X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FMainFrameApplication.java;h=9a9c233399f312a7468539fec1e71fe71dd58d29;hb=02afcdbc87b196aa929bcffabf83e409fd807077;hp=b688722af21136aec7111f3f654272cc0c13544b;hpb=6ebad4e2283f33540c6ed4a9b1c8efc839d62637;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java index b688722..9a9c233 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java @@ -1,2829 +1,2256 @@ -// $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.filechooser.FileFilter; -import javax.swing.plaf.synth.SynthLookAndFeel; - -import org.forester.analysis.TaxonomyDataManager; -import org.forester.archaeopteryx.AptxUtil.GraphicsExportType; -import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE; -import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION; -import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE; -import org.forester.archaeopteryx.tools.AncestralTaxonomyInferrer; -import org.forester.archaeopteryx.tools.InferenceManager; -import org.forester.archaeopteryx.tools.PhyloInferenceDialog; -import org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions; -import org.forester.archaeopteryx.tools.PhylogeneticInferrer; -import org.forester.archaeopteryx.tools.SequenceDataRetriver; -import org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient; -import org.forester.archaeopteryx.webservices.WebservicesManager; -import org.forester.io.parsers.FastaParser; -import org.forester.io.parsers.GeneralMsaParser; -import org.forester.io.parsers.PhylogenyParser; -import org.forester.io.parsers.nexus.NexusPhylogeniesParser; -import org.forester.io.parsers.nhx.NHXParser; -import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION; -import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException; -import org.forester.io.parsers.phyloxml.PhyloXmlParser; -import org.forester.io.parsers.phyloxml.PhyloXmlUtil; -import org.forester.io.parsers.tol.TolParser; -import org.forester.io.parsers.util.ParserUtils; -import org.forester.io.writers.PhylogenyWriter; -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.Taxonomy; -import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory; -import org.forester.phylogeny.factories.PhylogenyFactory; -import org.forester.phylogeny.iterators.PhylogenyNodeIterator; -import org.forester.sequence.Sequence; -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; -import org.forester.util.WindowsUtils; - -public final class MainFrameApplication extends MainFrame { - - static final String INFER_ANCESTOR_TAXONOMIES = "Infer Ancestor Taxonomies"; - static final String OBTAIN_DETAILED_TAXONOMIC_INFORMATION = "Obtain Detailed Taxonomic Information"; - private final static int FRAME_X_SIZE = 800; - private final static int FRAME_Y_SIZE = 800; - // Filters for the file-open dialog (classes defined in this file) - private final static NHFilter nhfilter = new NHFilter(); - private final static NHXFilter nhxfilter = new NHXFilter(); - private final static XMLFilter xmlfilter = new XMLFilter(); - private final static TolFilter tolfilter = new TolFilter(); - private final static NexusFilter nexusfilter = new NexusFilter(); - private final static PdfFilter pdffilter = new PdfFilter(); - private final static GraphicsFileFilter graphicsfilefilter = new GraphicsFileFilter(); - private final static MsaFileFilter msafilter = new MsaFileFilter(); - private final static SequencesFileFilter seqsfilter = new SequencesFileFilter(); - private final static DefaultFilter defaultfilter = new DefaultFilter(); - private static final long serialVersionUID = -799735726778865234L; - 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; - private final JFileChooser _save_filechooser; - private final JFileChooser _writetopdf_filechooser; - private final JFileChooser _writetographics_filechooser; - // Application-only print menu items - private JMenuItem _print_item; - private JMenuItem _write_to_pdf_item; - private JMenuItem _write_to_jpg_item; - private JMenuItem _write_to_gif_item; - private JMenuItem _write_to_tif_item; - private JMenuItem _write_to_png_item; - private JMenuItem _write_to_bmp_item; - private File _current_dir; - private ButtonGroup _radio_group_1; - private ButtonGroup _radio_group_2; - // Others: - double _min_not_collapse = Constants.MIN_NOT_COLLAPSE_DEFAULT; - // Phylogeny Inference menu - private JMenu _inference_menu; - private JMenuItem _inference_from_msa_item; - private JMenuItem _inference_from_seqs_item; - // Phylogeny Inference - private PhylogeneticInferenceOptions _phylogenetic_inference_options = null; - private Msa _msa = null; - private File _msa_file = null; - private List _seqs = null; - private File _seqs_file = null; - JMenuItem _read_values_jmi; - JMenuItem _read_seqs_jmi; - - private MainFrameApplication( final Phylogeny[] phys, final Configuration config ) { - _configuration = config; - if ( _configuration == null ) { - throw new IllegalArgumentException( "configuration is null" ); - } - setVisible( false ); - setOptions( Options.createInstance( _configuration ) ); - _mainpanel = new MainPanel( _configuration, this ); - _open_filechooser = null; - _open_filechooser_for_species_tree = null; - _save_filechooser = null; - _writetopdf_filechooser = null; - _writetographics_filechooser = null; - _msa_filechooser = null; - _seqs_pi_filechooser = null; - _values_filechooser = null; - _sequences_filechooser = null; - _jmenubar = new JMenuBar(); - buildFileMenu(); - buildTypeMenu(); - _contentpane = getContentPane(); - _contentpane.setLayout( new BorderLayout() ); - _contentpane.add( _mainpanel, BorderLayout.CENTER ); - // App is this big - setSize( MainFrameApplication.FRAME_X_SIZE, MainFrameApplication.FRAME_Y_SIZE ); - // The window listener - setDefaultCloseOperation( WindowConstants.DO_NOTHING_ON_CLOSE ); - addWindowListener( new WindowAdapter() { - - @Override - public void windowClosing( final WindowEvent e ) { - exit(); - } - } ); - // setVisible( true ); - if ( ( phys != null ) && ( phys.length > 0 ) ) { - AptxUtil.addPhylogeniesToTabs( phys, "", null, _configuration, _mainpanel ); - validate(); - getMainPanel().getControlPanel().showWholeAll(); - getMainPanel().getControlPanel().showWhole(); - } - //activateSaveAllIfNeeded(); - // ...and its children - _contentpane.repaint(); - } - - private MainFrameApplication( final Phylogeny[] phys, final Configuration config, final String title ) { - this( phys, config, title, null ); - } - - private MainFrameApplication( final Phylogeny[] phys, - final Configuration config, - final String title, - final File current_dir ) { - super(); - _configuration = config; - if ( _configuration == null ) { - throw new IllegalArgumentException( "configuration is null" ); - } - try { - boolean synth_exception = false; - if ( Constants.__SYNTH_LF ) { - try { - final SynthLookAndFeel synth = new SynthLookAndFeel(); - synth.load( MainFrameApplication.class.getResourceAsStream( "/resources/synth_look_and_feel_1.xml" ), - MainFrameApplication.class ); - UIManager.setLookAndFeel( synth ); - } - catch ( final Exception ex ) { - synth_exception = true; - ForesterUtil.printWarningMessage( Constants.PRG_NAME, - "could not create synth look and feel: " - + ex.getLocalizedMessage() ); - } - } - if ( !Constants.__SYNTH_LF || synth_exception ) { - if ( _configuration.isUseNativeUI() ) { - UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() ); - } - else { - UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() ); - } - } - //UIManager.setLookAndFeel( "com.sun.java.swing.plaf.nimbus.NimbusLookAndFeel" ); - } - 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 ) ); - // _textframe = null; #~~~~ - // set title - setTitle( Constants.PRG_NAME + " " + Constants.VERSION + " (" + Constants.PRG_DATE + ")" ); - _mainpanel = new MainPanel( _configuration, this ); - // The file dialogs - _open_filechooser = new JFileChooser(); - _open_filechooser.setCurrentDirectory( new File( "." ) ); - _open_filechooser.setMultiSelectionEnabled( false ); - _open_filechooser.addChoosableFileFilter( MainFrameApplication.xmlfilter ); - _open_filechooser.addChoosableFileFilter( MainFrameApplication.nhxfilter ); - _open_filechooser.addChoosableFileFilter( MainFrameApplication.nhfilter ); - _open_filechooser.addChoosableFileFilter( MainFrameApplication.nexusfilter ); - _open_filechooser.addChoosableFileFilter( MainFrameApplication.tolfilter ); - _open_filechooser.addChoosableFileFilter( _open_filechooser.getAcceptAllFileFilter() ); - _open_filechooser.setFileFilter( MainFrameApplication.defaultfilter ); - _open_filechooser_for_species_tree = new JFileChooser(); - _open_filechooser_for_species_tree.setCurrentDirectory( new File( "." ) ); - _open_filechooser_for_species_tree.setMultiSelectionEnabled( false ); - _open_filechooser_for_species_tree.addChoosableFileFilter( MainFrameApplication.xmlfilter ); - _open_filechooser_for_species_tree.addChoosableFileFilter( MainFrameApplication.tolfilter ); - _open_filechooser_for_species_tree.setFileFilter( MainFrameApplication.xmlfilter ); - _save_filechooser = new JFileChooser(); - _save_filechooser.setCurrentDirectory( new File( "." ) ); - _save_filechooser.setMultiSelectionEnabled( false ); - _save_filechooser.setFileFilter( MainFrameApplication.xmlfilter ); - _save_filechooser.addChoosableFileFilter( MainFrameApplication.nhfilter ); - _save_filechooser.addChoosableFileFilter( MainFrameApplication.nexusfilter ); - _save_filechooser.addChoosableFileFilter( _save_filechooser.getAcceptAllFileFilter() ); - _writetopdf_filechooser = new JFileChooser(); - _writetopdf_filechooser.addChoosableFileFilter( MainFrameApplication.pdffilter ); - _writetographics_filechooser = new JFileChooser(); - _writetographics_filechooser.addChoosableFileFilter( MainFrameApplication.graphicsfilefilter ); - // Msa: - _msa_filechooser = new JFileChooser(); - _msa_filechooser.setName( "Read Multiple Sequence Alignment File" ); - _msa_filechooser.setCurrentDirectory( new File( "." ) ); - _msa_filechooser.setMultiSelectionEnabled( false ); - _msa_filechooser.addChoosableFileFilter( _msa_filechooser.getAcceptAllFileFilter() ); - _msa_filechooser.addChoosableFileFilter( MainFrameApplication.msafilter ); - // Seqs: - _seqs_pi_filechooser = new JFileChooser(); - _seqs_pi_filechooser.setName( "Read Sequences File" ); - _seqs_pi_filechooser.setCurrentDirectory( new File( "." ) ); - _seqs_pi_filechooser.setMultiSelectionEnabled( false ); - _seqs_pi_filechooser.addChoosableFileFilter( _seqs_pi_filechooser.getAcceptAllFileFilter() ); - _seqs_pi_filechooser.addChoosableFileFilter( MainFrameApplication.seqsfilter ); - // Expression - _values_filechooser = new JFileChooser(); - _values_filechooser.setCurrentDirectory( new File( "." ) ); - _values_filechooser.setMultiSelectionEnabled( false ); - // Sequences - _sequences_filechooser = new JFileChooser(); - _sequences_filechooser.setCurrentDirectory( new File( "." ) ); - _sequences_filechooser.setMultiSelectionEnabled( false ); - // build the menu bar - _jmenubar = new JMenuBar(); - if ( !