-// $Id:\r
-// FORESTER -- software libraries and applications\r
-// for evolutionary biology research and applications.\r
-//\r
-// Copyright (C) 2008-2009 Christian M. Zmasek\r
-// Copyright (C) 2008-2009 Burnham Institute for Medical Research\r
-// Copyright (C) 2003-2007 Ethalinda K.S. Cannon\r
-// All rights reserved\r
-//\r
-// This library is free software; you can redistribute it and/or\r
-// modify it under the terms of the GNU Lesser General Public\r
-// License as published by the Free Software Foundation; either\r
-// version 2.1 of the License, or (at your option) any later version.\r
-//\r
-// This library is distributed in the hope that it will be useful,\r
-// but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU\r
-// Lesser General Public License for more details.\r
-//\r
-// You should have received a copy of the GNU Lesser General Public\r
-// License along with this library; if not, write to the Free Software\r
-// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-//\r
-// Contact: phylosoft @ gmail . com\r
-// WWW: https://sites.google.com/site/cmzmasek/home/software/forester\r
-\r
-package org.forester.archaeopteryx;\r
-\r
-import java.awt.BorderLayout;\r
-import java.awt.Font;\r
-import java.awt.event.ActionEvent;\r
-import java.awt.event.ComponentAdapter;\r
-import java.awt.event.ComponentEvent;\r
-import java.awt.event.WindowAdapter;\r
-import java.awt.event.WindowEvent;\r
-import java.io.File;\r
-import java.io.FileInputStream;\r
-import java.io.IOException;\r
-import java.io.InputStream;\r
-import java.net.MalformedURLException;\r
-import java.net.URL;\r
-import java.util.ArrayList;\r
-import java.util.HashSet;\r
-import java.util.List;\r
-import java.util.Set;\r
-\r
-import javax.swing.ButtonGroup;\r
-import javax.swing.JCheckBoxMenuItem;\r
-import javax.swing.JFileChooser;\r
-import javax.swing.JMenu;\r
-import javax.swing.JMenuBar;\r
-import javax.swing.JMenuItem;\r
-import javax.swing.JOptionPane;\r
-import javax.swing.JRadioButtonMenuItem;\r
-import javax.swing.UIManager;\r
-import javax.swing.UnsupportedLookAndFeelException;\r
-import javax.swing.WindowConstants;\r
-import javax.swing.event.ChangeEvent;\r
-import javax.swing.event.ChangeListener;\r
-import javax.swing.filechooser.FileFilter;\r
-import javax.swing.plaf.synth.SynthLookAndFeel;\r
-\r
-import org.forester.analysis.TaxonomyDataManager;\r
-import org.forester.archaeopteryx.AptxUtil.GraphicsExportType;\r
-import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;\r
-import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;\r
-import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;\r
-import org.forester.archaeopteryx.tools.AncestralTaxonomyInferrer;\r
-import org.forester.archaeopteryx.tools.InferenceManager;\r
-import org.forester.archaeopteryx.tools.PhyloInferenceDialog;\r
-import org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions;\r
-import org.forester.archaeopteryx.tools.PhylogeneticInferrer;\r
-import org.forester.archaeopteryx.tools.SequenceDataRetriver;\r
-import org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient;\r
-import org.forester.archaeopteryx.webservices.WebservicesManager;\r
-import org.forester.io.parsers.FastaParser;\r
-import org.forester.io.parsers.GeneralMsaParser;\r
-import org.forester.io.parsers.PhylogenyParser;\r
-import org.forester.io.parsers.nexus.NexusPhylogeniesParser;\r
-import org.forester.io.parsers.nhx.NHXParser;\r
-import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;\r
-import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;\r
-import org.forester.io.parsers.phyloxml.PhyloXmlParser;\r
-import org.forester.io.parsers.phyloxml.PhyloXmlUtil;\r
-import org.forester.io.parsers.tol.TolParser;\r
-import org.forester.io.parsers.util.ParserUtils;\r
-import org.forester.io.writers.PhylogenyWriter;\r
-import org.forester.io.writers.SequenceWriter;\r
-import org.forester.msa.Msa;\r
-import org.forester.msa.MsaFormatException;\r
-import org.forester.phylogeny.Phylogeny;\r
-import org.forester.phylogeny.PhylogenyMethods;\r
-import org.forester.phylogeny.PhylogenyNode;\r
-import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;\r
-import org.forester.phylogeny.data.Confidence;\r
-import org.forester.phylogeny.data.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
-import org.forester.util.WindowsUtils;\r
-\r
-public final class MainFrameApplication extends MainFrame {\r
-\r
- static final String INFER_ANCESTOR_TAXONOMIES = "Infer Ancestor Taxonomies";\r
- static final String OBTAIN_DETAILED_TAXONOMIC_INFORMATION = "Obtain Detailed Taxonomic Information";\r
- private final static int FRAME_X_SIZE = 800;\r
- private final static int FRAME_Y_SIZE = 800;\r
- // Filters for the file-open dialog (classes defined in this file)\r
- private final static NHFilter nhfilter = new NHFilter();\r
- private final static NHXFilter nhxfilter = new NHXFilter();\r
- private final static XMLFilter xmlfilter = new XMLFilter();\r
- private final static TolFilter tolfilter = new TolFilter();\r
- private final static NexusFilter nexusfilter = new NexusFilter();\r
- private final static PdfFilter pdffilter = new PdfFilter();\r
- private final static GraphicsFileFilter graphicsfilefilter = new GraphicsFileFilter();\r
- private final static MsaFileFilter msafilter = new MsaFileFilter();\r
- private final static SequencesFileFilter seqsfilter = new SequencesFileFilter();\r
- private final static DefaultFilter defaultfilter = new DefaultFilter();\r
- private static final long serialVersionUID = -799735726778865234L;\r
- private 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
- private final JFileChooser _save_filechooser;\r
- private final JFileChooser _writetopdf_filechooser;\r
- private final JFileChooser _writetographics_filechooser;\r
- // Application-only print menu items\r
- private JMenuItem _print_item;\r
- private JMenuItem _write_to_pdf_item;\r
- private JMenuItem _write_to_jpg_item;\r
- private JMenuItem _write_to_gif_item;\r
- private JMenuItem _write_to_tif_item;\r
- private JMenuItem _write_to_png_item;\r
- private JMenuItem _write_to_bmp_item;\r
- private JMenuItem _collapse_below_threshold;\r
- private JMenuItem _collapse_below_branch_length;\r
- private File _current_dir;\r
- private ButtonGroup _radio_group_1;\r
- private ButtonGroup _radio_group_2;\r
- // Others:\r
- double _min_not_collapse = Constants.MIN_NOT_COLLAPSE_DEFAULT;\r
- 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
- boolean synth_exception = false;\r
- if ( Constants.__SYNTH_LF ) {\r
- try {\r
- final SynthLookAndFeel synth = new SynthLookAndFeel();\r
- synth.load( MainFrameApplication.class.getResourceAsStream( "/resources/synth_look_and_feel_1.xml" ),\r
- MainFrameApplication.class );\r
- UIManager.setLookAndFeel( synth );\r
- }\r
- catch ( final Exception ex ) {\r
- synth_exception = true;\r
- ForesterUtil.printWarningMessage( Constants.PRG_NAME,\r
- "could not create synth look and feel: "\r
- + ex.getLocalizedMessage() );\r
- }\r
- }\r
- if ( !Constants.__SYNTH_LF || synth_exception ) {\r
- if ( _configuration.isUseNativeUI() ) {\r
- UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );\r
- }\r
- else {\r
- UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );\r
- }\r
- }\r
- //UIManager.setLookAndFeel( "com.sun.java.swing.plaf.nimbus.NimbusLookAndFeel" );\r
- }\r
- catch ( final UnsupportedLookAndFeelException e ) {\r
- AptxUtil.dieWithSystemError( "unsupported look and feel: " + e.toString() );\r
- }\r
- catch ( final ClassNotFoundException e ) {\r
- AptxUtil.dieWithSystemError( "class not found exception: " + e.toString() );\r
- }\r
- catch ( final InstantiationException e ) {\r
- AptxUtil.dieWithSystemError( "instantiation exception: " + e.toString() );\r
- }\r
- catch ( final IllegalAccessException e ) {\r
- AptxUtil.dieWithSystemError( "illegal access exception: " + e.toString() );\r
- }\r
- if ( ( current_dir != null ) && current_dir.canRead() && current_dir.isDirectory() ) {\r
- setCurrentDir( current_dir );\r
- }\r
- // hide until everything is ready\r
- setVisible( false );\r
- setOptions( Options.createInstance( _configuration ) );\r
- setInferenceManager( InferenceManager.createInstance( _configuration ) );\r
- setPhylogeneticInferenceOptions( PhylogeneticInferenceOptions.createInstance( _configuration ) );\r
- // _textframe = null; #~~~~\r
- // set title\r
- setTitle( Constants.PRG_NAME + " " + Constants.VERSION + " (" + Constants.PRG_DATE + ")" );\r
- _mainpanel = new MainPanel( _configuration, this );\r
- // The file dialogs\r
- _open_filechooser = new JFileChooser();\r
- _open_filechooser.setCurrentDirectory( new File( "." ) );\r
- _open_filechooser.setMultiSelectionEnabled( false );\r
- _open_filechooser.addChoosableFileFilter( MainFrameApplication.xmlfilter );\r
- _open_filechooser.addChoosableFileFilter( MainFrameApplication.nhxfilter );\r
- _open_filechooser.addChoosableFileFilter( MainFrameApplication.nhfilter );\r
- _open_filechooser.addChoosableFileFilter( MainFrameApplication.nexusfilter );\r
- _open_filechooser.addChoosableFileFilter( MainFrameApplication.tolfilter );\r
- _open_filechooser.addChoosableFileFilter( _open_filechooser.getAcceptAllFileFilter() );\r
- _open_filechooser.setFileFilter( MainFrameApplication.defaultfilter );\r
- _open_filechooser_for_species_tree = new JFileChooser();\r
- _open_filechooser_for_species_tree.setCurrentDirectory( new File( "." ) );\r
- _open_filechooser_for_species_tree.setMultiSelectionEnabled( false );\r
- _open_filechooser_for_species_tree.addChoosableFileFilter( MainFrameApplication.xmlfilter );\r
- _open_filechooser_for_species_tree.addChoosableFileFilter( MainFrameApplication.tolfilter );\r
- _open_filechooser_for_species_tree.setFileFilter( MainFrameApplication.xmlfilter );\r
- _save_filechooser = new JFileChooser();\r
- _save_filechooser.setCurrentDirectory( new File( "." ) );\r
- _save_filechooser.setMultiSelectionEnabled( false );\r
- _save_filechooser.setFileFilter( MainFrameApplication.xmlfilter );\r
- _save_filechooser.addChoosableFileFilter( MainFrameApplication.nhfilter );\r
- _save_filechooser.addChoosableFileFilter( MainFrameApplication.nexusfilter );\r
- _save_filechooser.addChoosableFileFilter( _save_filechooser.getAcceptAllFileFilter() );\r
- _writetopdf_filechooser = new JFileChooser();\r
- _writetopdf_filechooser.addChoosableFileFilter( MainFrameApplication.pdffilter );\r
- _writetographics_filechooser = new JFileChooser();\r
- _writetographics_filechooser.addChoosableFileFilter( MainFrameApplication.graphicsfilefilter );\r
- // Msa:\r
- _msa_filechooser = new JFileChooser();\r
- _msa_filechooser.setName( "Read Multiple Sequence Alignment File" );\r
- _msa_filechooser.setCurrentDirectory( new File( "." ) );\r
