog( this,
+ e.getLocalizedMessage(),
+ "Multiple sequence file format error",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ catch ( final IOException e ) {
+ setArrowCursor();
+ JOptionPane.showMessageDialog( this,
+ e.getLocalizedMessage(),
+ "Failed to read multiple sequence file",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ catch ( final Exception e ) {
+ setArrowCursor();
+ e.printStackTrace();
+ JOptionPane.showMessageDialog( this,
+ e.getLocalizedMessage(),
+ "Unexpected error during reading of multiple sequence file",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ if ( ( seqs == null ) || ( seqs.size() < 1 ) ) {
+ JOptionPane.showMessageDialog( this,
+ "Multiple sequence file is empty",
+ "Empty multiple sequence file",
+ JOptionPane.ERROR_MESSAGE );
+ setArrowCursor();
+ return;
+ }
+ }
+ if ( seqs != null ) {
+ for( final MolecularSequence seq : seqs ) {
+ System.out.println( seq.getIdentifier() );
+ }
+ final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
+ int total_counter = 0;
+ int attached_counter = 0;
+ for( final MolecularSequence seq : seqs ) {
+ ++total_counter;
+ final String seq_name = seq.getIdentifier();
+ if ( !ForesterUtil.isEmpty( seq_name ) ) {
+ List<PhylogenyNode> nodes = phy.getNodesViaSequenceName( seq_name );
+ if ( nodes.isEmpty() ) {
+ nodes = phy.getNodesViaSequenceSymbol( seq_name );
+ }
+ if ( nodes.isEmpty() ) {
+ nodes = phy.getNodesViaGeneName( seq_name );
+ }
+ if ( nodes.isEmpty() ) {
+ nodes = phy.getNodes( seq_name );
+ }
+ if ( nodes.size() > 1 ) {
+ JOptionPane.showMessageDialog( this,
+ "Sequence name \"" + seq_name + "\" is not unique",
+ "Sequence name not unique",
+ JOptionPane.ERROR_MESSAGE );
+ setArrowCursor();
+ return;
+ }
+ final String[] a = seq_name.split( "\\s" );
+ if ( nodes.isEmpty() && ( a.length > 1 ) ) {
+ final String seq_name_split = a[ 0 ];
+ nodes = phy.getNodesViaSequenceName( seq_name_split );
+ if ( nodes.isEmpty() ) {
+ nodes = phy.getNodesViaSequenceSymbol( seq_name_split );
+ }
+ if ( nodes.isEmpty() ) {
+ nodes = phy.getNodes( seq_name_split );
+ }
+ if ( nodes.size() > 1 ) {
+ JOptionPane.showMessageDialog( this, "Split sequence name \"" + seq_name_split
+ + "\" is not unique", "Sequence name not unique", JOptionPane.ERROR_MESSAGE );
+ setArrowCursor();
+ return;
+ }
+ }
+ if ( nodes.size() == 1 ) {
+ ++attached_counter;
+ final PhylogenyNode n = nodes.get( 0 );
+ if ( !n.getNodeData().isHasSequence() ) {
+ n.getNodeData().addSequence( new org.forester.phylogeny.data.Sequence() );
+ }
+ n.getNodeData().getSequence().setMolecularSequence( seq.getMolecularSequenceAsString() );
+ if ( ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) {
+ n.getNodeData().getSequence().setName( seq_name );
+ }
+ }
+ }
+ }
+ if ( attached_counter > 0 ) {
+ int ext_nodes = 0;
+ int ext_nodes_with_seq = 0;
+ for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
+ ++ext_nodes;
+ final PhylogenyNode n = iter.next();
+ if ( n.getNodeData().isHasSequence()
+ && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getMolecularSequence() ) ) {
+ ++ext_nodes_with_seq;
+ }
+ }
+ final String s;
+ if ( ext_nodes == ext_nodes_with_seq ) {
+ s = "All " + ext_nodes_with_seq + " external nodes now have a molecular sequence attached to them.";
+ }
+ else {
+ s = ext_nodes_with_seq + " out of " + ext_nodes
+ + " external nodes now have a molecular sequence attached to them.";
+ }
+ if ( ( attached_counter == total_counter ) && ( ext_nodes == ext_nodes_with_seq ) ) {
+ JOptionPane.showMessageDialog( this,
+ "Attached all " + total_counter + " sequences to tree nodes.\n" + s,
+ "All sequences attached",
+ JOptionPane.INFORMATION_MESSAGE );
+ }
+ else {
+ JOptionPane.showMessageDialog( this, "Attached " + attached_counter
+ + " sequences out of a total of " + total_counter + " sequences.\n" + s, attached_counter
+ + " sequences attached", JOptionPane.WARNING_MESSAGE );
+ }
+ }
+ else {
+ JOptionPane.showMessageDialog( this, "No maching tree node for any of the " + total_counter
+ + " sequences", "Could not attach any sequences", JOptionPane.ERROR_MESSAGE );
+ }
+ }
+ }
+
+ private void closeCurrentPane() {
+ if ( getMainPanel().getCurrentTreePanel() != null ) {
+ if ( getMainPanel().getCurrentTreePanel().isEdited() ) {
+ final int r = JOptionPane.showConfirmDialog( this,
+ "Close tab despite potentially unsaved changes?",
+ "Close Tab?",
+ JOptionPane.YES_NO_OPTION );
+ if ( r != JOptionPane.YES_OPTION ) {
+ return;
+ }
+ }
+ getMainPanel().closeCurrentPane();
+ activateSaveAllIfNeeded();
+ }
+ }
+
+ private void collapse( final Phylogeny phy ) {
+ final PhylogenyNodeIterator it = phy.iteratorPostorder();
+ final List<PhylogenyNode> to_be_removed = new ArrayList<PhylogenyNode>();
+ double min_support = Double.MAX_VALUE;
+ boolean conf_present = false;
+ while ( it.hasNext() ) {
+ final PhylogenyNode n = it.next();
+ if ( !n.isExternal() && !n.isRoot() ) {
+ final List<Confidence> c = n.getBranchData().getConfidences();
+ if ( ( c != null ) && ( c.size() > 0 ) ) {
+ conf_present = true;
+ double max = 0;
+ for( final Confidence confidence : c ) {
+ if ( confidence.getValue() > max ) {
+ max = confidence.getValue();
+ }
+ }
+ if ( max < getMinNotCollapseConfidenceValue() ) {
+ to_be_removed.add( n );
+ }
+ if ( max < min_support ) {
+ min_support = max;
+ }
+ }
+ }
+ }
+ if ( conf_present ) {
+ for( final PhylogenyNode node : to_be_removed ) {
+ PhylogenyMethods.removeNode( node, phy );
+ }
+ if ( to_be_removed.size() > 0 ) {
+ phy.externalNodesHaveChanged();
+ phy.clearHashIdToNodeMap();
+ phy.recalculateNumberOfExternalDescendants( true );
+ getCurrentTreePanel().resetNodeIdToDistToLeafMap();
+ getCurrentTreePanel().updateSetOfCollapsedExternalNodes();
+ getCurrentTreePanel().calculateLongestExtNodeInfo();
+ getCurrentTreePanel().setNodeInPreorderToNull();
+ getCurrentTreePanel().recalculateMaxDistanceToRoot();
+ getCurrentTreePanel().resetPreferredSize();
+ getCurrentTreePanel().setEdited( true );
+ getCurrentTreePanel().repaint();
+ repaint();
+ }
+ if ( to_be_removed.size() > 0 ) {
+ JOptionPane.showMessageDialog( this, "Collapsed " + to_be_removed.size()
+ + " branches with\nconfidence values below " + getMinNotCollapseConfidenceValue(), "Collapsed "
+ + to_be_removed.size() + " branches", JOptionPane.INFORMATION_MESSAGE );
+ }
+ else {
+ JOptionPane.showMessageDialog( this, "No branch collapsed,\nminimum confidence value per branch is "
+ + min_support, "No branch collapsed", JOptionPane.INFORMATION_MESSAGE );
+ }
+ }
+ else {
+ JOptionPane.showMessageDialog( this,
+ "No branch collapsed because no confidence values present",
+ "No confidence values present",
+ JOptionPane.INFORMATION_MESSAGE );
+ }
+ }
+
+ private void collapseBelowBranchLengthThreshold() {
+ if ( getCurrentTreePanel() != null ) {
+ final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
+ if ( ( phy != null ) && !phy.isEmpty() ) {
+ final String s = ( String ) JOptionPane
+ .showInputDialog( this,
+ "Please enter the minimum branch length value\n",
+ "Minimal Branch Length Value",
+ JOptionPane.QUESTION_MESSAGE,
+ null,
+ null,
+ getMinNotCollapseBlValue() );
+ if ( !ForesterUtil.isEmpty( s ) ) {
+ boolean success = true;
+ double m = 0.0;
+ final String m_str = s.trim();
+ if ( !ForesterUtil.isEmpty( m_str ) ) {
+ try {
+ m = Double.parseDouble( m_str );
+ }
+ catch ( final Exception ex ) {
+ success = false;
+ }
+ }
+ else {
+ success = false;
+ }
+ if ( success && ( m >= 0.0 ) ) {
+ setMinNotCollapseBlValue( m );
+ collapseBl( phy );
+ }
+ }
+ }
+ }
+ }
+
+ private void collapseBelowThreshold() {
+ if ( getCurrentTreePanel() != null ) {
+ final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
+ if ( ( phy != null ) && !phy.isEmpty() ) {
+ final String s = ( String ) JOptionPane.showInputDialog( this,
+ "Please enter the minimum confidence value\n",
+ "Minimal Confidence Value",
+ JOptionPane.QUESTION_MESSAGE,
+ null,
+ null,
+ getMinNotCollapseConfidenceValue() );
+ if ( !ForesterUtil.isEmpty( s ) ) {
+ boolean success = true;
+ double m = 0.0;
+ final String m_str = s.trim();
+ if ( !ForesterUtil.isEmpty( m_str ) ) {
+ try {
+ m = Double.parseDouble( m_str );
+ }
+ catch ( final Exception ex ) {
+ success = false;
+ }
+ }
+ else {
+ success = false;
+ }
+ if ( success && ( m >= 0.0 ) ) {
+ setMinNotCollapseConfidenceValue( m );
+ collapse( phy );
+ }
+ }
+ }
+ }
+ }
+
+ private void collapseBl( final Phylogeny phy ) {
+ final PhylogenyNodeIterator it = phy.iteratorPostorder();
+ final List<PhylogenyNode> to_be_removed = new ArrayList<PhylogenyNode>();
+ double min_bl = Double.MAX_VALUE;
+ boolean bl_present = false;
+ while ( it.hasNext() ) {
+ final PhylogenyNode n = it.next();
+ if ( !n.isExternal() && !n.isRoot() ) {
+ final double bl = n.getDistanceToParent();
+ if ( bl != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
+ bl_present = true;
+ if ( bl < getMinNotCollapseBlValue() ) {
+ to_be_removed.add( n );
+ }
+ if ( bl < min_bl ) {
+ min_bl = bl;
+ }
+ }
+ }
+ }
+ if ( bl_present ) {
+ for( final PhylogenyNode node : to_be_removed ) {
+ PhylogenyMethods.removeNode( node, phy );
+ }
+ if ( to_be_removed.size() > 0 ) {
+ phy.externalNodesHaveChanged();
+ phy.clearHashIdToNodeMap();
+ phy.recalculateNumberOfExternalDescendants( true );
+ getCurrentTreePanel().resetNodeIdToDistToLeafMap();
+ getCurrentTreePanel().updateSetOfCollapsedExternalNodes();
+ getCurrentTreePanel().calculateLongestExtNodeInfo();
+ getCurrentTreePanel().setNodeInPreorderToNull();
+ getCurrentTreePanel().recalculateMaxDistanceToRoot();
+ getCurrentTreePanel().resetPreferredSize();
+ getCurrentTreePanel().setEdited( true );
+ getCurrentTreePanel().repaint();
+ repaint();
+ }
+ if ( to_be_removed.size() > 0 ) {
+ JOptionPane.showMessageDialog( this, "Collapsed " + to_be_removed.size()
+ + " branches with\nbranch length values below " + getMinNotCollapseBlValue(), "Collapsed "
+ + to_be_removed.size() + " branches", JOptionPane.INFORMATION_MESSAGE );
+ }
+ else {
+ JOptionPane.showMessageDialog( this,
+ "No branch collapsed,\nminimum branch length is " + min_bl,
+ "No branch collapsed",
+ JOptionPane.INFORMATION_MESSAGE );
+ }
+ }
+ else {
+ JOptionPane.showMessageDialog( this,
+ "No branch collapsed because no branch length values present",
+ "No branch length values present",
+ JOptionPane.INFORMATION_MESSAGE );
+ }
+ }
+
+ private PhyloXmlParser createPhyloXmlParser() {
+ PhyloXmlParser xml_parser = null;
+ if ( getConfiguration().isValidatePhyloXmlAgainstSchema() ) {
+ try {
+ xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
+ }
+ catch ( final Exception e ) {
+ JOptionPane.showMessageDialog( this,
+ e.getLocalizedMessage(),
+ "failed to create validating XML parser",
+ JOptionPane.WARNING_MESSAGE );
+ }
+ }
+ if ( xml_parser == null ) {
+ xml_parser = PhyloXmlParser.createPhyloXmlParser();
+ }
+ return xml_parser;
+ }
+
+ private void executePhyleneticInference( final boolean from_unaligned_seqs ) {
+ final PhyloInferenceDialog dialog = new PhyloInferenceDialog( this,
+ getPhylogeneticInferenceOptions(),
+ from_unaligned_seqs );
+ dialog.activate();
+ if ( dialog.getValue() == JOptionPane.OK_OPTION ) {
+ if ( !from_unaligned_seqs ) {
+ if ( getMsa() != null ) {
+ final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getMsa(),
+ getPhylogeneticInferenceOptions()
+ .copy(), this );
+ new Thread( inferrer ).start();
+ }
+ else {
+ JOptionPane.showMessageDialog( this,
+ "No multiple sequence alignment selected",
+ "Phylogenetic Inference Not Launched",
+ JOptionPane.WARNING_MESSAGE );
+ }
+ }
+ else {
+ if ( getSeqs() != null ) {
+ final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getSeqs(),
+ getPhylogeneticInferenceOptions()
+ .copy(), this );
+ new Thread( inferrer ).start();
+ }
+ else {
+ JOptionPane.showMessageDialog( this,
+ "No input sequences selected",
+ "Phylogenetic Inference Not Launched",
+ JOptionPane.WARNING_MESSAGE );
+ }
+ }
+ }
+ }
+
+ private void extractTaxDataFromNodeNames() throws PhyloXmlDataFormatException {
+ final StringBuilder sb = new StringBuilder();
+ final StringBuilder sb_failed = new StringBuilder();
+ int counter = 0;
+ int counter_failed = 0;
+ if ( getCurrentTreePanel() != null ) {
+ final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
+ if ( ( phy != null ) && !phy.isEmpty() ) {
+ final PhylogenyNodeIterator it = phy.iteratorExternalForward();
+ while ( it.hasNext() ) {
+ final PhylogenyNode n = it.next();
+ final String name = n.getName().trim();
+ if ( !ForesterUtil.isEmpty( name ) ) {
+ final String nt = ParserUtils.extractTaxonomyDataFromNodeName( n,
+ TAXONOMY_EXTRACTION.AGGRESSIVE );
+ if ( !ForesterUtil.isEmpty( nt ) ) {
+ if ( counter < 15 ) {
+ sb.append( name + ": " + nt + "\n" );
+ }
+ else if ( counter == 15 ) {
+ sb.append( "...\n" );
+ }
+ counter++;
+ }
+ else {
+ if ( counter_failed < 15 ) {
+ sb_failed.append( name + "\n" );
+ }
+ else if ( counter_failed == 15 ) {
+ sb_failed.append( "...\n" );
+ }
+ counter_failed++;
+ }
+ }
+ }
+ if ( counter > 0 ) {
+ String failed = "";
+ String all = "all ";
+ if ( counter_failed > 0 ) {
+ all = "";
+ failed = "\nCould not extract taxonomic data for " + counter_failed
+ + " named external nodes:\n" + sb_failed;
+ }
+ JOptionPane.showMessageDialog( this,
+ "Extracted taxonomic data from " + all + counter
+ + " named external nodes:\n" + sb.toString() + failed,
+ "Taxonomic Data Extraction Completed",
+ counter_failed > 0 ? JOptionPane.WARNING_MESSAGE
+ : JOptionPane.INFORMATION_MESSAGE );
+ }
+ else {
+ JOptionPane
+ .showMessageDialog( this,
+ "Could not extract any taxonomic data.\nMaybe node names are empty\n"
+ + "or not in the forms \"XYZ_CAEEL\", \"XYZ_6239\", or \"XYZ_Caenorhabditis_elegans\"\n"
+ + "or nodes already have taxonomic data?\n",
+ "No Taxonomic Data Extracted",
+ JOptionPane.ERROR_MESSAGE );
+ }
+ }
+ }
+ }
+
+ private double getMinNotCollapseBlValue() {
+ return _min_not_collapse_bl;
+ }
+
+ private double getMinNotCollapseConfidenceValue() {
+ return _min_not_collapse;
+ }
+
+ private PhylogeneticInferenceOptions getPhylogeneticInferenceOptions() {
+ if ( _phylogenetic_inference_options == null ) {
+ _phylogenetic_inference_options = new PhylogeneticInferenceOptions();
+ }
+ return _phylogenetic_inference_options;
+ }
+
+ private boolean isUnsavedDataPresent() {
+ final List<TreePanel> tps = getMainPanel().getTreePanels();
+ for( final TreePanel tp : tps ) {
+ if ( tp.isEdited() ) {
+ return true;
+ }
+ }
+ return false;
+ }
+
+ private void moveNodeNamesToSeqNames() throws PhyloXmlDataFormatException {
+ if ( getCurrentTreePanel() != null ) {
+ final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
+ if ( ( phy != null ) && !phy.isEmpty() ) {
+ PhylogenyMethods
+ .transferNodeNameToField( phy, PhylogenyMethods.PhylogenyNodeField.SEQUENCE_NAME, false );
+ }
+ }
+ }
+
+ private void moveNodeNamesToTaxSn() throws PhyloXmlDataFormatException {
+ if ( getCurrentTreePanel() != null ) {
+ final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
+ if ( ( phy != null ) && !phy.isEmpty() ) {
+ PhylogenyMethods.transferNodeNameToField( phy,
+ PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME,
+ false );
+ }
+ }
+ }
+
+ private void newTree() {
+ final Phylogeny[] phys = new Phylogeny[ 1 ];
+ final Phylogeny phy = new Phylogeny();
+ final PhylogenyNode node = new PhylogenyNode();
+ phy.setRoot( node );
+ phy.setRooted( true );
+ phys[ 0 ] = phy;
+ AptxUtil.addPhylogeniesToTabs( phys, "", "", getConfiguration(), getMainPanel() );
+ _mainpanel.getControlPanel().showWhole();
+ _mainpanel.getCurrentTreePanel().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
+ _mainpanel.getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
+ if ( getMainPanel().getMainFrame() == null ) {
+ // Must be "E" applet version.
+ ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() )
+ .setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
+ }
+ else {
+ getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
+ }
+ activateSaveAllIfNeeded();
+ System.gc();
+ }
+
+ private void obtainDetailedTaxonomicInformation() {
+ if ( getCurrentTreePanel() != null ) {
+ final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
+ if ( ( phy != null ) && !phy.isEmpty() ) {
+ final TaxonomyDataManager t = new TaxonomyDataManager( this,
+ _mainpanel.getCurrentTreePanel(),
+ phy.copy(),
+ false,
+ true );
+ new Thread( t ).start();
+ }
+ }
+ }
+
+ private void obtainDetailedTaxonomicInformationDelete() {
+ if ( getCurrentTreePanel() != null ) {
+ final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
+ if ( ( phy != null ) && !phy.isEmpty() ) {
+ final TaxonomyDataManager t = new TaxonomyDataManager( this,
+ _mainpanel.getCurrentTreePanel(),
+ phy.copy(),
+ true,
+ true );
+ new Thread( t ).start();
+ }
+ }
+ }
+
+ private void obtainSequenceInformation() {
+ if ( getCurrentTreePanel() != null ) {
+ final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
+ if ( ( phy != null ) && !phy.isEmpty() ) {
+ final SequenceDataRetriver u = new SequenceDataRetriver( this,
+ _mainpanel.getCurrentTreePanel(),
+ phy.copy() );
+ new Thread( u ).start();
+ }
+ }
+ }
+
+ private void preProcessTreesUponReading( final Phylogeny[] phys ) {
+ for( final Phylogeny phy : phys ) {
+ if ( ( phy != null ) && !phy.isEmpty() ) {
+ for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) {
+ final PhylogenyNode n = it.next();
+ if ( n.isExternal() ) {
+ if ( n.getNodeData().isHasSequence() ) {
+ final Sequence s = n.getNodeData().getSequence();
+ if ( ForesterUtil.isEmpty( s.getGeneName() ) || s.getGeneName().startsWith( "LOC" ) ) {
+ if ( ( s.getAccession() != null )
+ && !ForesterUtil.isEmpty( s.getAccession().getValue() ) ) {
+ s.setGeneName( s.getAccession().getValue() );
+ }
+ else if ( !ForesterUtil.isEmpty( n.getName() ) ) {
+ s.setGeneName( n.getName() );
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+
+ private void readPhylogeniesFromFile() {
+ boolean exception = false;
+ Phylogeny[] phys = null;
+ // Set an initial directory if none set yet
+ final File my_dir = getCurrentDir();
+ // Open file-open dialog and set current directory
+ if ( my_dir != null ) {
+ _open_filechooser.setCurrentDirectory( my_dir );
+ }
+ final int result = _open_filechooser.showOpenDialog( _contentpane );
+ // All done: get the file
+ final File[] files = _open_filechooser.getSelectedFiles();
+ setCurrentDir( _open_filechooser.getCurrentDirectory() );
+ boolean nhx_or_nexus = false;
+ if ( ( files != null ) && ( files.length > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
+ for( final File file : files ) {
+ if ( ( file != null ) && !file.isDirectory() ) {
+ if ( _mainpanel.getCurrentTreePanel() != null ) {
+ _mainpanel.getCurrentTreePanel().setWaitCursor();
+ }
+ else {
+ _mainpanel.setWaitCursor();
+ }
+ if ( ( _open_filechooser.getFileFilter() == MainFrame.nhfilter )
+ || ( _open_filechooser.getFileFilter() == MainFrame.nhxfilter ) ) {
+ try {
+ final NHXParser nhx = new NHXParser();
+ setSpecialOptionsForNhxParser( nhx );
+ phys = PhylogenyMethods.readPhylogenies( nhx, file );
+ nhx_or_nexus = true;
+ }
+ catch ( final Exception e ) {
+ exception = true;
+ exceptionOccuredDuringOpenFile( e );
+ }
+ }
+ else if ( _open_filechooser.getFileFilter() == MainFrame.xmlfilter ) {
+ warnIfNotPhyloXmlValidation( getConfiguration() );
+ try {
+ final PhyloXmlParser xml_parser = createPhyloXmlParser();
+ phys = PhylogenyMethods.readPhylogenies( xml_parser, file );
+ }
+ catch ( final Exception e ) {
+ exception = true;
+ exceptionOccuredDuringOpenFile( e );
+ }
+ }
+ else if ( _open_filechooser.getFileFilter() == MainFrame.tolfilter ) {
+ try {
+ phys = PhylogenyMethods.readPhylogenies( new TolParser(), file );
+ }
+ catch ( final Exception e ) {
+ exception = true;
+ exceptionOccuredDuringOpenFile( e );
+ }
+ }
+ else if ( _open_filechooser.getFileFilter() == MainFrame.nexusfilter ) {
+ try {
+ final NexusPhylogeniesParser nex = new NexusPhylogeniesParser();
+ setSpecialOptionsForNexParser( nex );
+ phys = PhylogenyMethods.readPhylogenies( nex, file );
+ nhx_or_nexus = true;
+ }
+ catch ( final Exception e ) {
+ exception = true;
+ exceptionOccuredDuringOpenFile( e );
+ }
+ }
+ // "*.*":
+ else {
+ try {
+ final PhylogenyParser parser = ParserUtils
+ .createParserDependingOnFileType( file, getConfiguration()
+ .isValidatePhyloXmlAgainstSchema() );
+ if ( parser instanceof NexusPhylogeniesParser ) {
+ final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) parser;
+ setSpecialOptionsForNexParser( nex );
+ nhx_or_nexus = true;
+ }
+ else if ( parser instanceof NHXParser ) {
+ final NHXParser nhx = ( NHXParser ) parser;
+ setSpecialOptionsForNhxParser( nhx );
+ nhx_or_nexus = true;
+ }
+ else if ( parser instanceof PhyloXmlParser ) {
+ warnIfNotPhyloXmlValidation( getConfiguration() );
+ }
+ phys = PhylogenyMethods.readPhylogenies( parser, file );
+ }
+ catch ( final Exception e ) {
+ exception = true;
+ exceptionOccuredDuringOpenFile( e );
+ }
+ }
+ if ( _mainpanel.getCurrentTreePanel() != null ) {