_configuration.isUseNativeUI() ) { - _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() ); - } - buildFileMenu(); - if ( Constants.__ALLOW_PHYLOGENETIC_INFERENCE ) { - buildPhylogeneticInferenceMenu(); - } - buildAnalysisMenu(); - buildToolsMenu(); - buildViewMenu(); - buildFontSizeMenu(); - buildOptionsMenu(); - buildTypeMenu(); - buildHelpMenu(); - setJMenuBar( _jmenubar ); - _jmenubar.add( _help_jmenu ); - _contentpane = getContentPane(); - _contentpane.setLayout( new BorderLayout() ); - _contentpane.add( _mainpanel, BorderLayout.CENTER ); - // App is this big - setSize( MainFrameApplication.FRAME_X_SIZE, MainFrameApplication.FRAME_Y_SIZE ); - // addWindowFocusListener( new WindowAdapter() { - // - // @Override - // public void windowGainedFocus( WindowEvent e ) { - // requestFocusInWindow(); - // } - // } ); - // The window listener - setDefaultCloseOperation( WindowConstants.DO_NOTHING_ON_CLOSE ); - addWindowListener( new WindowAdapter() { - - @Override - public void windowClosing( final WindowEvent e ) { - if ( isUnsavedDataPresent() ) { - final int r = JOptionPane.showConfirmDialog( null, - "Exit despite potentially unsaved changes?", - "Exit?", - JOptionPane.YES_NO_OPTION ); - if ( r != JOptionPane.YES_OPTION ) { - return; - } - } - else { - final int r = JOptionPane.showConfirmDialog( null, - "Exit Archaeopteryx?", - "Exit?", - JOptionPane.YES_NO_OPTION ); - if ( r != JOptionPane.YES_OPTION ) { - return; - } - } - exit(); - } - } ); - // The component listener - addComponentListener( new ComponentAdapter() { - - @Override - public void componentResized( final ComponentEvent e ) { - if ( _mainpanel.getCurrentTreePanel() != null ) { - _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel() - .getWidth(), - _mainpanel.getCurrentTreePanel() - .getHeight(), - getOptions().isAllowFontSizeChange() ); - } - } - } ); - requestFocusInWindow(); - // addKeyListener( this ); - setVisible( true ); - if ( ( phys != null ) && ( phys.length > 0 ) ) { - AptxUtil.addPhylogeniesToTabs( phys, title, null, _configuration, _mainpanel ); - validate(); - getMainPanel().getControlPanel().showWholeAll(); - getMainPanel().getControlPanel().showWhole(); - } - activateSaveAllIfNeeded(); - // ...and its children - _contentpane.repaint(); - System.gc(); - } - - private MainFrameApplication( final Phylogeny[] phys, final String config_file, final String title ) { - // Reads the config file (false, false => not url, not applet): - this( phys, new Configuration( config_file, false, false, true ), title ); - } - - @Override - public void actionPerformed( final ActionEvent e ) { - try { - super.actionPerformed( e ); - final Object o = e.getSource(); - // Handle app-specific actions here: - if ( o == _open_item ) { - readPhylogeniesFromFile(); - } - if ( o == _open_url_item ) { - readPhylogeniesFromURL(); - } - else if ( o == _save_item ) { - writeToFile( _mainpanel.getCurrentPhylogeny() ); - // If subtree currently displayed, save it, instead of complete - // tree. - } - else if ( o == _new_item ) { - newTree(); - } - else if ( o == _save_all_item ) { - writeAllToFile(); - } - else if ( o == _close_item ) { - closeCurrentPane(); - } - else if ( o == _write_to_pdf_item ) { - writeToPdf( _mainpanel.getCurrentPhylogeny() ); - } - else if ( o == _write_to_jpg_item ) { - writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.JPG ); - } - else if ( o == _write_to_png_item ) { - writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.PNG ); - } - else if ( o == _write_to_gif_item ) { - writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.GIF ); - } - else if ( o == _write_to_tif_item ) { - writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.TIFF ); - } - else if ( o == _write_to_bmp_item ) { - writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.BMP ); - } - else if ( o == _print_item ) { - print(); - } - else if ( o == _load_species_tree_item ) { - readSpeciesTreeFromFile(); - } - else if ( o == _lineage_inference ) { - if ( isSubtreeDisplayed() ) { - JOptionPane.showMessageDialog( this, - "Subtree is shown.", - "Cannot infer ancestral taxonomies", - JOptionPane.ERROR_MESSAGE ); - return; - } - executeLineageInference(); - } - 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 == _graphics_export_visible_only_cbmi ) { - updateOptions( getOptions() ); - } - else if ( o == _antialias_print_cbmi ) { - updateOptions( getOptions() ); - } - else if ( o == _print_black_and_white_cbmi ) { - updateOptions( getOptions() ); - } - else if ( o == _print_using_actual_size_cbmi ) { - updateOptions( getOptions() ); - } - else if ( o == _graphics_export_using_actual_size_cbmi ) { - updateOptions( getOptions() ); - } - else if ( o == _print_size_mi ) { - choosePrintSize(); - } - else if ( o == _choose_pdf_width_mi ) { - choosePdfWidth(); - } - 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 == _extract_taxonomy_pfam_strict_rbmi ) || ( o == _extract_taxonomy_pfam_relaxed_rbmi ) - || ( o == _extract_taxonomy_agressive_rbmi ) ) { - if ( _replace_underscores_cbmi != null ) { - _replace_underscores_cbmi.setSelected( false ); - } - updateOptions( getOptions() ); - } - else if ( o == _extract_taxonomy_no_rbmi ) { - updateOptions( getOptions() ); - } - else if ( o == _inference_from_msa_item ) { - executePhyleneticInference( false ); - } - else if ( o == _inference_from_seqs_item ) { - executePhyleneticInference( true ); - } - _contentpane.repaint(); - } - catch ( final Exception ex ) { - AptxUtil.unexpectedException( ex ); - } - catch ( final Error err ) { - AptxUtil.unexpectedError( err ); - } - } - - public void end() { - _mainpanel.terminate(); - _contentpane.removeAll(); - setVisible( false ); - dispose(); - } - - @Override - public MainPanel getMainPanel() { - return _mainpanel; - } - - public Msa getMsa() { - return _msa; - } - - public File getMsaFile() { - return _msa_file; - } - - public List getSeqs() { - return _seqs; - } - - public File getSeqsFile() { - return _seqs_file; - } - - public void readMsaFromFile() { - // Set an initial directory if none set yet - final File my_dir = getCurrentDir(); - _msa_filechooser.setMultiSelectionEnabled( false ); - // Open file-open dialog and set current directory - if ( my_dir != null ) { - _msa_filechooser.setCurrentDirectory( my_dir ); - } - final int result = _msa_filechooser.showOpenDialog( _contentpane ); - // All done: get the msa - final File file = _msa_filechooser.getSelectedFile(); - setCurrentDir( _msa_filechooser.getCurrentDirectory() ); - if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) { - setMsaFile( null ); - setMsa( null ); - Msa msa = null; - try { - final InputStream is = new FileInputStream( file ); - if ( FastaParser.isLikelyFasta( file ) ) { - msa = FastaParser.parseMsa( is ); - } - else { - msa = GeneralMsaParser.parse( is ); - } - } - catch ( final MsaFormatException e ) { - setArrowCursor(); - JOptionPane.showMessageDialog( this, - e.getLocalizedMessage(), - "Multiple sequence alignment format error", - JOptionPane.ERROR_MESSAGE ); - return; - } - catch ( final IOException e ) { - setArrowCursor(); - JOptionPane.showMessageDialog( this, - e.getLocalizedMessage(), - "Failed to read multiple sequence alignment", - JOptionPane.ERROR_MESSAGE ); - return; - } - catch ( final IllegalArgumentException e ) { - setArrowCursor(); - JOptionPane.showMessageDialog( this, - e.getLocalizedMessage(), - "Unexpected error during reading of multiple sequence alignment", - JOptionPane.ERROR_MESSAGE ); - return; - } - catch ( final Exception e ) { - setArrowCursor(); - e.printStackTrace(); - JOptionPane.showMessageDialog( this, - e.getLocalizedMessage(), - "Unexpected error during reading of multiple sequence alignment", - JOptionPane.ERROR_MESSAGE ); - return; - } - if ( ( msa == null ) || ( msa.getNumberOfSequences() < 1 ) ) { - JOptionPane.showMessageDialog( this, - "Multiple sequence alignment is empty", - "Illegal Multiple Sequence Alignment", - JOptionPane.ERROR_MESSAGE ); - return; - } - if ( msa.getNumberOfSequences() < 4 ) { - JOptionPane.showMessageDialog( this, - "Multiple sequence alignment needs to contain at least 3 sequences", - "Illegal multiple sequence alignment", - JOptionPane.ERROR_MESSAGE ); - return; - } - if ( msa.getLength() < 2 ) { - JOptionPane.showMessageDialog( this, - "Multiple sequence alignment needs to contain at least 2 residues", - "Illegal multiple sequence alignment", - JOptionPane.ERROR_MESSAGE ); - return; - } - System.gc(); - setMsaFile( _msa_filechooser.getSelectedFile() ); - setMsa( msa ); - } - } - - public void readSeqsFromFileforPI() { - // Set an initial directory if none set yet - final File my_dir = getCurrentDir(); - _seqs_pi_filechooser.setMultiSelectionEnabled( false ); - // Open file-open dialog and set current directory - if ( my_dir != null ) { - _seqs_pi_filechooser.setCurrentDirectory( my_dir ); - } - final int result = _seqs_pi_filechooser.showOpenDialog( _contentpane ); - // All done: get the seqs - final File file = _seqs_pi_filechooser.getSelectedFile(); - setCurrentDir( _seqs_pi_filechooser.getCurrentDirectory() ); - if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) { - setSeqsFile( null ); - setSeqs( null ); - List seqs = null; - try { - if ( FastaParser.isLikelyFasta( new FileInputStream( file ) ) ) { - seqs = FastaParser.parse( new FileInputStream( file ) ); - for( final Sequence seq : seqs ) { - System.out.println( SequenceWriter.toFasta( seq, 60 ) ); - } - } - else { - //TODO error - } - } - catch ( final MsaFormatException e ) { - setArrowCursor(); - JOptionPane.showMessageDialog( this, - e.getLocalizedMessage(), - "Multiple sequence file format error", - JOptionPane.ERROR_MESSAGE ); - return; - } - catch ( final IOException e ) { - setArrowCursor(); - JOptionPane.showMessageDialog( this, - e.getLocalizedMessage(), - "Failed to read multiple sequence file", - JOptionPane.ERROR_MESSAGE ); - return; - } - catch ( final IllegalArgumentException e ) { - setArrowCursor(); - JOptionPane.showMessageDialog( this, - e.getLocalizedMessage(), - "Unexpected error during reading of multiple sequence file", - JOptionPane.ERROR_MESSAGE ); - return; - } - catch ( final Exception e ) { - setArrowCursor(); - e.printStackTrace(); - JOptionPane.showMessageDialog( this, - e.getLocalizedMessage(), - "Unexpected error during reading of multiple sequence file", - JOptionPane.ERROR_MESSAGE ); - return; - } - if ( ( seqs == null ) || ( seqs.size() < 1 ) ) { - JOptionPane.showMessageDialog( this, - "Multiple sequence file is empty", - "Illegal multiple sequence file", - JOptionPane.ERROR_MESSAGE ); - return; - } - if ( seqs.size() < 4 ) { - JOptionPane.showMessageDialog( this, - "Multiple sequence file needs to contain at least 3 sequences", - "Illegal multiple sequence file", - JOptionPane.ERROR_MESSAGE ); - return; - } - // if ( msa.getLength() < 2 ) { - // JOptionPane.showMessageDialog( this, - // "Multiple sequence alignment needs to contain at least 2 residues", - // "Illegal multiple sequence file", - // JOptionPane.ERROR_MESSAGE ); - // return; - // } - System.gc(); - setSeqsFile( _seqs_pi_filechooser.getSelectedFile() ); - setSeqs( seqs ); - } - } - - 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() ) ); - setTextForGraphicsSizeChooserMenuItem( _print_size_mi, getOptions() ); - setTextForPdfLineWidthChooserMenuItem( _choose_pdf_width_mi, getOptions() ); - MainFrame.updateOptionsMenuDependingOnPhylogenyType( getMainPanel(), - _show_scale_cbmi, - _show_branch_length_values_cbmi, - _non_lined_up_cladograms_rbmi, - _uniform_cladograms_rbmi, - _ext_node_dependent_cladogram_rbmi, - _label_direction_cbmi ); - MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() ); - MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() ); - MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() ); - } - } ); - _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( DISPLAY_SUBHEADER ), getConfiguration() ) ); - _options_jmenu - .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) ); - _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) ); - _options_jmenu.add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( NON_LINED_UP_CLADOGRAMS_LABEL ) ); - _radio_group_1 = new ButtonGroup(); - _radio_group_1.add( _ext_node_dependent_cladogram_rbmi ); - _radio_group_1.add( _uniform_cladograms_rbmi ); - _radio_group_1.add( _non_lined_up_cladograms_rbmi ); - /////// - _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( SHOW_OVERVIEW_LABEL ) ); - _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( DISPLAY_SCALE_LABEL ) ); - _options_jmenu - .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( DISPLAY_BRANCH_LENGTH_VALUES_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 ) ); - if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) { - _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( 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( 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( _inverse_search_result_cbmi = new JCheckBoxMenuItem( INVERSE_SEARCH_RESULT_LABEL ) ); - _options_jmenu.addSeparator(); - _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Graphics Export & Printing:" ), - getConfiguration() ) ); - _options_jmenu.add( _antialias_print_cbmi = new JCheckBoxMenuItem( "Antialias" ) ); - _options_jmenu.add( _print_black_and_white_cbmi = new JCheckBoxMenuItem( "Export in Black and White" ) ); - _options_jmenu - .add( _print_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PDF export and Printing" ) ); - _options_jmenu - .add( _graphics_export_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PNG, JPG, and GIF export" ) ); - _options_jmenu - .add( _graphics_export_visible_only_cbmi = new JCheckBoxMenuItem( "Limit to Visible ('Screenshot') for PNG, JPG, and GIF export" ) ); - _options_jmenu.add( _print_size_mi = new JMenuItem( "" ) ); - _options_jmenu.add( _choose_pdf_width_mi = new JMenuItem( "" ) ); - _options_jmenu.addSeparator(); - _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/NHX/Nexus Input:" ), getConfiguration() ) ); - _options_jmenu - .add( _internal_number_are_confidence_for_nh_parsing_cbmi = new JCheckBoxMenuItem( "Internal Node Names are Confidence Values" ) ); - _options_jmenu.add( _replace_underscores_cbmi = new JCheckBoxMenuItem( "Replace Underscores with Spaces" ) ); - _options_jmenu - .add( _allow_errors_in_distance_to_parent_cbmi = new JCheckBoxMenuItem( "Ignore Distance Values Format Errors" ) ); - // - _options_jmenu.add( _extract_taxonomy_no_rbmi = new JRadioButtonMenuItem( "No Taxonomy Extraction" ) ); - _options_jmenu - .add( _extract_taxonomy_pfam_strict_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style Node Names" ) ); - _options_jmenu - .add( _extract_taxonomy_pfam_relaxed_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style like Node Names" ) ); - _options_jmenu - .add( _extract_taxonomy_agressive_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids/Scientific Names from Node Names" ) ); - _extract_taxonomy_pfam_strict_rbmi - .setToolTipText( "To extract taxonomy codes/ids from node names in the form of e.g. \"BCL2_MOUSE/123-304\" or \"BCL2_10090/123-304\"" ); - _extract_taxonomy_pfam_relaxed_rbmi - .setToolTipText( "To extract taxonomy codes/ids from node names in the form of e.g. \"bax_MOUSE\" or \"bax_10090\"" ); - _extract_taxonomy_agressive_rbmi - .setToolTipText( "To extract taxonomy codes/ids or scientific names from node names in the form of e.g. \"MOUSE\" or \"10090\" or \"xyz_Nematostella_vectensis\"" ); - _radio_group_2 = new ButtonGroup(); - _radio_group_2.add( _extract_taxonomy_no_rbmi ); - _radio_group_2.add( _extract_taxonomy_pfam_strict_rbmi ); - _radio_group_2.add( _extract_taxonomy_pfam_relaxed_rbmi ); - _radio_group_2.add( _extract_taxonomy_agressive_rbmi ); - // - _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/Nexus Output:" ), getConfiguration() ) ); - _options_jmenu - .add( _use_brackets_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_BRACKETS_FOR_CONF_IN_NH_LABEL ) ); - _use_brackets_for_conf_in_nh_export_cbmi - .setToolTipText( "e.g. \"0.1[90]\" for a branch with support 90 and a length of 0.1" ); - _options_jmenu - .add( _use_internal_names_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL ) ); - customizeJMenuItem( _choose_font_mi ); - customizeJMenuItem( _choose_minimal_confidence_mi ); - customizeJMenuItem( _switch_colors_mi ); - customizeJMenuItem( _print_size_mi ); - customizeJMenuItem( _choose_pdf_width_mi ); - customizeJMenuItem( _overview_placment_mi ); - customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions() - .isShowDefaultNodeShapesExternal() ); - customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions() - .isShowDefaultNodeShapesInternal() ); - customizeJMenuItem( _cycle_node_shape_mi ); - customizeJMenuItem( _cycle_node_fill_mi ); - customizeJMenuItem( _choose_node_size_mi ); - customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() ); - customizeCheckBoxMenuItem( _color_by_taxonomic_group_cbmi, getOptions().isColorByTaxonomicGroup() ); - customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() ); - customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() ); - customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() ); - customizeCheckBoxMenuItem( _show_annotation_ref_source, getOptions().isShowAnnotationRefSource() ); - customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() ); - customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() ); - customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() ); - customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi, - getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP ); - customizeRadioButtonMenuItem( _uniform_cladograms_rbmi, - getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP ); - customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi, - getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP ); - customizeCheckBoxMenuItem( _show_branch_length_values_cbmi, getOptions().isShowBranchLengthValues() ); - 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_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() ); - customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() ); - customizeCheckBoxMenuItem( _graphics_export_visible_only_cbmi, getOptions().isGraphicsExportVisibleOnly() ); - customizeCheckBoxMenuItem( _print_using_actual_size_cbmi, getOptions().isPrintUsingActualSize() ); - customizeCheckBoxMenuItem( _graphics_export_using_actual_size_cbmi, getOptions() - .isGraphicsExportUsingActualSize() ); - 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 ); - _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( _deleted_selected_nodes_item = new JMenuItem( "Delete Selected Nodes" ) ); - customizeJMenuItem( _deleted_selected_nodes_item ); - _tools_menu.add( _deleted_not_selected_nodes_item = new JMenuItem( "Retain Selected Nodes" ) ); - customizeJMenuItem( _deleted_not_selected_nodes_item ); - _tools_menu.addSeparator(); - _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) ); - customizeJMenuItem( _collapse_species_specific_subtrees ); - _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 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.addSeparator(); - _tools_menu - .add( _extract_tax_code_from_node_names_jmi = new JMenuItem( "Extract Taxonomic Data from Node Names" ) ); - customizeJMenuItem( _extract_tax_code_from_node_names_jmi ); - _extract_tax_code_from_node_names_jmi - .setToolTipText( "To extract SwissProt/Uniprot taxonomic codes (mnemonics) from nodes names in the form of 'xyz_CAEEL', Uniprot/NCBI identifiers form of 'xyz_6239', or scientific names form of 'xyz_Caenorhabditis_elegans'" ); - _tools_menu - .add( _move_node_names_to_tax_sn_jmi = new JMenuItem( "Transfer Node Names to Taxonomic Scientific Names" ) ); - customizeJMenuItem( _move_node_names_to_tax_sn_jmi ); - _move_node_names_to_tax_sn_jmi.setToolTipText( "To interpret node names as taxonomic scientific names" ); - _tools_menu.add( _move_node_names_to_seq_names_jmi = new JMenuItem( "Transfer Node Names to Sequence Names" ) ); - customizeJMenuItem( _move_node_names_to_seq_names_jmi ); - _move_node_names_to_seq_names_jmi.setToolTipText( "To interpret node names as sequence (protein, gene) names" ); - _tools_menu.addSeparator(); - _tools_menu.add( _obtain_seq_information_jmi = new JMenuItem( "Obtain Sequence Information" ) ); - customizeJMenuItem( _obtain_seq_information_jmi ); - _obtain_seq_information_jmi.setToolTipText( "To add additional sequence information" ); - _tools_menu - .add( _obtain_detailed_taxonomic_information_jmi = new JMenuItem( OBTAIN_DETAILED_TAXONOMIC_INFORMATION ) ); - customizeJMenuItem( _obtain_detailed_taxonomic_information_jmi ); - _obtain_detailed_taxonomic_information_jmi - .setToolTipText( "To add additional taxonomic