- _msa_filechooser.setMultiSelectionEnabled( false );\r
- _msa_filechooser.addChoosableFileFilter( _msa_filechooser.getAcceptAllFileFilter() );\r
- _msa_filechooser.addChoosableFileFilter( MainFrameApplication.msafilter );\r
- // Seqs:\r
- _seqs_pi_filechooser = new JFileChooser();\r
- _seqs_pi_filechooser.setName( "Read Sequences File" );\r
- _seqs_pi_filechooser.setCurrentDirectory( new File( "." ) );\r
- _seqs_pi_filechooser.setMultiSelectionEnabled( false );\r
- _seqs_pi_filechooser.addChoosableFileFilter( _seqs_pi_filechooser.getAcceptAllFileFilter() );\r
- _seqs_pi_filechooser.addChoosableFileFilter( MainFrameApplication.seqsfilter );\r
- // Expression\r
- _values_filechooser = new JFileChooser();\r
- _values_filechooser.setCurrentDirectory( new File( "." ) );\r
- _values_filechooser.setMultiSelectionEnabled( false );\r
- // Sequences\r
- _sequences_filechooser = new JFileChooser();\r
- _sequences_filechooser.setCurrentDirectory( new File( "." ) );\r
- _sequences_filechooser.setMultiSelectionEnabled( false );\r
- // build the menu bar\r
- _jmenubar = new JMenuBar();\r
- if ( !_configuration.isUseNativeUI() ) {\r
- _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
- }\r
- buildFileMenu();\r
- if ( Constants.__ALLOW_PHYLOGENETIC_INFERENCE ) {\r
- buildPhylogeneticInferenceMenu();\r
- }\r
- buildAnalysisMenu();\r
- buildToolsMenu();\r
- buildViewMenu();\r
- buildFontSizeMenu();\r
- buildOptionsMenu();\r
- buildTypeMenu();\r
- buildHelpMenu();\r
- setJMenuBar( _jmenubar );\r
- _jmenubar.add( _help_jmenu );\r
- _contentpane = getContentPane();\r
- _contentpane.setLayout( new BorderLayout() );\r
- _contentpane.add( _mainpanel, BorderLayout.CENTER );\r
- // App is this big\r
- setSize( MainFrameApplication.FRAME_X_SIZE, MainFrameApplication.FRAME_Y_SIZE );\r
- // addWindowFocusListener( new WindowAdapter() {\r
- //\r
- // @Override\r
- // public void windowGainedFocus( WindowEvent e ) {\r
- // requestFocusInWindow();\r
- // }\r
- // } );\r
- // The window listener\r
- setDefaultCloseOperation( WindowConstants.DO_NOTHING_ON_CLOSE );\r
- addWindowListener( new WindowAdapter() {\r
-\r
- @Override\r
- public void windowClosing( final WindowEvent e ) {\r
- if ( isUnsavedDataPresent() ) {\r
- final int r = JOptionPane.showConfirmDialog( null,\r
- "Exit despite potentially unsaved changes?",\r
- "Exit?",\r
- JOptionPane.YES_NO_OPTION );\r
- if ( r != JOptionPane.YES_OPTION ) {\r
- return;\r
- }\r
- }\r
- else {\r
- final int r = JOptionPane.showConfirmDialog( null,\r
- "Exit Archaeopteryx?",\r
- "Exit?",\r
- JOptionPane.YES_NO_OPTION );\r
- if ( r != JOptionPane.YES_OPTION ) {\r
- return;\r
- }\r
- }\r
- exit();\r
- }\r
- } );\r
- // The component listener\r
- addComponentListener( new ComponentAdapter() {\r
-\r
- @Override\r
- public void componentResized( final ComponentEvent e ) {\r
- if ( _mainpanel.getCurrentTreePanel() != null ) {\r
- _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel()\r
- .getWidth(),\r
- _mainpanel.getCurrentTreePanel()\r
- .getHeight(),\r
- getOptions().isAllowFontSizeChange() );\r
- }\r
- }\r
- } );\r
- requestFocusInWindow();\r
- // addKeyListener( this );\r
- setVisible( true );\r
- if ( ( phys != null ) && ( phys.length > 0 ) ) {\r
- AptxUtil.addPhylogeniesToTabs( phys, title, null, _configuration, _mainpanel );\r
- validate();\r
- getMainPanel().getControlPanel().showWholeAll();\r
- getMainPanel().getControlPanel().showWhole();\r
- }\r
- activateSaveAllIfNeeded();\r
- // ...and its children\r
- _contentpane.repaint();\r
- System.gc();\r
- }\r
-\r
- private MainFrameApplication( final Phylogeny[] phys, final String config_file, final String title ) {\r
- // Reads the config file (false, false => not url, not applet):\r
- this( phys, new Configuration( config_file, false, false, true ), title );\r
- }\r
-\r
- @Override\r
- public void actionPerformed( final ActionEvent e ) {\r
- try {\r
- super.actionPerformed( e );\r
- final Object o = e.getSource();\r
- // Handle app-specific actions here:\r
- if ( o == _open_item ) {\r
- readPhylogeniesFromFile();\r
- }\r
- if ( o == _open_url_item ) {\r
- readPhylogeniesFromURL();\r
- }\r
- else if ( o == _save_item ) {\r
- writeToFile( _mainpanel.getCurrentPhylogeny() );\r
- // If subtree currently displayed, save it, instead of complete\r
- // tree.\r
- }\r
- else if ( o == _new_item ) {\r
- newTree();\r
- }\r
- else if ( o == _save_all_item ) {\r
- writeAllToFile();\r
- }\r
- else if ( o == _close_item ) {\r
- closeCurrentPane();\r
- }\r
- else if ( o == _write_to_pdf_item ) {\r
- writeToPdf( _mainpanel.getCurrentPhylogeny() );\r
- }\r
- else if ( o == _write_to_jpg_item ) {\r
- writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.JPG );\r
- }\r
- else if ( o == _write_to_png_item ) {\r
- writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.PNG );\r
- }\r
- else if ( o == _write_to_gif_item ) {\r
- writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.GIF );\r
- }\r
- else if ( o == _write_to_tif_item ) {\r
- writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.TIFF );\r
- }\r
- else if ( o == _write_to_bmp_item ) {\r
- writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.BMP );\r
- }\r
- else if ( o == _print_item ) {\r
- print();\r
- }\r
- else if ( o == _load_species_tree_item ) {\r
- readSpeciesTreeFromFile();\r
- }\r
- else if ( o == _lineage_inference ) {\r
- if ( isSubtreeDisplayed() ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Subtree is shown.",\r
- "Cannot infer ancestral taxonomies",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- executeLineageInference();\r
- }\r
- else if ( o == _obtain_detailed_taxonomic_information_jmi ) {\r
- if ( isSubtreeDisplayed() ) {\r
- return;\r
- }\r
- obtainDetailedTaxonomicInformation();\r
- }\r
- else if ( o == _obtain_detailed_taxonomic_information_deleting_jmi ) {\r
- if ( isSubtreeDisplayed() ) {\r
- return;\r
- }\r
- obtainDetailedTaxonomicInformationDelete();\r
- }\r
- else if ( o == _obtain_seq_information_jmi ) {\r
- obtainSequenceInformation();\r
- }\r
- else if ( o == _read_values_jmi ) {\r
- if ( isSubtreeDisplayed() ) {\r
- return;\r
- }\r
- addExpressionValuesFromFile();\r
- }\r
- else if ( o == _read_seqs_jmi ) {\r
- if ( isSubtreeDisplayed() ) {\r
- return;\r
- }\r
- addSequencesFromFile();\r
- }\r
- else if ( o == _move_node_names_to_tax_sn_jmi ) {\r
- moveNodeNamesToTaxSn();\r
- }\r
- else if ( o == _move_node_names_to_seq_names_jmi ) {\r
- moveNodeNamesToSeqNames();\r
- }\r
- else if ( o == _extract_tax_code_from_node_names_jmi ) {\r
- extractTaxDataFromNodeNames();\r
- }\r
- else if ( o == _graphics_export_visible_only_cbmi ) {\r
- updateOptions( getOptions() );\r
- }\r
- else if ( o == _antialias_print_cbmi ) {\r
- updateOptions( getOptions() );\r
- }\r
- else if ( o == _print_black_and_white_cbmi ) {\r
- updateOptions( getOptions() );\r
- }\r
- else if ( o == _print_using_actual_size_cbmi ) {\r
- updateOptions( getOptions() );\r
- }\r
- else if ( o == _graphics_export_using_actual_size_cbmi ) {\r
- updateOptions( getOptions() );\r
- }\r
- else if ( o == _print_size_mi ) {\r
- choosePrintSize();\r
- }\r
- else if ( o == _choose_pdf_width_mi ) {\r
- choosePdfWidth();\r
- }\r
- else if ( o == _internal_number_are_confidence_for_nh_parsing_cbmi ) {\r
- updateOptions( getOptions() );\r
- }\r
- else if ( o == _replace_underscores_cbmi ) {\r
- if ( ( _extract_taxonomy_no_rbmi != null ) && !_extract_taxonomy_no_rbmi.isSelected() ) {\r
- _extract_taxonomy_no_rbmi.setSelected( true );\r
- }\r
- updateOptions( getOptions() );\r
- }\r
- else if ( o == _allow_errors_in_distance_to_parent_cbmi ) {\r
- updateOptions( getOptions() );\r
- }\r
- else if ( o == _collapse_below_threshold ) {\r
- if ( isSubtreeDisplayed() ) {\r
- return;\r
- }\r
- collapseBelowThreshold();\r
- }\r
- else if ( o == _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
- void buildAnalysisMenu() {\r
- _analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );\r
- _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );\r
- _analysis_menu.add( _gsdir_item = new JMenuItem( "GSDIR (GSDI with re-rooting)" ) );\r
- _analysis_menu.add( _load_species_tree_item = new JMenuItem( "Load Species Tree..." ) );\r
- customizeJMenuItem( _gsdi_item );\r
- customizeJMenuItem( _gsdir_item );\r
- customizeJMenuItem( _load_species_tree_item );\r
- _analysis_menu.addSeparator();\r
- _analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) );\r
- customizeJMenuItem( _lineage_inference );\r
- _lineage_inference.setToolTipText( "Inference of ancestor taxonomies/lineages" );\r
- _jmenubar.add( _analysis_menu );\r
- }\r
-\r
- @Override\r
- void buildFileMenu() {\r
- _file_jmenu = MainFrame.createMenu( "File", getConfiguration() );\r
- _file_jmenu.add( _open_item = new JMenuItem( "Read Tree from File..." ) );\r
- _file_jmenu.addSeparator();\r
- _file_jmenu.add( _open_url_item = new JMenuItem( "Read Tree from URL/Webservice..." ) );\r
- _file_jmenu.addSeparator();\r
- final WebservicesManager webservices_manager = WebservicesManager.getInstance();\r
- _load_phylogeny_from_webservice_menu_items = new JMenuItem[ webservices_manager\r
- .getAvailablePhylogeniesWebserviceClients().size() ];\r
- for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {\r
- final PhylogeniesWebserviceClient client = webservices_manager.getAvailablePhylogeniesWebserviceClient( i );\r
- _load_phylogeny_from_webservice_menu_items[ i ] = new JMenuItem( client.getMenuName() );\r
- _file_jmenu.add( _load_phylogeny_from_webservice_menu_items[ i ] );\r
- }\r
- if ( getConfiguration().isEditable() ) {\r
- _file_jmenu.addSeparator();\r
- _file_jmenu.add( _new_item = new JMenuItem( "New" ) );\r
- _new_item.setToolTipText( "to create a new tree with one node, as source for manual tree construction" );\r
- }\r
- _file_jmenu.addSeparator();\r
- _file_jmenu.add( _save_item = new JMenuItem( "Save Tree As..." ) );\r
- _file_jmenu.add( _save_all_item = new JMenuItem( "Save All Trees As..." ) );\r
- _save_all_item.setToolTipText( "Write all phylogenies to one file." );\r
- _save_all_item.setEnabled( false );\r
- _file_jmenu.addSeparator();\r
- _file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) );\r
- if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" ) || AptxUtil.canWriteFormat( "TIF" ) ) {\r
- _file_jmenu.add( _write_to_tif_item = new JMenuItem( "Export to TIFF file..." ) );\r
- }\r
- _file_jmenu.add( _write_to_png_item = new JMenuItem( "Export to PNG file..." ) );\r
- _file_jmenu.add( _write_to_jpg_item = new JMenuItem( "Export to JPG file..." ) );\r
- if ( AptxUtil.canWriteFormat( "gif" ) ) {\r
- _file_jmenu.add( _write_to_gif_item = new JMenuItem( "Export to GIF file..." ) );\r
- }\r
- if ( AptxUtil.canWriteFormat( "bmp" ) ) {\r
- _file_jmenu.add( _write_to_bmp_item = new JMenuItem( "Export to BMP file..." ) );\r