+ _mainpanel.getCurrentTreePanel().setArrowCursor();
+ }
+ else {
+ _mainpanel.setArrowCursor();
+ }
+ if ( !exception && ( phys != null ) && ( phys.length > 0 ) ) {
+ boolean one_desc = false;
+ if ( nhx_or_nexus ) {
+ for( final Phylogeny phy : phys ) {
+ if ( getOptions().isInternalNumberAreConfidenceForNhParsing() ) {
+ PhylogenyMethods.transferInternalNodeNamesToConfidence( phy, "" );
+ }
+ if ( PhylogenyMethods.getMinimumDescendentsPerInternalNodes( phy ) == 1 ) {
+ one_desc = true;
+ break;
+ }
+ }
+ }
+ if ( PREPROCESS_TREES ) {
+ preProcessTreesUponReading( phys );
+ }
+ AptxUtil.addPhylogeniesToTabs( phys,
+ file.getName(),
+ file.getAbsolutePath(),
+ getConfiguration(),
+ getMainPanel() );
+ _mainpanel.getControlPanel().showWhole();
+ if ( nhx_or_nexus && one_desc ) {
+ JOptionPane
+ .showMessageDialog( this,
+ "One or more trees contain (a) node(s) with one descendant, "
+ + ForesterUtil.LINE_SEPARATOR
+ + "possibly indicating illegal parentheses within node names.",
+ "Warning: Possible Error in New Hampshire Formatted Data",
+ JOptionPane.WARNING_MESSAGE );
+ }
+ }
+ }
+ }
+ }
+ activateSaveAllIfNeeded();
+ System.gc();
+ }
+
+ private void readSpeciesTreeFromFile() {
+ Phylogeny t = null;
+ boolean exception = false;
+ final File my_dir = getCurrentDir();
+ _open_filechooser_for_species_tree.setSelectedFile( new File( "" ) );
+ if ( my_dir != null ) {
+ _open_filechooser_for_species_tree.setCurrentDirectory( my_dir );
+ }
+ final int result = _open_filechooser_for_species_tree.showOpenDialog( _contentpane );
+ final File file = _open_filechooser_for_species_tree.getSelectedFile();
+ if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
+ if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrame.xmlfilter ) {
+ try {
+ final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( PhyloXmlParser
+ .createPhyloXmlParserXsdValidating(), file );
+ t = trees[ 0 ];
+ }
+ catch ( final Exception e ) {
+ exception = true;
+ exceptionOccuredDuringOpenFile( e );
+ }
+ }
+ else if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrame.tolfilter ) {
+ try {
+ final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new TolParser(), file );
+ t = trees[ 0 ];
+ }
+ catch ( final Exception e ) {
+ exception = true;
+ exceptionOccuredDuringOpenFile( e );
+ }
+ }
+ // "*.*":
+ else {
+ try {
+ final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( PhyloXmlParser
+ .createPhyloXmlParserXsdValidating(), file );
+ t = trees[ 0 ];
+ }
+ catch ( final Exception e ) {
+ exception = true;
+ exceptionOccuredDuringOpenFile( e );
+ }
+ }
+ if ( !exception && ( t != null ) && !t.isRooted() ) {
+ exception = true;
+ t = null;
+ JOptionPane.showMessageDialog( this,
+ "Species tree is not rooted",
+ "Species tree not loaded",
+ JOptionPane.ERROR_MESSAGE );
+ }
+ if ( !exception && ( t != null ) ) {
+ final Set<Taxonomy> tax_set = new HashSet<Taxonomy>();
+ for( final PhylogenyNodeIterator it = t.iteratorExternalForward(); it.hasNext(); ) {
+ final PhylogenyNode node = it.next();
+ if ( !node.getNodeData().isHasTaxonomy() ) {
+ exception = true;
+ t = null;
+ JOptionPane
+ .showMessageDialog( this,
+ "Species tree contains external node(s) without taxonomy information",
+ "Species tree not loaded",
+ JOptionPane.ERROR_MESSAGE );
+ break;
+ }
+ else {
+ if ( tax_set.contains( node.getNodeData().getTaxonomy() ) ) {
+ exception = true;
+ t = null;
+ JOptionPane.showMessageDialog( this,
+ "Taxonomy ["
+ + node.getNodeData().getTaxonomy().asSimpleText()
+ + "] is not unique in species tree",
+ "Species tree not loaded",
+ JOptionPane.ERROR_MESSAGE );
+ break;
+ }
+ else {
+ tax_set.add( node.getNodeData().getTaxonomy() );
+ }
+ }
+ }
+ }
+ if ( !exception && ( t != null ) ) {
+ setSpeciesTree( t );
+ JOptionPane.showMessageDialog( this,
+ "Species tree successfully loaded",
+ "Species tree loaded",
+ JOptionPane.INFORMATION_MESSAGE );
+ }
+ _contentpane.repaint();
+ System.gc();
+ }
+ }
+
+ private void setArrowCursor() {
+ try {
+ _mainpanel.getCurrentTreePanel().setArrowCursor();
+ }
+ catch ( final Exception ex ) {
+ // Do nothing.
+ }
+ }
+
+ private void setMinNotCollapseBlValue( final double min_not_collapse_bl ) {
+ _min_not_collapse_bl = min_not_collapse_bl;
+ }
+
+ private void setMinNotCollapseConfidenceValue( final double min_not_collapse ) {
+ _min_not_collapse = min_not_collapse;
+ }
+
+ private void setPhylogeneticInferenceOptions( final PhylogeneticInferenceOptions phylogenetic_inference_options ) {
+ _phylogenetic_inference_options = phylogenetic_inference_options;
+ }
+
+ private void setSpecialOptionsForNexParser( final NexusPhylogeniesParser nex ) {
+ nex.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );
+ nex.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() );
+ nex.setParseBeastStyleExtendedTags( getOptions().isParseBeastStyleExtendedNexusTags() );
+ }
+
+ private void setSpecialOptionsForNhxParser( final NHXParser nhx ) {
+ nhx.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );
+ nhx.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() );
+ nhx.setAllowErrorsInDistanceToParent( getOptions().isAllowErrorsInDistanceToParent() );
+ nhx.setParseBeastStyleExtendedTags( getOptions().isParseBeastStyleExtendedNexusTags() );
+ }
+
+ void buildAnalysisMenu() {
+ _analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );
+ _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );
+ _analysis_menu.add( _gsdir_item = new JMenuItem( "GSDIR (GSDI with re-rooting)" ) );
+ _analysis_menu.add( _load_species_tree_item = new JMenuItem( "Load Species Tree..." ) );
+ customizeJMenuItem( _gsdi_item );
+ customizeJMenuItem( _gsdir_item );
+ customizeJMenuItem( _load_species_tree_item );
+ _analysis_menu.addSeparator();
+ _analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) );
+ customizeJMenuItem( _lineage_inference );
+ _lineage_inference.setToolTipText( "Inference of ancestor taxonomies/lineages" );
+ _jmenubar.add( _analysis_menu );
+ }
+
+ @Override
+ void buildFileMenu() {
+ _file_jmenu = MainFrame.createMenu( "File", getConfiguration() );
+ _file_jmenu.add( _open_item = new JMenuItem( "Read Tree from File..." ) );
+ _file_jmenu.addSeparator();
+ _file_jmenu.add( _open_url_item = new JMenuItem( "Read Tree from URL/Webservice..." ) );
+ _file_jmenu.addSeparator();
+ final WebservicesManager webservices_manager = WebservicesManager.getInstance();
+ _load_phylogeny_from_webservice_menu_items = new JMenuItem[ webservices_manager
+ .getAvailablePhylogeniesWebserviceClients().size() ];
+ for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {
+ final PhylogeniesWebserviceClient client = webservices_manager.getAvailablePhylogeniesWebserviceClient( i );
+ _load_phylogeny_from_webservice_menu_items[ i ] = new JMenuItem( client.getMenuName() );
+ _file_jmenu.add( _load_phylogeny_from_webservice_menu_items[ i ] );
+ }
+ if ( getConfiguration().isEditable() ) {
+ _file_jmenu.addSeparator();
+ _file_jmenu.add( _new_item = new JMenuItem( "New" ) );
+ _new_item.setToolTipText( "to create a new tree with one node, as source for manual tree construction" );
+ }
+ _file_jmenu.addSeparator();
+ _file_jmenu.add( _save_item = new JMenuItem( "Save Tree As..." ) );
+ _file_jmenu.add( _save_all_item = new JMenuItem( "Save All Trees As..." ) );
+ _save_all_item.setToolTipText( "Write all phylogenies to one file." );
+ _save_all_item.setEnabled( false );
+ _file_jmenu.addSeparator();
+ _file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) );
+ if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" ) || AptxUtil.canWriteFormat( "TIF" ) ) {
+ _file_jmenu.add( _write_to_tif_item = new JMenuItem( "Export to TIFF file..." ) );
+ }
+ _file_jmenu.add( _write_to_png_item = new JMenuItem( "Export to PNG file..." ) );
+ _file_jmenu.add( _write_to_jpg_item = new JMenuItem( "Export to JPG file..." ) );
+ if ( AptxUtil.canWriteFormat( "gif" ) ) {
+ _file_jmenu.add( _write_to_gif_item = new JMenuItem( "Export to GIF file..." ) );
+ }
+ if ( AptxUtil.canWriteFormat( "bmp" ) ) {
+ _file_jmenu.add( _write_to_bmp_item = new JMenuItem( "Export to BMP file..." ) );
+ }
+ _file_jmenu.addSeparator();
+ _file_jmenu.add( _print_item = new JMenuItem( "Print..." ) );
+ _file_jmenu.addSeparator();
+ _file_jmenu.add( _close_item = new JMenuItem( "Close Tab" ) );
+ _close_item.setToolTipText( "To close the current pane." );
+ _close_item.setEnabled( true );
+ _file_jmenu.addSeparator();
+ _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );
+ customizeJMenuItem( _open_item );
+ _open_item
+ .setFont( new Font( _open_item.getFont().getFontName(), Font.BOLD, _open_item.getFont().getSize() + 4 ) );
+ customizeJMenuItem( _open_url_item );
+ for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {
+ customizeJMenuItem( _load_phylogeny_from_webservice_menu_items[ i ] );
+ }
+ customizeJMenuItem( _save_item );
+ if ( getConfiguration().isEditable() ) {
+ customizeJMenuItem( _new_item );
+ }
+ customizeJMenuItem( _close_item );
+ customizeJMenuItem( _save_all_item );
+ customizeJMenuItem( _write_to_pdf_item );
+ customizeJMenuItem( _write_to_png_item );
+ customizeJMenuItem( _write_to_jpg_item );
+ customizeJMenuItem( _write_to_gif_item );
+ customizeJMenuItem( _write_to_tif_item );
+ customizeJMenuItem( _write_to_bmp_item );
+ customizeJMenuItem( _print_item );
+ customizeJMenuItem( _exit_item );
+ _jmenubar.add( _file_jmenu );
+ }
+
+ void buildOptionsMenu() {
+ _options_jmenu = MainFrame.createMenu( OPTIONS_HEADER, getConfiguration() );
+ _options_jmenu.addChangeListener( new ChangeListener() {
+
+ @Override
+ public void stateChanged( final ChangeEvent e ) {
+ MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
+ MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
+ MainFrame
+ .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
+ MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame
+ .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );
+ // MainFrame.setTextForGraphicsSizeChooserMenuItem( _print_size_mi, getOptions() );
+ MainFrame.setTextForPdfLineWidthChooserMenuItem( _choose_pdf_width_mi, getOptions() );
+ MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
+ MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
+ MainFrame.setCycleDataReturnMenuItem( _cycle_data_return, getOptions() );
+ MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
+ try {
+ getMainPanel().getControlPanel().setVisibilityOfDomainStrucureCB();
+ getMainPanel().getControlPanel().setVisibilityOfX();
+ }
+ catch ( final Exception ignore ) {
+ // do nothing, not important.