information (from UniProt Taxonomy)" ); - _tools_menu - .add( _obtain_detailed_taxonomic_information_deleting_jmi = new JMenuItem( "Obtain Detailed Taxonomic Information (deletes nodes!)" ) ); - customizeJMenuItem( _obtain_detailed_taxonomic_information_deleting_jmi ); - _obtain_detailed_taxonomic_information_deleting_jmi - .setToolTipText( "To add additional taxonomic information, deletes nodes for which taxonomy cannot found (from UniProt Taxonomy)" ); - _tools_menu.addSeparator(); - _tools_menu.add( _read_values_jmi = new JMenuItem( "Attach Vector/Expression Values" ) ); - customizeJMenuItem( _read_values_jmi ); - _read_values_jmi.setToolTipText( "To attach vector (e.g. gene expression) values to tree nodes (beta)" ); - _jmenubar.add( _tools_menu ); - _tools_menu.add( _read_seqs_jmi = new JMenuItem( "Attach Molecular Sequences" ) ); - customizeJMenuItem( _read_seqs_jmi ); - _read_seqs_jmi - .setToolTipText( "To attach molecular sequences to tree nodes (from Fasta-formatted file) (beta)" ); - _jmenubar.add( _tools_menu ); - } - - @Override - void close() { - if ( isUnsavedDataPresent() ) { - final int r = JOptionPane.showConfirmDialog( this, - "Exit despite potentially unsaved changes?", - "Exit?", - JOptionPane.YES_NO_OPTION ); - if ( r != JOptionPane.YES_OPTION ) { - return; - } - } - exit(); - } - - void executeLineageInference() { - if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) { - return; - } - if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) { - JOptionPane.showMessageDialog( this, - "Phylogeny is not rooted.", - "Cannot infer ancestral taxonomies", - JOptionPane.ERROR_MESSAGE ); - return; - } - final AncestralTaxonomyInferrer inferrer = new AncestralTaxonomyInferrer( this, - _mainpanel.getCurrentTreePanel(), - _mainpanel.getCurrentPhylogeny() - .copy() ); - new Thread( inferrer ).start(); - } - - void exit() { - removeAllTextFrames(); - _mainpanel.terminate(); - _contentpane.removeAll(); - setVisible( false ); - dispose(); - System.exit( 0 ); - } - - void readPhylogeniesFromURL() { - URL url = null; - Phylogeny[] phys = null; - final String message = "Please enter a complete URL, for example \"http://purl.org/phylo/treebase/phylows/study/TB2:S15480?format=nexus\""; - final String url_string = JOptionPane.showInputDialog( this, - message, - "Use URL/webservice to obtain a phylogeny", - JOptionPane.QUESTION_MESSAGE ); - boolean nhx_or_nexus = false; - if ( ( url_string != null ) && ( url_string.length() > 0 ) ) { - try { - url = new URL( url_string ); - PhylogenyParser parser = null; - if ( url.getHost().toLowerCase().indexOf( "tolweb" ) >= 0 ) { - parser = new TolParser(); - } - else { - parser = ParserUtils.createParserDependingOnUrlContents( url, getConfiguration() - .isValidatePhyloXmlAgainstSchema() ); - } - if ( parser instanceof NexusPhylogeniesParser ) { - nhx_or_nexus = true; - } - else if ( parser instanceof NHXParser ) { - nhx_or_nexus = true; - } - if ( _mainpanel.getCurrentTreePanel() != null ) { - _mainpanel.getCurrentTreePanel().setWaitCursor(); - } - else { - _mainpanel.setWaitCursor(); - } - final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - phys = factory.create( url.openStream(), parser ); - } - catch ( final MalformedURLException e ) { - JOptionPane.showMessageDialog( this, - "Malformed URL: " + url + "\n" + e.getLocalizedMessage(), - "Malformed URL", - JOptionPane.ERROR_MESSAGE ); - } - catch ( final IOException e ) { - JOptionPane.showMessageDialog( this, - "Could not read from " + url + "\n" - + ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ), - "Failed to read URL", - JOptionPane.ERROR_MESSAGE ); - } - catch ( final Exception e ) { - JOptionPane.showMessageDialog( this, - ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ), - "Unexpected Exception", - JOptionPane.ERROR_MESSAGE ); - } - finally { - if ( _mainpanel.getCurrentTreePanel() != null ) { - _mainpanel.getCurrentTreePanel().setArrowCursor(); - } - else { - _mainpanel.setArrowCursor(); - } - } - if ( ( phys != null ) && ( phys.length > 0 ) ) { - if ( nhx_or_nexus && getOptions().isInternalNumberAreConfidenceForNhParsing() ) { - for( final Phylogeny phy : phys ) { - - PhylogenyMethods.transferInternalNodeNamesToConfidence( phy, "" ); - } - } - AptxUtil.addPhylogeniesToTabs( phys, - new File( url.getFile() ).getName(), - new File( url.getFile() ).toString(), - getConfiguration(), - getMainPanel() ); - _mainpanel.getControlPanel().showWhole(); - } - } - activateSaveAllIfNeeded(); - System.gc(); - } - - void setMsa( final Msa msa ) { - _msa = msa; - } - - void setMsaFile( final File msa_file ) { - _msa_file = msa_file; - } - - void setSeqs( final List seqs ) { - _seqs = seqs; - } - - void setSeqsFile( final File seqs_file ) { - _seqs_file = seqs_file; - } - - void writePhylogenyToGraphicsFile( final String file_name, final GraphicsExportType type ) { - _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel().getWidth(), - _mainpanel.getCurrentTreePanel().getHeight(), - true ); - String file_written_to = ""; - boolean error = false; - try { - file_written_to = AptxUtil.writePhylogenyToGraphicsFile( file_name, - _mainpanel.getCurrentTreePanel().getWidth(), - _mainpanel.getCurrentTreePanel().getHeight(), - _mainpanel.getCurrentTreePanel(), - _mainpanel.getControlPanel(), - type, - getOptions() ); - } - catch ( final IOException e ) { - error = true; - JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE ); - } - if ( !error ) { - if ( ( file_written_to != null ) && ( file_written_to.length() > 0 ) ) { - JOptionPane.showMessageDialog( this, - "Wrote image to: " + file_written_to, - "Graphics Export", - JOptionPane.INFORMATION_MESSAGE ); - } - else { - JOptionPane.showMessageDialog( this, - "There was an unknown problem when attempting to write to an image file: \"" - + file_name + "\"", - "Error", - JOptionPane.ERROR_MESSAGE ); - } - } - _contentpane.repaint(); - } - - private void addExpressionValuesFromFile() { - if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) { - JOptionPane.showMessageDialog( this, - "Need to load evolutionary tree first", - "Can Not Read Expression Values", - JOptionPane.WARNING_MESSAGE ); - return; - } - final File my_dir = getCurrentDir(); - if ( my_dir != null ) { - _values_filechooser.setCurrentDirectory( my_dir ); - } - final int result = _values_filechooser.showOpenDialog( _contentpane ); - final File file = _values_filechooser.getSelectedFile(); - if ( ( file != null ) && ( file.length() > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) { - BasicTable t = null; - try { - t = BasicTableParser.parse( file, '\t' ); - if ( t.getNumberOfColumns() < 2 ) { - t = BasicTableParser.parse( file, ',' ); - } - if ( t.getNumberOfColumns() < 2 ) { - t = BasicTableParser.parse( file, ' ' ); - } - } - catch ( final IOException e ) { - JOptionPane.showMessageDialog( this, - e.getMessage(), - "Could Not Read Expression Value Table", - JOptionPane.ERROR_MESSAGE ); - return; - } - if ( t.getNumberOfColumns() < 2 ) { - JOptionPane.showMessageDialog( this, - "Table contains " + t.getNumberOfColumns() + " column(s)", - "Problem with Expression Value Table", - JOptionPane.ERROR_MESSAGE ); - return; - } - if ( t.getNumberOfRows() < 1 ) { - JOptionPane.showMessageDialog( this, - "Table contains zero rows", - "Problem with Expression Value Table", - JOptionPane.ERROR_MESSAGE ); - return; - } - final Phylogeny phy = getCurrentTreePanel().getPhylogeny(); - if ( t.getNumberOfRows() != phy.getNumberOfExternalNodes() ) { - JOptionPane.showMessageDialog( this, - "Table contains " + t.getNumberOfRows() + " rows, but tree contains " - + phy.getNumberOfExternalNodes() + " external nodes", - "Warning", - JOptionPane.WARNING_MESSAGE ); - } - final DescriptiveStatistics stats = new BasicDescriptiveStatistics(); - int not_found = 0; - for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) { - final PhylogenyNode node = iter.next(); - final String node_name = node.getName(); - if ( !ForesterUtil.isEmpty( node_name ) ) { - int row = -1; - try { - row = t.findRow( node_name ); - } - catch ( final IllegalArgumentException e ) { - JOptionPane - .showMessageDialog( this, - e.getMessage(), - "Error Mapping Node Identifiers to Expression Value Identifiers", - JOptionPane.ERROR_MESSAGE ); - return; - } - if ( row < 0 ) { - if ( node.isExternal() ) { - not_found++; - } - continue; - } - final List l = new ArrayList(); - for( int col = 1; col < t.getNumberOfColumns(); ++col ) { - double d = -100; - try { - d = Double.parseDouble( t.getValueAsString( col, row ) ); - } - catch ( final NumberFormatException e ) { - JOptionPane.showMessageDialog( this, - "Could not parse \"" + t.getValueAsString( col, row ) - + "\" into a decimal value", - "Issue with Expression Value Table", - JOptionPane.ERROR_MESSAGE ); - return; - } - stats.addValue( d ); - l.add( d ); - } - if ( !l.isEmpty() ) { - if ( node.getNodeData().getProperties() != null ) { - node.getNodeData().getProperties() - .removePropertiesWithGivenReferencePrefix( PhyloXmlUtil.VECTOR_PROPERTY_REF ); - } - node.getNodeData().setVector( l ); - } - } - } - if ( not_found > 0 ) { - JOptionPane.showMessageDialog( this, "Could not fine expression values for " + not_found - + " external node(s)", "Warning", JOptionPane.WARNING_MESSAGE ); - } - getCurrentTreePanel().setStatisticsForExpressionValues( stats ); - } - } - - private void addSequencesFromFile() { - if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) { - JOptionPane.showMessageDialog( this, - "Need to load evolutionary tree first", - "Can Not Read Sequences", - JOptionPane.WARNING_MESSAGE ); - return; - } - final File my_dir = getCurrentDir(); - if ( my_dir != null ) { - _sequences_filechooser.setCurrentDirectory( my_dir ); - } - final int result = _sequences_filechooser.showOpenDialog( _contentpane ); - final File file = _sequences_filechooser.getSelectedFile(); - List seqs = null; - if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) { - try { - if ( FastaParser.isLikelyFasta( new FileInputStream( file ) ) ) { - seqs = FastaParser.parse( new FileInputStream( file ) ); - } - else { - JOptionPane.showMessageDialog( this, - "Format does not appear to be Fasta", - "Multiple sequence file format error", - JOptionPane.ERROR_MESSAGE ); - return; - } - } - catch ( final MsaFormatException e ) { - setArrowCursor(); - JOptionPane.showMessageDialog( this, - e.getLocalizedMessage(), - "Multiple sequence file format error", - JOptionPane.ERROR_MESSAGE ); - return; - } - catch ( final IOException e ) { - setArrowCursor(); - JOptionPane.showMessageDialog( this, - e.getLocalizedMessage(), - "Failed