- }\r
- _file_jmenu.addSeparator();\r
- _file_jmenu.add( _print_item = new JMenuItem( "Print..." ) );\r
- _file_jmenu.addSeparator();\r
- _file_jmenu.add( _close_item = new JMenuItem( "Close Tab" ) );\r
- _close_item.setToolTipText( "To close the current pane." );\r
- _close_item.setEnabled( true );\r
- _file_jmenu.addSeparator();\r
- _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );\r
- customizeJMenuItem( _open_item );\r
- _open_item\r
- .setFont( new Font( _open_item.getFont().getFontName(), Font.BOLD, _open_item.getFont().getSize() + 4 ) );\r
- customizeJMenuItem( _open_url_item );\r
- for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {\r
- customizeJMenuItem( _load_phylogeny_from_webservice_menu_items[ i ] );\r
- }\r
- customizeJMenuItem( _save_item );\r
- if ( getConfiguration().isEditable() ) {\r
- customizeJMenuItem( _new_item );\r
- }\r
- customizeJMenuItem( _close_item );\r
- customizeJMenuItem( _save_all_item );\r
- customizeJMenuItem( _write_to_pdf_item );\r
- customizeJMenuItem( _write_to_png_item );\r
- customizeJMenuItem( _write_to_jpg_item );\r
- customizeJMenuItem( _write_to_gif_item );\r
- customizeJMenuItem( _write_to_tif_item );\r
- customizeJMenuItem( _write_to_bmp_item );\r
- customizeJMenuItem( _print_item );\r
- customizeJMenuItem( _exit_item );\r
- _jmenubar.add( _file_jmenu );\r
- }\r
-\r
- void buildOptionsMenu() {\r
- _options_jmenu = MainFrame.createMenu( OPTIONS_HEADER, getConfiguration() );\r
- _options_jmenu.addChangeListener( new ChangeListener() {\r
-\r
- @Override\r
- public void stateChanged( final ChangeEvent e ) {\r
- MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );\r
- MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );\r
- MainFrame\r
- .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );\r
- MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame\r
- .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );\r
- setTextForGraphicsSizeChooserMenuItem( _print_size_mi, getOptions() );\r
- setTextForPdfLineWidthChooserMenuItem( _choose_pdf_width_mi, getOptions() );\r
- MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );\r
- MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, 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( 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
- _options_jmenu.add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( INVERSE_SEARCH_RESULT_LABEL ) );\r
- _options_jmenu.addSeparator();\r
- _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Graphics Export & Printing:" ),\r
- getConfiguration() ) );\r
- _options_jmenu.add( _antialias_print_cbmi = new JCheckBoxMenuItem( "Antialias" ) );\r
- _options_jmenu.add( _print_black_and_white_cbmi = new JCheckBoxMenuItem( "Export in Black and White" ) );\r
- _options_jmenu\r
- .add( _print_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PDF export and Printing" ) );\r
- _options_jmenu\r
- .add( _graphics_export_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PNG, JPG, and GIF export" ) );\r
- _options_jmenu\r
- .add( _graphics_export_visible_only_cbmi = new JCheckBoxMenuItem( "Limit to Visible ('Screenshot') for PNG, JPG, and GIF export" ) );\r
- _options_jmenu.add( _print_size_mi = new JMenuItem( "" ) );\r
- _options_jmenu.add( _choose_pdf_width_mi = new JMenuItem( "" ) );\r
- _options_jmenu.addSeparator();\r
- _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/NHX/Nexus Input:" ), getConfiguration() ) );\r
- _options_jmenu\r
- .add( _internal_number_are_confidence_for_nh_parsing_cbmi = new JCheckBoxMenuItem( "Internal Node Names are Confidence Values" ) );\r
- _options_jmenu.add( _replace_underscores_cbmi = new JCheckBoxMenuItem( "Replace Underscores with Spaces" ) );\r
- _options_jmenu\r
- .add( _allow_errors_in_distance_to_parent_cbmi = new JCheckBoxMenuItem( "Ignore Distance Values Format Errors" ) );\r
- _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 Output:" ), getConfiguration() ) );\r
- _options_jmenu\r
- .add( _use_brackets_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_BRACKETS_FOR_CONF_IN_NH_LABEL ) );\r
- _use_brackets_for_conf_in_nh_export_cbmi\r
- .setToolTipText( "e.g. \"0.1[90]\" for a branch with support 90 and a length of 0.1" );\r
- _options_jmenu\r
- .add( _use_internal_names_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL ) );\r
- customizeJMenuItem( _choose_font_mi );\r
- customizeJMenuItem( _choose_minimal_confidence_mi );\r
- customizeJMenuItem( _switch_colors_mi );\r
- customizeJMenuItem( _print_size_mi );\r
- customizeJMenuItem( _choose_pdf_width_mi );\r
- customizeJMenuItem( _overview_placment_mi );\r
- customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions()\r
- .isShowDefaultNodeShapesExternal() );\r
- customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()\r
- .isShowDefaultNodeShapesInternal() );\r
- 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
- 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( _graphics_export_visible_only_cbmi, getOptions().isGraphicsExportVisibleOnly() );\r
- customizeCheckBoxMenuItem( _print_using_actual_size_cbmi, getOptions().isPrintUsingActualSize() );\r
- customizeCheckBoxMenuItem( _graphics_export_using_actual_size_cbmi, getOptions()\r
- .isGraphicsExportUsingActualSize() );\r
- customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );\r
- customizeCheckBoxMenuItem( _use_brackets_for_conf_in_nh_export_cbmi, getOptions()\r
- .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );\r
- customizeCheckBoxMenuItem( _use_internal_names_for_conf_in_nh_export_cbmi, getOptions()\r
- .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );\r
- 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 executeLineageInference() {\r
- if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) {\r
- return;\r
- }\r
- if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Phylogeny is not rooted.",\r
- "Cannot infer ancestral taxonomies",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- final AncestralTaxonomyInferrer inferrer = new AncestralTaxonomyInferrer( this,\r
- _mainpanel.getCurrentTreePanel(),\r
- _mainpanel.getCurrentPhylogeny()\r
- .copy() );\r
- new Thread( inferrer ).start();\r
- }\r
-\r
- void exit() {\r
- removeAllTextFrames();\r
- _mainpanel.terminate();\r
- _contentpane.removeAll();\r
- setVisible( false );\r
- dispose();\r
- System.exit( 0 );\r
- }\r
-\r
- void readPhylogeniesFromURL() {\r
- URL url = null;\r
- Phylogeny[] phys = null;\r
- final String message = "Please enter a complete URL, for example \"http://purl.org/phylo/treebase/phylows/study/TB2:S15480?format=nexus\"";\r
- final String url_string = JOptionPane.showInputDialog( this,\r
- message,\r
- "Use URL/webservice to obtain a phylogeny",\r
- JOptionPane.QUESTION_MESSAGE );\r
- boolean nhx_or_nexus = false;\r
- if ( ( url_string != null ) && ( url_string.length() > 0 ) ) {\r
- try {\r
- url = new URL( url_string );\r
- PhylogenyParser parser = null;\r
- if ( url.getHost().toLowerCase().indexOf( "tolweb" ) >= 0 ) {\r
- parser = new TolParser();\r
- }\r
- else {\r
- parser = ParserUtils.createParserDependingOnUrlContents( url, getConfiguration()\r
- .isValidatePhyloXmlAgainstSchema() );\r
- }\r
- if ( parser instanceof NexusPhylogeniesParser ) {\r
- nhx_or_nexus = true;\r
- }\r
- else if ( parser instanceof NHXParser ) {\r
- nhx_or_nexus = true;\r
- }\r
- if ( _mainpanel.getCurrentTreePanel() != null ) {\r
- _mainpanel.getCurrentTreePanel().setWaitCursor();\r
- }\r
- else {\r
- _mainpanel.setWaitCursor();\r
- }\r
- final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();\r
- phys = factory.create( url.openStream(), parser );\r
- }\r
- catch ( final MalformedURLException e ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Malformed URL: " + url + "\n" + e.getLocalizedMessage(),\r
- "Malformed URL",\r
- JOptionPane.ERROR_MESSAGE );\r
- }\r
- catch ( final IOException e ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Could not read from " + url + "\n"\r
- + ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),\r
- "Failed to read URL",\r
- JOptionPane.ERROR_MESSAGE );\r
- }\r
- catch ( final Exception e ) {\r
- JOptionPane.showMessageDialog( this,\r
- ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),\r
- "Unexpected Exception",\r
- JOptionPane.ERROR_MESSAGE );\r
- }\r
- finally {\r
- if ( _mainpanel.getCurrentTreePanel() != null ) {\r
- _mainpanel.getCurrentTreePanel().setArrowCursor();\r
- }\r
- else {\r
- _mainpanel.setArrowCursor();\r
- }\r
- }\r
- if ( ( phys != null ) && ( phys.length > 0 ) ) {\r
- if ( nhx_or_nexus && getOptions().isInternalNumberAreConfidenceForNhParsing() ) {\r
- for( final Phylogeny phy : phys ) {\r
- 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
- void writePhylogenyToGraphicsFile( final String file_name, final GraphicsExportType type ) {\r
- _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel().getWidth(),\r
- _mainpanel.getCurrentTreePanel().getHeight(),\r
- true );\r
- String file_written_to = "";\r
- boolean error = false;\r
- try {\r
- file_written_to = AptxUtil.writePhylogenyToGraphicsFile( file_name,\r
- _mainpanel.getCurrentTreePanel().getWidth(),\r
- _mainpanel.getCurrentTreePanel().getHeight(),\r
- _mainpanel.getCurrentTreePanel(),\r
- _mainpanel.getControlPanel(),\r
- type,\r
- getOptions() );\r
- }\r
- catch ( final IOException e ) {\r
- error = true;\r
- JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );\r
- }\r
- if ( !error ) {\r
- if ( ( file_written_to != null ) && ( file_written_to.length() > 0 ) ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Wrote image to: " + file_written_to,\r
- "Graphics Export",\r
- JOptionPane.INFORMATION_MESSAGE );\r
- }\r
- else {\r
- JOptionPane.showMessageDialog( this,\r
- "There was an unknown problem when attempting to write to an image file: \""\r
- + file_name + "\"",\r
- "Error",\r
- JOptionPane.ERROR_MESSAGE );\r
- }\r
- }\r
- _contentpane.repaint();\r
- }\r
-\r
- private void addExpressionValuesFromFile() {\r
- if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Need to load evolutionary tree first",\r
- "Can Not Read Expression Values",\r
- JOptionPane.WARNING_MESSAGE );\r
- return;\r
- }\r
- final File my_dir = getCurrentDir();\r
- if ( my_dir != null ) {\r
- _values_filechooser.setCurrentDirectory( my_dir );\r
- }\r
- final int result = _values_filechooser.showOpenDialog( _contentpane );\r
- final File file = _values_filechooser.getSelectedFile();\r
- if ( ( file != null ) && ( file.length() > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
- BasicTable<String> t = null;\r
- try {\r
- t = BasicTableParser.parse( file, '\t' );\r
- if ( t.getNumberOfColumns() < 2 ) {\r
- t = BasicTableParser.parse( file, ',' );\r
- }\r
- if ( t.getNumberOfColumns() < 2 ) {\r