+ }
+ }
+ } );
+ _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( DISPLAY_SUBHEADER ), getConfiguration() ) );
+ _options_jmenu
+ .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
+ _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );
+ _options_jmenu.add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( NON_LINED_UP_CLADOGRAMS_LABEL ) );
+ _radio_group_1 = new ButtonGroup();
+ _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
+ _radio_group_1.add( _uniform_cladograms_rbmi );
+ _radio_group_1.add( _non_lined_up_cladograms_rbmi );
+ _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( SHOW_OVERVIEW_LABEL ) );
+ _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( DISPLAY_SCALE_LABEL ) );
+ _options_jmenu
+ .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_INT ) );
+ _options_jmenu
+ .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_EXT ) );
+ _options_jmenu
+ .add( _show_default_node_shapes_for_marked_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_MARKED ) );
+ _options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) );
+ if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
+ _options_jmenu.add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) );
+ _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) );
+ }
+ _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( SHOW_ANN_REF_SOURCE_LABEL ) );
+ _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( SHOW_CONF_STDDEV_LABEL ) );
+ _options_jmenu.add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( COLOR_BY_TAXONOMIC_GROUP ) );
+ _options_jmenu.add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( COLOR_LABELS_LABEL ) );
+ _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
+ _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( ABBREV_SN_LABEL ) );
+ _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( LABEL_DIRECTION_LABEL ) );
+ _label_direction_cbmi.setToolTipText( LABEL_DIRECTION_TIP );
+ _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( SCREEN_ANTIALIAS_LABEL ) );
+ _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( BG_GRAD_LABEL ) );
+ _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
+ _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
+ _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
+ _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
+ _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
+ _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
+ _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
+ _options_jmenu.addSeparator();
+ _options_jmenu.add( _cycle_data_return = new JMenuItem( "Cycle Data Return" ) );
+ _options_jmenu.addSeparator();
+ _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( SEARCH_SUBHEADER ), getConfiguration() ) );
+ _options_jmenu.add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( SEARCH_CASE_SENSITIVE_LABEL ) );
+ _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( SEARCH_TERMS_ONLY_LABEL ) );
+ _options_jmenu.add( _search_with_regex_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_REGEX_LABEL ) );
+ _search_with_regex_cbmi.setToolTipText( MainFrame.SEARCH_WITH_REGEX_TIP );
+ _options_jmenu.add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( INVERSE_SEARCH_RESULT_LABEL ) );
+ _options_jmenu.add( _color_all_found_nodes_when_coloring_subtree_cbmi = new JCheckBoxMenuItem( "Colorize All Found Nodes When Colorizing Subtree(s)" ) );
+ _options_jmenu.addSeparator();
+ _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Graphics Export & Printing:" ),
+ getConfiguration() ) );
+ _options_jmenu.add( _antialias_print_cbmi = new JCheckBoxMenuItem( "Antialias" ) );
+ _options_jmenu.add( _print_black_and_white_cbmi = new JCheckBoxMenuItem( "Export in Black and White" ) );
+ _options_jmenu
+ .add( _graphics_export_visible_only_cbmi = new JCheckBoxMenuItem( "Limit to Visible ('Screenshot') for PNG, JPG, and GIF export" ) );
+ _options_jmenu.add( _choose_pdf_width_mi = new JMenuItem( "" ) );
+ _options_jmenu.addSeparator();
+ _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/NHX/Nexus Read:" ), getConfiguration() ) );
+ _options_jmenu
+ .add( _internal_number_are_confidence_for_nh_parsing_cbmi = new JCheckBoxMenuItem( "Internal Node Names are Confidence Values" ) );
+ _options_jmenu.add( _replace_underscores_cbmi = new JCheckBoxMenuItem( "Replace Underscores with Spaces" ) );
+ _options_jmenu.add( _parse_beast_style_extended_nexus_tags_cbmi = new JCheckBoxMenuItem( "Parse BEAST-style extended Newick/Nexus tags" ) );
+
+ _parse_beast_style_extended_nexus_tags_cbmi.setToolTipText( "to parse elements in the form of \"[&!color=#800080]\" in Newick/Nexus formatted trees" );
+
+
+ _options_jmenu
+ .add( _allow_errors_in_distance_to_parent_cbmi = new JCheckBoxMenuItem( "Ignore Distance Values Format Errors" ) );
+ _options_jmenu.add( _extract_taxonomy_no_rbmi = new JRadioButtonMenuItem( "No Taxonomy Extraction" ) );
+ _options_jmenu
+ .add( _extract_taxonomy_pfam_strict_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style Node Names" ) );
+ _options_jmenu
+ .add( _extract_taxonomy_pfam_relaxed_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style like Node Names" ) );
+ _options_jmenu
+ .add( _extract_taxonomy_agressive_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids/Scientific Names from Node Names" ) );
+ _extract_taxonomy_pfam_strict_rbmi
+ .setToolTipText( "To extract taxonomy codes/ids from node names in the form of e.g. \"BCL2_MOUSE/123-304\" or \"BCL2_10090/123-304\"" );
+ _extract_taxonomy_pfam_relaxed_rbmi
+ .setToolTipText( "To extract taxonomy codes/ids from node names in the form of e.g. \"bax_MOUSE\" or \"bax_10090\"" );
+ _extract_taxonomy_agressive_rbmi
+ .setToolTipText( "To extract taxonomy codes/ids or scientific names from node names in the form of e.g. \"MOUSE\" or \"10090\" or \"xyz_Nematostella_vectensis\"" );
+ _radio_group_2 = new ButtonGroup();
+ _radio_group_2.add( _extract_taxonomy_no_rbmi );
+ _radio_group_2.add( _extract_taxonomy_pfam_strict_rbmi );
+ _radio_group_2.add( _extract_taxonomy_pfam_relaxed_rbmi );
+ _radio_group_2.add( _extract_taxonomy_agressive_rbmi );
+ _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/Nexus Save:" ), getConfiguration() ) );
+ _options_jmenu
+ .add( _use_brackets_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_BRACKETS_FOR_CONF_IN_NH_LABEL ) );
+ _use_brackets_for_conf_in_nh_export_cbmi
+ .setToolTipText( "e.g. \"0.1[90]\" for a branch with support 90 and a length of 0.1" );
+ _options_jmenu
+ .add( _use_internal_names_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL ) );
+ customizeJMenuItem( _choose_font_mi );
+ customizeJMenuItem( _choose_minimal_confidence_mi );
+ customizeJMenuItem( _switch_colors_mi );
+ customizeJMenuItem( _choose_pdf_width_mi );
+ customizeJMenuItem( _overview_placment_mi );
+ customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions()
+ .isShowDefaultNodeShapesExternal() );
+ customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()
+ .isShowDefaultNodeShapesInternal() );
+ customizeCheckBoxMenuItem( _show_default_node_shapes_for_marked_cbmi, getOptions()
+ .isShowDefaultNodeShapesForMarkedNodes() );
+ customizeJMenuItem( _cycle_node_shape_mi );
+ customizeJMenuItem( _cycle_node_fill_mi );
+ customizeJMenuItem( _choose_node_size_mi );
+ customizeJMenuItem( _cycle_data_return );
+ customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
+ customizeCheckBoxMenuItem( _color_by_taxonomic_group_cbmi, getOptions().isColorByTaxonomicGroup() );
+ customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
+ customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
+ customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );
+ customizeCheckBoxMenuItem( _show_annotation_ref_source, getOptions().isShowAnnotationRefSource() );
+ customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
+ customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );
+ customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );
+ customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,
+ getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );
+ customizeRadioButtonMenuItem( _uniform_cladograms_rbmi,
+ getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
+ customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
+ getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
+ customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
+ customizeCheckBoxMenuItem( _label_direction_cbmi,
+ getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
+ customizeCheckBoxMenuItem( _antialias_print_cbmi, getOptions().isAntialiasPrint() );
+ customizeCheckBoxMenuItem( _print_black_and_white_cbmi, getOptions().isPrintBlackAndWhite() );
+ customizeCheckBoxMenuItem( _internal_number_are_confidence_for_nh_parsing_cbmi, getOptions()
+ .isInternalNumberAreConfidenceForNhParsing() );
+ customizeRadioButtonMenuItem( _extract_taxonomy_no_rbmi,
+ getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.NO );
+ customizeRadioButtonMenuItem( _extract_taxonomy_pfam_strict_rbmi,
+ getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ customizeRadioButtonMenuItem( _extract_taxonomy_pfam_relaxed_rbmi,
+ getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ customizeRadioButtonMenuItem( _extract_taxonomy_agressive_rbmi,
+ getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.AGGRESSIVE );
+ customizeCheckBoxMenuItem( _replace_underscores_cbmi, getOptions().isReplaceUnderscoresInNhParsing() );
+ customizeCheckBoxMenuItem( _allow_errors_in_distance_to_parent_cbmi, getOptions()
+ .isReplaceUnderscoresInNhParsing() );
+ customizeCheckBoxMenuItem( _search_with_regex_cbmi, getOptions().isSearchWithRegex() );
+ customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
+ customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
+ customizeCheckBoxMenuItem( _color_all_found_nodes_when_coloring_subtree_cbmi, getOptions().isColorAllFoundNodesWhenColoringSubtree() );
+ customizeCheckBoxMenuItem( _parse_beast_style_extended_nexus_tags_cbmi, getOptions().isParseBeastStyleExtendedNexusTags() );
+
+ customizeCheckBoxMenuItem( _graphics_export_visible_only_cbmi, getOptions().isGraphicsExportVisibleOnly() );
+ customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
+ customizeCheckBoxMenuItem( _use_brackets_for_conf_in_nh_export_cbmi, getOptions()
+ .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );
+ customizeCheckBoxMenuItem( _use_internal_names_for_conf_in_nh_export_cbmi, getOptions()
+ .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );
+ customizeCheckBoxMenuItem( _line_up_renderable_data_cbmi, getOptions().isLineUpRendarableNodeData() );
+ customizeCheckBoxMenuItem( _right_line_up_domains_cbmi, getOptions().isRightLineUpDomains() );
+ _jmenubar.add( _options_jmenu );
+ }
+
+ void buildPhylogeneticInferenceMenu() {
+ final InferenceManager im = getInferenceManager();