to read multiple sequence file", - JOptionPane.ERROR_MESSAGE ); - return; - } - catch ( final Exception e ) { - setArrowCursor(); - e.printStackTrace(); - JOptionPane.showMessageDialog( this, - e.getLocalizedMessage(), - "Unexpected error during reading of multiple sequence file", - JOptionPane.ERROR_MESSAGE ); - return; - } - if ( ( seqs == null ) || ( seqs.size() < 1 ) ) { - JOptionPane.showMessageDialog( this, - "Multiple sequence file is empty", - "Empty multiple sequence file", - JOptionPane.ERROR_MESSAGE ); - setArrowCursor(); - return; - } - } - if ( seqs != null ) { - for( final Sequence seq : seqs ) { - System.out.println( seq.getIdentifier() ); - } - final Phylogeny phy = getCurrentTreePanel().getPhylogeny(); - int total_counter = 0; - int attached_counter = 0; - for( final Sequence seq : seqs ) { - ++total_counter; - final String seq_name = seq.getIdentifier(); - if ( !ForesterUtil.isEmpty( seq_name ) ) { - List nodes = phy.getNodesViaSequenceName( seq_name ); - if ( nodes.isEmpty() ) { - nodes = phy.getNodesViaSequenceSymbol( seq_name ); - } - if ( nodes.isEmpty() ) { - nodes = phy.getNodesViaGeneName( seq_name ); - } - if ( nodes.isEmpty() ) { - nodes = phy.getNodes( seq_name ); - } - if ( nodes.size() > 1 ) { - JOptionPane.showMessageDialog( this, - "Sequence name \"" + seq_name + "\" is not unique", - "Sequence name not unique", - JOptionPane.ERROR_MESSAGE ); - setArrowCursor(); - return; - } - final String[] a = seq_name.split( "\\s" ); - if ( nodes.isEmpty() && ( a.length > 1 ) ) { - final String seq_name_split = a[ 0 ]; - nodes = phy.getNodesViaSequenceName( seq_name_split ); - if ( nodes.isEmpty() ) { - nodes = phy.getNodesViaSequenceSymbol( seq_name_split ); - } - if ( nodes.isEmpty() ) { - nodes = phy.getNodes( seq_name_split ); - } - if ( nodes.size() > 1 ) { - JOptionPane.showMessageDialog( this, "Split sequence name \"" + seq_name_split - + "\" is not unique", "Sequence name not unique", JOptionPane.ERROR_MESSAGE ); - setArrowCursor(); - return; - } - } - if ( nodes.size() == 1 ) { - ++attached_counter; - final PhylogenyNode n = nodes.get( 0 ); - if ( !n.getNodeData().isHasSequence() ) { - n.getNodeData().addSequence( new org.forester.phylogeny.data.Sequence() ); - } - n.getNodeData().getSequence().setMolecularSequence( seq.getMolecularSequenceAsString() ); - if ( ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) { - n.getNodeData().getSequence().setName( seq_name ); - } - } - } - } - if ( attached_counter > 0 ) { - int ext_nodes = 0; - int ext_nodes_with_seq = 0; - for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) { - ++ext_nodes; - final PhylogenyNode n = iter.next(); - if ( n.getNodeData().isHasSequence() - && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getMolecularSequence() ) ) { - ++ext_nodes_with_seq; - } - } - final String s; - if ( ext_nodes == ext_nodes_with_seq ) { - s = "All " + ext_nodes_with_seq + " external nodes now have a molecular sequence attached to them."; - } - else { - s = ext_nodes_with_seq + " out of " + ext_nodes - + " external nodes now have a molecular sequence attached to them."; - } - if ( ( attached_counter == total_counter ) && ( ext_nodes == ext_nodes_with_seq ) ) { - JOptionPane.showMessageDialog( this, - "Attached all " + total_counter + " sequences to tree nodes.\n" + s, - "All sequences attached", - JOptionPane.INFORMATION_MESSAGE ); - } - else { - JOptionPane.showMessageDialog( this, "Attached " + attached_counter - + " sequences out of a total of " + total_counter + " sequences.\n" + s, attached_counter - + " sequences attached", JOptionPane.WARNING_MESSAGE ); - } - } - else { - JOptionPane.showMessageDialog( this, "No maching tree node for any of the " + total_counter - + " sequences", "Could not attach any sequences", JOptionPane.ERROR_MESSAGE ); - } - } - } - - private void choosePdfWidth() { - final String s = ( String ) JOptionPane.showInputDialog( this, - "Please enter the default line width for PDF export.\n" - + "[current value: " - + getOptions().getPrintLineWidth() + "]\n", - "Line Width for PDF Export", - JOptionPane.QUESTION_MESSAGE, - null, - null, - getOptions().getPrintLineWidth() ); - if ( !ForesterUtil.isEmpty( s ) ) { - boolean success = true; - float f = 0.0f; - final String m_str = s.trim(); - if ( !ForesterUtil.isEmpty( m_str ) ) { - try { - f = Float.parseFloat( m_str ); - } - catch ( final Exception ex ) { - success = false; - } - } - else { - success = false; - } - if ( success && ( f > 0.0 ) ) { - getOptions().setPrintLineWidth( f ); - } - } - } - - private void choosePrintSize() { - final String s = ( String ) JOptionPane.showInputDialog( this, - "Please enter values for width and height,\nseparated by a comma.\n" - + "[current values: " - + getOptions().getPrintSizeX() + ", " - + getOptions().getPrintSizeY() + "]\n" - + "[A4: " + Constants.A4_SIZE_X + ", " - + Constants.A4_SIZE_Y + "]\n" + "[US Letter: " - + Constants.US_LETTER_SIZE_X + ", " - + Constants.US_LETTER_SIZE_Y + "]", - "Default Size for Graphics Export", - JOptionPane.QUESTION_MESSAGE, - null, - null, - getOptions().getPrintSizeX() + ", " - + getOptions().getPrintSizeY() ); - if ( !ForesterUtil.isEmpty( s ) && ( s.indexOf( ',' ) > 0 ) ) { - boolean success = true; - int x = 0; - int y = 0; - final String[] str_ary = s.split( "," ); - if ( str_ary.length == 2 ) { - final String x_str = str_ary[ 0 ].trim(); - final String y_str = str_ary[ 1 ].trim(); - if ( !ForesterUtil.isEmpty( x_str ) && !ForesterUtil.isEmpty( y_str ) ) { - try { - x = Integer.parseInt( x_str ); - y = Integer.parseInt( y_str ); - } - catch ( final Exception ex ) { - success = false; - } - } - else { - success = false; - } - } - else { - success = false; - } - if ( success && ( x > 1 ) && ( y > 1 ) ) { - getOptions().setPrintSizeX( x ); - getOptions().setPrintSizeY( y ); - } - } - } - - private void closeCurrentPane() { - if ( getMainPanel().getCurrentTreePanel() != null ) { - if ( getMainPanel().getCurrentTreePanel().isEdited() ) { - final int r = JOptionPane.showConfirmDialog( this, - "Close tab despite potentially unsaved changes?", - "Close Tab?", - JOptionPane.YES_NO_OPTION ); - if ( r != JOptionPane.YES_OPTION ) { - return; - } - } - getMainPanel().closeCurrentPane(); - activateSaveAllIfNeeded(); - } - } - - private void collapse( final Phylogeny phy, final double m ) { - final PhylogenyNodeIterator it = phy.iteratorPostorder(); - final List to_be_removed = new ArrayList(); - double min_support = Double.MAX_VALUE; - boolean conf_present = false; - while ( it.hasNext() ) { - final PhylogenyNode n = it.next(); - if ( !n.isExternal() && !n.isRoot() ) { - final List c = n.getBranchData().getConfidences(); - if ( ( c != null ) && ( c.size() > 0 ) ) { - conf_present = true; - double max = 0; - for( final Confidence confidence : c ) { - if ( confidence.getValue() > max ) { - max = confidence.getValue(); - } - } - if ( max < getMinNotCollapseConfidenceValue() ) { - to_be_removed.add( n ); - } - if ( max < min_support ) { - min_support = max; - } - } - } - } - if ( conf_present ) { - for( final PhylogenyNode node : to_be_removed ) { - PhylogenyMethods.removeNode( node, phy ); - } - if ( to_be_removed.size() > 0 ) { - phy.externalNodesHaveChanged(); - phy.clearHashIdToNodeMap(); - phy.recalculateNumberOfExternalDescendants( true ); - getCurrentTreePanel().resetNodeIdToDistToLeafMap(); - getCurrentTreePanel().updateSetOfCollapsedExternalNodes(); - getCurrentTreePanel().calculateLongestExtNodeInfo(); - getCurrentTreePanel().setNodeInPreorderToNull(); - getCurrentTreePanel().recalculateMaxDistanceToRoot(); - getCurrentTreePanel().resetPreferredSize(); - getCurrentTreePanel().setEdited( true ); - getCurrentTreePanel().repaint(); - repaint(); - } - if ( to_be_removed.size() > 0 ) { - JOptionPane.showMessageDialog( this, "Collapsed " + to_be_removed.size() - + " branches with\nconfidence values below " + getMinNotCollapseConfidenceValue(), "Collapsed " - + to_be_removed.size() + " branches", JOptionPane.INFORMATION_MESSAGE ); - } - else { - JOptionPane.showMessageDialog( this, "No branch collapsed,\nminimum confidence value per branch is " - + min_support, "No branch collapsed", JOptionPane.INFORMATION_MESSAGE ); - } - } - else { - JOptionPane.showMessageDialog( this, - "No branch collapsed because no confidence values present", - "No confidence values present", - JOptionPane.INFORMATION_MESSAGE ); - } - } - - private void collapseBelowThreshold() { - if ( getCurrentTreePanel() != null ) { - final Phylogeny phy = getCurrentTreePanel().getPhylogeny(); - if ( ( phy != null ) && !phy.isEmpty() ) { - final String s = ( String ) JOptionPane.showInputDialog( this, - "Please enter the minimum confidence value\n", - "Minimal Confidence Value", - JOptionPane.QUESTION_MESSAGE, - null, - null, - getMinNotCollapseConfidenceValue() ); - if ( !ForesterUtil.isEmpty( s ) ) { - boolean success = true; - double m = 0.0; - final String m_str = s.trim(); - if ( !ForesterUtil.isEmpty( m_str ) ) { - try { - m = Double.parseDouble( m_str ); - } - catch ( final Exception ex ) { - success = false; - } - } - else { - success = false; - } - if ( success && ( m >= 0.0 ) ) { - setMinNotCollapseConfidenceValue( m ); - collapse( phy, m ); - } - } - } - } - } - - private PhyloXmlParser createPhyloXmlParser() { - PhyloXmlParser xml_parser = null; - if ( getConfiguration().isValidatePhyloXmlAgainstSchema() ) { - try { - xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating(); - } - catch ( final Exception e ) { - JOptionPane.showMessageDialog( this, - e.getLocalizedMessage(), - "failed to create validating XML parser", - JOptionPane.WARNING_MESSAGE ); - } - } - if ( xml_parser == null ) { - xml_parser = PhyloXmlParser.createPhyloXmlParser(); - } - return xml_parser; - } - - private void executePhyleneticInference( final boolean from_unaligned_seqs ) { - final PhyloInferenceDialog dialog = new PhyloInferenceDialog( this, - getPhylogeneticInferenceOptions(), - from_unaligned_seqs ); - dialog.activate(); - if ( dialog.getValue() == JOptionPane.OK_OPTION ) { - if ( !from_unaligned_seqs ) { - if ( getMsa() != null ) { - final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getMsa(), - getPhylogeneticInferenceOptions() - .copy(), this ); - new Thread( inferrer ).start(); - } - else { - JOptionPane.showMessageDialog( this, - "No multiple sequence alignment selected", - "Phylogenetic Inference Not Launched", - JOptionPane.WARNING_MESSAGE ); - } - } - else { - if ( getSeqs() != null ) { - final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getSeqs(), - getPhylogeneticInferenceOptions() - .copy(), this ); - new Thread( inferrer ).start(); - } - else { - JOptionPane.showMessageDialog( this, - "No input sequences selected", - "Phylogenetic Inference Not Launched", - JOptionPane.WARNING_MESSAGE ); - } - } - } - } - - private void extractTaxDataFromNodeNames() throws PhyloXmlDataFormatException { - final StringBuilder sb = new StringBuilder(); - final StringBuilder sb_failed = new StringBuilder(); - int counter = 0; - int counter_failed = 0; - if ( getCurrentTreePanel() != null ) { - final Phylogeny phy = getCurrentTreePanel().getPhylogeny(); - if ( ( phy != null ) && !phy.isEmpty() ) { - final PhylogenyNodeIterator it = phy.iteratorExternalForward(); - while ( it.hasNext() ) { - final PhylogenyNode n = it.next(); - final String name = n.getName().trim(); - if ( !ForesterUtil.isEmpty( name ) ) { - final String nt = ParserUtils.extractTaxonomyDataFromNodeName( n, - TAXONOMY_EXTRACTION.AGGRESSIVE ); - if ( !ForesterUtil.isEmpty( nt ) ) { - if ( counter < 15 ) { - sb.append( name + ": " + nt + "\n" ); - } - else if ( counter == 15 ) { - sb.append( "...