- t = BasicTableParser.parse( file, ' ' );\r
- }\r
- }\r
- catch ( final IOException e ) {\r
- JOptionPane.showMessageDialog( this,\r
- e.getMessage(),\r
- "Could Not Read Expression Value Table",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- if ( t.getNumberOfColumns() < 2 ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Table contains " + t.getNumberOfColumns() + " column(s)",\r
- "Problem with Expression Value Table",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- if ( t.getNumberOfRows() < 1 ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Table contains zero rows",\r
- "Problem with Expression Value Table",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- final Phylogeny phy = getCurrentTreePanel().getPhylogeny();\r
- if ( t.getNumberOfRows() != phy.getNumberOfExternalNodes() ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Table contains " + t.getNumberOfRows() + " rows, but tree contains "\r
- + phy.getNumberOfExternalNodes() + " external nodes",\r
- "Warning",\r
- JOptionPane.WARNING_MESSAGE );\r
- }\r
- final DescriptiveStatistics stats = new BasicDescriptiveStatistics();\r
- int not_found = 0;\r
- for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {\r
- final PhylogenyNode node = iter.next();\r
- final String node_name = node.getName();\r
- if ( !ForesterUtil.isEmpty( node_name ) ) {\r
- int row = -1;\r
- try {\r
- row = t.findRow( node_name );\r
- }\r
- catch ( final IllegalArgumentException e ) {\r
- JOptionPane\r
- .showMessageDialog( this,\r
- e.getMessage(),\r
- "Error Mapping Node Identifiers to Expression Value Identifiers",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- if ( row < 0 ) {\r
- if ( node.isExternal() ) {\r
- not_found++;\r
- }\r
- continue;\r
- }\r
- final List<Double> l = new ArrayList<Double>();\r
- for( int col = 1; col < t.getNumberOfColumns(); ++col ) {\r
- double d = -100;\r
- try {\r
- d = Double.parseDouble( t.getValueAsString( col, row ) );\r
- }\r
- catch ( final NumberFormatException e ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Could not parse \"" + t.getValueAsString( col, row )\r
- + "\" into a decimal value",\r
- "Issue with Expression Value Table",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- stats.addValue( d );\r
- l.add( d );\r
- }\r
- if ( !l.isEmpty() ) {\r
- if ( node.getNodeData().getProperties() != null ) {\r
- node.getNodeData().getProperties()\r
- .removePropertiesWithGivenReferencePrefix( PhyloXmlUtil.VECTOR_PROPERTY_REF );\r
- }\r
- node.getNodeData().setVector( l );\r
- }\r
- }\r
- }\r
- if ( not_found > 0 ) {\r
- JOptionPane.showMessageDialog( this, "Could not fine expression values for " + not_found\r
- + " external node(s)", "Warning", JOptionPane.WARNING_MESSAGE );\r
- }\r
- getCurrentTreePanel().setStatisticsForExpressionValues( stats );\r
- }\r
- }\r
-\r
- private void addSequencesFromFile() {\r
- if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Need to load evolutionary tree first",\r
- "Can Not Read Sequences",\r
- JOptionPane.WARNING_MESSAGE );\r
- return;\r
- }\r
- final File my_dir = getCurrentDir();\r
- if ( my_dir != null ) {\r
- _sequences_filechooser.setCurrentDirectory( my_dir );\r
- }\r
- final int result = _sequences_filechooser.showOpenDialog( _contentpane );\r
- final File file = _sequences_filechooser.getSelectedFile();\r
- List<MolecularSequence> seqs = null;\r
- if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
- try {\r
- if ( FastaParser.isLikelyFasta( new FileInputStream( file ) ) ) {\r
- seqs = FastaParser.parse( new FileInputStream( file ) );\r
- }\r
- else {\r
- JOptionPane.showMessageDialog( this,\r
- "Format does not appear to be Fasta",\r
- "Multiple sequence file format error",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- }\r
- catch ( final MsaFormatException e ) {\r
- setArrowCursor();\r
- JOptionPane.showMessageDialog( this,\r
- e.getLocalizedMessage(),\r
- "Multiple sequence file format error",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- catch ( final IOException e ) {\r
- setArrowCursor();\r
- JOptionPane.showMessageDialog( this,\r
- e.getLocalizedMessage(),\r
- "Failed to read multiple sequence file",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- catch ( final Exception e ) {\r
- setArrowCursor();\r
- e.printStackTrace();\r
- JOptionPane.showMessageDialog( this,\r
- e.getLocalizedMessage(),\r
- "Unexpected error during reading of multiple sequence file",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- if ( ( seqs == null ) || ( seqs.size() < 1 ) ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Multiple sequence file is empty",\r
- "Empty multiple sequence file",\r
- JOptionPane.ERROR_MESSAGE );\r
- setArrowCursor();\r
- return;\r
- }\r
- }\r
- if ( seqs != null ) {\r
- for( final 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 choosePdfWidth() {\r
- final String s = ( String ) JOptionPane.showInputDialog( this,\r
- "Please enter the default line width for PDF export.\n"\r
- + "[current value: "\r
- + getOptions().getPrintLineWidth() + "]\n",\r
- "Line Width for PDF Export",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null,\r
- null,\r
- getOptions().getPrintLineWidth() );\r
- if ( !ForesterUtil.isEmpty( s ) ) {\r
- boolean success = true;\r
- float f = 0.0f;\r
- final String m_str = s.trim();\r
- if ( !ForesterUtil.isEmpty( m_str ) ) {\r
- try {\r
- f = Float.parseFloat( m_str );\r
- }\r
- catch ( final Exception ex ) {\r
- success = false;\r
- }\r
- }\r
- else {\r
- success = false;\r
- }\r
- if ( success && ( f > 0.0 ) ) {\r
- getOptions().setPrintLineWidth( f );\r
- }\r
- }\r
- }\r
-\r
- private void choosePrintSize() {\r
- final String s = ( String ) JOptionPane.showInputDialog( this,\r
- "Please enter values for width and height,\nseparated by a comma.\n"\r
- + "[current values: "\r
- + getOptions().getPrintSizeX() + ", "\r
- + getOptions().getPrintSizeY() + "]\n"\r
- + "[A4: " + Constants.A4_SIZE_X + ", "\r
- + Constants.A4_SIZE_Y + "]\n" + "[US Letter: "\r
- + Constants.US_LETTER_SIZE_X + ", "\r
- + Constants.US_LETTER_SIZE_Y + "]",\r
- "Default Size for Graphics Export",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null,\r
- null,\r
- getOptions().getPrintSizeX() + ", "\r
- + getOptions().getPrintSizeY() );\r
- if ( !ForesterUtil.isEmpty( s ) && ( s.indexOf( ',' ) > 0 ) ) {\r
- boolean success = true;\r
- int x = 0;\r
- int y = 0;\r
- final String[] str_ary = s.split( "," );\r
- if ( str_ary.length == 2 ) {\r
- final String x_str = str_ary[ 0 ].trim();\r
- final String y_str = str_ary[ 1 ].trim();\r
- if ( !ForesterUtil.isEmpty( x_str ) && !ForesterUtil.isEmpty( y_str ) ) {\r
- try {\r
- x = Integer.parseInt( x_str );\r
- y = Integer.parseInt( y_str );\r
- }\r
- catch ( final Exception ex ) {\r
- success = false;\r
- }\r
- }\r
- else {\r
- success = false;\r
- }\r
- }\r
- else {\r
- success = false;\r
- }\r
- if ( success && ( x > 1 ) && ( y > 1 ) ) {\r
- getOptions().setPrintSizeX( x );\r
- getOptions().setPrintSizeY( y );\r
- }\r
- }\r
- }\r
-\r
- private void closeCurrentPane() {\r
- if ( getMainPanel().getCurrentTreePanel() != null ) {\r
- if ( getMainPanel().getCurrentTreePanel().isEdited() ) {\r
- final int r = JOptionPane.showConfirmDialog( this,\r
- "Close tab despite potentially unsaved changes?",\r
- "Close Tab?",\r
- JOptionPane.YES_NO_OPTION );\r
- if ( r != JOptionPane.YES_OPTION ) {\r
- return;\r
- }\r
- }\r
- getMainPanel().closeCurrentPane();\r
- activateSaveAllIfNeeded();\r
- }\r
- }\r
-\r
- private void 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 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 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 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 PhyloXmlParser createPhyloXmlParser() {\r
- PhyloXmlParser xml_parser = null;\r
- if ( getConfiguration().isValidatePhyloXmlAgainstSchema() ) {\r
- try {\r
- xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();\r
- }\r
- catch ( final Exception e ) {\r
- JOptionPane.showMessageDialog( this,\r
- e.getLocalizedMessage(),\r
- "failed to create validating XML parser",\r
- JOptionPane.WARNING_MESSAGE );\r
- }\r
- }\r
- if ( xml_parser == null ) {\r
- xml_parser = PhyloXmlParser.createPhyloXmlParser();\r
- }\r
- return xml_parser;\r
- }\r
-\r
- private void executePhyleneticInference( final boolean from_unaligned_seqs ) {\r
- final PhyloInferenceDialog dialog = new PhyloInferenceDialog( this,\r
- getPhylogeneticInferenceOptions(),\r
- from_unaligned_seqs );\r
- dialog.activate();\r
- if ( dialog.getValue() == JOptionPane.OK_OPTION ) {\r
- if ( !from_unaligned_seqs ) {\r
- if ( getMsa() != null ) {\r
- final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getMsa(),\r
- getPhylogeneticInferenceOptions()\r
- .copy(), this );\r
- new Thread( inferrer ).start();\r
- }\r
- else {\r
- JOptionPane.showMessageDialog( this,\r
- "No multiple sequence alignment selected",\r
- "Phylogenetic Inference Not Launched",\r
- JOptionPane.WARNING_MESSAGE );\r
- }\r
- }\r
- else {\r
- if ( getSeqs() != null ) {\r
- final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getSeqs(),\r
- getPhylogeneticInferenceOptions()\r
- .copy(), this );\r
- new Thread( inferrer ).start();\r
- }\r
- else {\r
- JOptionPane.showMessageDialog( this,\r
- "No input sequences selected",\r
- "Phylogenetic Inference Not Launched",\r
- JOptionPane.WARNING_MESSAGE );\r
- }\r
- }\r
- }\r
- }\r
-\r
- private void extractTaxDataFromNodeNames() throws PhyloXmlDataFormatException {\r
- final StringBuilder sb = new StringBuilder();\r
- final StringBuilder sb_failed = new StringBuilder();\r
- int counter = 0;\r
- int counter_failed = 0;\r
- if ( getCurrentTreePanel() != null ) {\r
- final Phylogeny phy = getCurrentTreePanel().getPhylogeny();\r
- if ( ( phy != null ) && !phy.isEmpty() ) {\r
- final PhylogenyNodeIterator it = phy.iteratorExternalForward();\r
- while ( it.hasNext() ) {\r
- final PhylogenyNode n = it.next();\r
- final String name = n.getName().trim();\r
- if ( !ForesterUtil.isEmpty( name ) ) {\r
- final String nt = ParserUtils.extractTaxonomyDataFromNodeName( n,\r
- TAXONOMY_EXTRACTION.AGGRESSIVE );\r
- if ( !ForesterUtil.isEmpty( nt ) ) {\r
- if ( counter < 15 ) {\r
- sb.append( name + ": " + nt + "\n" );\r
- }\r
- else if ( counter == 15 ) {\r
- sb.append( "...\n" );\r
- }\r
- counter++;\r
- }\r
- else {\r
- if ( counter_failed < 15 ) {\r
- sb_failed.append( name + "\n" );\r
- }\r
- else if ( counter_failed == 15 ) {\r
- sb_failed.append( "...\n" );\r
- }\r
- counter_failed++;\r
- }\r
- }\r
- }\r
- if ( counter > 0 ) {\r
- String failed = "";\r
- String all = "all ";\r
- if ( counter_failed > 0 ) {\r
- all = "";\r
- failed = "\nCould not extract taxonomic data for " + counter_failed\r
- + " named external nodes:\n" + sb_failed;\r
- }\r