+ _inference_menu = MainFrame.createMenu( "Inference", getConfiguration() );
+ _inference_menu.add( _inference_from_msa_item = new JMenuItem( "From Multiple Sequence Alignment..." ) );
+ customizeJMenuItem( _inference_from_msa_item );
+ _inference_from_msa_item.setToolTipText( "Basic phylogenetic inference from MSA" );
+ if ( im.canDoMsa() ) {
+ _inference_menu.add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences..." ) );
+ customizeJMenuItem( _inference_from_seqs_item );
+ _inference_from_seqs_item
+ .setToolTipText( "Basic phylogenetic inference including multiple sequence alignment" );
+ }
+ else {
+ _inference_menu
+ .add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences (no program found)" ) );
+ customizeJMenuItem( _inference_from_seqs_item );
+ _inference_from_seqs_item.setEnabled( false );
+ }
+ _jmenubar.add( _inference_menu );
+ }
+
+ void buildToolsMenu() {
+ _tools_menu = createMenu( "Tools", getConfiguration() );
+ _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );
+ customizeJMenuItem( _confcolor_item );
+ _tools_menu.add( _color_rank_jmi = new JMenuItem( "Colorize Subtrees via Taxonomic Rank" ) );
+ customizeJMenuItem( _color_rank_jmi );
+ _color_rank_jmi.setToolTipText( "for example, at \"Class\" level, colorize mammal specific subtree red" );
+ _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );
+ customizeJMenuItem( _taxcolor_item );
+ _tools_menu.addSeparator();
+ _tools_menu.add( _remove_visual_styles_item = new JMenuItem( "Delete All Visual Styles From Nodes" ) );
+ _remove_visual_styles_item
+ .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny" );
+ customizeJMenuItem( _remove_visual_styles_item );
+ _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete All Colors From Branches" ) );
+ _remove_branch_color_item.setToolTipText( "To remove all branch color values from the current phylogeny" );
+ customizeJMenuItem( _remove_branch_color_item );
+ _tools_menu.addSeparator();
+ _tools_menu.add( _annotate_item = new JMenuItem( "Annotate Sequences of Selected Nodes" ) );
+ customizeJMenuItem( _annotate_item );
+ _tools_menu.addSeparator();
+ _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );
+ customizeJMenuItem( _midpoint_root_item );
+ _tools_menu.addSeparator();
+ _tools_menu.add( _delete_selected_nodes_item = new JMenuItem( "Delete Selected Nodes" ) );
+ _delete_selected_nodes_item.setToolTipText( "To delete all selected external nodes" );
+ customizeJMenuItem( _delete_selected_nodes_item );
+ _tools_menu.add( _delete_not_selected_nodes_item = new JMenuItem( "Retain Selected Nodes" ) );
+ _delete_not_selected_nodes_item.setToolTipText( "To delete all not selected external nodes" );
+ customizeJMenuItem( _delete_not_selected_nodes_item );
+ _tools_menu.addSeparator();
+ _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );
+ customizeJMenuItem( _collapse_species_specific_subtrees );
+ _collapse_species_specific_subtrees.setToolTipText( "To (reversibly) collapse species-specific subtrees" );
+ _tools_menu
+ .add( _collapse_below_threshold = new JMenuItem( "Collapse Branches with Confidence Below Threshold into Multifurcations" ) );
+ customizeJMenuItem( _collapse_below_threshold );
+ _collapse_below_threshold
+ .setToolTipText( "To (permanently) collapse branches with confidence values below a threshold into multifurcations (in the case of multiple confidences per branch: without at least one confidence value above a threshold)" );
+ //
+ _tools_menu
+ .add( _collapse_below_branch_length = new JMenuItem( "Collapse Branches with Branch Lengths Below Threshold into Multifurcations" ) );
+ customizeJMenuItem( _collapse_below_branch_length );
+ _collapse_below_branch_length
+ .setToolTipText( "To (permanently) collapse branches with branches with branch lengths below a threshold into multifurcations" );
+ //
+ _tools_menu.addSeparator();
+ _tools_menu
+ .add( _extract_tax_code_from_node_names_jmi = new JMenuItem( "Extract Taxonomic Data from Node Names" ) );
+ customizeJMenuItem( _extract_tax_code_from_node_names_jmi );
+ _extract_tax_code_from_node_names_jmi
+ .setToolTipText( "To extract SwissProt/Uniprot taxonomic codes (mnemonics) from nodes names in the form of 'xyz_CAEEL', Uniprot/NCBI identifiers form of 'xyz_6239', or scientific names form of 'xyz_Caenorhabditis_elegans'" );
+ _tools_menu
+ .add( _move_node_names_to_tax_sn_jmi = new JMenuItem( "Transfer Node Names to Taxonomic Scientific Names" ) );
+ customizeJMenuItem( _move_node_names_to_tax_sn_jmi );
+ _move_node_names_to_tax_sn_jmi.setToolTipText( "To interpret node names as taxonomic scientific names" );
+ _tools_menu.add( _move_node_names_to_seq_names_jmi = new JMenuItem( "Transfer Node Names to Sequence Names" ) );
+ customizeJMenuItem( _move_node_names_to_seq_names_jmi );
+ _move_node_names_to_seq_names_jmi.setToolTipText( "To interpret node names as sequence (protein, gene) names" );
+ _tools_menu.addSeparator();
+ _tools_menu.add( _obtain_seq_information_jmi = new JMenuItem( "Obtain Sequence Information" ) );
+ customizeJMenuItem( _obtain_seq_information_jmi );
+ _obtain_seq_information_jmi.setToolTipText( "To add additional sequence information" );
+ _tools_menu
+ .add( _obtain_detailed_taxonomic_information_jmi = new JMenuItem( OBTAIN_DETAILED_TAXONOMIC_INFORMATION ) );
+ customizeJMenuItem( _obtain_detailed_taxonomic_information_jmi );
+ _obtain_detailed_taxonomic_information_jmi
+ .setToolTipText( "To add additional taxonomic information (from UniProt Taxonomy)" );
+ _tools_menu
+ .add( _obtain_detailed_taxonomic_information_deleting_jmi = new JMenuItem( "Obtain Detailed Taxonomic Information (deletes nodes!)" ) );
+ customizeJMenuItem( _obtain_detailed_taxonomic_information_deleting_jmi );
+ _obtain_detailed_taxonomic_information_deleting_jmi
+ .setToolTipText( "To add additional taxonomic information, deletes nodes for which taxonomy cannot found (from UniProt Taxonomy)" );
+ _tools_menu.addSeparator();
+ _tools_menu.add( _read_values_jmi = new JMenuItem( "Attach Vector/Expression Values" ) );
+ customizeJMenuItem( _read_values_jmi );
+ _read_values_jmi.setToolTipText( "To attach vector (e.g. gene expression) values to tree nodes (beta)" );
+ _jmenubar.add( _tools_menu );
+ _tools_menu.add( _read_seqs_jmi = new JMenuItem( "Attach Molecular Sequences" ) );
+ customizeJMenuItem( _read_seqs_jmi );
+ _read_seqs_jmi
+ .setToolTipText( "To attach molecular sequences to tree nodes (from Fasta-formatted file) (beta)" );
+ _jmenubar.add( _tools_menu );
+ }
+
+ @Override
+ void close() {
+ if ( isUnsavedDataPresent() ) {
+ final int r = JOptionPane.showConfirmDialog( this,
+ "Exit despite potentially unsaved changes?",
+ "Exit?",
+ JOptionPane.YES_NO_OPTION );
+ if ( r != JOptionPane.YES_OPTION ) {
+ return;
+ }
+ }
+ exit();
+ }
+
+ void exit() {
+ removeAllTextFrames();
+ _mainpanel.terminate();
+ _contentpane.removeAll();
+ setVisible( false );
+ dispose();
+ // System.exit( 0 ); //TODO reconfirm that this is OK, then remove.
+ }
+
+ void readPhylogeniesFromURL() {
+ URL url = null;
+ Phylogeny[] phys = null;
+ final String message = "Please enter a complete URL, for example \"http://purl.org/phylo/treebase/phylows/study/TB2:S15480?format=nexus\"";
+ final String url_string = JOptionPane.showInputDialog( this,
+ message,
+ "Use URL/webservice to obtain a phylogeny",
+ JOptionPane.QUESTION_MESSAGE );
+ boolean nhx_or_nexus = false;
+ if ( ( url_string != null ) && ( url_string.length() > 0 ) ) {
+ try {
+ url = new URL( url_string );
+ PhylogenyParser parser = null;
+ if ( url.getHost().toLowerCase().indexOf( "tolweb" ) >= 0 ) {
+ parser = new TolParser();
+ }
+ else {
+ parser = ParserUtils.createParserDependingOnUrlContents( url, getConfiguration()
+ .isValidatePhyloXmlAgainstSchema() );
+ }
+ if ( parser instanceof NexusPhylogeniesParser ) {
+ nhx_or_nexus = true;
+ }
+ else if ( parser instanceof NHXParser ) {
+ nhx_or_nexus = true;
+ }
+ if ( _mainpanel.getCurrentTreePanel() != null ) {
+ _mainpanel.getCurrentTreePanel().setWaitCursor();
+ }
+ else {
+ _mainpanel.setWaitCursor();
+ }
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ phys = factory.create( url.openStream(), parser );
+ }
+ catch ( final MalformedURLException e ) {
+ JOptionPane.showMessageDialog( this,
+ "Malformed URL: " + url + "\n" + e.getLocalizedMessage(),
+ "Malformed URL",
+ JOptionPane.ERROR_MESSAGE );
+ }
+ catch ( final IOException e ) {
+ JOptionPane.showMessageDialog( this,
+ "Could not read from " + url + "\n"
+ + ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
+ "Failed to read URL",
+ JOptionPane.ERROR_MESSAGE );
+ }
+ catch ( final Exception e ) {
+ JOptionPane.showMessageDialog( this,
+ ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
+ "Unexpected Exception",
+ JOptionPane.ERROR_MESSAGE );
+ }
+ finally {
+ if ( _mainpanel.getCurrentTreePanel() != null ) {
+ _mainpanel.getCurrentTreePanel().setArrowCursor();
+ }
+ else {
+ _mainpanel.setArrowCursor();
+ }
+ }
+ if ( ( phys != null ) && ( phys.length > 0 ) ) {
+ if ( nhx_or_nexus && getOptions().isInternalNumberAreConfidenceForNhParsing() ) {
+ for( final Phylogeny phy : phys ) {
+ PhylogenyMethods.transferInternalNodeNamesToConfidence( phy, "" );
+ }
+ }
+ AptxUtil.addPhylogeniesToTabs( phys,
+ new File( url.getFile() ).getName(),
+ new File( url.getFile() ).toString(),
+ getConfiguration(),
+ getMainPanel() );
+ _mainpanel.getControlPanel().showWhole();
+ }
+ }
+ activateSaveAllIfNeeded();
+ System.gc();
+ }
+
+ void setMsa( final Msa msa ) {
+ _msa = msa;
+ }
+
+ void setMsaFile( final File msa_file ) {
+ _msa_file = msa_file;
+ }
+
+ void setSeqs( final List<MolecularSequence> seqs ) {
+ _seqs = seqs;
+ }
+
+ void setSeqsFile( final File seqs_file ) {
+ _seqs_file = seqs_file;
+ }
+
+ public static MainFrameApplication createInstance( final Phylogeny[] phys, final Configuration config ) {
+ return new MainFrameApplication( phys, config );
+ }
+
+ public static MainFrame createInstance( final Phylogeny[] phys,
+ final Configuration config,
+ final String title,
+ final File current_dir ) {
+ return new MainFrameApplication( phys, config, title, current_dir );
+ }
+
+ static MainFrame createInstance( final Phylogeny[] phys, final Configuration config, final String title ) {
+ return new MainFrameApplication( phys, config, title );
+ }
+
+ static MainFrame createInstance( final Phylogeny[] phys, final String config_file_name, final String title ) {
+ return new MainFrameApplication( phys, config_file_name, title );
+ }
+
+ static void warnIfNotPhyloXmlValidation( final Configuration c ) {
+ if ( !c.isValidatePhyloXmlAgainstSchema() ) {
+ JOptionPane
+ .showMessageDialog( null,
+ ForesterUtil
+ .wordWrap( "phyloXML XSD-based validation is turned off [enable with line 'validate_against_phyloxml_xsd_schem: true' in configuration file]",
+ 80 ),
+ "Warning",
+ JOptionPane.WARNING_MESSAGE );
+ }
+ }
+} // MainFrameApplication.