\n" ); - } - counter++; - } - else { - if ( counter_failed < 15 ) { - sb_failed.append( name + "\n" ); - } - else if ( counter_failed == 15 ) { - sb_failed.append( "...\n" ); - } - counter_failed++; - } - } - } - if ( counter > 0 ) { - String failed = ""; - String all = "all "; - if ( counter_failed > 0 ) { - all = ""; - failed = "\nCould not extract taxonomic data for " + counter_failed - + " named external nodes:\n" + sb_failed; - } - JOptionPane.showMessageDialog( this, - "Extracted taxonomic data from " + all + counter - + " named external nodes:\n" + sb.toString() + failed, - "Taxonomic Data Extraction Completed", - counter_failed > 0 ? JOptionPane.WARNING_MESSAGE - : JOptionPane.INFORMATION_MESSAGE ); - } - else { - JOptionPane - .showMessageDialog( this, - "Could not extract any taxonomic data.\nMaybe node names are empty\n" - + "or not in the forms \"XYZ_CAEEL\", \"XYZ_6239\", or \"XYZ_Caenorhabditis_elegans\"\n" - + "or nodes already have taxonomic data?\n", - "No Taxonomic Data Extracted", - JOptionPane.ERROR_MESSAGE ); - } - } - } - } - - private ControlPanel getControlPanel() { - return getMainPanel().getControlPanel(); - } - - private File getCurrentDir() { - if ( ( _current_dir == null ) || !_current_dir.canRead() ) { - if ( ForesterUtil.isWindows() ) { - try { - _current_dir = new File( WindowsUtils.getCurrentUserDesktopPath() ); - } - catch ( final Exception e ) { - _current_dir = null; - } - } - } - if ( ( _current_dir == null ) || !_current_dir.canRead() ) { - if ( System.getProperty( "user.home" ) != null ) { - _current_dir = new File( System.getProperty( "user.home" ) ); - } - else if ( System.getProperty( "user.dir" ) != null ) { - _current_dir = new File( System.getProperty( "user.dir" ) ); - } - } - return _current_dir; - } - - private double getMinNotCollapseConfidenceValue() { - return _min_not_collapse; - } - - private PhylogeneticInferenceOptions getPhylogeneticInferenceOptions() { - if ( _phylogenetic_inference_options == null ) { - _phylogenetic_inference_options = new PhylogeneticInferenceOptions(); - } - return _phylogenetic_inference_options; - } - - private boolean isUnsavedDataPresent() { - final List tps = getMainPanel().getTreePanels(); - for( final TreePanel tp : tps ) { - if ( tp.isEdited() ) { - return true; - } - } - return false; - } - - private void moveNodeNamesToSeqNames() throws PhyloXmlDataFormatException { - if ( getCurrentTreePanel() != null ) { - final Phylogeny phy = getCurrentTreePanel().getPhylogeny(); - if ( ( phy != null ) && !phy.isEmpty() ) { - PhylogenyMethods - .transferNodeNameToField( phy, PhylogenyMethods.PhylogenyNodeField.SEQUENCE_NAME, false ); - } - } - } - - private void moveNodeNamesToTaxSn() throws PhyloXmlDataFormatException { - if ( getCurrentTreePanel() != null ) { - final Phylogeny phy = getCurrentTreePanel().getPhylogeny(); - if ( ( phy != null ) && !phy.isEmpty() ) { - PhylogenyMethods.transferNodeNameToField( phy, - PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME, - false ); - } - } - } - - private void newTree() { - final Phylogeny[] phys = new Phylogeny[ 1 ]; - final Phylogeny phy = new Phylogeny(); - final PhylogenyNode node = new PhylogenyNode(); - phy.setRoot( node ); - phy.setRooted( true ); - phys[ 0 ] = phy; - AptxUtil.addPhylogeniesToTabs( phys, "", "", getConfiguration(), getMainPanel() ); - _mainpanel.getControlPanel().showWhole(); - _mainpanel.getCurrentTreePanel().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ); - _mainpanel.getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ); - if ( getMainPanel().getMainFrame() == null ) { - // Must be "E" applet version. - ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() ) - .setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ); - } - else { - getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ); - } - activateSaveAllIfNeeded(); - System.gc(); - } - - private void obtainDetailedTaxonomicInformation() { - if ( getCurrentTreePanel() != null ) { - final Phylogeny phy = getCurrentTreePanel().getPhylogeny(); - if ( ( phy != null ) && !phy.isEmpty() ) { - final TaxonomyDataManager t = new TaxonomyDataManager( this, - _mainpanel.getCurrentTreePanel(), - phy.copy(), - false, - true ); - new Thread( t ).start(); - } - } - } - - private void obtainDetailedTaxonomicInformationDelete() { - if ( getCurrentTreePanel() != null ) { - final Phylogeny phy = getCurrentTreePanel().getPhylogeny(); - if ( ( phy != null ) && !phy.isEmpty() ) { - final TaxonomyDataManager t = new TaxonomyDataManager( this, - _mainpanel.getCurrentTreePanel(), - phy.copy(), - true, - true ); - new Thread( t ).start(); - } - } - } - - private void obtainSequenceInformation() { - if ( getCurrentTreePanel() != null ) { - final Phylogeny phy = getCurrentTreePanel().getPhylogeny(); - if ( ( phy != null ) && !phy.isEmpty() ) { - final SequenceDataRetriver u = new SequenceDataRetriver( this, - _mainpanel.getCurrentTreePanel(), - phy.copy() ); - new Thread( u ).start(); - } - } - } - - private void print() { - if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) - || getCurrentTreePanel().getPhylogeny().isEmpty() ) { - return; - } - if ( !getOptions().isPrintUsingActualSize() ) { - getCurrentTreePanel().calcParametersForPainting( getOptions().getPrintSizeX() - 80, - getOptions().getPrintSizeY() - 140, - true ); - getCurrentTreePanel().resetPreferredSize(); - getCurrentTreePanel().repaint(); - } - final String job_name = Constants.PRG_NAME; - boolean error = false; - String printer_name = null; - try { - printer_name = Printer.print( getCurrentTreePanel(), job_name ); - } - catch ( final Exception e ) { - error = true; - JOptionPane.showMessageDialog( this, e.getMessage(), "Printing Error", JOptionPane.ERROR_MESSAGE ); - } - if ( !error && ( printer_name != null ) ) { - String msg = "Printing data sent to printer"; - if ( printer_name.length() > 1 ) { - msg += " [" + printer_name + "]"; - } - JOptionPane.showMessageDialog( this, msg, "Printing...", JOptionPane.INFORMATION_MESSAGE ); - } - if ( !getOptions().isPrintUsingActualSize() ) { - getControlPanel().showWhole(); - } - } - - private void printPhylogenyToPdf( final String file_name ) { - if ( !getOptions().isPrintUsingActualSize() ) { - getCurrentTreePanel().calcParametersForPainting( getOptions().getPrintSizeX(), - getOptions().getPrintSizeY(), - true ); - getCurrentTreePanel().resetPreferredSize(); - getCurrentTreePanel().repaint(); - } - String pdf_written_to = ""; - boolean error = false; - try { - if ( getOptions().isPrintUsingActualSize() ) { - pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name, - getCurrentTreePanel(), - getCurrentTreePanel().getWidth(), - getCurrentTreePanel().getHeight() ); - } - else { - pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name, getCurrentTreePanel(), getOptions() - .getPrintSizeX(), getOptions().getPrintSizeY() ); - } - } - catch ( final IOException e ) { - error = true; - JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE ); - } - if ( !error ) { - if ( !ForesterUtil.isEmpty( pdf_written_to ) ) { - JOptionPane.showMessageDialog( this, - "Wrote PDF to: " + pdf_written_to, - "Information", - JOptionPane.INFORMATION_MESSAGE ); - } - else { - JOptionPane.showMessageDialog( this, - "There was an unknown problem when attempting to write to PDF file: \"" - + file_name + "\"", - "Error", - JOptionPane.ERROR_MESSAGE ); - } - } - if ( !getOptions().isPrintUsingActualSize() ) { - getControlPanel().showWhole(); - } - } - - private void readPhylogeniesFromFile() { - boolean exception = false; - Phylogeny[] phys = null; - // Set an initial directory if none set yet - final File my_dir = getCurrentDir(); - _open_filechooser.setMultiSelectionEnabled( true ); - // 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() == MainFrameApplication.nhfilter ) - || ( _open_filechooser.getFileFilter() == MainFrameApplication.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() == MainFrameApplication.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() == MainFrameApplication.tolfilter ) { - try { - phys = PhylogenyMethods.readPhylogenies( new TolParser(), file ); - } - catch ( final Exception e ) { - exception = true; - exceptionOccuredDuringOpenFile( e ); - } - } - else if ( _open_filechooser.getFileFilter() == MainFrameApplication.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; - } - } - } - AptxUtil.addPhylogeniesToTabs( phys, - file.getName(), - file.getAbsolutePath(), - getConfiguration(), - getMainPanel() ); - _mainpanel.getControlPanel().showWhole(); - if ( nhx_or_nexus && one_desc ) { - JOptionPane - .showMessageDialog( this, - "One or more trees contain (a) node(s) with one descendant, " - + ForesterUtil.LINE_SEPARATOR - + "possibly indicating illegal parentheses within node names.", - "Warning: Possible Error in New Hampshire Formatted Data", - JOptionPane.WARNING_MESSAGE ); - } - } - } - } - } - activateSaveAllIfNeeded(); - System.gc(); - } - - private void readSpeciesTreeFromFile() { - Phylogeny t = null; - boolean exception = false; - final File my_dir = getCurrentDir(); - _open_filechooser_for_species_tree.setSelectedFile( new File( "" ) ); - if ( my_dir != null ) { - _open_filechooser_for_species_tree.setCurrentDirectory( my_dir ); - } - final int result = _open_filechooser_for_species_tree.showOpenDialog( _contentpane ); - final File file = _open_filechooser_for_species_tree.getSelectedFile(); - if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) { - if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrameApplication.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() == MainFrameApplication.tolfilter ) { - try { - final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new TolParser(), file ); - t = trees[ 0 ]; - } - catch ( final Exception e ) { - exception = true; - exceptionOccuredDuringOpenFile( e ); - } - } - // "*.*": - else { - try { - final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( PhyloXmlParser - .createPhyloXmlParserXsdValidating(), file ); - t = trees[ 0 ]; - } - catch ( final Exception e ) { - exception = true; - exceptionOccuredDuringOpenFile( e ); - } - } - if ( !exception && ( t != null ) && !t.isRooted() ) { - exception = true; - t = null; - JOptionPane.showMessageDialog( this, - "Species tree is not rooted", - "Species tree not loaded", - JOptionPane.ERROR_MESSAGE ); - } - if ( !exception && ( t != null ) ) { - final Set tax_set = new HashSet(); - for( final PhylogenyNodeIterator it = t.iteratorExternalForward(); it.hasNext(); ) { - final PhylogenyNode node = it.next(); - if ( !node.getNodeData().isHasTaxonomy() ) { - exception = true; - t = null; - JOptionPane - .showMessageDialog( this, - "Species tree contains external node(s) without taxonomy information", - "Species tree not loaded", - JOptionPane.ERROR_MESSAGE ); - break; - } - else { - if ( tax_set.contains( node.getNodeData().getTaxonomy() ) ) { - exception = true; - t = null; - JOptionPane.showMessageDialog( this, - "Taxonomy [" - + node.getNodeData().getTaxonomy().asSimpleText() - + "] is not unique in species tree", - "Species tree not loaded", - JOptionPane.ERROR_MESSAGE ); - break; - } - else { - tax_set.add( node.getNodeData().getTaxonomy() ); - } - } - } - } - if ( !exception && ( t != null ) ) { - setSpeciesTree( t ); - JOptionPane.showMessageDialog( this, - "Species tree successfully loaded", - "Species tree loaded", - JOptionPane.INFORMATION_MESSAGE ); - } - _contentpane.repaint(); - System.gc(); - } - } - - private void setArrowCursor() { - try { - _mainpanel.getCurrentTreePanel().setArrowCursor(); - } - catch ( final Exception ex ) { - // Do nothing. - } - } - - private void setCurrentDir( final File current_dir ) { - _current_dir = current_dir; - } - - private void setMinNotCollapseConfidenceValue( final double min_not_collapse ) { - _min_not_collapse = min_not_collapse; - } - - private void setPhylogeneticInferenceOptions( final PhylogeneticInferenceOptions phylogenetic_inference_options ) { - _phylogenetic_inference_options = phylogenetic_inference_options; - } - - private void setSpecialOptionsForNexParser( final NexusPhylogeniesParser nex ) { - nex.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() ); - nex.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() ); - } - - private void setSpecialOptionsForNhxParser( final NHXParser nhx ) { - nhx.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() ); - nhx.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() ); - nhx.setAllowErrorsInDistanceToParent( getOptions().isAllowErrorsInDistanceToParent() ); - } - - private void writeAllToFile() { - if ( ( getMainPanel().getTabbedPane() == null ) || ( getMainPanel().getTabbedPane().getTabCount() < 1 ) ) { - return; - } - final File my_dir = getCurrentDir(); - if ( my_dir != null ) { - _save_filechooser.setCurrentDirectory( my_dir ); - } - _save_filechooser.setSelectedFile( new File( "" ) ); - final int result = _save_filechooser.showSaveDialog( _contentpane ); - final File file = _save_filechooser.getSelectedFile(); - setCurrentDir( _save_filechooser.getCurrentDirectory() ); - if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) { - if ( file.exists() ) { - final int i = JOptionPane.showConfirmDialog( this, - file + " already exists. Overwrite?", - "Warning", - JOptionPane.OK_CANCEL_OPTION, - JOptionPane.WARNING_MESSAGE ); - if ( i != JOptionPane.OK_OPTION ) { - return; - } - else { - try { - file.delete(); - } - catch ( final Exception e ) { - JOptionPane.showMessageDialog( this, - "Failed to delete: " + file, - "Error", - JOptionPane.WARNING_MESSAGE ); - } - } - } - final int count = getMainPanel().getTabbedPane().getTabCount(); - final List trees = new ArrayList(); - for( int i = 0; i < count; ++i ) { - final Phylogeny phy = getMainPanel().getPhylogeny( i ); - if ( ForesterUtil.isEmpty( phy.getName() ) - && !ForesterUtil.isEmpty( getMainPanel().getTabbedPane().getTitleAt( i ) ) ) { - phy.setName( getMainPanel().getTabbedPane().getTitleAt( i ) ); - } - trees.add( phy ); - getMainPanel().getTreePanels().get( i ).setEdited( false ); - } - final PhylogenyWriter writer = new PhylogenyWriter(); - try { - writer.toPhyloXML( file, trees, 0, ForesterUtil.LINE_SEPARATOR ); - } - catch ( final IOException e ) { - JOptionPane.showMessageDialog( this, - "Failed to write to: " + file, - "Error", - JOptionPane.WARNING_MESSAGE ); - } - } - } - - private boolean writeAsNewHampshire( final Phylogeny t, boolean exception, final File file ) { - try { - final PhylogenyWriter writer = new PhylogenyWriter(); - writer.toNewHampshire( t, true, getOptions().getNhConversionSupportValueStyle(), file ); - } - catch ( final Exception e ) { - exception = true; - exceptionOccuredDuringSaveAs( e ); - } - return exception; - } - - private boolean writeAsNexus( final Phylogeny t, boolean exception, final File file ) { - try { - final PhylogenyWriter writer = new PhylogenyWriter(); - writer.toNexus( file, t, getOptions().getNhConversionSupportValueStyle() ); - } - catch ( final Exception e ) { - exception = true; - exceptionOccuredDuringSaveAs( e ); - } - return exception; - } - - private boolean writeAsPhyloXml( final Phylogeny t, boolean exception, final File file ) { - try { - final PhylogenyWriter writer = new PhylogenyWriter(); - writer.toPhyloXML( file, t, 0 ); - } - catch ( final Exception e ) { - exception = true; - exceptionOccuredDuringSaveAs( e ); - } - return exception; - } - - private void writeToFile( final Phylogeny t ) { - if ( t == null ) { - return; - } - String initial_filename = null; - if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) { - try { - initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().getCanonicalPath(); - } - catch ( final IOException e ) { - initial_filename = null; - } - } - if ( !ForesterUtil.isEmpty( initial_filename ) ) { - _save_filechooser.setSelectedFile( new File( initial_filename ) ); - } - else { - _save_filechooser.setSelectedFile( new File( "" ) ); - } - final File my_dir = getCurrentDir(); - if ( my_dir != null ) { - _save_filechooser.setCurrentDirectory( my_dir ); - } - final int result = _save_filechooser.showSaveDialog( _contentpane ); - final File file = _save_filechooser.getSelectedFile(); - setCurrentDir( _save_filechooser.getCurrentDirectory() ); - boolean exception = false; - if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) { - if ( file.exists() ) { - final int i = JOptionPane.showConfirmDialog( this, - file + " already exists.\nOverwrite?", - "Overwrite?", - JOptionPane.OK_CANCEL_OPTION, - JOptionPane.QUESTION_MESSAGE ); - if ( i != JOptionPane.OK_OPTION ) { - return; - } - else { - final File to = new File( file.getAbsoluteFile().toString() + Constants.BACKUP_FILE_SUFFIX ); - try { - ForesterUtil.copyFile( file, to ); - } - catch ( final Exception e ) { - JOptionPane.showMessageDialog( this, - "Failed to create backup copy " + to, - "Failed to Create Backup Copy", - JOptionPane.WARNING_MESSAGE ); - } - try { - file.delete(); - } - catch ( final Exception e ) { - JOptionPane.showMessageDialog( this, - "Failed to delete: " + file, - "Failed to Delete", - JOptionPane.WARNING_MESSAGE ); - } - } - } - if ( _save_filechooser.getFileFilter() == MainFrameApplication.nhfilter ) { - exception = writeAsNewHampshire( t, exception, file ); - } - else if ( _save_filechooser.getFileFilter() == MainFrameApplication.xmlfilter ) { - exception = writeAsPhyloXml( t, exception, file ); - } - else if ( _save_filechooser.getFileFilter() == MainFrameApplication.nexusfilter ) { - exception = writeAsNexus( t, exception, file ); - } - // "*.*": - else { - final String file_name = file.getName().trim().toLowerCase(); - if ( file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" ) - || file_name.endsWith( ".tree" ) ) { - exception = writeAsNewHampshire( t, exception, file ); - } - else if ( file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) ) { - exception = writeAsNexus( t, exception, file ); - } - // XML is default: - else { - exception = writeAsPhyloXml( t, exception, file ); - } - } - if ( !exception ) { - getMainPanel().setTitleOfSelectedTab( file.getName() ); - getMainPanel().getCurrentTreePanel().setTreeFile( file ); - getMainPanel().getCurrentTreePanel().setEdited( false ); - } - } - } - - private void writeToGraphicsFile( final Phylogeny t, final GraphicsExportType type ) { - if ( ( t == null ) || t.isEmpty() ) { - return; - } - String initial_filename = ""; - if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) { - initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().toString(); - } - if ( initial_filename.indexOf( '.' ) > 0 ) { - initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) ); - } - initial_filename = initial_filename + "." + type; - _writetographics_filechooser.setSelectedFile( new File( initial_filename ) ); - final File my_dir = getCurrentDir(); - if ( my_dir != null ) { - _writetographics_filechooser.setCurrentDirectory( my_dir ); - } - final int result = _writetographics_filechooser.showSaveDialog( _contentpane ); - File file = _writetographics_filechooser.getSelectedFile(); - setCurrentDir( _writetographics_filechooser.getCurrentDirectory() ); - if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) { - if ( !file.toString().toLowerCase().endsWith( type.toString() ) ) { - file = new File( file.toString() + "." + type ); - } - if ( file.exists() ) { - final int i = JOptionPane.showConfirmDialog( this, - file + " already exists. Overwrite?", - "Warning", - JOptionPane.OK_CANCEL_OPTION, - JOptionPane.WARNING_MESSAGE ); - if ( i != JOptionPane.OK_OPTION ) { - return; - } - else { - try { - file.delete(); - } - catch ( final Exception e ) { - JOptionPane.showMessageDialog( this, - "Failed to delete: " + file, - "Error", - JOptionPane.WARNING_MESSAGE ); - } - } - } - writePhylogenyToGraphicsFile( file.toString(), type ); - } - } - - private void writeToPdf( final Phylogeny t ) { - if ( ( t == null ) || t.isEmpty() ) { - return; - } - String initial_filename = ""; - if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) { - initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().toString(); - } - if ( initial_filename.indexOf( '.' ) > 0 ) { - initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) ); - } - initial_filename = initial_filename + ".pdf"; - _writetopdf_filechooser.setSelectedFile( new File( initial_filename ) ); - final File my_dir = getCurrentDir(); - if ( my_dir != null ) { - _writetopdf_filechooser.setCurrentDirectory( my_dir ); - } - final int result = _writetopdf_filechooser.showSaveDialog( _contentpane ); - File file = _writetopdf_filechooser.getSelectedFile(); - setCurrentDir( _writetopdf_filechooser.getCurrentDirectory() ); - if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) { - if ( !file.toString().toLowerCase().endsWith( ".pdf" ) ) { - file = new File( file.toString() + ".pdf" ); - } - if ( file.exists() ) { - final int i = JOptionPane.showConfirmDialog( this, - file + " already exists. Overwrite?", - "WARNING", - JOptionPane.OK_CANCEL_OPTION, - JOptionPane.WARNING_MESSAGE ); - if ( i != JOptionPane.OK_OPTION ) { - return; - } - } - printPhylogenyToPdf( file.toString() ); - } - } - - 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 setTextForGraphicsSizeChooserMenuItem( final JMenuItem mi, final Options o ) { - mi.setText( "Enter Default Size for Graphics Export... (current: " + o.getPrintSizeX() + ", " - + o.getPrintSizeY() + ")" ); - } - - static void setTextForPdfLineWidthChooserMenuItem( final JMenuItem mi, final Options o ) { - mi.setText( "Enter Default Line Width for PDF Export... (current: " + o.getPrintLineWidth() + ")" ); - } - - 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. - -class DefaultFilter extends FileFilter { - - @Override - public boolean accept( final File f ) { - final String file_name = f.getName().trim().toLowerCase(); - return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" ) - || file_name.endsWith( ".nwk" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".ph" ) - || file_name.endsWith( ".tr" ) || file_name.endsWith( ".dnd" ) || file_name.endsWith( ".tree" ) - || file_name.endsWith( ".nhx" ) || file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" ) - || file_name.endsWith( "phylo.xml" ) || file_name.endsWith( ".pxml" ) || file_name.endsWith( ".nexus" ) - || file_name.endsWith( ".nx" ) || file_name.endsWith( ".nex" ) || file_name.endsWith( ".tre" ) - || file_name.endsWith( ".zip" ) || file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" ) - || file_name.endsWith( ".con" ) || f.isDirectory(); - } - - @Override - public String getDescription() { - return "All supported files (*.xml, *.phyloxml, *phylo.xml, *.nhx, *.nh, *.newick, *.nex, *.nexus, *.phy, *.tre, *.tree, *.tol, ...)"; - } -} - -class GraphicsFileFilter extends FileFilter { - - @Override - public boolean accept( final File f ) { - final String file_name = f.getName().trim().toLowerCase(); - return file_name.endsWith( ".jpg" ) || file_name.endsWith( ".jpeg" ) || file_name.endsWith( ".png" ) - || file_name.endsWith( ".gif" ) || file_name.endsWith( ".bmp" ) || f.isDirectory(); - } - - @Override - public String getDescription() { - return "Image files (*.jpg, *.jpeg, *.png, *.gif, *.bmp)"; - } -} - -class MsaFileFilter extends FileFilter { - - @Override - public boolean accept( final File f ) { - final String file_name = f.getName().trim().toLowerCase(); - return file_name.endsWith( ".msa" ) || file_name.endsWith( ".aln" ) || file_name.endsWith( ".fasta" ) - || file_name.endsWith( ".fas" ) || file_name.endsWith( ".fa" ) || f.isDirectory(); - } - - @Override - public String getDescription() { - return "Multiple sequence alignment files (*.msa, *.aln, *.fasta, *.fa, *.fas)"; - } -} - -class NexusFilter extends FileFilter { - - @Override - public boolean accept( final File f ) { - final String file_name = f.getName().trim().toLowerCase(); - return file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) || file_name.endsWith( ".nx" ) - || file_name.endsWith( ".tre" ) || f.isDirectory(); - } - - @Override - public String getDescription() { - return "Nexus files (*.nex, *.nexus, *.nx, *.tre)"; - } -} // NexusFilter - -class NHFilter extends FileFilter { - - @Override - public boolean accept( final File f ) { - final String file_name = f.getName().trim().toLowerCase(); - return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" ) - || file_name.endsWith( ".tr" ) || file_name.endsWith( ".tree" ) || file_name.endsWith( ".dnd" ) - || file_name.endsWith( ".ph" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".nwk" ) - || f.isDirectory(); - } - - @Override - public String getDescription() { - return "New Hampshire - Newick files (*.nh, *.newick, *.phy, *.tree, *.dnd, *.tr, *.ph, *.phb, *.nwk)"; - } -} // NHFilter - -class NHXFilter extends FileFilter { - - @Override - public boolean accept( final File f ) { - final String file_name = f.getName().trim().toLowerCase(); - return file_name.endsWith( ".nhx" ) || f.isDirectory(); - } - - @Override - public String getDescription() { - return "NHX files (*.nhx) [deprecated]"; - } -} - -class PdfFilter extends FileFilter { - - @Override - public boolean accept( final File f ) { - return f.getName().trim().toLowerCase().endsWith( ".pdf" ) || f.isDirectory(); - } - - @Override - public String getDescription() { - return "PDF files (*.pdf)"; - } -} // PdfFilter - -class SequencesFileFilter extends FileFilter { - - @Override - public boolean accept( final File f ) { - final String file_name = f.getName().trim().toLowerCase(); - return file_name.endsWith( ".fasta" ) || file_name.endsWith( ".fa" ) || file_name.endsWith( ".fas" ) - || file_name.endsWith( ".seqs" ) || f.isDirectory(); - } - - @Override - public String getDescription() { - return "Sequences files (*.fasta, *.fa, *.fas, *.seqs )"; - } -} - -class TolFilter extends FileFilter { - - @Override - public boolean accept( final File f ) { - final String file_name = f.getName().trim().toLowerCase(); - return ( file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" ) || file_name.endsWith( ".zip" ) || f - .isDirectory() ) && ( !file_name.endsWith( ".xml.zip" ) ); - } - - @Override - public String getDescription() { - return "Tree of Life files (*.tol, *.tolxml)"; - } -} // TolFilter - -class XMLFilter extends FileFilter { - - @Override - public boolean accept( final File f ) { - final String file_name = f.getName().trim().toLowerCase(); - return file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" ) || file_name.endsWith( "phylo.xml" ) - || file_name.endsWith( ".pxml" ) || file_name.endsWith( ".zip" ) || f.isDirectory(); - } - - @Override - public String getDescription() { - return "phyloXML files (*.xml, *.phyloxml, *phylo.xml, *.pxml, *.zip)"; - } -} // XMLFilter +// $Id: +// FORESTER -- software libraries and applications +// for evolutionary biology research and applications. +// +// Copyright (C) 2008-2009 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 _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 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 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 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 l = new ArrayList(); + for( int col = 1; col < t.getNumberOfColumns(); ++col ) { + double d = -100; + try { + d = Double.parseDouble( t.getValueAsString( col, row ) ); + } + catch ( final NumberFormatException e ) { + JOptionPane.showMessageDialog( 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 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 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 to_be_removed = new ArrayList(); + double min_support = Double.MAX_VALUE; + boolean conf_present = false; + while ( it.hasNext() ) { + final PhylogenyNode n = it.next(); + if ( !n.isExternal() && !n.isRoot() ) { + final List c = n.getBranchData().getConfidences(); + if ( ( c != null ) && ( c.size() > 0 ) ) { + conf_present = true; + double max = 0; + for( final Confidence confidence : c ) { + if ( confidence.getValue() > max ) { + max = confidence.getValue(); + } + } + if ( max < getMinNotCollapseConfidenceValue() ) { + to_be_removed.add( n ); + } + if ( max < min_support ) { + min_support = max; + } + } + } + } + if ( conf_present ) { + for( final PhylogenyNode node : to_be_removed ) { + PhylogenyMethods.removeNode( node, phy ); + } + if ( to_be_removed.size() > 0 ) { + phy.externalNodesHaveChanged(); + phy.clearHashIdToNodeMap(); + phy.recalculateNumberOfExternalDescendants( true ); + getCurrentTreePanel().resetNodeIdToDistToLeafMap(); + getCurrentTreePanel().updateSetOfCollapsedExternalNodes(); + getCurrentTreePanel().calculateLongestExtNodeInfo(); + getCurrentTreePanel().setNodeInPreorderToNull(); + getCurrentTreePanel().recalculateMaxDistanceToRoot(); + getCurrentTreePanel().resetPreferredSize(); + getCurrentTreePanel().setEdited( true ); + getCurrentTreePanel().repaint(); + repaint(); + } + if ( to_be_removed.size() > 0 ) { + JOptionPane.showMessageDialog( 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 to_be_removed = new ArrayList(); + double min_bl = Double.MAX_VALUE; + boolean bl_present = false; + while ( it.hasNext() ) { + final PhylogenyNode n = it.next(); + if ( !n.isExternal() && !n.isRoot() ) { + final double bl = n.getDistanceToParent(); + if ( bl != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) { + bl_present = true; + if ( bl < getMinNotCollapseBlValue() ) { + to_be_removed.add( n ); + } + if ( bl < min_bl ) { + min_bl = bl; + } + } + } + } + if ( bl_present ) { + for( final PhylogenyNode node : to_be_removed ) { + PhylogenyMethods.removeNode( node, phy ); + } + if ( to_be_removed.size() > 0 ) { + phy.externalNodesHaveChanged(); + phy.clearHashIdToNodeMap(); + phy.recalculateNumberOfExternalDescendants( true ); + getCurrentTreePanel().resetNodeIdToDistToLeafMap(); + getCurrentTreePanel().updateSetOfCollapsedExternalNodes(); + getCurrentTreePanel().calculateLongestExtNodeInfo(); + getCurrentTreePanel().setNodeInPreorderToNull(); + getCurrentTreePanel().recalculateMaxDistanceToRoot(); + getCurrentTreePanel().resetPreferredSize(); + getCurrentTreePanel().setEdited( true ); + getCurrentTreePanel().repaint(); + repaint(); + } + if ( to_be_removed.size() > 0 ) { + JOptionPane.showMessageDialog( 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 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 tax_set = new HashSet(); + for( final PhylogenyNodeIterator it = t.iteratorExternalForward(); it.hasNext(); ) { + final PhylogenyNode node = it.next(); + if ( !node.getNodeData().isHasTaxonomy() ) { + exception = true; + t = null; + JOptionPane.showMessageDialog( 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 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.