- JOptionPane.showMessageDialog( this,\r
- "Extracted taxonomic data from " + all + counter\r
- + " named external nodes:\n" + sb.toString() + failed,\r
- "Taxonomic Data Extraction Completed",\r
- counter_failed > 0 ? JOptionPane.WARNING_MESSAGE\r
- : JOptionPane.INFORMATION_MESSAGE );\r
- }\r
- else {\r
- JOptionPane\r
- .showMessageDialog( this,\r
- "Could not extract any taxonomic data.\nMaybe node names are empty\n"\r
- + "or not in the forms \"XYZ_CAEEL\", \"XYZ_6239\", or \"XYZ_Caenorhabditis_elegans\"\n"\r
- + "or nodes already have taxonomic data?\n",\r
- "No Taxonomic Data Extracted",\r
- JOptionPane.ERROR_MESSAGE );\r
- }\r
- }\r
- }\r
- }\r
-\r
- private ControlPanel getControlPanel() {\r
- return getMainPanel().getControlPanel();\r
- }\r
-\r
- private File getCurrentDir() {\r
- if ( ( _current_dir == null ) || !_current_dir.canRead() ) {\r
- if ( ForesterUtil.isWindows() ) {\r
- try {\r
- _current_dir = new File( WindowsUtils.getCurrentUserDesktopPath() );\r
- }\r
- catch ( final Exception e ) {\r
- _current_dir = null;\r
- }\r
- }\r
- }\r
- if ( ( _current_dir == null ) || !_current_dir.canRead() ) {\r
- if ( System.getProperty( "user.home" ) != null ) {\r
- _current_dir = new File( System.getProperty( "user.home" ) );\r
- }\r
- else if ( System.getProperty( "user.dir" ) != null ) {\r
- _current_dir = new File( System.getProperty( "user.dir" ) );\r
- }\r
- }\r
- return _current_dir;\r
- }\r
-\r
- private double getMinNotCollapseConfidenceValue() {\r
- return _min_not_collapse;\r
- }\r
-\r
- private double getMinNotCollapseBlValue() {\r
- return _min_not_collapse_bl;\r
- }\r
-\r
- private PhylogeneticInferenceOptions getPhylogeneticInferenceOptions() {\r
- if ( _phylogenetic_inference_options == null ) {\r
- _phylogenetic_inference_options = new PhylogeneticInferenceOptions();\r
- }\r
- return _phylogenetic_inference_options;\r
- }\r
-\r
- private boolean isUnsavedDataPresent() {\r
- final List<TreePanel> tps = getMainPanel().getTreePanels();\r
- for( final TreePanel tp : tps ) {\r
- if ( tp.isEdited() ) {\r
- return true;\r
- }\r
- }\r
- return false;\r
- }\r
-\r
- private void moveNodeNamesToSeqNames() throws PhyloXmlDataFormatException {\r
- if ( getCurrentTreePanel() != null ) {\r
- final Phylogeny phy = getCurrentTreePanel().getPhylogeny();\r
- if ( ( phy != null ) && !phy.isEmpty() ) {\r
- PhylogenyMethods\r
- .transferNodeNameToField( phy, PhylogenyMethods.PhylogenyNodeField.SEQUENCE_NAME, false );\r
- }\r
- }\r
- }\r
-\r
- private void moveNodeNamesToTaxSn() throws PhyloXmlDataFormatException {\r
- if ( getCurrentTreePanel() != null ) {\r
- final Phylogeny phy = getCurrentTreePanel().getPhylogeny();\r
- if ( ( phy != null ) && !phy.isEmpty() ) {\r
- PhylogenyMethods.transferNodeNameToField( phy,\r
- PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME,\r
- false );\r
- }\r
- }\r
- }\r
-\r
- private void newTree() {\r
- final Phylogeny[] phys = new Phylogeny[ 1 ];\r
- final Phylogeny phy = new Phylogeny();\r
- final PhylogenyNode node = new PhylogenyNode();\r
- phy.setRoot( node );\r
- phy.setRooted( true );\r
- phys[ 0 ] = phy;\r
- AptxUtil.addPhylogeniesToTabs( phys, "", "", getConfiguration(), getMainPanel() );\r
- _mainpanel.getControlPanel().showWhole();\r
- _mainpanel.getCurrentTreePanel().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );\r
- _mainpanel.getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );\r
- if ( getMainPanel().getMainFrame() == null ) {\r
- // Must be "E" applet version.\r
- ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() )\r
- .setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );\r
- }\r
- else {\r
- getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );\r
- }\r
- activateSaveAllIfNeeded();\r
- System.gc();\r
- }\r
-\r
- private void obtainDetailedTaxonomicInformation() {\r
- if ( getCurrentTreePanel() != null ) {\r
- final Phylogeny phy = getCurrentTreePanel().getPhylogeny();\r
- if ( ( phy != null ) && !phy.isEmpty() ) {\r
- final TaxonomyDataManager t = new TaxonomyDataManager( this,\r
- _mainpanel.getCurrentTreePanel(),\r
- phy.copy(),\r
- false,\r
- true );\r
- new Thread( t ).start();\r
- }\r
- }\r
- }\r
-\r
- private void obtainDetailedTaxonomicInformationDelete() {\r
- if ( getCurrentTreePanel() != null ) {\r
- final Phylogeny phy = getCurrentTreePanel().getPhylogeny();\r
- if ( ( phy != null ) && !phy.isEmpty() ) {\r
- final TaxonomyDataManager t = new TaxonomyDataManager( this,\r
- _mainpanel.getCurrentTreePanel(),\r
- phy.copy(),\r
- true,\r
- true );\r
- new Thread( t ).start();\r
- }\r
- }\r
- }\r
-\r
- private void obtainSequenceInformation() {\r
- if ( getCurrentTreePanel() != null ) {\r
- final Phylogeny phy = getCurrentTreePanel().getPhylogeny();\r
- if ( ( phy != null ) && !phy.isEmpty() ) {\r
- final SequenceDataRetriver u = new SequenceDataRetriver( this,\r
- _mainpanel.getCurrentTreePanel(),\r
- phy.copy() );\r
- new Thread( u ).start();\r
- }\r
- }\r
- }\r
-\r
- private void print() {\r
- if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null )\r
- || getCurrentTreePanel().getPhylogeny().isEmpty() ) {\r
- return;\r
- }\r
- if ( !getOptions().isPrintUsingActualSize() ) {\r
- getCurrentTreePanel().calcParametersForPainting( getOptions().getPrintSizeX() - 80,\r
- getOptions().getPrintSizeY() - 140,\r
- true );\r
- getCurrentTreePanel().resetPreferredSize();\r
- getCurrentTreePanel().repaint();\r
- }\r
- final String job_name = Constants.PRG_NAME;\r
- boolean error = false;\r
- String printer_name = null;\r
- try {\r
- printer_name = Printer.print( getCurrentTreePanel(), job_name );\r
- }\r
- catch ( final Exception e ) {\r
- error = true;\r
- JOptionPane.showMessageDialog( this, e.getMessage(), "Printing Error", JOptionPane.ERROR_MESSAGE );\r
- }\r
- if ( !error && ( printer_name != null ) ) {\r
- String msg = "Printing data sent to printer";\r
- if ( printer_name.length() > 1 ) {\r
- msg += " [" + printer_name + "]";\r
- }\r
- JOptionPane.showMessageDialog( this, msg, "Printing...", JOptionPane.INFORMATION_MESSAGE );\r
- }\r
- if ( !getOptions().isPrintUsingActualSize() ) {\r
- getControlPanel().showWhole();\r
- }\r
- }\r
-\r
- private void printPhylogenyToPdf( final String file_name ) {\r
- if ( !getOptions().isPrintUsingActualSize() ) {\r
- getCurrentTreePanel().calcParametersForPainting( getOptions().getPrintSizeX(),\r
- getOptions().getPrintSizeY(),\r
- true );\r
- getCurrentTreePanel().resetPreferredSize();\r
- getCurrentTreePanel().repaint();\r
- }\r
- String pdf_written_to = "";\r
- boolean error = false;\r
- try {\r
- if ( getOptions().isPrintUsingActualSize() ) {\r
- pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name,\r
- getCurrentTreePanel(),\r
- getCurrentTreePanel().getWidth(),\r
- getCurrentTreePanel().getHeight() );\r
- }\r
- else {\r
- pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name, getCurrentTreePanel(), getOptions()\r
- .getPrintSizeX(), getOptions().getPrintSizeY() );\r
- }\r
- }\r
- catch ( final IOException e ) {\r
- error = true;\r
- JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );\r
- }\r
- if ( !error ) {\r
- if ( !ForesterUtil.isEmpty( pdf_written_to ) ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Wrote PDF to: " + pdf_written_to,\r
- "Information",\r
- JOptionPane.INFORMATION_MESSAGE );\r
- }\r
- else {\r
- JOptionPane.showMessageDialog( this,\r
- "There was an unknown problem when attempting to write to PDF file: \""\r
- + file_name + "\"",\r
- "Error",\r
- JOptionPane.ERROR_MESSAGE );\r
- }\r
- }\r
- if ( !getOptions().isPrintUsingActualSize() ) {\r
- getControlPanel().showWhole();\r
- }\r
- }\r
-\r
- private void readPhylogeniesFromFile() {\r
- boolean exception = false;\r
- Phylogeny[] phys = null;\r
- // Set an initial directory if none set yet\r
- final File my_dir = getCurrentDir();\r
- _open_filechooser.setMultiSelectionEnabled( true );\r
- // Open file-open dialog and set current directory\r
- if ( my_dir != null ) {\r
- _open_filechooser.setCurrentDirectory( my_dir );\r
- }\r
- final int result = _open_filechooser.showOpenDialog( _contentpane );\r
- // All done: get the file\r
- final File[] files = _open_filechooser.getSelectedFiles();\r
- setCurrentDir( _open_filechooser.getCurrentDirectory() );\r
- boolean nhx_or_nexus = false;\r
- if ( ( files != null ) && ( files.length > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
- for( final File file : files ) {\r
- if ( ( file != null ) && !file.isDirectory() ) {\r
- if ( _mainpanel.getCurrentTreePanel() != null ) {\r
- _mainpanel.getCurrentTreePanel().setWaitCursor();\r
- }\r
- else {\r
- _mainpanel.setWaitCursor();\r
- }\r
- if ( ( _open_filechooser.getFileFilter() == MainFrameApplication.nhfilter )\r
- || ( _open_filechooser.getFileFilter() == MainFrameApplication.nhxfilter ) ) {\r
- try {\r
- final NHXParser nhx = new NHXParser();\r
- setSpecialOptionsForNhxParser( nhx );\r
- phys = PhylogenyMethods.readPhylogenies( nhx, file );\r
- nhx_or_nexus = true;\r
- }\r
- catch ( final Exception e ) {\r
- exception = true;\r
- exceptionOccuredDuringOpenFile( e );\r
- }\r
- }\r
- else if ( _open_filechooser.getFileFilter() == MainFrameApplication.xmlfilter ) {\r
- warnIfNotPhyloXmlValidation( getConfiguration() );\r
- try {\r
- final PhyloXmlParser xml_parser = createPhyloXmlParser();\r
- phys = PhylogenyMethods.readPhylogenies( xml_parser, file );\r
- }\r
- catch ( final Exception e ) {\r
- exception = true;\r
- exceptionOccuredDuringOpenFile( e );\r
- }\r
- }\r
- else if ( _open_filechooser.getFileFilter() == MainFrameApplication.tolfilter ) {\r
- try {\r
- phys = PhylogenyMethods.readPhylogenies( new TolParser(), file );\r
- }\r
- catch ( final Exception e ) {\r
- exception = true;\r
- exceptionOccuredDuringOpenFile( e );\r
- }\r
- }\r
- else if ( _open_filechooser.getFileFilter() == MainFrameApplication.nexusfilter ) {\r
- try {\r
- final NexusPhylogeniesParser nex = new NexusPhylogeniesParser();\r
- setSpecialOptionsForNexParser( nex );\r
- phys = PhylogenyMethods.readPhylogenies( nex, file );\r
- nhx_or_nexus = true;\r
- }\r
- catch ( final Exception e ) {\r
- exception = true;\r
- exceptionOccuredDuringOpenFile( e );\r
- }\r
- }\r
- // "*.*":\r
- else {\r
- try {\r
- final PhylogenyParser parser = ParserUtils\r
- .createParserDependingOnFileType( file, getConfiguration()\r
- .isValidatePhyloXmlAgainstSchema() );\r
- if ( parser instanceof NexusPhylogeniesParser ) {\r
- final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) parser;\r
- setSpecialOptionsForNexParser( nex );\r
- nhx_or_nexus = true;\r
- }\r
- else if ( parser instanceof NHXParser ) {\r
- final NHXParser nhx = ( NHXParser ) parser;\r
- setSpecialOptionsForNhxParser( nhx );\r
- nhx_or_nexus = true;\r
- }\r
- else if ( parser instanceof PhyloXmlParser ) {\r