private boolean _line_up_renderable_node_data;
private boolean _right_align_domains;
private boolean _color_all_found_nodes_when_coloring_subtree;
+ private boolean _parse_beast_style_extended_nexus_tags;
private Options() {
init();
_show_default_node_shapes_external = false;
_show_default_node_shapes_for_marked_nodes = false;
_color_all_found_nodes_when_coloring_subtree = false;
+ _parse_beast_style_extended_nexus_tags= true;
_min_confidence_value = MIN_CONFIDENCE_DEFAULT;
_print_black_and_white = false;
_phylogeny_graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
final void setColorAllFoundNodesWhenColoringSubtree( final boolean color_all_found_nodes_when_coloring_subtree ) {
_color_all_found_nodes_when_coloring_subtree = color_all_found_nodes_when_coloring_subtree;
}
+
+ final boolean isParseBeastStyleExtendedNexusTags() {
+ return _parse_beast_style_extended_nexus_tags;
+ }
+
+ final void setParseBeastStyleExtendedNexusTags( boolean parse_beast_style_extended_nexus_tags ) {
+ _parse_beast_style_extended_nexus_tags = parse_beast_style_extended_nexus_tags;
+ }
}
.equalsIgnoreCase( "uniprot" ) ) ) {
try {
uri_str = "http://www.uniprot.org/taxonomy/"
- + URLEncoder.encode( tax.getIdentifier().getValue(), ForesterConstants.UTF8 );
+ + URLEncoder.encode( tax.getIdentifier().getValue(), ForesterConstants.UTF_8 );
}
catch ( final UnsupportedEncodingException e ) {
AptxUtil.showErrorMessage( this, e.toString() );
else if ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
try {
uri_str = "http://www.uniprot.org/taxonomy/?query="
- + URLEncoder.encode( tax.getScientificName(), ForesterConstants.UTF8 );
+ + URLEncoder.encode( tax.getScientificName(), ForesterConstants.UTF_8 );
}
catch ( final UnsupportedEncodingException e ) {
AptxUtil.showErrorMessage( this, e.toString() );
else if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
try {
uri_str = "http://www.uniprot.org/taxonomy/?query="
- + URLEncoder.encode( tax.getTaxonomyCode(), ForesterConstants.UTF8 );
+ + URLEncoder.encode( tax.getTaxonomyCode(), ForesterConstants.UTF_8 );
}
catch ( final UnsupportedEncodingException e ) {
AptxUtil.showErrorMessage( this, e.toString() );
else if ( !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
try {
uri_str = "http://www.uniprot.org/taxonomy/?query="
- + URLEncoder.encode( tax.getCommonName(), ForesterConstants.UTF8 );
+ + URLEncoder.encode( tax.getCommonName(), ForesterConstants.UTF_8 );
}
catch ( final UnsupportedEncodingException e ) {
AptxUtil.showErrorMessage( this, e.toString() );
final String upkb = SequenceAccessionTools.obtainUniProtAccessorFromDataFields( node );
if ( !ForesterUtil.isEmpty( upkb ) ) {
try {
- uri_str = ForesterUtil.UNIPROT_KB + URLEncoder.encode( upkb, ForesterConstants.UTF8 );
+ uri_str = ForesterUtil.UNIPROT_KB + URLEncoder.encode( upkb, ForesterConstants.UTF_8 );
}
catch ( final UnsupportedEncodingException e ) {
AptxUtil.showErrorMessage( tp, e.toString() );
if ( !ForesterUtil.isEmpty( v ) ) {
try {
if ( SequenceAccessionTools.isProteinDbQuery( v ) ) {
- uri_str = ForesterUtil.NCBI_PROTEIN + URLEncoder.encode( v, ForesterConstants.UTF8 );
+ uri_str = ForesterUtil.NCBI_PROTEIN + URLEncoder.encode( v, ForesterConstants.UTF_8 );
}
else {
- uri_str = ForesterUtil.NCBI_NUCCORE + URLEncoder.encode( v, ForesterConstants.UTF8 );
+ uri_str = ForesterUtil.NCBI_NUCCORE + URLEncoder.encode( v, ForesterConstants.UTF_8 );
}
}
catch ( final UnsupportedEncodingException e ) {
if ( !ForesterUtil.isEmpty( v ) ) {
try {
if ( SequenceAccessionTools.isProteinDbQuery( v ) ) {
- uri_str = ForesterUtil.NCBI_PROTEIN + URLEncoder.encode( v, ForesterConstants.UTF8 );
+ uri_str = ForesterUtil.NCBI_PROTEIN + URLEncoder.encode( v, ForesterConstants.UTF_8 );
}
else {
- uri_str = ForesterUtil.NCBI_NUCCORE + URLEncoder.encode( v, ForesterConstants.UTF8 );
+ uri_str = ForesterUtil.NCBI_NUCCORE + URLEncoder.encode( v, ForesterConstants.UTF_8 );
}
}
catch ( final UnsupportedEncodingException e ) {
final String v = SequenceAccessionTools.obtainGiNumberFromDataFields( node );
if ( !ForesterUtil.isEmpty( v ) ) {
try {
- uri_str = ForesterUtil.NCBI_GI + URLEncoder.encode( v, ForesterConstants.UTF8 );
+ uri_str = ForesterUtil.NCBI_GI + URLEncoder.encode( v, ForesterConstants.UTF_8 );
}
catch ( final UnsupportedEncodingException e ) {
AptxUtil.showErrorMessage( tp, e.toString() );
import org.forester.evoinference.matrix.character.CharacterStateMatrix.BinaryStates;
import org.forester.io.parsers.util.ParserUtils;
import org.forester.io.parsers.util.PhylogenyParserException;
+import org.forester.util.ForesterConstants;
public class NexusBinaryStatesMatrixParser {
- private static final String UTF_8 = "UTF-8";
private Object _nexus_source;
private CharacterStateMatrix<BinaryStates> _matrix;
private int _nchar;
public void parse() throws IOException {
reset();
- final BufferedReader reader = ParserUtils.createReader( getNexusSource(), UTF_8 );
+ final BufferedReader reader = ParserUtils.createReader( getNexusSource(), ForesterConstants.UTF_8 );
String line;
boolean in_matrix = false;
int identifier_index = 0;
import org.forester.io.parsers.util.ParserUtils;
import org.forester.io.parsers.util.PhylogenyParserException;
+import org.forester.util.ForesterConstants;
import org.forester.util.ForesterUtil;
public class NexusCharactersParser {
- private static final String UTF_8 = "UTF-8";
- final private static String charstatelabels = NexusConstants.CHARSTATELABELS.toLowerCase();
+ final private static String charstatelabels = NexusConstants.CHARSTATELABELS.toLowerCase();
private Object _nexus_source;
private String[] _char_state_labels;
public void parse() throws IOException {
reset();
- final BufferedReader reader = ParserUtils.createReader( getNexusSource(), UTF_8 );
+ final BufferedReader reader = ParserUtils.createReader( getNexusSource(), ForesterConstants.UTF_8 );
String line;
boolean in_charstatelabels = false;
final List<String> labels_list = new ArrayList<String>();
import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
import org.forester.sequence.BasicSequence;
import org.forester.sequence.MolecularSequence;
+import org.forester.util.ForesterConstants;
import org.forester.util.ForesterUtil;
public final class NexusPhylogeniesParser implements IteratingPhylogenyParser, PhylogenyParser {
- private static final String UTF_8 = "UTF-8";
-
+
final private static boolean DEBUG = false;
final private static String begin_trees = NexusConstants.BEGIN_TREES.toLowerCase();
private StringBuilder _translate_sb;
private Map<String, MolecularSequence> _seqs;
private final boolean _add_sequences = true;
+ private boolean _parse_beast_style_extended_tags = false;
+
@Override
public String getName() {
_rooted_info_present = false;
_is_rooted = false;
_seqs = new HashMap<String, MolecularSequence>();
- _br = ParserUtils.createReader( _nexus_source, UTF_8 );
+ _br = ParserUtils.createReader( _nexus_source, ForesterConstants.UTF_8 );
getNext();
}
pars.setTaxonomyExtraction( _taxonomy_extraction );
pars.setReplaceUnderscores( _replace_underscores );
pars.setIgnoreQuotes( _ignore_quotes_in_nh_data );
+ pars.setParseBeastStyleExtendedTags( _parse_beast_style_extended_tags );
if ( rooted_info_present ) {
pars.setGuessRootedness( false );
}
_translate_map.put( key, value );
}
}
-
+
+ public final void setParseBeastStyleExtendedTags( final boolean parse_beast_style_extended_tags ) {
+ _parse_beast_style_extended_tags = parse_beast_style_extended_tags;
+ }
+
private final static String removeWhiteSpaceBeforeSemicolon( final String s ) {
return s.replaceAll( "\\s+;", ";" );
}
package org.forester.io.parsers.nhx;
+import java.awt.Color;
import java.io.BufferedReader;
import java.io.ByteArrayInputStream;
import java.io.File;
import org.forester.phylogeny.PhylogenyMethods;
import org.forester.phylogeny.PhylogenyNode;
import org.forester.phylogeny.data.Accession;
+import org.forester.phylogeny.data.BranchColor;
import org.forester.phylogeny.data.Confidence;
import org.forester.phylogeny.data.Event;
import org.forester.phylogeny.data.Identifier;
import org.forester.phylogeny.data.Sequence;
import org.forester.phylogeny.data.Taxonomy;
import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
+import org.forester.util.ForesterConstants;
import org.forester.util.ForesterUtil;
public final class NHXParser implements PhylogenyParser, IteratingPhylogenyParser {
- public final static Pattern MB_BL_PATTERN = Pattern.compile( "length.median=([^,]+)" );
- public final static Pattern MB_PROB_PATTERN = Pattern.compile( "prob=([^,]+)" );
- public final static Pattern MB_PROB_SD_PATTERN = Pattern.compile( "prob.stddev=([^,]+)" );
- public final static Pattern NUMBERS_ONLY_PATTERN = Pattern.compile( "^[0-9\\.]+$" );
- final static public boolean REPLACE_UNDERSCORES_DEFAULT = false;
- private static final boolean ALLOW_ERRORS_IN_DISTANCE_TO_PARENT_DEFAULT = false;
- final static private byte BUFFERED_READER = 3;
- final static private byte CHAR_ARRAY = 2;
- final static private boolean GUESS_IF_SUPPORT_VALUES = true;
- final static private boolean GUESS_ROOTEDNESS_DEFAULT = true;
- final static private boolean IGNORE_QUOTES_DEFAULT = false;
+ private final static Pattern MB_BL_PATTERN = Pattern.compile( "length.median=([-+eE0-9\\.]+)" );
+ private final static Pattern MB_PROB_PATTERN = Pattern.compile( "prob=([-+eE0-9\\.]+)" );
+ private final static Pattern MB_PROB_SD_PATTERN = Pattern.compile( "prob.stddev=([-+eE0-9\\.]+)" );
+ private final static Pattern NUMBERS_ONLY_PATTERN = Pattern.compile( "^[0-9\\.]+$" );
+
+ private final static Pattern BEAST_STYLE_EXTENDED_BOOTSTRAP_PATTERN = Pattern.compile( "boot?strap=([\\d\\.]+)" );
+ private final static Pattern BEAST_STYLE_EXTENDED_COLOR_PATTERN = Pattern.compile( "colou?r=(#[\\da-fA-F]{6})" );
+ private final static Pattern ENDS_WITH_NUMBER_PATTERN = Pattern.compile( "(:[-+eE0-9\\.]+$)" );
+
+
+ public final static boolean REPLACE_UNDERSCORES_DEFAULT = false;
+ private final static boolean ALLOW_ERRORS_IN_DISTANCE_TO_PARENT_DEFAULT = false;
+ private final static byte BUFFERED_READER = 3;
+ private final static byte CHAR_ARRAY = 2;
+ private final static boolean GUESS_IF_SUPPORT_VALUES = true;
+ private final static boolean GUESS_ROOTEDNESS_DEFAULT = true;
+ private final static boolean IGNORE_QUOTES_DEFAULT = false;
- final static private char BELL = 7;
- public final static String UTF_8 = "UTF-8";
- public final static String ISO_8859_1 = "ISO-8859-1";
- private final static String ENCODING_DEFAULT = UTF_8;
+ private final static char BELL = 7;