- warnIfNotPhyloXmlValidation( getConfiguration() );\r
- }\r
- phys = PhylogenyMethods.readPhylogenies( parser, file );\r
- }\r
- catch ( final Exception e ) {\r
- exception = true;\r
- exceptionOccuredDuringOpenFile( e );\r
- }\r
- }\r
- if ( _mainpanel.getCurrentTreePanel() != null ) {\r
- _mainpanel.getCurrentTreePanel().setArrowCursor();\r
- }\r
- else {\r
- _mainpanel.setArrowCursor();\r
- }\r
- if ( !exception && ( phys != null ) && ( phys.length > 0 ) ) {\r
- boolean one_desc = false;\r
- if ( nhx_or_nexus ) {\r
- for( final Phylogeny phy : phys ) {\r
- if ( getOptions().isInternalNumberAreConfidenceForNhParsing() ) {\r
- PhylogenyMethods.transferInternalNodeNamesToConfidence( phy, "" );\r
- }\r
- if ( PhylogenyMethods.getMinimumDescendentsPerInternalNodes( phy ) == 1 ) {\r
- one_desc = true;\r
- break;\r
- }\r
- }\r
- }\r
- 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 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 readSpeciesTreeFromFile() {\r
- Phylogeny t = null;\r
- boolean exception = false;\r
- final File my_dir = getCurrentDir();\r
- _open_filechooser_for_species_tree.setSelectedFile( new File( "" ) );\r
- if ( my_dir != null ) {\r
- _open_filechooser_for_species_tree.setCurrentDirectory( my_dir );\r
- }\r
- final int result = _open_filechooser_for_species_tree.showOpenDialog( _contentpane );\r
- final File file = _open_filechooser_for_species_tree.getSelectedFile();\r
- if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
- if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrameApplication.xmlfilter ) {\r
- try {\r
- final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( PhyloXmlParser\r
- .createPhyloXmlParserXsdValidating(), file );\r
- t = trees[ 0 ];\r
- }\r
- catch ( final Exception e ) {\r
- exception = true;\r
- exceptionOccuredDuringOpenFile( e );\r
- }\r
- }\r
- else if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrameApplication.tolfilter ) {\r
- try {\r
- final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new TolParser(), file );\r
- t = trees[ 0 ];\r
- }\r
- catch ( final Exception e ) {\r
- exception = true;\r
- exceptionOccuredDuringOpenFile( e );\r
- }\r
- }\r
- // "*.*":\r
- else {\r
- try {\r
- final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( PhyloXmlParser\r
- .createPhyloXmlParserXsdValidating(), file );\r
- t = trees[ 0 ];\r
- }\r
- catch ( final Exception e ) {\r
- exception = true;\r
- exceptionOccuredDuringOpenFile( e );\r
- }\r
- }\r
- if ( !exception && ( t != null ) && !t.isRooted() ) {\r
- exception = true;\r
- t = null;\r
- JOptionPane.showMessageDialog( this,\r
- "Species tree is not rooted",\r
- "Species tree not loaded",\r
- JOptionPane.ERROR_MESSAGE );\r
- }\r
- if ( !exception && ( t != null ) ) {\r
- final Set<Taxonomy> tax_set = new HashSet<Taxonomy>();\r
- for( final PhylogenyNodeIterator it = t.iteratorExternalForward(); it.hasNext(); ) {\r
- final PhylogenyNode node = it.next();\r
- if ( !node.getNodeData().isHasTaxonomy() ) {\r
- exception = true;\r
- t = null;\r
- JOptionPane\r
- .showMessageDialog( this,\r
- "Species tree contains external node(s) without taxonomy information",\r
- "Species tree not loaded",\r
- JOptionPane.ERROR_MESSAGE );\r
- break;\r
- }\r
- else {\r
- if ( tax_set.contains( node.getNodeData().getTaxonomy() ) ) {\r
- exception = true;\r
- t = null;\r
- JOptionPane.showMessageDialog( this,\r
- "Taxonomy ["\r
- + node.getNodeData().getTaxonomy().asSimpleText()\r
- + "] is not unique in species tree",\r
- "Species tree not loaded",\r
- JOptionPane.ERROR_MESSAGE );\r
- break;\r
- }\r
- else {\r
- tax_set.add( node.getNodeData().getTaxonomy() );\r
- }\r
- }\r
- }\r
- }\r
- if ( !exception && ( t != null ) ) {\r
- setSpeciesTree( t );\r
- JOptionPane.showMessageDialog( this,\r
- "Species tree successfully loaded",\r
- "Species tree loaded",\r
- JOptionPane.INFORMATION_MESSAGE );\r
- }\r
- _contentpane.repaint();\r
- System.gc();\r
- }\r
- }\r
-\r
- private void setArrowCursor() {\r
- try {\r
- _mainpanel.getCurrentTreePanel().setArrowCursor();\r
- }\r
- catch ( final Exception ex ) {\r
- // Do nothing.\r
- }\r
- }\r
-\r
- private void setCurrentDir( final File current_dir ) {\r
- _current_dir = current_dir;\r
- }\r
-\r
- private void setMinNotCollapseConfidenceValue( final double min_not_collapse ) {\r
- _min_not_collapse = min_not_collapse;\r
- }\r
-\r
- private void setMinNotCollapseBlValue( final double min_not_collapse_bl ) {\r
- _min_not_collapse_bl = min_not_collapse_bl;\r
- }\r
-\r
- private void setPhylogeneticInferenceOptions( final PhylogeneticInferenceOptions phylogenetic_inference_options ) {\r
- _phylogenetic_inference_options = phylogenetic_inference_options;\r
- }\r
-\r
- private void setSpecialOptionsForNexParser( final NexusPhylogeniesParser nex ) {\r
- nex.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );\r
- nex.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() );\r
- }\r
-\r
- private void setSpecialOptionsForNhxParser( final NHXParser nhx ) {\r
- nhx.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );\r
- nhx.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() );\r
- nhx.setAllowErrorsInDistanceToParent( getOptions().isAllowErrorsInDistanceToParent() );\r
- }\r
-\r
- private void writeAllToFile() {\r
- if ( ( getMainPanel().getTabbedPane() == null ) || ( getMainPanel().getTabbedPane().getTabCount() < 1 ) ) {\r
- return;\r
- }\r
- final File my_dir = getCurrentDir();\r
- if ( my_dir != null ) {\r
- _save_filechooser.setCurrentDirectory( my_dir );\r
- }\r
- _save_filechooser.setSelectedFile( new File( "" ) );\r
- final int result = _save_filechooser.showSaveDialog( _contentpane );\r
- final File file = _save_filechooser.getSelectedFile();\r
- setCurrentDir( _save_filechooser.getCurrentDirectory() );\r
- if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
- if ( file.exists() ) {\r
- final int i = JOptionPane.showConfirmDialog( this,\r
- file + " already exists. Overwrite?",\r
- "Warning",\r
- JOptionPane.OK_CANCEL_OPTION,\r
- JOptionPane.WARNING_MESSAGE );\r
- if ( i != JOptionPane.OK_OPTION ) {\r
- return;\r
- }\r
- else {\r
- try {\r
- file.delete();\r
- }\r
- catch ( final Exception e ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Failed to delete: " + file,\r
- "Error",\r
- JOptionPane.WARNING_MESSAGE );\r
- }\r
- }\r
- }\r
- final int count = getMainPanel().getTabbedPane().getTabCount();\r
- final List<Phylogeny> trees = new ArrayList<Phylogeny>();\r
- for( int i = 0; i < count; ++i ) {\r
- final Phylogeny phy = getMainPanel().getPhylogeny( i );\r
- if ( ForesterUtil.isEmpty( phy.getName() )\r
- && !ForesterUtil.isEmpty( getMainPanel().getTabbedPane().getTitleAt( i ) ) ) {\r
- phy.setName( getMainPanel().getTabbedPane().getTitleAt( i ) );\r
- }\r
- trees.add( phy );\r
- getMainPanel().getTreePanels().get( i ).setEdited( false );\r
- }\r
- final PhylogenyWriter writer = new PhylogenyWriter();\r
- try {\r
- writer.toPhyloXML( file, trees, 0, ForesterUtil.LINE_SEPARATOR );\r
- }\r
- catch ( final IOException e ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Failed to write to: " + file,\r
- "Error",\r
- JOptionPane.WARNING_MESSAGE );\r
- }\r
- }\r
- }\r
-\r
- private boolean writeAsNewHampshire( final Phylogeny t, boolean exception, final File file ) {\r
- try {\r
- final PhylogenyWriter writer = new PhylogenyWriter();\r
- writer.toNewHampshire( t, true, getOptions().getNhConversionSupportValueStyle(), file );\r
- }\r
- catch ( final Exception e ) {\r
- exception = true;\r
- exceptionOccuredDuringSaveAs( e );\r
- }\r
- return exception;\r
- }\r
-\r
- private boolean writeAsNexus( final Phylogeny t, boolean exception, final File file ) {\r
- try {\r
- final PhylogenyWriter writer = new PhylogenyWriter();\r
- writer.toNexus( file, t, getOptions().getNhConversionSupportValueStyle() );\r
- }\r
- catch ( final Exception e ) {\r
- exception = true;\r
- exceptionOccuredDuringSaveAs( e );\r
- }\r
- return exception;\r
- }\r
-\r
- private boolean writeAsPhyloXml( final Phylogeny t, boolean exception, final File file ) {\r
- try {\r
- final PhylogenyWriter writer = new PhylogenyWriter();\r
- writer.toPhyloXML( file, t, 0 );\r
- }\r
- catch ( final Exception e ) {\r
- exception = true;\r
- exceptionOccuredDuringSaveAs( e );\r
- }\r
- return exception;\r
- }\r
-\r
- private void writeToFile( final Phylogeny t ) {\r
- if ( t == null ) {\r
- return;\r
- }\r
- String initial_filename = null;\r
- if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {\r
- try {\r
- initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().getCanonicalPath();\r
- }\r
- catch ( final IOException e ) {\r
- initial_filename = null;\r
- }\r
- }\r
- if ( !ForesterUtil.isEmpty( initial_filename ) ) {\r
- _save_filechooser.setSelectedFile( new File( initial_filename ) );\r
- }\r
- else {\r
- _save_filechooser.setSelectedFile( new File( "" ) );\r
- }\r
- final File my_dir = getCurrentDir();\r
- if ( my_dir != null ) {\r
- _save_filechooser.setCurrentDirectory( my_dir );\r
- }\r
- final int result = _save_filechooser.showSaveDialog( _contentpane );\r
- final File file = _save_filechooser.getSelectedFile();\r
- setCurrentDir( _save_filechooser.getCurrentDirectory() );\r
- boolean exception = false;\r
- if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
- if ( file.exists() ) {\r
- final int i = JOptionPane.showConfirmDialog( this,\r
- file + " already exists.\nOverwrite?",\r
- "Overwrite?",\r
- JOptionPane.OK_CANCEL_OPTION,\r
- JOptionPane.QUESTION_MESSAGE );\r
- if ( i != JOptionPane.OK_OPTION ) {\r
- return;\r
- }\r
- else {\r
- final File to = new File( file.getAbsoluteFile().toString() + Constants.BACKUP_FILE_SUFFIX );\r
- try {\r
- ForesterUtil.copyFile( file, to );\r
- }\r
- catch ( final Exception e ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Failed to create backup copy " + to,\r
- "Failed to Create Backup Copy",\r
- JOptionPane.WARNING_MESSAGE );\r
- }\r
- try {\r
- file.delete();\r
- }\r
- catch ( final Exception e ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Failed to delete: " + file,\r
- "Failed to Delete",\r
- JOptionPane.WARNING_MESSAGE );\r
- }\r
- }\r
- }\r
- if ( _save_filechooser.getFileFilter() == MainFrameApplication.nhfilter ) {\r
- exception = writeAsNewHampshire( t, exception, file );\r
- }\r
- else if ( _save_filechooser.getFileFilter() == MainFrameApplication.xmlfilter ) {\r
- exception = writeAsPhyloXml( t, exception, file );\r
- }\r
- else if ( _save_filechooser.getFileFilter() == MainFrameApplication.nexusfilter ) {\r
- exception = writeAsNexus( t, exception, file );\r
- }\r
- // "*.*":\r
- else {\r
- final String file_name = file.getName().trim().toLowerCase();\r
- if ( file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )\r
- || file_name.endsWith( ".tree" ) ) {\r
- exception = writeAsNewHampshire( t, exception, file );\r
- }\r
- else if ( file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) ) {\r
- exception = writeAsNexus( t, exception, file );\r
- }\r
- // XML is default:\r
- else {\r
- exception = writeAsPhyloXml( t, exception, file );\r
- }\r
- }\r
- if ( !exception ) {\r
- getMainPanel().setTitleOfSelectedTab( file.getName() );\r
- getMainPanel().getCurrentTreePanel().setTreeFile( file );\r
- getMainPanel().getCurrentTreePanel().setEdited( false );\r
- }\r
- }\r
- }\r
-\r
- private void writeToGraphicsFile( final Phylogeny t, final GraphicsExportType type ) {\r
- if ( ( t == null ) || t.isEmpty() ) {\r
- return;\r
- }\r
- String initial_filename = "";\r
- if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {\r
- initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().toString();\r
- }\r
- if ( initial_filename.indexOf( '.' ) > 0 ) {\r
- initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );\r
- }\r
- initial_filename = initial_filename + "." + type;\r
- _writetographics_filechooser.setSelectedFile( new File( initial_filename ) );\r
- final File my_dir = getCurrentDir();\r
- if ( my_dir != null ) {\r
- _writetographics_filechooser.setCurrentDirectory( my_dir );\r
- }\r
- final int result = _writetographics_filechooser.showSaveDialog( _contentpane );\r
- File file = _writetographics_filechooser.getSelectedFile();\r
- setCurrentDir( _writetographics_filechooser.getCurrentDirectory() );\r
- if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
- if ( !file.toString().toLowerCase().endsWith( type.toString() ) ) {\r
- file = new File( file.toString() + "." + type );\r
- }\r
- if ( file.exists() ) {\r
- final int i = JOptionPane.showConfirmDialog( this,\r
- file + " already exists. Overwrite?",\r
- "Warning",\r
- JOptionPane.OK_CANCEL_OPTION,\r
- JOptionPane.WARNING_MESSAGE );\r
- if ( i != JOptionPane.OK_OPTION ) {\r
- return;\r
- }\r
- else {\r
- try {\r
- file.delete();\r
- }\r
- catch ( final Exception e ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Failed to delete: " + file,\r
- "Error",\r
- JOptionPane.WARNING_MESSAGE );\r
- }\r
- }\r
- }\r
- writePhylogenyToGraphicsFile( file.toString(), type );\r
- }\r
- }\r
-\r
- private void writeToPdf( final Phylogeny t ) {\r
- if ( ( t == null ) || t.isEmpty() ) {\r
- return;\r
- }\r
- String initial_filename = "";\r
- if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {\r
- initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().toString();\r
- }\r
- if ( initial_filename.indexOf( '.' ) > 0 ) {\r
- initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );\r
- }\r
- initial_filename = initial_filename + ".pdf";\r
- _writetopdf_filechooser.setSelectedFile( new File( initial_filename ) );\r
- final File my_dir = getCurrentDir();\r
- if ( my_dir != null ) {\r
- _writetopdf_filechooser.setCurrentDirectory( my_dir );\r
- }\r
- final int result = _writetopdf_filechooser.showSaveDialog( _contentpane );\r
- File file = _writetopdf_filechooser.getSelectedFile();\r
- setCurrentDir( _writetopdf_filechooser.getCurrentDirectory() );\r
- if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
- if ( !file.toString().toLowerCase().endsWith( ".pdf" ) ) {\r
- file = new File( file.toString() + ".pdf" );\r
- }\r
- if ( file.exists() ) {\r
- final int i = JOptionPane.showConfirmDialog( this,\r
- file + " already exists. Overwrite?",\r
- "WARNING",\r
- JOptionPane.OK_CANCEL_OPTION,\r
- JOptionPane.WARNING_MESSAGE );\r
- if ( i != JOptionPane.OK_OPTION ) {\r
- return;\r
- }\r
- }\r
- printPhylogenyToPdf( file.toString() );\r
- }\r
- }\r
-\r
- public static MainFrameApplication createInstance( final Phylogeny[] phys, final Configuration config ) {\r
- return new MainFrameApplication( phys, config );\r
- }\r
-\r
- public static MainFrame createInstance( final Phylogeny[] phys,\r
- final Configuration config,\r
- final String title,\r
- final File current_dir ) {\r
- return new MainFrameApplication( phys, config, title, current_dir );\r
- }\r
-\r
- static MainFrame createInstance( final Phylogeny[] phys, final Configuration config, final String title ) {\r
- return new MainFrameApplication( phys, config, title );\r
- }\r
-\r
- static MainFrame createInstance( final Phylogeny[] phys, final String config_file_name, final String title ) {\r
- return new MainFrameApplication( phys, config_file_name, title );\r
- }\r
-\r
- static void setTextForGraphicsSizeChooserMenuItem( final JMenuItem mi, final Options o ) {\r
- mi.setText( "Enter Default Size for Graphics Export... (current: " + o.getPrintSizeX() + ", "\r
- + o.getPrintSizeY() + ")" );\r
- }\r
-\r
- static void setTextForPdfLineWidthChooserMenuItem( final JMenuItem mi, final Options o ) {\r
- mi.setText( "Enter Default Line Width for PDF Export... (current: " + o.getPrintLineWidth() + ")" );\r
- }\r
-\r
- static void warnIfNotPhyloXmlValidation( final Configuration c ) {\r
- if ( !c.isValidatePhyloXmlAgainstSchema() ) {\r
- JOptionPane\r
- .showMessageDialog( null,\r
- ForesterUtil\r
- .wordWrap( "phyloXML XSD-based validation is turned off [enable with line 'validate_against_phyloxml_xsd_schem: true' in configuration file]",\r
- 80 ),\r
- "Warning",\r
- JOptionPane.WARNING_MESSAGE );\r
- }\r
- }\r
-} // MainFrameApplication.\r
-\r
-class DefaultFilter extends FileFilter {\r
-\r
- @Override\r
- public boolean accept( final File f ) {\r
- final String file_name = f.getName().trim().toLowerCase();\r
- return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )\r
- || file_name.endsWith( ".nwk" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".ph" )\r
- || file_name.endsWith( ".tr" ) || file_name.endsWith( ".dnd" ) || file_name.endsWith( ".tree" )\r
- || file_name.endsWith( ".nhx" ) || file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" )\r
- || file_name.endsWith( "phylo.xml" ) || file_name.endsWith( ".pxml" ) || file_name.endsWith( ".nexus" )\r
- || file_name.endsWith( ".nx" ) || file_name.endsWith( ".nex" ) || file_name.endsWith( ".tre" )\r
- || file_name.endsWith( ".zip" ) || file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" )\r
- || file_name.endsWith( ".con" ) || f.isDirectory();\r
- }\r
-\r
- @Override\r
- public String getDescription() {\r
- return "All supported files (*.xml, *.phyloxml, *phylo.xml, *.nhx, *.nh, *.newick, *.nex, *.nexus, *.phy, *.tre, *.tree, *.tol, ...)";\r
- }\r
-}\r
-\r
-class GraphicsFileFilter extends FileFilter {\r
-\r
- @Override\r
- public boolean accept( final File f ) {\r
- final String file_name = f.getName().trim().toLowerCase();\r
- return file_name.endsWith( ".jpg" ) || file_name.endsWith( ".jpeg" ) || file_name.endsWith( ".png" )\r
- || file_name.endsWith( ".gif" ) || file_name.endsWith( ".bmp" ) || f.isDirectory();\r
- }\r
-\r
- @Override\r
- public String getDescription() {\r
- return "Image files (*.jpg, *.jpeg, *.png, *.gif, *.bmp)";\r
- }\r
-}\r
-\r
-class MsaFileFilter extends FileFilter {\r
-\r
- @Override\r
- public boolean accept( final File f ) {\r
- final String file_name = f.getName().trim().toLowerCase();\r
- return file_name.endsWith( ".msa" ) || file_name.endsWith( ".aln" ) || file_name.endsWith( ".fasta" )\r
- || file_name.endsWith( ".fas" ) || file_name.endsWith( ".fa" ) || f.isDirectory();\r
- }\r
-\r
- @Override\r
- public String getDescription() {\r
- return "Multiple sequence alignment files (*.msa, *.aln, *.fasta, *.fa, *.fas)";\r
- }\r
-}\r
-\r
-class NexusFilter extends FileFilter {\r
-\r
- @Override\r
- public boolean accept( final File f ) {\r
- final String file_name = f.getName().trim().toLowerCase();\r
- return file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) || file_name.endsWith( ".nx" )\r
- || file_name.endsWith( ".tre" ) || f.isDirectory();\r
- }\r
-\r
- @Override\r
- public String getDescription() {\r
- return "Nexus files (*.nex, *.nexus, *.nx, *.tre)";\r
- }\r
-} // NexusFilter\r
-\r
-class NHFilter extends FileFilter {\r
-\r
- @Override\r
- public boolean accept( final File f ) {\r
- final String file_name = f.getName().trim().toLowerCase();\r
- return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )\r
- || file_name.endsWith( ".tr" ) || file_name.endsWith( ".tree" ) || file_name.endsWith( ".dnd" )\r
- || file_name.endsWith( ".ph" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".nwk" )\r
- || f.isDirectory();\r
- }\r
-\r
- @Override\r
- public String getDescription() {\r
- return "New Hampshire - Newick files (*.nh, *.newick, *.phy, *.tree, *.dnd, *.tr, *.ph, *.phb, *.nwk)";\r
- }\r
-} // NHFilter\r
-\r
-class NHXFilter extends FileFilter {\r
-\r
- @Override\r
- public boolean accept( final File f ) {\r
- final String file_name = f.getName().trim().toLowerCase();\r
- return file_name.endsWith( ".nhx" ) || f.isDirectory();\r
- }\r
-\r
- @Override\r
- public String getDescription() {\r
- return "NHX files (*.nhx) [deprecated]";\r
- }\r
-}\r
-\r
-class PdfFilter extends FileFilter {\r
-\r
- @Override\r
- public boolean accept( final File f ) {\r
- return f.getName().trim().toLowerCase().endsWith( ".pdf" ) || f.isDirectory();\r
- }\r
-\r
- @Override\r
- public String getDescription() {\r
- return "PDF files (*.pdf)";\r
- }\r
-} // PdfFilter\r
-\r
-class SequencesFileFilter extends FileFilter {\r
-\r
- @Override\r
- public boolean accept( final File f ) {\r
- final String file_name = f.getName().trim().toLowerCase();\r
- return file_name.endsWith( ".fasta" ) || file_name.endsWith( ".fa" ) || file_name.endsWith( ".fas" )\r
- || file_name.endsWith( ".seqs" ) || f.isDirectory();\r
- }\r
-\r
- @Override\r
- public String getDescription() {\r
- return "Sequences files (*.fasta, *.fa, *.fas, *.seqs )";\r
- }\r
-}\r
-\r
-class TolFilter extends FileFilter {\r
-\r
- @Override\r
- public boolean accept( final File f ) {\r
- final String file_name = f.getName().trim().toLowerCase();\r
- return ( file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" ) || file_name.endsWith( ".zip" ) || f\r
- .isDirectory() ) && ( !file_name.endsWith( ".xml.zip" ) );\r
- }\r
-\r
- @Override\r
- public String getDescription() {\r
- return "Tree of Life files (*.tol, *.tolxml)";\r
- }\r
-} // TolFilter\r
-\r
-class XMLFilter extends FileFilter {\r
-\r
- @Override\r
- public boolean accept( final File f ) {\r
- final String file_name = f.getName().trim().toLowerCase();\r
- return file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" ) || file_name.endsWith( "phylo.xml" )\r
- || file_name.endsWith( ".pxml" ) || file_name.endsWith( ".zip" ) || f.isDirectory();\r
- }\r
-\r
- @Override\r
- public String getDescription() {\r
- return "phyloXML files (*.xml, *.phyloxml, *phylo.xml, *.pxml, *.zip)";\r
- }\r
-} // XMLFilter\r
+// $Id:
+// FORESTER -- software libraries and applications
+// for evolutionary biology research and applications.