+ private final static String ENCODING_DEFAULT = ForesterConstants.UTF_8;
private boolean _allow_errors_in_distance_to_parent;
private int _clade_level;
private StringBuilder _current_anotation;
private Object _source;
private int _source_length;
private TAXONOMY_EXTRACTION _taxonomy_extraction;
+ private boolean _parse_beast_style_extended_tags = false;
private final String _encoding;
public NHXParser() {
getTaxonomyExtraction(),
isReplaceUnderscores(),
isAllowErrorsInDistanceToParent(),
- true );
+ true,
+ isParseBeastStyleExtendedTags());
if ( GUESS_IF_SUPPORT_VALUES ) {
if ( isBranchLengthsLikeBootstrapValues( _current_phylogeny ) ) {
moveBranchLengthsToConfidenceValues( _current_phylogeny );
getTaxonomyExtraction(),
isReplaceUnderscores(),
isAllowErrorsInDistanceToParent(),
- true );
+ true,
+ isParseBeastStyleExtendedTags());
_current_phylogeny = new Phylogeny();
_current_phylogeny.setRoot( new_node );
return _current_phylogeny;
setGuessRootedness( GUESS_ROOTEDNESS_DEFAULT );
setIgnoreQuotes( IGNORE_QUOTES_DEFAULT );
setAllowErrorsInDistanceToParent( ALLOW_ERRORS_IN_DISTANCE_TO_PARENT_DEFAULT );
+ setParseBeastStyleExtendedTags( false );
}
private final boolean isAllowErrorsInDistanceToParent() {
if ( c == ':' ) {
_saw_colon = true;
}
- else if ( !( ( c < 33 ) || ( c > 126 ) ) && _saw_colon
+ else if ( !( ( c < 33 ) || ( c == 127 ) ) && _saw_colon
&& ( ( c != '[' ) && ( c != '.' ) && ( ( c < 48 ) || ( c > 57 ) ) ) ) {
_saw_colon = false;
}
getTaxonomyExtraction(),
isReplaceUnderscores(),
isAllowErrorsInDistanceToParent(),
- true );
+ true,
+ isParseBeastStyleExtendedTags());
_current_anotation = new StringBuilder();
_current_node.addAsChild( new_node );
}
getTaxonomyExtraction(),
isReplaceUnderscores(),
isAllowErrorsInDistanceToParent(),
- true );
+ true,
+ isParseBeastStyleExtendedTags());
_current_anotation = new StringBuilder();
}
if ( !_current_node.isRoot() ) {
getTaxonomyExtraction(),
isReplaceUnderscores(),
isAllowErrorsInDistanceToParent(),
- true );
+ true,
+ isParseBeastStyleExtendedTags());
if ( _current_node == null ) {
throw new NHXFormatException( "format might not be NH or NHX" );
}
getTaxonomyExtraction(),
isReplaceUnderscores(),
isAllowErrorsInDistanceToParent(),
- true );
+ true,
+ isParseBeastStyleExtendedTags());
}
_current_anotation = new StringBuilder();
_saw_closing_paren = false;
final TAXONOMY_EXTRACTION taxonomy_extraction,
final boolean replace_underscores,
final boolean allow_errors_in_distance_to_parent,
- final boolean replace_bell ) throws NHXFormatException,
+ final boolean replace_bell,
+ final boolean parse_beast_style_extended_tags ) throws NHXFormatException,
PhyloXmlDataFormatException {
if ( ( taxonomy_extraction != TAXONOMY_EXTRACTION.NO ) && replace_underscores ) {
throw new IllegalArgumentException( "cannot extract taxonomies and replace under scores at the same time" );
else if ( s.indexOf( "prob=" ) > -1 ) {
processMrBayes3Data( s, node_to_annotate );
}
+ if ( parse_beast_style_extended_tags ) {
+ processBeastStyleExtendedData( s, node_to_annotate );
+ }
+ final Matcher ewn_matcher = ENDS_WITH_NUMBER_PATTERN.matcher( s );
+ if ( ewn_matcher.find() ) {
+ b = ewn_matcher.group(1);
+ }
}
s = s.substring( 0, ob ) + b;
if ( ( s.indexOf( "[" ) > -1 ) || ( s.indexOf( "]" ) > -1 ) ) {
}
}
final StringTokenizer t = new StringTokenizer( s, ":" );
+
if ( t.countTokens() > 0 ) {
if ( !s.startsWith( ":" ) ) {
if ( ( s.indexOf( BELL ) <= -1 ) || !replace_bell ) {
}
}
+ private final static void processBeastStyleExtendedData( final String s,
+ final PhylogenyNode node_to_annotate )
+ throws NHXFormatException {
+ final Matcher ft_bs_matcher = BEAST_STYLE_EXTENDED_BOOTSTRAP_PATTERN.matcher( s );
+
+ double bs = -1;
+ if ( ft_bs_matcher.find() ) {
+ try {
+ bs = Double.parseDouble( ft_bs_matcher.group( 1 ) );
+ }
+ catch ( final NumberFormatException e ) {
+ throw new NHXFormatException( "failed to parse bootstrap support from \""
+ + s + "\"" );
+ }
+ if ( bs >= 0.0 ) {
+ node_to_annotate.getBranchData()
+ .addConfidence( new Confidence( bs, "bootstrap" ) );
+ }
+ }
+ final Matcher ft_color_matcher = BEAST_STYLE_EXTENDED_COLOR_PATTERN.matcher( s );
+ Color c = null;
+ if ( ft_color_matcher.find() ) {
+ try {
+ c = Color.decode(ft_color_matcher.group( 1 ) );
+ }
+ catch ( final NumberFormatException e ) {
+ throw new NHXFormatException( "failed to parse color from \""
+ + s + "\"" );
+ }
+ }
+ if ( c != null ) {
+ node_to_annotate.getBranchData().setBranchColor( new BranchColor( c ) );
+ }
+ }
+
private final static void processMrBayes3Data( final String s, final PhylogenyNode node_to_annotate )
throws NHXFormatException {
double sd = -1;
return _encoding;
}
+ private final boolean isParseBeastStyleExtendedTags() {
+ return _parse_beast_style_extended_tags;
+ }
+
+ public final void setParseBeastStyleExtendedTags( final boolean parse_beast_style_extended_tags ) {
+ _parse_beast_style_extended_tags = parse_beast_style_extended_tags;
+ }
+
public static enum TAXONOMY_EXTRACTION {
AGGRESSIVE, NO, PFAM_STYLE_RELAXED, PFAM_STYLE_STRICT;
}
public static final String COLOR_BLUE = "blue";
public static final String COLOR_GREEN = "green";
public static final String COLOR_RED = "red";
+ public static final String COLOR_ALPHA = "alpha";
public static final String CONFIDENCE = "confidence";
public static final String CONFIDENCE_SD_ATTR = "stddev";
public static final String CONFIDENCE_TYPE_ATTR = "type";
public class PhyloXmlParser implements PhylogenyParser {
- private static final String UTF_8 = "UTF-8";
final public static String JAXP_SCHEMA_LANGUAGE = "http://java.sun.com/xml/jaxp/properties/schemaLanguage";
final public static String W3C_XML_SCHEMA = "http://www.w3.org/2001/XMLSchema";
final public static String JAXP_SCHEMA_SOURCE = "http://java.sun.com/xml/jaxp/properties/schemaSource";
final ZipEntry zip_file_entry = ( ZipEntry ) zip_file_entries.nextElement();
if ( !zip_file_entry.isDirectory() && ( zip_file_entry.getSize() > 0 ) ) {
final InputStream is = zip_file.getInputStream( zip_file_entry );
- reader = new InputStreamReader( is, UTF_8 );
+ reader = new InputStreamReader( is, ForesterConstants.UTF_8 );
break;
}
}
if ( getSource() instanceof File ) {
if ( !getSource().toString().toLowerCase().endsWith( ".zip" ) ) {
final InputStream is = new FileInputStream( (File) getSource() );
- final InputStreamReader isr = new InputStreamReader( is, UTF_8 );
+ final InputStreamReader isr = new InputStreamReader( is, ForesterConstants.UTF_8 );
xml_reader.parse( new InputSource( new BufferedReader( isr ) ) );
}
else {
}
else if ( getSource() instanceof InputSource ) {
final InputSource is = ( InputSource ) getSource();
- is.setEncoding( UTF_8 );
+ is.setEncoding( ForesterConstants.UTF_8 );
xml_reader.parse( is );
}
else if ( getSource() instanceof InputStream ) {
if ( !isZippedInputstream() ) {
final InputStream is = ( InputStream ) getSource();
- xml_reader.parse( new InputSource( new BufferedReader( new InputStreamReader( is, UTF_8 ) ) ) );
+ xml_reader.parse( new InputSource( new BufferedReader( new InputStreamReader( is, ForesterConstants.UTF_8 ) ) ) );
}
else {
final ZipInputStream zip_is = new ZipInputStream( ( InputStream ) getSource() );
zip_is.getNextEntry();
- xml_reader.parse( new InputSource( new BufferedReader( new InputStreamReader( zip_is, UTF_8 ) ) ) );
+ xml_reader.parse( new InputSource( new BufferedReader( new InputStreamReader( zip_is, ForesterConstants.UTF_8 ) ) ) );
}
}
else if ( getSource() instanceof StringBuffer ) {
int red = 0;
int green = 0;
int blue = 0;
+ int alpha = -1;
for( int j = 0; j < element.getNumberOfChildElements(); ++j ) {
final XmlElement c = element.getChildElement( j );
if ( c.getQualifiedName().equals( PhyloXmlMapping.COLOR_RED ) ) {
else if ( c.getQualifiedName().equals( PhyloXmlMapping.COLOR_BLUE ) ) {
blue = c.getValueAsInt();
}
+ else if ( c.getQualifiedName().equals( PhyloXmlMapping.COLOR_ALPHA ) ) {
+ alpha = c.getValueAsInt();
+ }
}
final BranchColor color = new BranchColor();
- color.setValue( new Color( red, green, blue ) );
+ if ( alpha < 0 ) {
+ color.setValue( new Color( red, green, blue ) );
+ }
+ else {
+ color.setValue( new Color( red, green, blue ) );
+ }
return color;
}
public final class PhylogenyWriter {
- private static final String UTF_8 = "UTF-8";
public final static boolean INDENT_PHYLOXML_DEAFULT = true;
public final static String PHYLO_XML_INTENDATION_BASE = " ";
public final static String PHYLO_XML_VERSION_ENCODING_LINE = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>";
public void toNexus( final File out_file, final Phylogeny tree, final NH_CONVERSION_SUPPORT_VALUE_STYLE svs )
throws IOException {
- final Writer writer = new BufferedWriter( new PrintWriter( out_file, UTF_8 ) );
+ final Writer writer = new BufferedWriter( new PrintWriter( out_file, ForesterConstants.UTF_8 ) );
final List<Phylogeny> trees = new ArrayList<Phylogeny>( 1 );
trees.add( tree );
writeNexusStart( writer );
final List<Phylogeny> trees,
final int phyloxml_level,
final String separator ) throws IOException {
- final Writer writer = new BufferedWriter( new PrintWriter( out_file, UTF_8 ) );
+ final Writer writer = new BufferedWriter( new PrintWriter( out_file, ForesterConstants.UTF_8 ) );
toPhyloXML( writer, trees, phyloxml_level, separator );
writer.flush();
writer.close();
}
public void toPhyloXML( final File out_file, final Phylogeny tree, final int phyloxml_level ) throws IOException {
- final Writer writer = new BufferedWriter( new PrintWriter( out_file, UTF_8 ) );
+ final Writer writer = new BufferedWriter( new PrintWriter( out_file, ForesterConstants.UTF_8 ) );
writePhyloXmlStart( writer );
toPhyloXMLNoPhyloXmlSource( writer, tree, phyloxml_level );
writePhyloXmlEnd( writer );
if ( out_file.exists() ) {
throw new IOException( "attempt to overwrite existing file \"" + out_file.getAbsolutePath() + "\"" );
}
- final PrintWriter out = new PrintWriter( out_file, UTF_8 );
+ final PrintWriter out = new PrintWriter( out_file, ForesterConstants.UTF_8 );
out.print( sb );
out.flush();
out.close();
private PhylogenyNode( final String nhx,
final NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction,
final boolean replace_underscores ) throws NHXFormatException, PhyloXmlDataFormatException {
- NHXParser.parseNHX( nhx, this, taxonomy_extraction, replace_underscores, false, false );
+ NHXParser.parseNHX( nhx, this, taxonomy_extraction, replace_underscores, false, false, false );
+ setId( PhylogenyNode.getNodeCount() );
+ PhylogenyNode.increaseNodeCount();
+ setSumExtNodes( 1 ); // For ext node, this number is 1 (not 0!!).