+//
+// Copyright (C) 2008-2009 Christian M. Zmasek
+// Copyright (C) 2008-2009 Burnham Institute for Medical Research
+// 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 javax.swing.event.InternalFrameAdapter;
+import javax.swing.event.InternalFrameEvent;
+
+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.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 = 900;
+ private final static int FRAME_Y_SIZE = 900;
+ // 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 );
+ addFrameListener( new FrameAdapter() {
+
+ @Override
+ public void FrameClosing () {
+
+ 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,
+ final boolean isEmbedded) {
+ super(isEmbedded);
+ _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 );
+
+ addFrameListener( new FrameAdapter() {
+
+ @Override
+ public void FrameClosing( ) {
+ if (MainFrameApplication.this.getParent() == null) {
+ if ( isUnsavedDataPresent() ) {
+ final int r = JOptionPane.showConfirmDialog( _mainpanel,
+ "Close Archaeopteryx despite potentially unsaved changes?",
+ "Close viewer?",
+ 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 Configuration config,
+ final String title,
+ final File current_dir ) {
+ this(phys,config,title,current_dir,false);
+ }
+
+ 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.parseMsa( is );
+ }
+ }
+ catch ( final MsaFormatException e ) {
+ setArrowCursor();
+ JOptionPane.showMessageDialog( getThisFrame(),
+ e.getLocalizedMessage(),
+ "Multiple sequence alignment format error",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ catch ( final IOException e ) {
+ setArrowCursor();
+ JOptionPane.showMessageDialog( getThisFrame(),
+ e.getLocalizedMessage(),
+ "Failed to read multiple sequence alignment",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ catch ( final IllegalArgumentException e ) {
+ setArrowCursor();
+ JOptionPane.showMessageDialog( getThisFrame(),
+ e.getLocalizedMessage(),
+ "Unexpected error during reading of multiple sequence alignment",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ catch ( final Exception e ) {
+ setArrowCursor();
+ e.printStackTrace();
+ JOptionPane.showMessageDialog( getThisFrame(),
+ e.getLocalizedMessage(),
+ "Unexpected error during reading of multiple sequence alignment",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ if ( ( msa == null ) || ( msa.getNumberOfSequences() < 1 ) ) {
+ JOptionPane.showMessageDialog( getThisFrame(),
+ "Multiple sequence alignment is empty",
+ "Illegal Multiple Sequence Alignment",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ if ( msa.getNumberOfSequences() < 4 ) {
+ JOptionPane.showMessageDialog( getThisFrame(),
+ "Multiple sequence alignment needs to contain at least 3 sequences",
+ "Illegal multiple sequence alignment",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ if ( msa.getLength() < 2 ) {
+ JOptionPane.showMessageDialog( getThisFrame(),
+ "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( getThisFrame(),
+ e.getLocalizedMessage(),
+ "Multiple sequence file format error",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ catch ( final IOException e ) {
+ setArrowCursor();
+ JOptionPane.showMessageDialog( getThisFrame(),
+ e.getLocalizedMessage(),
+ "Failed to read multiple sequence file",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ catch ( final IllegalArgumentException e ) {
+ setArrowCursor();
+ JOptionPane.showMessageDialog( getThisFrame(),
+ e.getLocalizedMessage(),
+ "Unexpected error during reading of multiple sequence file",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ catch ( final Exception e ) {
+ setArrowCursor();
+ e.printStackTrace();
+ JOptionPane.showMessageDialog( getThisFrame(),
+ e.getLocalizedMessage(),
+ "Unexpected error during reading of multiple sequence file",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ if ( ( seqs == null ) || ( seqs.size() < 1 ) ) {
+ JOptionPane.showMessageDialog( getThisFrame(),
+ "Multiple sequence file is empty",
+ "Illegal multiple sequence file",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ if ( seqs.size() < 4 ) {
+ JOptionPane.showMessageDialog( getThisFrame(),
+ "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( getThisFrame(),
+ "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( getThisFrame(),
+ e.getMessage(),
+ "Could Not Read Expression Value Table",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ if ( t.getNumberOfColumns() < 2 ) {
+ JOptionPane.showMessageDialog( getThisFrame(),
+ "Table contains " + t.getNumberOfColumns() + " column(s)",
+ "Problem with Expression Value Table",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ if ( t.getNumberOfRows() < 1 ) {
+ JOptionPane.showMessageDialog( getThisFrame(),
+ "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( getThisFrame(),
+ "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( getThisFrame(),
+ 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( getThisFrame(),
+ "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() ) {
+
+ node.getNodeData().setVector( l );
+ }
+ }
+ }
+ if ( not_found > 0 ) {
+ JOptionPane
+ .showMessageDialog( getThisFrame(),
+ "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( getThisFrame(),
+ "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( getThisFrame(),
+ "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( getThisFrame(),
+ e.getLocalizedMessage(),
+ "Multiple sequence file format error",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ catch ( final IOException e ) {
+ setArrowCursor();
+ JOptionPane.showMessageDialog( getThisFrame(),
+ e.getLocalizedMessage(),
+ "Failed to read multiple sequence file",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ catch ( final Exception e ) {
+ setArrowCursor();
+ e.printStackTrace();
+ JOptionPane.showMessageDialog( getThisFrame(),
+ e.getLocalizedMessage(),
+ "Unexpected error during reading of multiple sequence file",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ if ( ( seqs == null ) || ( seqs.size() < 1 ) ) {
+ JOptionPane.showMessageDialog( getThisFrame(),
+ "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( getThisFrame(),
+ "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( getThisFrame(),
+ "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( getThisFrame(),
+ "Attached all " + total_counter + " sequences to tree nodes.\n" + s,
+ "All sequences attached",
+ JOptionPane.INFORMATION_MESSAGE );
+ }
+ else {
+ JOptionPane.showMessageDialog( getThisFrame(),
+ "Attached " + attached_counter + " sequences out of a total of "
+ + total_counter + " sequences.\n" + s,
+ attached_counter + " sequences attached",
+ JOptionPane.WARNING_MESSAGE );
+ }
+ }
+ else {
+ JOptionPane.showMessageDialog( getThisFrame(),
+ "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( getThisFrame(),
+ "Close tab despite potentially unsaved changes?",
+ "Close Tab?",
+ JOptionPane.YES_NO_OPTION );
+ if ( r != JOptionPane.YES_OPTION ) {
+ return;
+ }
+ }
+ getMainPanel().closeCurrentPane();
+ activateSaveAllIfNeeded();
+ }
+ }
+
+ private void collapseBelowThreshold( 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( getThisFrame(),
+ "Collapsed " + to_be_removed.size()
+ + " branches with\nconfidence values below "
+ + getMinNotCollapseConfidenceValue(),
+ "Collapsed " + to_be_removed.size() + " branches",
+ JOptionPane.INFORMATION_MESSAGE );
+ }
+ else {
+ JOptionPane.showMessageDialog( getThisFrame(),
+ "No branch collapsed,\nminimum confidence value per branch is "
+ + min_support,
+ "No branch collapsed",
+ JOptionPane.INFORMATION_MESSAGE );
+ }
+ }
+ else {
+ JOptionPane.showMessageDialog( getThisFrame(),
+ "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( getThisFrame(),
+ "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( getThisFrame(),
+ "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 );
+ collapseBelowThreshold( 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( getThisFrame(),
+ "Collapsed " + to_be_removed.size()
+ + " branches with\nbranch length values below "
+ + getMinNotCollapseBlValue(),
+ "Collapsed " + to_be_removed.size() + " branches",
+ JOptionPane.INFORMATION_MESSAGE );
+ }
+ else {
+ JOptionPane.showMessageDialog( getThisFrame(),
+ "No branch collapsed,\nminimum branch length is " + min_bl,
+ "No branch collapsed",
+ JOptionPane.INFORMATION_MESSAGE );
+ }
+ }
+ else {
+ JOptionPane.showMessageDialog( getThisFrame(),
+ "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( getThisFrame(),
+ 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( getThisFrame(),
+ "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( getThisFrame(),
+ "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( getThisFrame(),
+ "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( getThisFrame(),
+ "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 );
+
+ 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( getThisFrame(),
+ "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( getThisFrame(),
+ "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( getThisFrame(),
+ "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( getThisFrame(),
+ "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( getThisFrame(),
+ "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( _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( _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( _collapsed_with_average_height_cbmi = new JCheckBoxMenuItem( "Proportional Height of Collapsed Subtrees" ) );
+
+
+ _options_jmenu
+ .add( _show_abbreviated_labels_for_collapsed_nodes_cbmi = new JCheckBoxMenuItem( "Add Abbreviated Labels to Collapsed Subtrees" ) );
+
+
+
+ _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() );
+ customizeCheckBoxMenuItem( _collapsed_with_average_height_cbmi, getOptions().isCollapsedWithAverageHeigh() );
+ customizeCheckBoxMenuItem( _show_abbreviated_labels_for_collapsed_nodes_cbmi, getOptions().isShowAbbreviatedLabelsForCollapsedNodes() );
+
+ customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,
+ getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );
+ customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
+ getOptions().getCladogramType() == CLADOGRAM_TYPE.LINED_UP );
+ 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 Single Taxonomy-Subtrees" ) );
+ customizeJMenuItem( _collapse_species_specific_subtrees );
+ _collapse_species_specific_subtrees.setToolTipText( "To (reversibly) collapse subtrees associated with only one taxonomy (such as 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( getThisFrame(),
+ "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( getThisFrame(),
+ 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( getThisFrame(),
+ "Malformed URL: " + url + "\n" + e.getLocalizedMessage(),
+ "Malformed URL",
+ JOptionPane.ERROR_MESSAGE );
+ }
+ catch ( final IOException e ) {
+ JOptionPane.showMessageDialog( getThisFrame(),
+ "Could not read from " + url + "\n"
+ + ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
+ "Failed to read URL",
+ JOptionPane.ERROR_MESSAGE );
+ }
+ catch ( final Exception e ) {
+ JOptionPane.showMessageDialog( getThisFrame(),
+ 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.
git://source.jalview.org / jalview.git / blobdiff