+ }
+
+ private PhylogenyNode( final String nhx,
+ final NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction,
+ final boolean replace_underscores,
+ final boolean parse_extended_tags ) throws NHXFormatException, PhyloXmlDataFormatException {
+ NHXParser.parseNHX( nhx,
+ this,
+ taxonomy_extraction,
+ replace_underscores,
+ false,
+ false,
+ parse_extended_tags );
setId( PhylogenyNode.getNodeCount() );
PhylogenyNode.increaseNodeCount();
setSumExtNodes( 1 ); // For ext node, this number is 1 (not 0!!).
throws NHXFormatException, PhyloXmlDataFormatException {
return new PhylogenyNode( nhx, taxonomy_extraction, replace_underscores );
}
+
+ public static PhylogenyNode createInstanceFromNhxString( final String nhx,
+ final NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction,
+ final boolean replace_underscores,
+ final boolean parse_extended_tags )
+ throws NHXFormatException, PhyloXmlDataFormatException {
+ return new PhylogenyNode( nhx, taxonomy_extraction, replace_underscores, parse_extended_tags );
+ }
/**
* Returns the total number of all Nodes created so far.
PhylogenyDataUtil.appendElement( writer, PhyloXmlMapping.COLOR_RED, getValue().getRed() + "", indentation );
PhylogenyDataUtil.appendElement( writer, PhyloXmlMapping.COLOR_GREEN, getValue().getGreen() + "", indentation );
PhylogenyDataUtil.appendElement( writer, PhyloXmlMapping.COLOR_BLUE, getValue().getBlue() + "", indentation );
+ if ( getValue().getAlpha() != 255 ) {
+ PhylogenyDataUtil.appendElement( writer, PhyloXmlMapping.COLOR_ALPHA, getValue().getAlpha() + "", indentation );
+ }
writer.write( ForesterUtil.LINE_SEPARATOR );
writer.write( indentation );
PhylogenyDataUtil.appendClose( writer, PhyloXmlMapping.COLOR );
@Override
public StringBuffer asSimpleText() {
- // TODO Auto-generated method stub
return null;
}
@Override
public StringBuffer asText() {
- // TODO Auto-generated method stub
return null;
}
System.out.println( "failed." );
failed++;
}
+ System.out.print( "Node construction and parsing of NHX (node level): " );
+ if ( Test.testNHXNodeParsing2() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
System.out.print( "NHX parsing iterating: " );
if ( Test.testNHParsingIter() ) {
System.out.println( "OK." );
return true;
}
+
+ private static boolean testNHXNodeParsing2() {
+ try {
+
+ final PhylogenyNode n0_0 = PhylogenyNode
+ .createInstanceFromNhxString( "n0:[ignore me 123]:1E-3", NHXParser.TAXONOMY_EXTRACTION.NO, true, true );
+ if ( !n0_0.getName().equals( "n0" ) ) {
+ return false;
+ }
+ if ( !isEqual( n0_0.getDistanceToParent(), 0.001 ) ) {
+ return false;
+ }
+ final PhylogenyNode n0_1 = PhylogenyNode
+ .createInstanceFromNhxString( "n0[ignore me 123]:1E-3", NHXParser.TAXONOMY_EXTRACTION.NO, true, true );
+ if ( !n0_1.getName().equals( "n0" ) ) {
+ return false;
+ }
+ if ( !isEqual( n0_1.getDistanceToParent(), 0.001 ) ) {
+ return false;
+ }
+ final PhylogenyNode n0_2 = PhylogenyNode
+ .createInstanceFromNhxString( "n0:1E-3[ignore me 123]", NHXParser.TAXONOMY_EXTRACTION.NO, true, true );
+ if ( !n0_2.getName().equals( "n0" ) ) {
+ return false;
+ }
+ if ( !isEqual( n0_2.getDistanceToParent(), 0.001 ) ) {
+ return false;
+ }
+ final PhylogenyNode n0_3 = PhylogenyNode
+ .createInstanceFromNhxString( "n0:1E-3:[ignore me 123]", NHXParser.TAXONOMY_EXTRACTION.NO, true, true );
+ if ( !n0_3.getName().equals( "n0" ) ) {
+ return false;
+ }
+ if ( !isEqual( n0_3.getDistanceToParent(), 0.001 ) ) {
+ return false;
+ }
+ final PhylogenyNode n0_4 = PhylogenyNode
+ .createInstanceFromNhxString( "n0:0.001:[ignore me 123]", NHXParser.TAXONOMY_EXTRACTION.NO, true, true );
+ if ( !n0_4.getName().equals( "n0" ) ) {
+ return false;
+ }
+ if ( !isEqual( n0_4.getDistanceToParent(), 0.001 ) ) {
+ return false;
+ }
+ final PhylogenyNode n1_0 = PhylogenyNode
+ .createInstanceFromNhxString( "xyz|A/American_duck/NH/00321/|Duck|Canada[&!color=#FFFFFF]", NHXParser.TAXONOMY_EXTRACTION.NO, true, true );
+ if ( !n1_0.getName().equals( "xyz|A/American duck/NH/00321/|Duck|Canada" ) ) {
+ return false;
+ }
+ if ( n1_0.getBranchData().getBranchColor().getValue().getGreen()!=255 ) {
+ return false;
+ }
+ final PhylogenyNode n1_1 = PhylogenyNode
+ .createInstanceFromNhxString( "xyz|A/American_duck/NH/00321/|Duck|Canada[&!color=#FFFFFF]:0.001", NHXParser.TAXONOMY_EXTRACTION.NO, true, true );
+ if ( !n1_1.getName().equals( "xyz|A/American duck/NH/00321/|Duck|Canada" ) ) {
+ return false;
+ }
+ if ( n1_1.getBranchData().getBranchColor().getValue().getGreen()!=255 ) {
+ return false;
+ }
+ if ( !isEqual( n1_1.getDistanceToParent(), 0.001 ) ) {
+ return false;
+ }
+ final PhylogenyNode n1_2 = PhylogenyNode
+ .createInstanceFromNhxString( "xyz|A/American_duck/NH/00321/|Duck|Canada:0.001[&!color=#FFFFFF]", NHXParser.TAXONOMY_EXTRACTION.NO, true, true );
+ if ( !n1_2.getName().equals( "xyz|A/American duck/NH/00321/|Duck|Canada" ) ) {
+ return false;
+ }
+ if ( n1_2.getBranchData().getBranchColor().getValue().getGreen()!=255 ) {
+ return false;
+ }
+ if ( !isEqual( n1_2.getDistanceToParent(), 0.001 ) ) {
+ return false;
+ }
+ final PhylogenyNode n1_3 = PhylogenyNode
+ .createInstanceFromNhxString( "xyz|A/American_duck/NH/00321/|Duck|Canada:1e-3[&boostrap=69,&!color=#FFFFFF]", NHXParser.TAXONOMY_EXTRACTION.NO, true, true );
+ if ( !n1_3.getName().equals( "xyz|A/American duck/NH/00321/|Duck|Canada" ) ) {
+ return false;
+ }
+ if ( n1_3.getBranchData().getBranchColor().getValue().getGreen()!=255 ) {
+ return false;
+ }
+ if ( !isEqual( n1_3.getDistanceToParent(), 0.001 ) ) {
+ return false;
+ }
+ if ( !isEqual( n1_3.getBranchData().getConfidence( 0 ).getValue(), 69 ) ) {
+ return false;
+ }
+ if ( !n1_3.getBranchData().getConfidence( 0 ).getType().equals( "bootstrap" ) ) {
+ return false;
+ }
+ final PhylogenyNode n1_4 = PhylogenyNode
+ .createInstanceFromNhxString( "xyz|A/American_duck/NH/00321/|Duck|Canada[&bootstrap=69,&!colour=#FFFFFF]:1e-3", NHXParser.TAXONOMY_EXTRACTION.NO, true, true );
+ if ( !n1_4.getName().equals( "xyz|A/American duck/NH/00321/|Duck|Canada" ) ) {
+ return false;
+ }
+ if ( n1_4.getBranchData().getBranchColor().getValue().getGreen()!=255 ) {
+ return false;
+ }
+ if ( !isEqual( n1_4.getDistanceToParent(), 0.001 ) ) {
+ return false;
+ }
+ if ( !isEqual( n1_4.getBranchData().getConfidence( 0 ).getValue(), 69 ) ) {
+ return false;
+ }
+ if ( !n1_4.getBranchData().getConfidence( 0 ).getType().equals( "bootstrap" ) ) {
+ return false;
+ }
+ final PhylogenyNode n1_5 = PhylogenyNode
+ .createInstanceFromNhxString( "xyz|A/American_duck/NH/00321/|Duck|Canada:1e-3[69.0]", NHXParser.TAXONOMY_EXTRACTION.NO, true, true );
+ if ( !n1_5.getName().equals( "xyz|A/American duck/NH/00321/|Duck|Canada" ) ) {
+ return false;
+ }
+ if ( !isEqual( n1_5.getDistanceToParent(), 0.001 ) ) {
+ return false;
+ }
+ if ( !isEqual( n1_5.getBranchData().getConfidence( 0 ).getValue(), 69 ) ) {
+ return false;
+ }
+ final PhylogenyNode n1_6 = PhylogenyNode
+ .createInstanceFromNhxString( "xyz|A/American_duck/NH/00321/|Duck|Canada[&prob=0.9500000000000000e+00,prob_stddev=0.1100000000000000e+00]:1e-3", NHXParser.TAXONOMY_EXTRACTION.NO, true, true );
+ if ( !n1_6.getName().equals( "xyz|A/American duck/NH/00321/|Duck|Canada" ) ) {
+ return false;
+ }
+
+ if ( !isEqual( n1_6.getDistanceToParent(), 0.001 ) ) {
+ return false;
+ }
+ if ( !isEqual( n1_6.getBranchData().getConfidence( 0 ).getStandardDeviation(), 0.11 ) ) {
+ return false;
+ }
+ if ( !isEqual( n1_6.getBranchData().getConfidence( 0 ).getValue(), 0.95 ) ) {
+ return false;
+ }
+ if ( !n1_6.getBranchData().getConfidence( 0 ).getType().equals( "posterior probability" ) ) {
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace( System.out );
+ return false;
+ }
+ return true;
+ }
+
private static boolean testNHXParsing() {
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
public final class ForesterConstants {
- public final static String FORESTER_VERSION = "1.041";
- public final static String FORESTER_DATE = "160701";
+ public final static String FORESTER_VERSION = "1.042";
+ public final static String FORESTER_DATE = "160712";
public final static String PHYLO_XML_VERSION = "1.10";
public final static String PHYLO_XML_LOCATION = "http://www.phyloxml.org";
public final static String PHYLO_XML_XSD = "phyloxml.xsd";
public final static String XML_SCHEMA_INSTANCE = "http://www.w3.org/2001/XMLSchema-instance";
public final static String LOCAL_PHYLOXML_XSD_RESOURCE = "resources/phyloxml.xsd";
public final static String PHYLO_XML_SUFFIX = ".xml";
- public final static String UTF8 = "UTF-8";
+ public final static String UTF_8 = "UTF-8";
+ public final static String ISO_8859_1 = "ISO-8859-1";
public final static String PHYLO_XML_REFERENCE = "Han MV and Zmasek CM (2009): \"phyloXML: XML for evolutionary biology and comparative genomics\", BMC Bioinformatics 10:356";
public final static boolean RELEASE = false;
public enum PhylogeneticTreeFormats {
NH, NHX, NEXUS, PHYLOXML
}
+
+
}
git://source.jalview.org / jalview.git / commitdiff